diff --git a/data/covid/preprints-summary.csv b/data/covid/preprints-summary.csv index c1878841..35fd7e7e 100644 --- a/data/covid/preprints-summary.csv +++ b/data/covid/preprints-summary.csv @@ -1,49 +1,49 @@ -biophysics,immunology,epidemiology,health informatics,infectious diseases,microbiology,neurology,geriatric medicine,pediatrics,emergency medicine,cardiovascular medicine,bioinformatics,evolutionary biology,dentistry and oral medicine,oncology,genomics,dermatology,psychiatry and clinical psychology,Total,health economics,health policy,genetic and genomic medicine,allergy and immunology,pharmacology and therapeutics,health systems and quality improvement,public and global health,primary care research,pathology,molecular biology,systems biology,occupational and environmental health,month,radiology and imaging,hiv aids,intensive care and critical care medicine,obstetrics and gynecology,ophthalmology,surgery,biochemistry,respiratory medicine -,,,,,,,,,,,,,,,,,,2,,,,,,,2,,,,,,Jan-24,,,,,,,, -,,4,,,,1,,,,1,,,,,,,,10,2,,,,,,1,,,,,1,Dec-23,,,,,,,, -,,2,,1,,,,,,,,,,1,,,,4,,,,,,,,,,,,,Nov-23,,,,,,,, -,1,1,1,1,,,,,,,,,,,,,,5,,,,,,,,,,,,,Oct-23,,,,,,,,1 -,,,,1,,,,,,,,,,,,,,1,,,,,,,,,,,,,Sep-23,,,,,,,, -,,4,,,,,,,,,,,,,,,,7,,,,,,,1,1,,,,1,Aug-23,,,,,,,, -,,3,,,,,,,,,,,,,,,,7,,,1,,,2,1,,,,,,Jul-23,,,,,,,, -,,1,1,2,,,,,,,,,,,,,,5,,,,,,,,,,,,1,Jun-23,,,,,,,, -,1,2,,1,,,,,,,,,,,,,,6,,,,,,,1,,,,,,May-23,,,,,,,,1 -,,,,1,,,,,,,,,,,,,,3,,,,,,,2,,,,,,Apr-23,,,,,,,, -,,2,,3,,,,,,,,,,,,,1,9,,,,,,,2,,,,,1,Mar-23,,,,,,,, -,,4,,,,1,,,,,,,,,,,,8,,,,,,,2,,,,,,Feb-23,,,,,,,,1 -,,5,,1,,,,,,,,,,,,,,6,,,,,,,,,,,,,Jan-23,,,,,,,, -,,3,,4,,,,,,,,,,,,,,12,,1,,,,,1,,1,,,,Dec-22,,,,,,,,2 -,,,,4,,,,,,,,,,,,,,4,,,,,,,,,,,,,Nov-22,,,,,,,, -,,1,,2,,,,,,1,,,,,,,,6,,,,,,,2,,,,,,Oct-22,,,,,,,, -,,1,,2,1,,,1,,,,,,,,,,9,,,,,,,1,,,,,2,Sep-22,,,,,,,,1 -,,4,,3,,,,,,,,,,,,,,10,,,,,,,3,,,,,,Aug-22,,,,,,,, -,1,2,1,3,,,,1,,,,,,,,,,8,,,,,,,,,,,,,Jul-22,,,,,,,, -,,6,1,4,,,,,,,,,,,,,4,17,,,1,,,,1,,,,,,Jun-22,,,,,,,, -,,2,,4,1,,,,,,,,,,,,2,13,1,,,,,1,1,1,,,,,May-22,,,,,,,, -,,5,,3,1,,,,,1,,,,,,,,16,1,,,,,2,1,,,,,1,Apr-22,,,,,,,,1 -,,9,,5,,,,,,,,1,,,,,1,18,,,,,,,,1,,,,,Mar-22,,,,,,,,1 -,,6,,4,,1,,,,,,,,,,,,12,,,,,,,1,,,,,,Feb-22,,,,,,,, -,1,5,2,3,,,,,,1,,,,,,,,14,,,,,,,1,,,,,1,Jan-22,,,,,,,, -,,9,,8,1,1,,1,,1,,,,,,,,23,,,,,,,1,1,,,,,Dec-21,,,,,,,, -1,,9,,5,,1,,,,,,,,,1,,1,25,,,,,,2,3,1,,,,,Nov-21,,,1,,,,, -,,4,,3,,,1,1,,,,,,,,,2,11,,,,,,,,,,,,,Oct-21,,,,,,,, -,,6,1,5,,,,,,1,,,,,,,,17,,,,,1,,2,,,,,,Sep-21,,,1,,,,, -,,2,1,3,,,,,,1,,,,,,,,11,,,,,,,2,,,,,1,Aug-21,,,,,,,,1 -,,3,,12,,,,1,1,,,,,1,,,,26,,,1,,,,4,,,,,,Jul-21,,,1,,,,,2 -,,7,1,7,,1,,1,,,,,,,,,1,27,,,,1,,1,4,1,,,,1,Jun-21,,,1,,,,, -,,11,1,8,,,,,,,,,,,,1,1,24,,,1,,,,1,,,,,,May-21,,,,,,,, -,,4,1,7,1,,,,,,,,,,,,1,20,,,,1,,1,1,1,,,,2,Apr-21,,,,,,,, -,,6,2,16,,1,2,1,,,,,,,,,,37,,,1,,,,5,,,,,,Mar-21,1,,,,,1,1, -,,9,1,8,,,,,,1,,,,,,,,23,1,,,,,1,1,,,,,,Feb-21,,,,,,1,, -,1,4,,8,,,1,,,,,,1,,,,1,23,,1,,,,1,3,1,,,,,Jan-21,,,1,,,,, -,,4,3,4,1,,,,,2,,,,,2,,2,23,,,,,,1,3,1,,,,,Dec-20,,,,,,,, -,1,5,1,13,,,,,,,1,,,,,,,26,,1,,,,,4,,,,,,Nov-20,,,,,,,, -,1,6,1,11,,,1,,,,1,,,1,,,3,29,,1,,,,,,1,,,1,,Oct-20,,,1,,,,, -,,6,1,7,1,,,,3,,,,,,,,2,26,,,,,,,3,1,,,,,Sep-20,,1,1,,,,, -,,6,,12,,,,,2,,,,,,,,,27,,,1,,,1,2,,,1,,1,Aug-20,,,,1,,,, -,1,10,,8,,,,,,1,,,,,1,,1,27,,,,,,,3,,,,,,Jul-20,,,1,,,,,1 -,1,7,1,10,,,1,,,1,1,,,1,,,4,36,,1,,,,1,3,,,,,,Jun-20,,,2,,1,,,1 -,,8,1,10,,,1,,,2,1,,,1,,,,37,1,,,,,,9,,,,,1,May-20,,,1,,,,,1 -,,6,,7,,,,,,,,,,,1,,,18,,,2,,,1,1,,,,,,Apr-20,,,,,,,, -,,4,,1,,,,,,,,,,,,,,8,,,,,,,3,,,,,,Mar-20,,,,,,,, -,,3,,1,,,,,,,,,,,,,,6,,,,,,,2,,,,,,Feb-20,,,,,,,, +epidemiology,dentistry and oral medicine,microbiology,systems biology,pathology,molecular biology,primary care research,biophysics,dermatology,Total,genetic and genomic medicine,health economics,emergency medicine,health policy,month,oncology,respiratory medicine,immunology,pediatrics,obstetrics and gynecology,infectious diseases,geriatric medicine,scientific communication and education,cardiovascular medicine,hiv aids,allergy and immunology,pharmacology and therapeutics,genomics,health systems and quality improvement,public and global health,neurology,biochemistry,psychiatry and clinical psychology,ophthalmology,evolutionary biology,health informatics,occupational and environmental health,intensive care and critical care medicine,bioinformatics,orthopedics,surgery,radiology and imaging +,,,,,,,,,2,,,,,Jan-24,,,,,,,,,,,,,,,2,,,,,,,,,,,, +3,,,,,,,,,9,,2,,,Dec-23,,,,,,,,,1,,,,,,1,1,,,,,,1,,,,, +2,,,,,,,,,4,,,,,Nov-23,1,,,,,1,,,,,,,,,,,,,,,,,,,,, +1,,,,,,,,,4,,,,,Oct-23,,1,,,,1,,,,,,,,,,,,,,,1,,,,,, +,,,,,,,,,1,,,,,Sep-23,,,,,,1,,,,,,,,,,,,,,,,,,,,, +4,,,,,,1,,,7,,,,,Aug-23,,,,,,,,,,,,,,,1,,,,,,,1,,,,, +3,,,,,,,,,7,1,,,,Jul-23,,,,,,,,,,,,,,2,1,,,,,,,,,,,, +1,,,,,,,,,7,,,,,Jun-23,,,,,,2,,1,,,,,,,,,,,,,1,1,,,1,, +2,,,,,,,,,6,,,,,May-23,,1,1,,,1,,,,,,,,,1,,,,,,,,,,,, +,,,,,,,,,3,,,,,Apr-23,,,,,,1,,,,,,,,,2,,,,,,,,,,,, +2,,,,,,,,,8,,,,,Mar-23,,,,,,3,,,,,,,,,2,,,1,,,,,,,,, +4,,,,,,,,,8,,,,,Feb-23,,1,,,,,,,,,,,,,2,1,,,,,,,,,,, +5,,,,,,,,,6,,,,,Jan-23,,,,,,1,,,,,,,,,,,,,,,,,,,,, +3,,,,1,,,,,12,,,,1,Dec-22,,2,,,,4,,,,,,,,,1,,,,,,,,,,,, +,,,,,,,,,4,,,,,Nov-22,,,,,,4,,,,,,,,,,,,,,,,,,,,, +1,,,,,,,,,6,,,,,Oct-22,,,,,,2,,,1,,,,,,2,,,,,,,,,,,, +1,,1,,,,,,,9,,,,,Sep-22,,1,,1,,2,,,,,,,,,1,,,,,,,2,,,,, +4,,,,,,,,,10,,,,,Aug-22,,,,,,3,,,,,,,,,3,,,,,,,,,,,, +2,,,,,,,,,8,,,,,Jul-22,,,1,1,,3,,,,,,,,,,,,,,,1,,,,,, +5,,,,,,,,,17,1,,,,Jun-22,,,,,,4,,,,,,,,,1,,,5,,,1,,,,,, +2,,1,,,,1,,,12,,1,,,May-22,,,,,,4,,,,,,,,1,,,,2,,,,,,,,, +5,,1,,,,,,,15,,1,,,Apr-22,,1,,,,2,,,1,,,,,2,1,,,,,,,1,,,,, +9,,,,,,1,,,18,,,,,Mar-22,,1,,,,5,,,,,,,,,,,,1,,1,,,,,,, +6,,,,,,,,,12,,,,,Feb-22,,,,,,4,,,,,,,,,1,1,,,,,,,,,,, +5,,,,,,,,,13,,,,,Jan-22,,,1,,,3,,,1,,,,,,1,,,,,,1,1,,,,, +10,,1,,,,1,,,24,,,,,Dec-21,,,,1,,8,,,1,,,,,,1,1,,,,,,,,,,, +9,,,,,,1,1,,25,,,,,Nov-21,,,,,,5,,,,,,,1,2,3,1,,1,,,,,1,,,, +4,,,,,,,,,11,,,,,Oct-21,,,,1,,3,1,,,,,,,,,,,2,,,,,,,,, +6,,,,,,,,,16,,,,,Sep-21,,,,,,5,,,1,,,1,,,2,,,,,,1,,,,,, +2,,,,,,,,,13,,,,,Aug-21,,1,,,,3,,,1,,,,,,3,,,,,,1,1,1,,,, +3,,,,,,,,,26,1,,1,,Jul-21,1,2,,1,,12,,,,,,,,,4,,,,,,,,1,,,, +6,,,,,,1,,,27,,,,,Jun-21,,,1,1,,7,,,,,1,,,1,4,1,,1,,,1,1,1,,,, +10,,,,,,,,1,22,,,,,May-21,,,,,,8,,,,,,,,,1,,,1,,,1,,,,,, +4,,1,,,,1,,,20,,,,,Apr-21,,,,,,7,,,,,1,,,1,1,,,1,,,1,2,,,,, +6,,,,,,,,,39,1,,,,Mar-21,,,,1,,17,2,,,,,,,,5,1,1,1,,,2,,,,,1,1 +9,,,,,,,,,24,,1,,,Feb-21,,,,,,9,,,1,,,,,1,1,,,,,,1,,,,,1, +4,1,,,,,1,,,23,,,,1,Jan-21,,,1,,,8,1,,,,,,,1,3,,,1,,,,,1,,,, +4,,1,,,,1,,,23,,,,,Dec-20,,,,,,4,,,2,,,,2,1,3,,,2,,,3,,,,,, +6,,,,,,,,,27,,,,1,Nov-20,,,1,,,12,,,,,,,,,5,,,,,,1,,,1,,, +6,,,1,,,1,,,30,,,,1,Oct-20,1,,1,,,12,1,,,,,,,,,,,3,,,1,,1,1,,, +5,,1,,,,1,,,26,,,3,,Sep-20,,,,,,8,,,,1,,,,,3,,,2,,,1,,1,,,, +6,,,,,1,,,,27,1,,2,,Aug-20,,,,,1,12,,,,,,,,1,2,,,,,,,1,,,,, +10,,,,,,,,,28,,,,,Jul-20,,1,1,,,8,,,1,,,,1,,4,,,1,,,,,1,,,, +7,,,,,,,,,36,,,,1,Jun-20,1,1,1,,,9,1,,1,,,,,1,3,,,4,1,,1,,3,1,,, +7,,,,,,,,,34,,1,,,May-20,1,1,,,,9,1,,1,,,,,,9,,,,,,1,1,1,1,,, +7,,,,,,,,,18,1,,,,Apr-20,,,,,,7,,,,,,,1,1,1,,,,,,,,,,,, +4,,,,,,,,,8,,,,,Mar-20,,,,,,1,,,,,,,,,3,,,,,,,,,,,, +4,,,,,,,,,7,,,,,Feb-20,,,,,,1,,,,,,,,,2,,,,,,,,,,,, diff --git a/data/covid/preprints.csv b/data/covid/preprints.csv index 2f46a6a1..9bb7a5fe 100644 --- a/data/covid/preprints.csv +++ b/data/covid/preprints.csv @@ -95,13 +95,6 @@ OutcomesWe considered eight outcomes: depression, serious mental illness, genera InterpretationIncidence of mental illness is elevated for up to a year following severe COVID-19 in unvaccinated people. Vaccination mitigates the adverse effect of COVID-19 on mental health. FundingMedical Research Council (MC_PC_20059) and NIHR (COV-LT-0009).",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2023.12.04.23299364,2023-12-04,https://medrxiv.org/cgi/content/short/2023.12.04.23299364,Clinical coding of long COVID in primary care 2020-2023 in a cohort of 19 million adults: an OpenSAFELY analysis,Alasdair D Henderson; Ben FC Butler-Cole; John Tazare; Laurie A Tomlinson; Michael Marks; Mark Jit; Andrew Briggs; Liang-Yu Lin; Oliver Carlile; Christopher Bates; John Parry; Sebastian CJ Bacon; Iain Dillingham; William A Dennison; Ruth E Costello; Yinghui Wei; Alex J Walker; William Hulme; Ben Goldacre; Amir Mehrkar; Brian MacKenna; The OpenSAFELY Collaborative; Emily Herrett; Rosalind M Eggo,"London School of Hygiene & Tropical Medicine; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; TPP, TPP House, 129 Low Lane, Horsforth, Leeds; TPP, TPP House, 129 Low Lane, Horsforth, Leeds; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Patient and Public Involvement Steering Committee, London,; London School of Hygiene & Tropical Medicine; Centre for Mathematical Sciences, School of Engineering, Computing and Mathematics, University of Plymouth, Plymouth; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine","BackgroundLong COVID is the patient-coined term for the persistent symptoms of COVID-19 illness for weeks, months or years following the acute infection. There is a large burden of long COVID globally from self-reported data, but the epidemiology, causes and treatments remain poorly understood. Primary care is used to help identify and treat patients with long COVID and therefore Electronic Health Records (EHRs) of past COVID-19 patients could be used to help fill these knowledge gaps. We aimed to describe those with long COVID in primary care records in England. - -MethodsWith the approval of NHS England we used routine clinical data from over 19 million adults in England linked to SARS-COV-2 test result, hospitalisation and vaccination data to describe trends in the recording of 16 clinical codes related to long COVID between November 2020 and January 2023. We calculated rates per 100,000 person-years and plotted how these changed over time. We compared crude and minimally adjusted rates of recorded long COVID in patient records between different key demographic and vaccination characteristics using negative binomial models. - -FindingsWe identified a total of 55,465 people recorded to have long COVID over the study period, with incidence of new long COVID records increasing steadily over 2021, and declining over 2022. The overall rate per 100,000 person-years was 177.5 cases in women (95% CI: 175.5-179) and 100.5 men (99.5-102). In terms of vaccination against COVID-19, the lowest rates were observed in those with 3+ vaccine doses (103.5 [95% CI: 101.5-105]). Finally, the majority of those with a long COVID record did not have a recorded positive SARS-COV-2 test 12 weeks before the long COVID record. - -InterpretationEHR recorded long COVID remains very low compared and incident records of long COVID declined over 2022. We found the lowest rates of recorded long COVID in people with 3 or more vaccine doses. We summarised several sources of possible bias for researchers using EHRs to study long COVID.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.11.30.23299229,2023-12-01,https://medrxiv.org/cgi/content/short/2023.11.30.23299229,Population age as a key factor in the COVID-19 pandemic dynamics,Igor Nesteruk; Matt Keeling,"Institute of Hydromechanics National Academy of sciences of Ukraine; School of Life Sciences & Mathematics Institute, University of Warwick, UK","The population and governments of many countries are losing interest in the SARS-CoV-2 infection, the number of tests and the number of new cases detected is sharply decreasing. To compare the accumulated numbers CC of cases and deaths DC per million and to answer the question why the less vaccinated Africa has accumulated 36 times lower CC values and 15 times lower DC values than Europe, simple statistical analysis have been performed. CC and DC values demonstrated rather strong correlation with the median age of populations. One-year increment in the median year yields 12-18 thousand increase in CC values and 52-83 increase in DC values. Zero-COVID countries succeed to have much lower numbers of deaths per capita and case fatality ratios DC/CC.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.11.28.23299156,2023-11-29,https://medrxiv.org/cgi/content/short/2023.11.28.23299156,Examining the association of live virus neutralisation activity of capillary microsamples and risk of SARS-CoV-2 infections: a nested case control study within the Virus Watch community cohort,Alexei Yavlinsky; Vincent Nguyen; Sarah Beale; Emma Wall; Mary Y Wu; Isobel Braithwaite; Jana Kovar; Madhumita Shrotri; Annalan Mathew Dwight Navaratnam; Wing Lam Erica Fong; Thomas Edward Byrne; Francois Balloux; Ibrahim Abubakar; Benjamin J Cowling; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; The Francis Crick Institute; The Francis Crick Institute; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; The University of Hong Kong; University College London; University College London,"Due to the proliferation of new SARS-CoV-2 variants, most COVID-19 cases are now caused by post-vaccine infections and a substantial proportion are reinfections. While prior research on correlates of protection has focused on the role of anti-spike antibodies, the results of the corresponding antibody assays may not accurately predict the risk of infection with new SARS-CoV-2 variants. In this study, we investigated the association between live virus neutralising antibody activity and SARS-CoV-2 infection risk using self-administered capillary microsample blood tests from VirusWatch participants. The study was conducted during the transition between the dominance of the B.1.617.2 (Delta) and B.1.1.529 (Omicron BA.1) SARS-CoV-2 variants, enabling us to investigate the association between variant-specific virus inhibition and subsequent infections within each dominance period. Greater inhibition of Omicron BA.1 live virus was associated with a reduction in infection risk during both the Delta and Omicron BA.1 dominance periods. Delta virus inhibition was associated with infection risk reduction during the Delta dominance period, but we found no association between Delta inhibition and protection against infection during the Omicron BA.1 dominance period. Our results are consistent with earlier findings and suggest that variant-specific serosurveillance of immunity and protection against SARS-CoV-2 infection at the population level could inform public health policy in near-real time using inexpensive and accessible home-based testing.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.11.24.23296021,2023-11-27,https://medrxiv.org/cgi/content/short/2023.11.24.23296021,Severe acute myositis and myocarditis upon initiation of six-weekly Pembrolizumab post-COVID-19 mRNA vaccination,Robert Aerwyn Watson; Weiyu Ye; Chelsea Alice Taylor; Rosalin Anisha Cooper; Orion Tong; Tim James; Brian Shine; Monika Hofer; Damian Jenkins; Robert Pell; Eleni Ieremia; Stephanie Jones; David Maldonado-Perez; Ian Roberts; Nicholas Coupe; Mark Ross Middleton; Miranda Jane Payne; Benjamin Peter Fairfax,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford,"We describe three cases of critical acute myositis with myocarditis occurring within 22 days of each other at a single institution, all within one month of receiving the initial cycle of the anti-PD-1 drug Pembrolizumab. Analysis of T cell receptor repertoires from peripheral blood and tissues revealed a high degree of clonal expansion and public clones between cases, with several T cell clones expanded within the skeletal muscle putatively recognising viral epitopes. All patients had recently received a COVID-19 mRNA booster vaccine prior to treatment and were positive for SARS-CoV2 Spike antibody. In conclusion, we report a series of unusually severe myositis and myocarditis following PD-1 blockade and the COVID-19 mRNA vaccination.",oncology,fuzzy,100,100 @@ -122,13 +115,6 @@ MethodsConcentrations for black carbon(BC), particulate matter 10(PM10), particu ResultsSingle pollutant analysis showed the direct effect of higher risk of SARS-CoV-2 infection with increased exposure to PM2.5(RR1.11,95%CI 1.08;1.15), PM10(RR1.06,95%CI 1.04;1.09), NO2(RR1.04,95%CI 1.04;1.05) and NOx(RR1.02,95%CI 1.02;1.02) per 1{micro}g/m3 increment with DEFRA 2015-19 data. Sensitivity analyses altering covariates, exposure window and modelled air pollution data source produced similar estimates. Higher risk of SARS-CoV-2 per 10-5m-1 increment of BC (RR1.86, 95%CI 1.62;2.14) was observed using ELAPSE data. ConclusionLong term exposure to higher concentrations of air pollutions increases the risk of SARS-CoV-2 infection, highlighting that adverse health effects of air pollution is not only limited to non-communicable diseases.",epidemiology,fuzzy,100,100 -bioRxiv,10.1101/2023.10.22.563481,2023-10-24,https://biorxiv.org/cgi/content/short/2023.10.22.563481,Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy,Ashley Priddey; Michael Xin Hua Chen-Xu; Daniel James Cooper; Serena MacMillan; Georg Meisl; Catherine K Xu; Myra Hosmillo; Ian G Goodfellow; Rafael Kollyfas; Rainer Doffinger; John R Bradley; Irina I Mohorianu; Rachel Jones; Tuomas P.J. Knowles; Rona Smith; Vasilis Kosmoliaptsis,"Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D","BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. - -MethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). - -ResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. - -DiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.",immunology,fuzzy,100,100 medRxiv,10.1101/2023.10.12.23296948,2023-10-13,https://medrxiv.org/cgi/content/short/2023.10.12.23296948,"A nationwide study of 331 rare diseases among 58 million individuals: prevalence, demographics, and COVID-19 outcomes",Johan H Thygesen; HUAYU ZHANG; Hanane Issa; Jinge Wu; Tuankasfee Hama; Ana-Catarina Pinho-Gomes; Tudor Groza; Sara Khalid; Richard Lumbers; Mevhibe Hocaoglu; Kamlesh Khunti; Rouven Priedon; Amitava Banerjee; Nikolas Pontikos; Christopher Tomlinson; Ana Torralbo; Paul Taylor; Cathie Sudlow; Spiros Denaxas; Harry Hemingway; Honghan Wu,"Institute of Health Informatics, University College London, London, UK; Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, UK.; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK; Institute of Health Informatics, University College London, London, UK; Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, Kings College London, London, UK; College of Life Sciences, University of Leicester, Leicester, UK; Health Data Research UK, London, UK; Institute of Health Informatics, University College London, London, UK; UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Health Data Research UK, London, UK; British Heart Foundation Data Science Centre, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edin; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK","BackgroundThe Global Burden of Disease study has provided key evidence to inform clinicians, researchers, and policy makers across common diseases, but no similar effort with single study design exists for hundreds of rare diseases. Consequently, many rare conditions lack population-level evidence including prevalence and clinical vulnerability. This has led to the absence of evidence-based care for rare diseases, prominently in the COVID-19 pandemic. MethodThis study used electronic health records (EHRs) of more than 58 million people in England, linking nine National Health Service datasets spanning healthcare settings for people alive on Jan 23, 2020. Starting with all rare diseases listed in Orphanet, we quality assured and filtered down to analyse 331 conditions with ICD-10 or SNOMED-CT mappings clinically validated in our dataset. We report 1) population prevalence, clinical and demographic details of rare diseases, and 2) investigate differences in mortality with SARs-CoV-2. @@ -326,6 +312,21 @@ MethodsRetrospective cohort study of non-hospitalised patients diagnosed with CO ResultsA total of 2548 patients were included (492: sotrovimab, 276: nirmatrelvir/ritonavir, 71: molnupiravir, and 1709 eligible highest-risk untreated). Patients aged [≥]75 years accounted for 6.9% (n=34/492) of the sotrovimab-treated group, 21.0% (n=58/276) of those treated with nirmatrelvir/ritonavir, 16.9% (n=12/71) of those treated with molnupiravir and 13.2% (n=225/1709) of untreated patients. Advanced renal disease was reported for 6.7% (n=33/492) of sotrovimab-treated and 4.7% (n=81/1709) of untreated patients, and five or fewer patients in the nirmatrelvir/ritonavir and molnupiravir cohorts. A high proportion of treated patients did not have a highest-risk condition reported in the database (71.7% for sotrovimab [n=353/492], 85.1% for nirmatrelvir/ritonavir [n=235/276], 85.9% for molnupiravir [n=61/71]). Five or fewer patients in each treated cohort experienced COVID-19-related hospitalisations during the 28-day acute period. For untreated patients, the percentage of COVID-19-related hospitalisations was 3.0% (n=48/1622). All-cause hospitalisations were experienced by 5.3% (n=25/476) of sotrovimab-treated patients, 6.9% (n=12/175) of nirmatrelvir/ritonavir-treated patients and 13.3% (n=216/1622) of untreated patients. Five or fewer patients in the molnupiravir cohort experienced all-cause hospitalisation. There were no deaths within 28 days of index for patients in the treated cohorts. Mortality was 4.3% (n=70/1622) in untreated patients (18.6% [n=13/70] had COVID-19 as the primary cause). In our analyses of outcomes for sotrovimab-treated and untreated patients during BA.1, BA.2 and BA.5 predominance, COVID-19-related hospitalisation rates were consistent, with n[≤]5 for sotrovimab-treated patients in each period. ConclusionsOur findings indicate that sotrovimab was often used amongst patients who were aged <75 years old and had advanced renal disease. Among patients who received early COVID-19 treatment, proportions of all-cause hospitalisation and death within 28 days of treatment were low.",infectious diseases,fuzzy,100,92 +bioRxiv,10.1101/2023.06.12.544667,2023-06-12,https://biorxiv.org/cgi/content/short/2023.06.12.544667,Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic,Katharine Sherratt; Anna C Carnegie; Adam Kucharski; Anne Cori; Carl AB Pearson; Christopher I Jarvis; Christopher Overton; Dale Weston; Edward M Hill; Edward Knock; Elizabeth Fearon; Emily Nightingale; Joel Hellewell; W John Edmunds; Julian Villabona Arenas; Kiesha Prem; Li Pi; Marc Baguelin; Michelle Kendall; Neil Ferguson; Nicholas Davies; Rosalind M Eggo; Sabine van Elsland; Timothy Russell; Sebastian Funk; Yang Liu; Sam Abbott,"Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & South African DSI-NRF Centre of Excellence in Epide; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; All Hazards Intelligence, Data Analytics and Surveillance, UK Health Security Agency, UK & Department of Mathematical Sciences, University of Liverpool, UK & De; Emergency Response Department Science & Technology Behavioural Science, UK Health Security Agency, UK; Warwick Mathematics Institute and The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, UK & Joint UNIvers; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK; Institute for Global Health, University College London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & Saw Swee Hock School of Public Health, National Uni; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & MRC Centre for Global Infectious Disease Analysis, ; Warwick Mathematics Institute and The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & European Molecular Biology Laboratory, European Bio; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK","The COVID-19 pandemic both relied and placed significant burdens on the experts involved from research and public health sectors. The sustained high pressure of a pandemic on responders, such as healthcare workers, can lead to lasting psychological impacts including acute stress disorder, post-traumatic stress disorder, burnout, and moral injury, which can impact individual wellbeing and productivity. As members of the infectious disease modelling community, we convened a reflective workshop to understand the professional and personal impacts of response work on our community and to propose recommendations for future epidemic responses. The attendees represented a range of career stages, institutions, and disciplines. This piece was collectively produced by those present at the session based on our collective experiences. Key issues we identified at the workshop were lack of institutional support, insecure contracts, unequal credit and recognition, and mental health impacts. Our recommendations include rewarding impactful work, fostering academia-public health collaboration, decreasing dependence on key individuals by developing teams, increasing transparency in decision-making, and implementing sustainable work practices. Despite limitations in representation, this workshop provided valuable insights into the UK COVID-19 modelling experience and guidance for future public health crises. Recognising and addressing the issues highlighted is crucial, in our view, for ensuring the effectiveness of epidemic response work in the future.",scientific communication and education,fuzzy,100,100 +medRxiv,10.1101/2023.05.31.23290774,2023-06-05,https://medrxiv.org/cgi/content/short/2023.05.31.23290774,POST-COVID ORTHOPAEDIC ELECTIVE RESOURCE PLANNING USING SIMULATION MODELLING,Alison Harper; Thomas Monks; Rebecca Wilson; Maria Theresa Redaniel; Emily Eyles; Timothy Jones; Chris Penfold; Andrew Elliott; Tim Keen; Martin Pitt; Ashley Blom; Michael Whitehouse; Andrew Judge,University of Exeter; University of Exeter; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; North Bristol NHS Foundation Trust; North Bristol NHS Foundation Trust; University of Exeter; University of Sheffield; University of Bristol; University of Bristol,"ObjectivesTo develop a simulation model to support orthopaedic elective capacity planning. + +MethodsAn open-source, generalisable discrete-event simulation was developed, including a web-based application. The model used anonymised patient records between 2016-2019 of elective orthopaedic procedures from an NHS Trust in England. In this paper, it is used to investigate scenarios including resourcing (beds and theatres) and productivity (lengths-of-stay, delayed discharges, theatre activity) to support planning for meeting new NHS targets aimed at reducing elective orthopaedic surgical backlogs in a proposed ring fenced orthopaedic surgical facility. The simulation is interactive and intended for use by health service planners and clinicians. + +ResultsA higher number of beds (65-70) than the proposed number (40 beds) will be required if lengths-of-stay and delayed discharge rates remain unchanged. Reducing lengths-of-stay in line with national benchmarks reduces bed utilisation to an estimated 60%, allowing for additional theatre activity such as weekend working. Further, reducing the proportion of patients with a delayed discharge by 75% reduces bed utilisation to below 40%, even with weekend working. A range of other scenarios can also be investigated directly by NHS planners using the interactive web app. + +ConclusionsThe simulation model is intended to support capacity planning of orthopaedic elective services by identifying a balance of capacity across theatres and beds and predicting the impact of productivity measures on capacity requirements. It is applicable beyond the study site and can be adapted for other specialties. + +Strengths and Limitations of this studyO_LIThe simulation model provides rapid quantitative estimates to support post-COVID elective services recovery toward medium-term elective targets. +C_LIO_LIParameter combinations include changes to both resourcing and productivity. +C_LIO_LIThe interactive web app enables intuitive parameter changes by users while underlying source code can be adapted or re-used for similar applications. +C_LIO_LIPatient attributes such as complexity are not included in the model but are reflected in variables such as length-of-stay and delayed discharge rates. +C_LIO_LITheatre schedules are simplified, incorporating the five key orthopaedic elective surgical procedures. +C_LI",orthopedics,fuzzy,100,100 medRxiv,10.1101/2023.05.23.23290354,2023-05-28,https://medrxiv.org/cgi/content/short/2023.05.23.23290354,Long COVID and financial outcomes: Evidence from four longitudinal population surveys,Rebecca Rhead; Jacques Wels; Bettina Moltrecht; Richard John Shaw; Richard John Silverwood; Jingmin Zhu; Alun Hughes; Nishi Chaturvedi; Evangelia Demou; Srinivasa Vittal Katikireddi; George Ploubidis,King's College London Institute of Psychiatry Psychology and Neuroscience; University College London; University College London; University of Glasgow; University College London; University College London; UCL; University College London; University of Glasgow; University of Glasgow; University College London,"BackgroundLong-term sequelae of COVID-19 (long COVID) include muscle weakness, fatigue, breathing difficulties and sleep disturbance over weeks or months. Using UK longitudinal data, we assessed the relationship between long COVID and financial disruption. MethodsWe estimated associations between long COVID (derived using self-reported length of COVID-19 symptoms) and measures of financial disruption (subjective financial well-being, new benefit claims, changes in household income) by analysing data from four longitudinal population studies, gathered during the first year of the pandemic. We employed modified Poisson regression in a pooled analysis of the four cohorts adjusting for a range of potential confounders, including pre-pandemic (pre-long COVID) factors. @@ -380,15 +381,6 @@ MethodsWe included UK COVID-19 Infection Survey participants who tested positive ResultsOverall, Long Covid was reported by those [≥]16 years after 4.0% and 2.4% of first and second infections, respectively; the corresponding estimates among those <16 years were 1.0% and 0.6%. The aOR for Long Covid after second compared to first infections was 0.72 (95% confidence interval: 0.63-0.81) for those [≥]16 years and 0.93 (0.57-1.53) for those <16 years. ConclusionsThe risk of new-onset Long Covid after a second SARS-CoV-2 infection is lower than that after a first infection for those [≥]16 years, though there is no evidence of a difference in risk for those <16 years. However, there remains some risk of new-onset Long Covid after a second infection, with around 1 in 40 of those [≥]16 years and 1 in 165 of those <16 years reporting Long Covid after a second infection.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2023.03.24.23287700,2023-03-26,https://medrxiv.org/cgi/content/short/2023.03.24.23287700,The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey,Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes,University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester,"ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection. - -DesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups. - -Setting - -ResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage. - -ConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2023.03.24.23287666,2023-03-24,https://medrxiv.org/cgi/content/short/2023.03.24.23287666,Occupational differences in the prevalence and severity of long-COVID: Analysis of the ONS Coronavirus (COVID-19) Infection Survey,Theocharis Kromydas; Evangelia Demou; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Neil Pearce; Martie van Tongeren; Jack Wilkinson; Sarah Rhodes,University of Glasgow; University of Glasgow; Lancaster University; University of Manchester; University of Glasgow; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester,"ObjectivesTo establish whether prevalence and severity of long-COVID symptoms vary by industry and occupation. MethodsWe utilised ONS Coronavirus Infection Survey (CIS) data (February 2021-April 2022) of working-age participants (16-65 years). Exposures were industrial sector, occupation and major Standard Occupational Classification (SOC) group. Outcomes were self-reported: (1) long-COVID symptoms; and (2) reduced function due to long-COVID. Binary (outcome 1) and ordered (outcome 2) logistic regression were used to estimate odds ratios (OR) and prevalence (marginal means) for all exposures. @@ -1072,7 +1064,6 @@ MethodsCOVIDENCE UK is a longitudinal population-based study that investigates r ResultsThe study was launched on 1st May 2020 and closed to recruitment on 6th October 2021. A total of 19,981 participants enrolled and consented to 5-year follow-up with medical record linkage. Their mean age was 59.1 years (range 16.0 to 94.4 years), 70.2% were female, and 93.7% identified their ethnic origin as White. Analyses conducted to date have provided key insights into risk factors for SARS-CoV-2 infection and COVID-19 disease, determinants of SARS-CoV-2 vaccine immunogenicity and efficacy, and impacts of COVID-19 on health economic outcomes. The cohort has also supported conduct of a Phase 3 randomised trial-within-cohort study (CORONAVIT) evaluating implementation of a test-and-treat approach to correcting sub-optimal vitamin D status on incidence and severity of acute respiratory infections, including COVID-19. ConclusionsThe COVIDENCE UK dataset represents a valuable resource containing granular information on factors influencing susceptibility to, and impacts of, COVID-19 in UK adults. Researchers wishing to access anonymised participant-level data should contacting the corresponding author for further information.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.06.20.22275994,2022-06-20,https://medrxiv.org/cgi/content/short/2022.06.20.22275994,Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies,Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood,King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London,"Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.06.18.22276437,2022-06-19,https://medrxiv.org/cgi/content/short/2022.06.18.22276437,A patient-centric characterization of systemic recovery from SARS-CoV-2 infection,Hélène Ruffieux; Aimee Hanson; Samantha Lodge; Nathan Lawler; Luke Whiley; Nicola Gray; Tui Nolan; Laura Bergamaschi; Federica Mescia; - CITIID-NIHR COVID BioResource Collaboration; Nathalie Kingston; John Bradley; Elaine Holmes; Julien Wist; Jeremy Nicholson; Paul Lyons; Kenneth Smith; Sylvia Richardson; Glenn Bantug; Christoph Hess,University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; ; University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; University and University Hospital Basel; University of Cambridge,"The biology driving individual patient responses to SARS-CoV-2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data, covering a year post disease onset, from 215 SARS-CoV-2 infected subjects with differing disease severities. Our analyses revealed distinct ""systemic recovery"" profiles with specific progression and resolution of the inflammatory, immune, metabolic and clinical responses, over weeks to several months after infection. In particular, we found a strong intra-patient temporal covariation of innate immune cell numbers, kynurenine- and host lipid-metabolites, which suggested candidate immunometabolic pathways putatively influencing restoration of homeostasis, the risk of death and of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery on the patient level, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool http://shiny.mrc-bsu.cam.ac.uk/apps/covid-systemic-recovery-prediction-app, designed to test our findings prospectively. Graphical abstract @@ -1094,6 +1085,19 @@ HighlightsO_LIClinical frontline healthcare workers (HCWs) have been exposed to C_LIO_LIHCWs described the significant adverse impact of this exposure on their mental health, including increased anxiety and depression symptoms and sleep disturbance C_LIO_LIMost HCWs interviewed believed that organisational change within the NHS was necessary to prevent excess PMIE exposure and promote resolution of moral distress C_LI",psychiatry and clinical psychology,fuzzy,100,100 +medRxiv,10.1101/2022.06.16.22276479,2022-06-16,https://medrxiv.org/cgi/content/short/2022.06.16.22276479,Mental health of healthcare workers in England during the COVID-19 pandemic: a longitudinal cohort study,Danielle Lamb; Rafael Gafoor; Hannah Scott; Ewan Carr; Sharon Stevelink; Rosalind Raine; Matthew Hotopf; Neil Greenberg; Siobhan Hegarty; Ira Madan; Paul Moran; Richard Morriss; Dominic Murphy; Anne Marie Rafferty; Scott Weich; Sarah Dorrington; Simon Wessely,UCL; University College London; King's College London; King's College London; King's College London; University College London; King's College London; King's College London; King's College London; Guy's and St Thomas' NHS Foundation Trust; University of Bristol; University of Nottingham; Combat Stress; King's College London; University of Sheffield; King's College London; King's College London,"ObjectiveTo examine variations in impact of the COVID-19 pandemic on the mental health of all types of healthcare workers (HCWs) in England over the first 17 months of the pandemic. + +MethodWe undertook a prospective cohort study of 22,501 HCWs from 18 English acute and mental health NHS Trusts, collecting online survey data on common mental disorders (CMDs), depression, anxiety, alcohol use, and PTSD, from April 2020 to August 2021. We analysed these data cross-sectionally by time period (corresponding to periods the NHS was under most pressure), and longitudinally. Data were weighted to better represent Trust population demographics. + +ResultsThe proportion of those with probable CMDs was greater during periods when the NHS was under most pressure (measured by average monthly deaths). For example, 55% (95%CI 53%, 58%) of participants reported symptoms of CMDs in April-June 2020 versus 47% (95%CI 46%, 48%) July-October 2020. Contrary to expectation, there were no major differences between professional groups (i.e. clinical and non-clinical staff). Younger, female, lower paid staff, who felt poorly supported by colleagues/managers, and who experienced potentially morally injurious events were most at risk of negative mental health outcomes. + +ConclusionAmong HCWs, the prevalence of probable CMDs increased during periods of escalating pressure on the NHS, suggesting staff support should be increased at such points in the future, and staff should be better prepared for such situations via training. All staff, regardless of role, experienced poorer mental health during these periods, suggesting that support should be provided for all staff groups. + +Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSExisting evidence about the mental health of healthcare workers (HCWs) through the COVID-19 pandemic comes mainly from cross-sectional studies using unrepresentative convenience samples, typically focussing on clinical staff rather than all HCWs. Such studies show high prevalence of symptoms of mental disorders, but the strength of this evidence is uncertain. + +What this study addsUsing a defined sampling frame, with longitudinal, weighted data, we show that during periods of greater pressure on the NHS (as indicated by average monthly national COVID-19 death rates), prevalence of mental disorder symptoms increased, and, importantly, that this effect was seen in non-clinical as well as clinical staff. + +How this study might affect research, practice or policyThese findings indicate that provision of support for HCWs should not only focus on those providing clinical care, but also on non-clinical staff such as porters, cleaners, and administrative staff, and additional support should be provided during higher pressure periods. Better preparation of staff for such situations is also suggested.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2022.06.16.22276487,2022-06-16,https://medrxiv.org/cgi/content/short/2022.06.16.22276487,"Capturing the experiences of UK healthcare workers during the COVID-19 pandemic: A structural topic modelling analysis of 7,412 free-text survey responses",Danielle Lamb; Liam Wright; Hannah Scott; Bethany Croak; Sam Gnanapragasam; Mary Jane Docherty; Neil Greenberg; Matthew Hotopf; Sharon Stevelink; Rosalind Raine; Simon Wessely,UCL; University College London; King's College London; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; University College London; King's College London,"BackgroundHealthcare workers (HCWs) have provided vital services during the COVID-19 pandemic, but existing research consists of quantitative surveys (lacking in depth or context) or qualitative interviews (with limited generalisability). Structural Topic Modelling (STM) of large-scale free-text survey data offers a way of capturing the perspectives of a wide range of HCWs in their own words about their experiences of the pandemic. MethodsIn an online survey distributed to all staff at 18 geographically dispersed NHS Trusts, we asked respondents, ""Is there anything else you think we should know about your experiences of the COVID-19 pandemic?"". We used STM on 7,412 responses to identify topics, and thematic analysis on the resultant topics and text excerpts. @@ -1172,6 +1176,7 @@ MethodsOn average, risk of infection is proportional to infection prevalence. Th ResultsFollowing an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was masked by the effects of vaccination and the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups. ConclusionHigh-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was highly effective at reducing risk of infection with school holidays/closures playing a significant part.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2022.05.23.22275458,2022-05-25,https://medrxiv.org/cgi/content/short/2022.05.23.22275458,Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States,Seth Flaxman; Charles Whittaker; Elizaveta Semenova; Theo Rashid; Robbie Parks; Alexandra Blenkinsop; H Juliette T Unwin; Swapnil Mishra; Samir Bhatt; Deepti Gurdasani; Oliver Ratmann,"Oxford; Imperial College London; AstraZeneca; Imperial College London; Columbia University; Imperial College London; Imperial College London; University of Copenhagen; University of Copenhagen, Imperial College London; Queen Mary University of London; Imperial College London","Covid-19 has caused more than 1 million deaths in the US, including at least 1,204 deaths among children and young people (CYP) aged 0-19 years, with 796 occurring in the one year period April 1, 2021 - March 31, 2022. Deaths among US CYP are rare in general, and so we argue here that the mortality burden of Covid-19 in CYP is best understood in the context of all other causes of CYP death. Using publicly available data from CDC WONDER on NCHSs 113 Selected Causes of Death, and comparing to mortality in 2019, the immediate pre-pandemic period, we find that Covid-19 mortality is among the 10 leading causes of death in CYP aged 0-19 years in the US, ranking 8th among all causes of deaths, 5th in disease-related causes of deaths (excluding accidents, assault and suicide), and 1st in deaths caused by infectious or respiratory diseases. Covid-19 deaths constitute 2.3% of the 10 leading causes of death in this age group. Covid-19 caused substantially more deaths in CYP than major vaccine-preventable diseases did historically in the period before vaccines became available. Various factors including underreporting and Covid-19s role as a contributing cause of death from other diseases mean that our estimates may understate the true mortality burden of Covid-19. Our findings underscore the public health relevance of Covid-19 to CYP. In the likely future context of sustained SARS-CoV-2 circulation, pharmaceutical and non-pharmaceutical interventions will continue to play an important role in limiting transmission of the virus in CYP and mitigating severe disease.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.05.22.22275417,2022-05-23,https://medrxiv.org/cgi/content/short/2022.05.22.22275417,Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe COVID-19 outcomes in non-hospitalised patients: an observational cohort study using the OpenSAFELY platform,Bang Zheng; Amelia CA Green; John Tazare; Helen J Curtis; Louis Fisher; Linda Nab; Anna Schultze; Viyaasan Mahalingasivam; Edward Parker; William J Hulme; Sebastian CJ Bacon; Nicholas J DeVito; Christopher Bates; David Evans; Peter Inglesby; Henry Drysdale; Simon Davy; Jonathan Cockburn; Caroline E Morton; George Hickman; Tom Ward; Rebecca M Smith; John Parry; Frank Hester; Sam Harper; Amir Mehrkar; Rosalind M Eggo; Alex J Walker; Stephen JW Evans; Ian J Douglas; Brian MacKenna; Ben Goldacre; Laurie A Tomlinson,London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Trop. Med.; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; TPP; TPP; University of Oxford; London School of Hygiene & Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine,"ObjectiveTo compare the effectiveness of sotrovimab (a neutralising monoclonal antibody) vs. molnupiravir (an antiviral) in preventing severe COVID-19 outcomes in non-hospitalised high-risk COVID-19 adult patients. DesignWith the approval of NHS England, we conducted a real-world cohort study using the OpenSAFELY-TPP platform. @@ -1187,7 +1192,6 @@ Main outcome measureCOVID-19 related hospitalisation or COVID-19 related death w ResultsBetween December 16, 2021 and February 10, 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, with no substantial differences in their baseline characteristics. The mean age of all 6020 patients was 52 (SD=16) years; 59% were female, 89% White and 88% had three or more COVID-19 vaccinations. Within 28 days after treatment initiation, 87 (1.4%) COVID-19 related hospitalisations/deaths were observed (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographics, high-risk cohort categories, vaccination status, calendar time, body mass index and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio, HR=0.54, 95% CI: 0.33 to 0.88; P=0.014). Consistent results were obtained from propensity score weighted Cox models (HR=0.50, 95% CI: 0.31 to 0.81; P=0.005) and when restricted to fully vaccinated people (HR=0.53, 95% CI: 0.31 to 0.90; P=0.019). No substantial effect modifications by other characteristics were detected (all P values for interaction>0.10). Findings were similar in an exploratory analysis of patients treated between February 16 and May 1, 2022 when the Omicron BA.2 variant was dominant in England. ConclusionIn routine care of non-hospitalised high-risk adult patients with COVID-19 in England, those who received sotrovimab were at lower risk of severe COVID-19 outcomes than those receiving molnupiravir.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.05.21.22275368,2022-05-23,https://medrxiv.org/cgi/content/short/2022.05.21.22275368,"Variant-specific symptoms of COVID-19 among 1,542,510 people in England",Matthew Whitaker; Joshua Elliott; Barbara Bodinier; Wendy S Barclay; Helen Ward; Graham Cooke; Christl A Donnelly; Marc Chadeau-Hyam; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health,"Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.",infectious diseases,fuzzy,96,100 medRxiv,10.1101/2022.05.19.22275214,2022-05-22,https://medrxiv.org/cgi/content/short/2022.05.19.22275214,Antibody levels following vaccination against SARS-CoV-2: associations with post-vaccination infection and risk factors,Nathan J Cheetham; Milla Kibble; Andrew Wong; Richard J Silverwood; Anika Knuppel; Dylan M Williams; Olivia K L Hamilton; Paul H Lee; Charis Bridger Staatz; Giorgio Di Gessa; Jingmin Zhu; Srinivasa Vittal Katikireddi; George B Ploubidis; Ellen J Thompson; Ruth C E Bowyer; Xinyuan Zhang; Golboo Abbasian; Maria Paz Garcia; Deborah Hart; Jeffrew Seow; Carl Graham; Neophytos Kouphou; Sam Acors; Michael H Malim; Ruth E Mitchell; Kate Northstone; Daniel Major-Smith; Sarah Matthews; Thomas Breeze; Michael Crawford; Lynn Molloy; Alex Siu Fung Kwong; Katie J Doores; Nishi Chaturvedi; Emma L Duncan; Nicholas J Timpson; Claire J Steves,King's College London; University of Cambridge; University College London; University College London; University College London; University College London; University of Glasgow; University of Leicester; University College London; University College London; University College London; University of Glasgow; University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; King's College London; University College London; King's College London; University of Bristol; King's College London,"SARS-CoV-2 antibody levels can be used to assess humoral immune responses following SARS-CoV-2 infection or vaccination, and may predict risk of future infection. From cross-sectional antibody testing of 9,361 individuals from TwinsUK and ALSPAC UK population-based longitudinal studies (jointly in April-May 2021, and TwinsUK only in November 2021-January 2022), we tested associations between antibody levels following vaccination and: (1) SARS-CoV-2 infection following vaccination(s); (2) health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables. Within TwinsUK, single-vaccinated individuals with the lowest 20% of anti-Spike antibody levels at initial testing had 3-fold greater odds of SARS-CoV-2 infection over the next six to nine months, compared to the top 20%. In TwinsUK and ALSPAC, individuals identified as at increased risk of COVID-19 complication through the UK ""Shielded Patient List"" had consistently greater odds (2 to 4-fold) of having antibody levels in the lowest 10%. Third vaccination increased absolute antibody levels for almost all individuals, and reduced relative disparities compared with earlier vaccinations. @@ -1204,23 +1208,6 @@ OutcomesPooled estimates of the standardized difference in outcome between those InterpretationSelf-reporting COVID-19 was longitudinally associated with deterioration in mental health and life satisfaction. Our findings have important implications for mental health service provision, given the substantial prevalence of COVID-19 in the UK and worldwide. FundingMRC and NIHR",psychiatry and clinical psychology,fuzzy,100,100 -medRxiv,10.1101/2022.05.09.22274769,2022-05-11,https://medrxiv.org/cgi/content/short/2022.05.09.22274769,"COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from the Born In Wales study",Mohamed Mhereeg; Hope Jones; Jonathan Kennedy; Michael Seaborne; Michael Parker; Natasha Kennedy; Sarah Beeson; Luisa Zuccolo; Alisha Davies; Sinead Brophy,"Swansea University Medical School, Swansea, Wales, UK; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Bristol Medical School, University of Bristol, Bristol, England, UK.; Public Health Wales, UK; Swansea University Medical School, Swansea, Wales, UK","BackgroundVaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics. - -ObjectivesThe aims of this study were to 1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health records (EHR) linkage, and 2) explore pregnant womens views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born in Wales Cohort). - -DesignA mixed methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) (Objective 1) and the Born In Wales Birth Cohort participants (Objective 2). SAIL combines data from general practice, hospital admissions, the national community child health dataset, maternal indicators dataset, and COVID-19 vaccination databases. - -Setting and participantsObjective 1) All women documented as being pregnant on or after 13th April 2021, aged 18 years or older, and eligible for COVID-19 vaccination were identified in routine health care. They were linked to the vaccination data up to and including 31st December 2021. Objective 2) Separately, a cross-section of pregnant women in Wales were invited to complete an online survey via social media advertising. The survey asked what their views were on having the COVID-19 vaccination during pregnancy, and if they had already received, or intended to receive, the COVID-19 vaccination during their pregnancies. They were also asked to give reasons for their decisions. - -Outcomes1 (a). Rate of vaccination uptake per month during pregnancy among women eligible for vaccination. 1 (b). Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnicity, and deprivation area was examined using hazard ratios (HR) from Cox regression. 2.Expectant mothers views of the COVID-19 vaccination during pregnancy. - -Results - -Population-level data linkage (objective 1)Within the population cohort, 32.7% (n = 8,203) were vaccinated (at least one dose of the vaccine) during pregnancy, 34.1% (n = 8,572) remained unvaccinated throughout follow-up period, and 33.2% (n = 8,336) received the vaccine postpartum. Younger women (<30 years) were less likely to have the vaccine and those living in areas of high deprivation were also less likely to have the vaccine (HR=0.88, 95% CI 0.82 to 0.95). Asian and other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared to women of White ethnicity (HR=1.12, 95% CI 1.00 to 1.25) and (HR=1.18, 95% CI 1.03 to 1.37) respectively. - -Survey responses (objective 2)69% of participants stated that they would be happy to have the vaccine during pregnancy (n = 207). The remainder, 31%, indicated that they would not have the vaccine during pregnancy (n = 94). Reasons for having the vaccine related to protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy. - -ConclusionPotentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and to decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation level areas.",public and global health,fuzzy,100,100 bioRxiv,10.1101/2022.05.07.491004,2022-05-10,https://biorxiv.org/cgi/content/short/2022.05.07.491004,SARS-CoV-2 Spike N-Terminal Domain modulates TMPRSS2-dependent viral entry and fusogenicity,Bo Meng; Rawlings Datir; Jinwook Choi; - CITIID-NIHR BioResource COVID-19 Collaboration; John Bradley; Kenneth GC Smith; Joo Hyeon Lee; Ravindra K Gupta,University of Cambridge; University of Cambridge; University of Cambridge; -; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge,"Over 20 mutations have been identified in the N-Terminal Domain (NTD) of SARS-CoV-2 spike and yet few of them are fully characterised. Here we first examined the contribution of the NTD to infection and cell-cell fusion by constructing different VOC-based chimeric spikes bearing B.1617 lineage (Delta and Kappa variants) NTDs and generating spike pseudotyped lentivirus (PV). We found the Delta NTD on a Kappa or WT background increased spike S1/S2 cleavage efficiency and virus entry, specifically in Calu-3 lung cells and airway organoids, through use of TMPRSS2. We have previously shown Delta spike confers rapid cell-cell fusion kinetics; here we show that increased fusogenicity can be conferred to WT and Kappa variant spikes by transfer of the Delta NTD. Moving to contemporary variants, we found that BA.2 had higher entry efficiency in a range of cell types as compared to BA.1. BA.2 showed higher fusogenic activity than BA.1, but the BA.2 NTD could not confer higher fusion to BA.1 spike. There was low efficiency of TMPRSS2 usage by both BA.1 and BA.2, and chimeras of Omicron BA.1 and BA.2 spikes with a Delta NTD did not result in more efficient use of TMRPSS2 or cell-cell fusogenicity. We conclude that the NTD allosterically modulates S1/S2 cleavage and spike-mediated functions such as entry and cell-cell fusion in a spike context dependent manner, and allosteric interactions may be lost when combining regions from more distantly related spike proteins. These data may explain the lack of successful SARS-CoV-2 inter-variant recombinants bearing breakpoints within spike.",microbiology,fuzzy,100,100 medRxiv,10.1101/2022.05.10.22274890,2022-05-10,https://medrxiv.org/cgi/content/short/2022.05.10.22274890,Biopsychosocial response to the COVID-19 lockdown in people with major depressive disorder and multiple sclerosis.,Sara Siddi; Iago Gine Vazquez; Raquel Bailon; Faith Matcham; Femke Lamers; Spyridon Kontaxis; Estela Laporta Puyal; Esther Garcia; Belen Arranz; Gloria Dallacosta; Anna Isabel Guerrero Perez; Anna Zabalza; Mathias Buron; Giancarlo Comi; Letizia Leocani; Peter Annas; Matthew Hotopf; Brenda Penninx; Melinda Magyari; Per Sorensen; Xavier Montalban; Grace Lavalle; Alina Ivan; Carolin Oetzmann; Katie White; Sonia Difrancesco; Patrick Locatelli; Jordi Aguilo; Vaibhav Narayan; Amos Folarin; Richard Dobson; Judith Anne Dineley; Daniel Leightley; Nicholas Cummins; Yarharth Ranjan; Zulqarnain Rashid; Aki Rintala; Giovanni De Girolamo; Antonio Preti; Sara Simblett; Til Wykes; Inez Myin-Germeys; Josep Maria Haro,"Parc Sanitari Sant Joan de Deu Cibersam; Parc Sanitari Sant Joan de Deu Cibersam; Universidad de Zaragoza; King's College London; Amsterdam UMC Locatie AMC, Amsterdam, North Holland, NL; Universidad de Zaragoza; Universidad de Zaragoza; Universitat Autonoma de Barcelona; Parc Sanitari Sant Joan de Deu Cibersam; Istituto di Ricovero e Cura a Carattere Scientifico Ospedale San Raffaele Milano; Vall d'Hebron Institut de Recerca; Vall d'Hebron Institut de Recerca; Copenhagen University Hospital Kobenhavn; Istituto di Ricovero e Cura a Carattere Scientifico Ospedale San Raffaele Milano; Istituto di Ricovero e Cura a Carattere Scientifico Ospedale San Raffaele Milano; H Lundbeck AS Valby; Institute of Psychiatry, Psychological Medicine; Amsterdam UMC Locatie AMC, Amsterdam, North Holland, NL; Copenhagen University Hospital Kobenhavn; Copenhagen University Hospital Kobenhavn; Vall d'Hebron Institut de Recerca; King's College London; King's College London; King's College London; King's College London; Amsterdam UMC Locatie AMC, Amsterdam, North Holland, NL; University of Bergamo; Universitat Autonoma de Barcelona; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Katholieke Universiteit Leuven; Centro San Giovanni di Dio Fatebenefratelli; Universita degli Studi di Torino; King's College London; King's College London; KU Leuven; Parc Sanitari Sant Joan de Deu Cibersam","BackgroundChanges in lifestyle, finances and work status during COVID-19 lockdowns may have led to biopsychosocial changes in people with pre-existing vulnerabilities such as Major Depressive Disorders (MDD) and Multiple Sclerosis (MS). @@ -1343,13 +1330,6 @@ Several reported interventions or factors suggest the potential to mitigate the Approximately one per cent of the global population resides in care homes, while care home residents account for nearly one-third of deaths attributed to COVID-19 in the 25 countries studied. Reducing this ratio requires analysing current care home infrastructures, funding models, and incentives for providing high-quality care. The scale of the problem in care homes requires robust evaluation and coordinated strategies to improve outcomes for those most vulnerable to COVID-19. Failure to address these systemic problems could mean global care home populations will be similarly affected by future crises and pandemics.",public and global health,fuzzy,90,100 medRxiv,10.1101/2022.04.11.22273690,2022-04-17,https://medrxiv.org/cgi/content/short/2022.04.11.22273690,Evaluation of isotype specific salivary antibody assays for detecting previous SARS-CoV-2 infection in children and adults,Amy C Thomas; Elizabeth Oliver; Holly Baum; Kapil Gupter; Kathryn Shelley; Anna Long; Hayley Jones; Joyce Smith; Benjamin Hitchings; Natalie di Bartolo; Kate Vasileiou; Fruzsina Rabi; Hanin Alamir; Malak Eghleilib; Ore Francis; Jennifer Oliver; Begonia Morales-Aza; Ulrike Obst; Debbie Shattock; Rachael Barr; Lucy Collingwood; Kaltun Duale; Niall Grace; Guillaume Gonnage Livera; Lindsay Bishop; Harriet Downing; Fernanda Rodrigues; Nicholas J Timpson; Caroline J Relton; Ashley Mark Toye; Derek N Woolfson; Imre Berger; Anu Goenka; Andrew D. Mark Davidson; Kathleen M Gillespie; Alistair JK Williams; Mick Bailey; Ellen Brooks-Pollock; Adam Finn; Alice Halliday; - CoMMinS Study Team,University of Bristol; University of Bristol; University of Bristol; University of Bristol and Imophoron Ltd.; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; Universidade de Coimbra; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; -,"Saliva is easily obtainable non-invasively and potentially suitable for detecting both current and previous SARS-CoV-2 infection. We established 6 standardised enzyme linked immunosorbent assays (ELISA) capable of detecting IgA and IgG antibodies to whole SARS-CoV-2 spike protein, to its receptor binding domain region and to nucleocapsid protein in saliva. In test accuracy (n=320), we found that spike IgG performed best (ROC AUC: 95.0%, 92.8-97.3%), followed by spike IgA (ROC AUC: 89.9%, 86.5-93.2%) for discriminating between pre-pandemic and post COVID-19 saliva samples. Using machine learning, diagnostic performance was improved when a combination of tests was used. As expected, salivary IgA was poorly correlated with serum, indicating an oral mucosal response whereas salivary IgG responses were predictive of those in serum. When deployed to 20 household outbreaks undergoing Delta and Omicron infection, antibody responses were heterogeneous but remained a reliable indicator of recent infection. Intriguingly, unvaccinated children showed evidence of exposure almost exclusively through specific IgA responses in the absence of evidence of viral infection. We have provided robust standardisation, evaluation, and field-testing of salivary antibody assays as tools for monitoring SARS-CoV-2 immune responses. Future work should focus on investigating salivary antibody responses following infection and vaccination to understand patterns of SARS-CoV-2 transmission and inform ongoing vaccination strategies.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2022.04.14.22272888,2022-04-14,https://medrxiv.org/cgi/content/short/2022.04.14.22272888,Anti-inflammatory therapy with nebulised dornase alfa in patients with severe COVID-19 pneumonia,Joanna Porter; Jamie Inshaw; Vincente Joel Solis; Emma Denneny; Rebecca Evans; Mia I. Temkin; Nathalia De Vasconcelos; Iker Valle Aramburu; Dennis Hoving; Donna Basire; Tracey Crissell; Jesusa Guinto; Alison Webb; Hanif Esmail; Victoria Johnston; Anna Last; Thomas Rampling; Elisa Theresa Helbig; Lena Lippert; Florian Kurth; Bryan Williams; Aiden Flynn; Pauline Lukey; Veronique Birault; Venizelos Papayannopoulos,"UCL Respiratory, University College London, UK; Exploristics, Belfast, N. Ireland; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; UCL Respiratory, University College London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Exploristics, Belfast, N. Ireland; Target to Treatment Consulting Ltd, Stevenage, UK; Translation, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK","BackgroundCell-free (cf)-DNA, from cellular sources, including Neutrophil Extracellular Traps (NETs), is found in the circulation of COVID-19 patients and may contribute to immune dysregulation. This study determined whether pulmonary administration of the endonuclease, dornase alfa, reduced systemic inflammation by degrading local and systemic cf-DNA. - -MethodsEligible patients were randomized (3:1) to receive twice-daily nebulised dornase alfa in addition to best available care (BAC) or BAC alone for seven days or until discharge. A 2:1 ratio of matched contemporary controls (CC-BAC) provided additional comparators. The primary endpoint was improvement in C-reactive protein (CRP) over time, analysed using a repeated-measures mixed model, adjusted for baseline factors. - -ResultsBetween June 2020-October 2021 we recruited 39 evaluable patients: 30 randomised to dornase alfa (R-BAC+DA); 9 randomised to BAC (R-BAC); with the addition of 60 CC-BAC participants. Dornase alfa was well tolerated and reduced CRP by 33% compared to combined BAC groups (T-BAC). Least squares (LS) mean post-dexamethasone CRP fell from 101.9mg/L to 23.23 mg/L in the BAC+ dornase alfa group versus a fall from 99.5mg/L to 34.82 mg/L in the T-BAC group at 7 days; P=0.01. This effect of dornase alfa on CRP was confirmed with subgroup and sensitivity analyses that mitigated potential biases associated with the use of the CC-BAC group. Dornase alfa increased the chance of live discharge by 63% (HR 1.63, 95% CI 1.01 to 2.61, P=0.03), increased lymphocyte counts (LS mean: 1.08 vs 0.87, P=0.02) and reduced circulating cf-DNA and the coagulopathy marker D-dimer (LS mean: 570.78 vs 1656.96 g/mL, P=0.004). - -ConclusionWe provide proof-of-concept evidence that dornase alfa reduces pathogenic inflammation in hospitalised patients with COVID-19 pneumonia, suggesting that best available care can be improved by the inclusion of anti-inflammatory treatments that target damage-associated molecules.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.04.12.22273752,2022-04-13,https://medrxiv.org/cgi/content/short/2022.04.12.22273752,Protection conferred by vaccine plus previous infection (hybrid immunity) with vaccines of three different platforms during the Omicron variant period in Brazil,Thiago Cerqueira-Silva; Vinicius de Araújo Oliveira; Enny S. Paixão; Pilar Florentino; Gerson O. Penna; Neil Pearce; Guilherme L. Werneck; Maurício L. Barreto; Viviane S. Boaventura; Manoel Barral-Netto,"Faculdade de Medicina - Universidade Federal da Bahia; Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fiocruz, Salvador, Bahia, Brazil; London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Nuúcleo de Medicina Tropical, Universidade de Brasiília. Escola Fiocruz de Governo, Fiocruz, DF, Brazil; London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Universidade Federal do Rio de Janeiro, Rio de Janeiro,Brazil; Instituto de Saúde Coletiva - Universidade Federal da Bahia; Faculdade de Medicina - Universidade Federal da Bahia; Faculdade de Medicina - Universidade Federal da Bahia","Hybrid immunity (infection plus vaccination) provided high protection against infection and severe disease in the periods of delta and gamma variants of concern. However, the protection of hybrid immunity in the Omicron era remains unknown. We performed a test-negative study using Brazilian national databases between January 01 and March 22, 2022, a period of predominant circulation of the Omicron variant in Brazil. Hybrid immunity offered low protection against infection, with rapid waning, compared to unvaccinated with or without previous infection. For severe illness (hospitalisation or death), the protection, although already high for unvaccinated pre-infected increased regardless of the type of vaccine (Ad26.COV2.S, BNT162b2, ChAdOx-1 or CoronaVac). In conclusion, during the Omicron-dominant period in Brazil, hybrid immunity offered high protection against severe illness and low protection against infection.",epidemiology,fuzzy,100,100 @@ -1790,11 +1770,6 @@ ResultsBetween October-2020 and April-2022, 120,995 SARS-CoV-2 PCR-positive epis ConclusionsIncreases in sore throat (also common in the general community), and a marked reduction in loss of taste/smell, make Omicron harder to detect with symptom-based testing algorithms, with implications for institutional and national testing policies. SummaryIn a UK community study, loss of taste/smell was markedly less commonly reported with Omicron BA.1/BA.2 than Delta SARS-CoV-2 infections, with smaller declines in reported shortness of breath, myalgia and fatigue/weakness, but increases in sore throat, challenging symptom-based testing algorithms.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.01.16.22269146,2022-01-17,https://medrxiv.org/cgi/content/short/2022.01.16.22269146,Development and validation of the Symptom Burden Questionnaire™ for Long COVID: a Rasch analysis,Sarah E Hughes; Shamil Haroon; Anuradhaa Subramanian; Christel McMullan; Olalekan L Aiyegbusi; Grace M Turner; Louise Jackson; Elin Haf Davies; Chris Frost; Gary McNamara; Gary Price; Karen Matthews; Jennifer Camaradou; Jane Ormerod; Anita Walker; Melanie J Calvert,"University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito Limited; Aparito Limited; Aparito Limited; University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; University of Birmingham; University of BIrmingham","ObjectiveTo describe the development and initial validation of a novel patient-reported outcome measure of Long COVID symptom burden, the Symptom-Burden Questionnaire for Long COVID (SBQ-LC). - -Method and FindingsThis multi-phase, prospective mixed-methods study took place between April and August 2021 in the United Kingdom (UK). A conceptual framework and initial item pool were developed from published systematic reviews. Further concept elicitation and content validation was undertaken with adults with lived experience (n = 13) and clinicians (n = 10), and face validity was confirmed by the Therapies for Long COVID Study Patient and Public Involvement group (n = 25). The draft SBQ-LC was field tested by adults with self-reported Long COVID recruited via social media and international Long COVID support groups (n = 274). Thematic analysis of interview and survey transcripts established content validity and informed construction of the draft questionnaire. Rasch analysis of field test data guided item and scale refinement and provided evidence of the final SBQ-LCs measurement properties. The Rasch-derived SBQ-LC is composed of 17 independent scales with promising psychometric properties. Respondents rate symptom burden during the past 7-days using a dichotomous response or 4-point rating scale. Each scale provides coverage of a different symptom domain and returns a summed raw score that may be converted to a linear (0 - 100) score. Higher scores represent higher symptom burden. - -ConclusionsThe SBQ-LC is a comprehensive patient-reported assessment of Long COVID symptom burden developed using modern psychometric methods. It measures symptoms of Long COVID important to individuals with lived experience and may be used to evaluate the impact of interventions and inform best practice in clinical management.",health informatics,fuzzy,100,100 medRxiv,10.1101/2022.01.13.22268948,2022-01-14,https://medrxiv.org/cgi/content/short/2022.01.13.22268948,Algorithmic Fairness and Bias Mitigation for Clinical Machine Learning: Insights from Rapid COVID-19 Diagnosis by Adversarial Learning,Jenny Yang; Andrew AS Soltan; Yang Yang; David A Clifton,The University of Oxford; University of Oxford; The University of Oxford; The University of Oxford,"Machine learning is becoming increasingly prominent in healthcare. Although its benefits are clear, growing attention is being given to how machine learning may exacerbate existing biases and disparities. In this study, we introduce an adversarial training framework that is capable of mitigating biases that may have been acquired through data collection or magnified during model development. For example, if one class is over-presented or errors/inconsistencies in practice are reflected in the training data, then a model can be biased by these. To evaluate our adversarial training framework, we used the statistical definition of equalized odds. We evaluated our model for the task of rapidly predicting COVID-19 for patients presenting to hospital emergency departments, and aimed to mitigate regional (hospital) and ethnic biases present. We trained our framework on a large, real-world COVID-19 dataset and demonstrated that adversarial training demonstrably improves outcome fairness (with respect to equalized odds), while still achieving clinically-effective screening performances (NPV>0.98). We compared our method to the benchmark set by related previous work, and performed prospective and external validation on four independent hospital cohorts. Our method can be generalized to any outcomes, models, and definitions of fairness.",health informatics,fuzzy,100,100 medRxiv,10.1101/2022.01.05.21268323,2022-01-06,https://medrxiv.org/cgi/content/short/2022.01.05.21268323,Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey,Katrina A Lythgoe; Tanya Golubchik; Matthew Hall; Thomas House; Roberto Cahuantzi; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; Mahan Ghafari; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Christophe Fraser; Ian Diamond; Jeff Barrett; Ann Sarah Walker; David Bonsall,University of Oxford; University of Oxford; University of Oxford; University of Manchester; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Wellcome Sanger Institute; Office for National Statistics; ; University of Oxford; Office for National Statistics; Wellcome Sanger Institute; University of Oxford; University of Oxford,"The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non- SGTF over time. Evolution was characterised by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly in the current phase of the pandemic with routine RT-PCR testing now ended in the community.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.01.01.21268131,2022-01-05,https://medrxiv.org/cgi/content/short/2022.01.01.21268131,Bayesian Estimation of real-time Epidemic Growth Rates using Gaussian Processes: local dynamics of SARS-CoV-2 in England,Laura Marcela Guzman Rincon; Edward M Hill; Louise Dyson; Michael J Tildesley; Matt J Keeling,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"Quantitative assessments of the recent state of an epidemic and short-term projections into the near future are key public health tools that have substantial policy impacts, helping to determine if existing control measures are sufficient or need to be strengthened. Key to these quantitative assessments is the ability to rapidly and robustly measure the speed with which the epidemic is growing or decaying. Frequently, epidemiological trends are addressed in terms of the (time-varying) reproductive number R. Here, we take a more parsimonious approach and calculate the exponential growth rate, r, using a Bayesian hierarchical model to fit a Gaussian process to the epidemiological data. We show how the method can be employed when only case data from positive tests are available, and the improvement gained by including the total number of tests as a measure of heterogeneous testing effort. Although the methods are generic, we apply them to SARS-CoV-2 cases and testing in England, making use of the available high-resolution spatio-temporal data to determine long-term patterns of national growth, highlight regional growth and spatial heterogeneity.",epidemiology,fuzzy,100,100 @@ -1913,6 +1888,13 @@ ResultsAmong the 1226855 CYP in the cohort, there were 378402 tests, 19005 PCR c ConclusionsInfants, and CYP with chronic conditions are at highest risk of admission with COVID-19, however the majority of admitted CYP have no chronic conditions. These results provide evidence to support risk/benefit analyses for paediatric COVID-19 vaccination programmes. Studies examining whether maternal vaccine during pregnancy prevents COVID-19 admissions in infants are urgently needed. FundingUK Research and Innovation-Medical Research Council",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.12.14.21267806,2021-12-16,https://medrxiv.org/cgi/content/short/2021.12.14.21267806,"REACT-1 round 15 final report: Increased breakthrough SARS-CoV-2 infections among adults who had received two doses of vaccine, but booster doses and first doses in children are providing important protection",Marc Chadeau-Hyam; Oliver Eales; Barbara Bodinier; Haowei Wang; David Haw; Matthew Whitaker; Caroline E. Walters; Jakob Jonnerby; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Deborah Ashby; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Christl A Donnelly; Paul Elliott,"School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research","BackgroundIt has been nearly a year since the first vaccinations against SARS-CoV-2 were delivered in England. The third wave of COVID-19 in England began in May 2021 as the Delta variant began to outcompete and largely replace other strains. The REal-time Assessment of Community Transmission-1 (REACT-1) series of community surveys for SARS-CoV-2 infection has provided insights into transmission dynamics since May 2020. Round 15 of the REACT-1 study was carried out from 19 October to 5 November 2021. + +MethodsWe estimated prevalence of SARS-CoV2 infection and used multiple logistic regression to analyse associations between SARS-CoV-2 infection in England and demographic and other risk factors, based on RT-PCR results from self-administered throat and nose swabs in over 100,000 participants. We estimated (single-dose) vaccine effectiveness among children aged 12 to 17 years, and among adults compared swab-positivity in people who had received a third (booster) dose with those who had received two vaccine doses. We used splines to analyse time trends in swab-positivity. + +ResultsDuring mid-October to early-November 2021, weighted prevalence was 1.57% (1.48%, 1.66%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). Weighted prevalence increased between rounds 14 and 15 across most age groups (including older ages, 65 years and over) and regions, with average reproduction number across rounds of R=1.09 (1.08, 1.11). During round 15, there was a fall in prevalence from a maximum around 20-21 October, with an R of 0.76 (0.70, 0.83), reflecting falls in prevalence at ages 17 years and below and 18 to 54 years. School-aged children had the highest weighted prevalence of infection: 4.95% (4.39%, 5.58%) in those aged 5 to 12 years and 5.21% (4.61%, 5.87%) in those aged 13 to 17 years. In multiple logistic regression, age, sex, key worker status and presence of one or more children in the home were associated with swab positivity. There was evidence of heterogeneity between rounds in swab positivity rates among vaccinated individuals at ages 18 to 64 years, and differences in key demographic and other variables between vaccinated and unvaccinated adults at these ages. Vaccine effectiveness against infection in children was estimated to be 56.2% (41.3%, 67.4%) in rounds 13, 14 and 15 combined, adjusted for demographic factors, with a similar estimate obtained for round 15 only. Among adults we found that those who received a third dose of vaccine were less likely to test positive compared to those who received only two vaccine doses, with adjusted odds ratio (OR) =0.38 (0.26, 0.55). + +DiscussionSwab-positivity was very high at the start of round 15, reaching a maximum around 20 to 21 October 2021, and then falling through late October with an uncertain trend in the last few days of data collection. The observational nature of survey data and the relatively small proportion of unvaccinated adults call into question the comparability of vaccinated and unvaccinated groups at this relatively late stage in the vaccination programme. However, third vaccine doses for eligible adults and the vaccination of children aged 12 years and over are associated with lower infection risk and, thus, remain a high priority (with possible extension to children aged 5-12 years). These should help reduce SARS-CoV-2 transmission during the winter period when healthcare demands typically rise.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.12.16.21267906,2021-12-16,https://medrxiv.org/cgi/content/short/2021.12.16.21267906,Workplace Contact Patterns in England during the COVID-19 Pandemic: Analysis of the Virus Watch prospective cohort study,Sarah Beale; Susan J Hoskins; Thomas Edward Byrne; Erica Wing Lam Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Parth Patel; Alexei Yavlinsky; Anne M Johnson; Robert W Aldridge; Andrew Hayward,University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London,"BackgroundWorkplaces are an important potential source of SARS-CoV-2 exposure; however, investigation into workplace contact patterns is lacking. This study aimed to investigate how workplace attendance and features of contact varied between occupations and over time during the COVID-19 pandemic in England. MethodsData were obtained from electronic contact diaries submitted between November 2020 and November 2021 by employed/self-employed prospective cohort study participants (n=4,616). We used mixed models to investigate the main effects and potential interactions between occupation and time for: workplace attendance, number of people in shared workspace, time spent sharing workspace, number of close contacts, and usage of face coverings. @@ -2481,11 +2463,15 @@ FindingsOf 4,091,537 RT-PCR results from 482,677 individuals, 29,903 (0{middle d InterpretationPopulation-level demographic and behavioural surveillance can be a valuable tool in identifying the varying characteristics driving current SARS-CoV-2 positivity, allowing monitoring to inform public health policy. FundingDepartment of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.09.02.21262965,2021-09-02,https://medrxiv.org/cgi/content/short/2021.09.02.21262965,Whole genome sequencing identifies multiple loci for critical illness caused by COVID-19,Athanasios Kousathanas; Erola Pairo-Castineira; Konrad Rawlik; Alex Stuckey; Christopher A Odhams; Susan Walker; Clark D Russell; Tomas Malinauskas; Jonathan Millar; Katherine S Elliott; Fiona Griffiths; Wilna Oosthuyzen; Kirstie Morrice; Sean Keating; Bo Wang; Daniel Rhodes; Lucija Klaric; Marie Zechner; Nick Parkinson; Andrew D. Bretherick; Afshan Siddiq; Peter Goddard; Sally Donovan; David Maslove; Alistair Nichol; Malcolm G Semple; Tala Zainy; Fiona Maleady-Crowe; Linda Todd; Shahla Salehi; Julian Knight; Greg Elgar; Georgia Chan; Prabhu Arumugam; Tom A Fowler; Augusto Rendon; Manu Shankar-Hari; Charlotte Summers; Charles Hinds; Peter Horby; Danny McAuley; Hugh Montgomery; Peter J.M. Openshaw; Yang Wu; Jian Yang; Paul Elliott; Timothy Walsh; - GenoMICC Investigators; - 23andMe Investigators; - Covid-19 Human Genetics Initiative; Angie Fawkes; Lee Murphy; Kathy Rowan; Chris P Ponting; Veronique Vitart; James F Wilson; Richard H Scott; Sara Clohisey; Loukas Moutsianas; Andy Law; Mark J Caulfield; J. Kenneth Baillie,"Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, ON, Canada.; Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland.; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, L; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Department of Intensive Care Medicine, Guy's and St. Thomas NHS Foundation Trust, London, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK; UCL Centre for Human Health and Performance, London, W1T 7HA, UK.; National Heart and Lung Institute, Imperial College London, London, UK; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Imperial College, London; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; ; ; ; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Intensive Care National Audit & Research Centre, London, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK","Critical illness in COVID-19 is caused by inflammatory lung injury, mediated by the host immune system. We and others have shown that host genetic variation influences the development of illness requiring critical care1 or hospitalisation2;3;4 following SARS-Co-V2 infection. The GenOMICC (Genetics of Mortality in Critical Care) study recruits critically-ill cases and compares their genomes with population controls in order to find underlying disease mechanisms. +medRxiv,10.1101/2021.08.26.21262523,2021-08-28,https://medrxiv.org/cgi/content/short/2021.08.26.21262523,"Association between tocilizumab, sarilumab and all-cause mortality at 28 days in hospitalized patients with COVID-19: A network meta-analysis",Peter J Godolphin; David J Fisher; Lindsay R Berry; Lennie PG Derde; Janet V Diaz; Anthony C Gordon; Elizabeth Lorenzi; John C Marshall; Srinivas Murthy; Manu Shankar-Hari; Jonathan AC Sterne; Jayne F Tierney; Claire L Vale,University College London; University College London; Berry Consultants; University Medical Center Utrecht; World Health Organization; Imperial College London; Berry Consultants; University of Toronto; University of British Columbia; King's College London; University of Bristol; University College London; University College London,"ObjectiveTo estimate pairwise associations between administration of tocilizumab, sarilumab and usual care or placebo with 28-day mortality, in COVID-19 patients receiving concomitant corticosteroids and non-invasive or mechanical ventilation, based on all available direct and indirect evidence. + +MethodsEligible trials randomized hospitalized patients with COVID-19 that compared either interleukin-6 receptor antagonist with usual care or placebo in a recent prospective meta-analysis (27 trials, 10930 patients) or that directly compared tocilizumab with sarilumab. Data were restricted to patients receiving corticosteroids and either non-invasive or invasive ventilation at randomization. -Here, we use whole genome sequencing and statistical fine mapping in 7,491 critically-ill cases compared with 48,400 population controls to discover and replicate 22 independent variants that significantly predispose to life-threatening COVID-19. We identify 15 new independent associations with critical COVID-19, including variants within genes involved in interferon signalling (IL10RB, PLSCR1), leucocyte differentiation (BCL11A), and blood type antigen secretor status (FUT2). Using transcriptome-wide association and colocalisation to infer the effect of gene expression on disease severity, we find evidence implicating expression of multiple genes, including reduced expression of a membrane flippase (ATP11A), and increased mucin expression (MUC1), in critical disease. +Pairwise associations between tocilizumab, sarilumab and usual care or placebo for all-cause mortality 28 days after randomization were estimated using a frequentist contrast-based network meta-analysis of odds ratios (ORs), implementing multivariate fixed-effects models that assume consistency between the direct and indirect evidence. -We show that comparison between critically-ill cases and population controls is highly efficient for genetic association analysis and enables detection of therapeutically-relevant mechanisms of disease. Therapeutic predictions arising from these findings require testing in clinical trials.",intensive care and critical care medicine,fuzzy,100,100 +ResultsOne trial (REMAP-CAP) was identified that directly compared tocilizumab with sarilumab and supplied results on all-cause mortality at 28-days. This network meta-analysis was based on 898 eligible patients (278 deaths) from REMAP-CAP and 3710 eligible patients from 18 trials (1278 deaths) from the prospective meta-analysis. Summary ORs were similar for tocilizumab [0.82 [0.71-0.95, P=0.008]] and sarilumab [0.80 [0.61-1.04, P=0.09]] compared with usual care or placebo. The summary OR for 28-day mortality comparing tocilizumab with sarilumab was 1.03 [95%CI 0.81-1.32, P=0.80]. The P value for the global test for inconsistency was 0.28. + +ConclusionAdministration of either tocilizumab or sarilumab was associated with lower 28-day all-cause mortality compared with usual care or placebo. The association is not dependent on the choice of interleukin-6 receptor antagonist.",intensive care and critical care medicine,fuzzy,100,100 medRxiv,10.1101/2021.08.23.21261638,2021-08-26,https://medrxiv.org/cgi/content/short/2021.08.23.21261638,Unexplained longitudinal variability in COVID-19 antibody status by Lateral Flow Immuno-Antibody testing,Katrina A S Davis; Carolin Oetzmann; Ewan Carr; Michael Malim; Vanessa J Boshell; Grace Lavelle; Daniel J Leightley; Catherine Polling; Sharon Stevelink; Valentina Vitiello; Alice Wickersham; Reza Razavi; Matthew H Hotopf; - KCL-CHECK team,"KCL Institute of Psychiatry, Psychology and Neuroscience; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; ","BackgroundCOVID-19 antibody testing allows population studies to classify participants by previous SARS-CoV-2 infection status. Home lateral flow immune-antibody testing devices offer a very convenient way of doing this, but relatively little is known about how measurement and antibody variability will affect consistency in results over time. We examined consistency by looking at the outcome of two tests three months apart while COVID-19 infection rates were low (summer 2020 in the UK). MethodsThe KCL-Coronavirus Health and Experiences in Colleagues at Kings is an occupational cohort of staff and postgraduate research students. Lateral flow immune-antibody testing kits were sent to participants homes in late June 2020 and late September 2020. Participants also completed regular surveys that included asking about COVID-19 symptoms and whether they thought they had been infected. @@ -2567,6 +2553,13 @@ ConclusionsThose that self-harmed and sought help during the COVID-19 pandemic p Relevance statementThis study provides novel findings on how the COVID-19 pandemic and the measures taken to curb its spread affected self-harm healthcare service presentations. To our knowledge no other population-based studies in the UK have linked routinely collected general practice (GP), emergency department (ED) and hospital admission data covering Waves 1 and 2 of the pandemic. Reductions in presentations with self-harm during the pandemic may be the result of those not requiring ED care or hospitalisation avoiding seeking help during the pandemic as often as before. Those that did seek help potentially encountered more stringent criteria for hospitalisation, particularly during Wave 2. This likely resulted in unmet healthcare needs which may later emerge placing further burden on individuals and healthcare services. Measures should be put in place to ensure that those who self-harm receive appropriate assessment and intervention.",health informatics,fuzzy,100,100 +medRxiv,10.1101/2021.08.05.21259863,2021-08-07,https://medrxiv.org/cgi/content/short/2021.08.05.21259863,Recording of 'COVID-19 vaccine declined' among vaccination priority groups: a cohort study on 57.9 million NHS patients' primary care records in situ using OpenSAFELY,Helen J Curtis; Peter Inglesby; Brian MacKenna; Richard Croker; William J Hulme; Christopher T Rentsch; Krishnan Bhaskaran; Alex J Walker; Caroline E Morton; David Evans; Amir Mehrkar; Sebastian CJ Bacon; Christopher Bates; George Hickman; Tom Ward; Jessica Morley; Jonathan Cockburn; Simon Davy; Anna Schultze; Elizabeth J Williamson; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; John Tazare; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundAll patients in England within vaccine priority groups were offered a COVID-19 vaccine by mid-April 2021. Clinical record systems contain codes to denote when such an offer has been declined by a patient (although these can in some cases be entered for a variety of other reasons including vaccination delay, or other administrative issues). We set out to describe the patterns of usage of codes for COVID-19 vaccines being declined. + +MethodsWith the approval of NHS England and using the full pseudonymised primary care records for 57.9 million NHS patients, we identified all patients in key vaccine priority groups: aged over 50, or over 16 and at increased risk from COVID-19 (Clinically Extremely Vulnerable [CEV] or otherwise ""at risk""). We describe the proportion of patients recorded as declining a COVID-19 vaccination for each priority group, and by other clinical and demographic factors; whether patients recorded as ""declined"" subsequently went on to receive a vaccination; and the distribution of code usage across GP practices. + +ResultsOf 24.5 million patients in priority groups as of May 25th 2021, 89.2% had received a vaccine, 8.8% had neither a vaccination nor a decline recorded, and 663,033 (2.7%) had a decline code recorded. Of patients with a recorded decline, 125,587 (18.9%) were subsequently vaccinated. Subsequent vaccination was slightly more common in the South Asian population than other ethnicities (e.g. 32.3% vs 22.8%, over 65s). The proportion of declining-unvaccinated patients varied strongly with ethnicity (Black 15.3%, South Asian 5.6%, White 1.5% in over 80s); and was higher in patients from more deprived areas. COVID-19 vaccine decline codes were present in almost all practices (98.8%), but with wide variation between practices in rates of usage. Among all priority groups, declining-unvaccinated status was most common in CEV (3.3%). + +ConclusionsClinical codes indicative of COVID-19 vaccinations being declined are widely used in English general practice. They are substantially more common among Black and South Asian patients, and patients from more deprived areas. There is a need for more detailed survey and/or qualitative research with patients and clinicians to determine the most common reasons for these recorded declines.",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.07.29.21261190,2021-07-31,https://medrxiv.org/cgi/content/short/2021.07.29.21261190,Right Ventricular Dysfunction in Ventilated Patients with COVID-19 (COVID-RV),Philip McCall; Jennifer Willder; Bethany Stanley; Claudia-Martina Messow; John Allan; Lisa Gemmell; Alex Puxty; Dominic Strachan; Colin Berry; Ben Shelley; - The COVID-RV investigators.,"Anaesthesia, Critical Care & Peri-operative Medicine Research Group, University of Glasgow, Glasgow, UK.; West of Scotland School of Anaesthesia, NHS Education for Scotland, Glasgow, UK.; Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK.; Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK.; Intensive Care Unit, University Hospital Crosshouse, Kilmarnock, UK.; Intensive Care Unit, Royal Alexandra Hospital, Paisley, UK.; Intensive Care Unit, Glasgow Royal Infirmary, Glasgow, UK.; Intensive Care Unit, University Hospital Wishaw, Wishaw, UK.; Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK.; Anaesthesia, Critical Care & Peri-operative Medicine Research Group, University of Glasgow, UK.; ","PurposeCOVID-19 is associated with cardiovascular complications, with right ventricular dysfunction (RVD) commonly reported. The combination of acute respiratory distress syndrome (ARDS), injurious invasive ventilation, micro/macro thrombi and the potential for direct myocardial injury create conditions where RVD is likely to occur. No study has prospectively explored the prevalence of RVD, and its association with mortality, in a cohort requiring mechanical ventilation. MethodsProspective, multi-centre, trans-thoracic echocardiographic, cohort study of ventilated patients with COVID-19 in Scottish intensive care units. RVD was defined as the presence of severe RV dilatation and interventricular septal flattening. To explore role of myocardial injury, high sensitivity troponin and N-terminal pro B-type natriuretic peptide (NT-proBNP) were measured in all patients. @@ -2861,6 +2854,9 @@ MethodsThe REal-time Assessment of Community Transmision-1 (REACT-1) study measu ResultsBetween rounds 11 and 12, national prevalence increased from 0.10% (0.08%, 0.13%) to 0.15% (0.12%, 0.18%). During round 12, we detected exponential growth with a doubling time of 11 (7.1, 23) days and an R number of 1.44 (1.20, 1.73). The highest prevalence was found in the North West at 0.26% (0.16%, 0.41%) compared to 0.05% (0.02%, 0.12%) in the South West. In the North West, the locations of positive samples suggested a cluster in Greater Manchester and the east Lancashire area. Prevalence in those aged 5-49 was 2.5 times higher at 0.20% (0.16%, 0.26%) compared with those aged 50 years and above at 0.08% (0.06%, 0.11%). At the beginning of February 2021, the link between infection rates and hospitalisations and deaths started to weaken, although in late April 2021, infection rates and hospital admissions started to reconverge. When split by age, the weakened link between infection rates and hospitalisations at ages 65 years and above was maintained, while the trends converged below the age of 65 years. The majority of the infections in the younger group occurred in the unvaccinated population or those without a stated vaccine history. We observed the rapid replacement of the Alpha (B.1.1.7) variant of SARS-CoV-2 with the Delta variant during the period covered by rounds 11 and 12 of the study. DiscussionThe extent to which exponential growth continues, or slows down as a consequence of the continued rapid roll-out of the vaccination programme, including to young adults, requires close monitoring. Data on community prevalence are vital to track the course of the epidemic and inform ongoing decisions about the timing of further lifting of restrictions in England.",infectious diseases,fuzzy,100,100 +bioRxiv,10.1101/2021.06.21.449178,2021-06-21,https://biorxiv.org/cgi/content/short/2021.06.21.449178,Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune pathways related to tissue injury,Amy R Cross; Carlos de Andrea; Maria Villalba-Esparza; Manuel Landecho Acha; Lucia Cerundolo; Praveen Weeratunga; Rachel Etherington; Laura Denney; Graham Ogg; Ling-Pei Ho; Ian Roberts; Joanna Hester; Paul Klenerman; Ignacio Melero; Stephen Sansom; Fadi Issa,"University of Oxford; Universidad de Navarra; Department of Pathology, Clinica de la Universidad de Navarra, Pamplona, Spain; Clinica Universidad de Navarra; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Universidad de Navarra; University of Oxford; University of Oxford","Severe lung damage in COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways and genes present across the spectrum of histopathological damage in COVID-19 lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from areas of interest within well preserved post-mortem lung samples from three patients. Despite substantial inter-patient heterogeneity we discovered evidence for a common immune cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines including CXCL9, CXCL10 and CXCL11 which are known to promote the recruitment of CXCR3+ immune cells. The tumour necrosis factor (TNF) superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were found to be consistently upregulated in the areas with severe tissue damage. We used published spatial and single cell SARS-CoV-2 datasets to confirm our findings in the lung tissue from additional cohorts of COVID-19 patients. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies. + +One Sentence SummarySpatial analysis identifies IFN{gamma} response signatures as focal to severe alveolar damage in COVID-19 pneumonitis.",immunology,fuzzy,100,100 medRxiv,10.1101/2021.06.17.21259100,2021-06-20,https://medrxiv.org/cgi/content/short/2021.06.17.21259100,COVID-19 Transmission Dynamics Underlying Epidemic Waves in Kenya,Samuel P C Brand; John Ojal; Rabia Aziza; Vincent Were; Emelda Okiro; Ivy Kombe; Caroline Mburu; Morris Ogero; Ambrose Agweyu; George M Warimwe; James Nyagwange; Henry Karanja; John Gitonga; Daisy Mugo; Sophie Uyoga; Ifedayo M O Adetifa; J Anthony G Scott; Edward Otieno; Nickson Murunga; Mark Otiende; Lynette I Ochola-Oyier; Charles N Agoti; George Githinji; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Benjamin Tsofa; Philip Bejon; Matt J Keeling; D James Nokes; Edwine Barasa,"University of Warwick; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; University of Warwick; Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Ministry of Health, Government of Kenya, Nairobi, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; University of Warwick; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya; Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme (KWTRP), Kilifi, Kenya","Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of SARS-CoV-2 transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or when infection spreads to susceptible sub-populations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of a new higher-transmissibility variant. Reopening schools led to a minor increase in transmission between the second and third waves. Our predictions of current population exposure in Kenya ([~]75% June 1st) have implications for a fourth wave and future control strategies. One Sentence SummaryCOVID-19 spread in Kenya is explained by mixing heterogeneity and a variant less constrained by high population exposure",epidemiology,fuzzy,100,100 @@ -2949,13 +2945,6 @@ MethodsIsolated neutrophils from 41 hospitalised, non-ICU COVID-19 patients and ResultsCompared to AMC, COVID-19 neutrophils demonstrated elevated transmigration (p=0.0397) and NETosis (p=0.0366), but impaired phagocytosis (p=0.0236) associated with impaired ROS generation (p<0.0001). Surface expression of CD54 (p<0.0001) and CD11c (p=0.0008) was significantly increased and CD11b significantly decreased (p=0.0229) on COVID-19 patient neutrophils. COVID-19 patients showed increased systemic markers of NETosis including increased cfDNA (p=0.0153) and impaired DNAse activity (p<0.0.001). MPO (p<0.0001), VEGF (p<0.0001), TNFRI (p<0.0001) and IL-6 (p=0.009) were elevated in COVID-19, which positively correlated with disease severity by 4C score. ConclusionCOVID-19 is associated with neutrophil dysfunction across all main effector functions, with altered phenotype, elevated migration, impaired antimicrobial responses and elevated NETosis. These changes represent a clear mechanism for tissue damage and highlight that targeting neutrophil function may help modulate COVID-19 severity.",intensive care and critical care medicine,fuzzy,100,92 -medRxiv,10.1101/2021.06.08.21258531,2021-06-08,https://medrxiv.org/cgi/content/short/2021.06.08.21258531,"The UK Coronavirus Job Retention Scheme and changes in diet, physical activity and sleep during the COVID-19 pandemic: Evidence from eight longitudinal studies",Bozena Wielgoszewska; Jane Maddock; Michael J Green; Giorgio Di Gessa; Sam Parsons; Gareth J Griffith; Jazz Croft; Anna J Stevenson; Charlotte Booth; Richard J Silverwood; David Bann; Praveetha Patalay; Alun D Hughes; Nishi Chaturvedi; Laura D Howe; Emla Fitzsimons; Srinivasa Vittal Katikireddi; George B Ploubidis,"Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Institute of Epidemiology and Health Care, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; UCL; MRC Unit for Lifelong Health and Ageing, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London","BackgroundIn March 2020 the UK implemented the Coronavirus Job Retention Scheme (furlough) to minimize job losses. Our aim was to investigate associations between furlough and diet, physical activity, and sleep during the early stages of the COVID-19 pandemic. - -MethodsWe analysed data from 25,092 participants aged 16 to 66 years from eight UK longitudinal studies. Changes in employment (including being furloughed) were defined by comparing employment status pre- and during the first lockdown. Health behaviours included fruit and vegetable consumption, physical activity, and sleeping patterns. Study-specific estimates obtained using modified Poisson regression, adjusting for socio-demographic characteristics and pre-pandemic health and health behaviours, were statistically pooled using random effects meta-analysis. Associations were also stratified by sex, age, and education. - -ResultsAcross studies, between 8 and 25% of participants were furloughed. Compared to those who remained working, furloughed workers were slightly less likely to be physically inactive (RR:0.85, [0.75-0.97], I2=59%) and did not differ in diet and sleep behaviours, although findings for sleep were heterogenous (I2=85%). In stratified analyses, furlough was associated with low fruit and vegetable consumption among males (RR=1.11; 95%CI: 1.01-1.22; I2: 0%) but not females (RR=0.84; 95%CI: 0.68-1.04; I2: 65%). Considering change in these health behaviours, furloughed workers were more likely than those who remained working to report increased fruit and vegetable consumption, exercise, and hours of sleep. - -ConclusionsThose furloughed exhibited broadly similar levels of health behaviours to those who remained in employment during the initial stages of the pandemic. There was little evidence to suggest that such social protection policies if used in the post-pandemic recovery period and during future economic crises would have adverse impacts on population health behaviours.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.06.08.21258132,2021-06-08,https://medrxiv.org/cgi/content/short/2021.06.08.21258132,"Aspirin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Guilherme Pessoa-Amorim; Natalie Staplin; Jonathan R Emberson; Enti Spata; Mark Campbell; Leon Peto; Nigel Brunskill; Simon Tiberi; Victor Chew; Thomas Brown; Hasan Tahir; Beate Ebert; David R Chadwick; Tony Whitehouse; Rahuldeb Sarkar; Jonathan Clive Graham; J Kenneth Baillie; Buddha Basnyat; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Raph Hamers; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; University of Leicester, Leicester, United Kingdom; Barts Health NHS Foundation Trust, London, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom; Royal Free London NHS Foundation Trust, London, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; James Cook University Hospital, Middlesbrough, United Kingdom; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Medway NHS Foundation Trust, Gillingham, UK; North Cumbria Integrated Care NHS Foundation Trust, Carlisle, UK; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Oxford University Clinical Research Unit, Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, Kings College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia, and Centre for Tropical Medicine; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundAspirin has been proposed as a treatment for COVID-19 on the basis of its antithrombotic properties. MethodsIn this randomised, controlled, open-label platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care plus 150mg aspirin once daily until discharge or usual standard of care alone using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). @@ -3023,7 +3012,6 @@ Implications of all the available evidenceSome individuals still contract COVID- medRxiv,10.1101/2021.05.25.21257505,2021-05-25,https://medrxiv.org/cgi/content/short/2021.05.25.21257505,Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization.,Jose F. Varona; Pedro Landete; Jose A Lopez-Martin; Vicente Estrada; Roger Paredes; Pablo Guisado-Vasco; Lucia Fernandez de Orueta; Miguel Torralba; Jesus Fortun; Roberto Vates; Jose Barberan; Bonaventura Clotet; Julio Ancochea; Daniel Carnevali; Noemi Cabello; Lourdes Porras; Paloma Gijon; Alfonso Monereo; Daniel Abad; Sonia Zuñiga; Isabel Sola; Jordi Rodon; Nuria Izquierdo-Useros; Salvador Fudio; Maria Jose Pontes; Beatriz de Rivas; Patricia Giron de Velasco; Belen Sopesen; Antonio Nieto; Javier Gomez; Pablo Aviles; Rubin Lubomirov; Kris M White; Romel Rosales; Soner Yildiz; Ann-Kathrin Reuschl; Lucy G. Thorne; Clare Jolly; Greg J. Towers; Lorena Zuliani-Alvarez; Mehdi Bouhaddou; Kirsten Obernier; Luis Enjuanes; Jose M Fernandez-Sousa; - Plitidepsin COVID Study Group; Nevan J Krogan; Jose M. Jimeno; Adolfo Garcia-Sastre,"Departamento de Medicina Interna, Hospital Universitario HM Monteprincipe, HM Hospitales, Madrid, Spain. Facultad de Medicina, Universidad San Pablo-CEU, Madrid; Hospital Universitario de La Princesa. Madrid, Spain. Universidad Autonoma de Madrid, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; Hospital Clinico San Carlos, Madrid, Spain. Universidad Complutense de Madrid, Madrid, Spain.; IrsiCaixa AIDS Research Institute; Internal Medicine Department, Hospital Universitario Quironsalud, Madrid, Spain. Universidad Europea, Madrid, Spain.; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain.; Internal Medicine, Guadalajara University Hospital, Guadalajara, Spain. University of Alcala, Madrid, Spain.; Hospital Universitario Ramon y Cajal, Madrid, Spain.; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain.; Hospital Universitario HM Monteprincipe, Madrid, Spain. Facultad de Medicina San Pablo CEU, Madrid, Spain.; Head of Infectious Diseases Department, Director of the Research Lab, IrsiCaixa, Barcelone, Spain. Professor of the UAB and the UVIC-UCC, Barcelone, Spain.; Hospital Universitario La Princesa, Madrid, Spain. Centro de Investigacion en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII; Hospital Universitario Quironsalud, Madrid, Spain Universidad Europea, Madrid, Spain.; Infectious Diseases Department, San Carlos University Hospital. Madrid Spain.; Internal Medicine, Hospital General de Ciudad Real, Ciudad Real, Spain.; Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañon, Instituto de Investigacion Sanitaria Gregorio Marañon; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain.; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain.; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain.; IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Bellaterra, Spain; IrsiCaixa AIDS Research Institute, 08916, Badalona, Spain. Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, 08916, Badalona, Spain.; PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain; PharmaMar - Medical Affairs Unit. Colmenar Viejo. Madrid, Spain.; PharmaMar - Medical Affairs Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain. Sylentis, S.A.U., Tres Cantos, Madrid, Spain. Biocross, S.L., Valladolid, Spain.; PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar - Preclinical Unit. Colmenar Viejo, Madrid, Spain; PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain.; PharmaMar, S.A., Colmenar Viejo, Madrid, Spain.; ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. ; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ","Plitidepsin is a marine-derived cyclic-peptide that inhibits SARS-CoV-2 replication at low nanomolar concentrations by the targeting of host protein eEF1A (eukaryotic translation-elongation-factor-1A). We evaluated a model of intervention with plitidepsin in hospitalized COVID-19 adult patients where three doses were assessed (1.5, 2 and 2.5 mg/day for 3 days, as a 90-minute intravenous infusion) in 45 patients (15 per dose-cohort). Treatment was well tolerated, with only two Grade 3 treatment-related adverse events observed (hypersensitivity and diarrhea). The discharge rates by Days 8 and 15 were 56.8% and 81.8%, respectively, with data sustaining dose-effect. A mean 4.2 log10 viral load reduction was attained by Day 15. Improvement in inflammation markers was also noted in a seemingly dose-dependent manner. These results suggest that plitidepsin impacts the outcome of patients with COVID-19. One-Sentence SummaryPlitidepsin, an inhibitor of SARS-Cov-2 in vitro, is safe and positively influences the outcome of patients hospitalized with COVID-19.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.05.18.21257396,2021-05-23,https://medrxiv.org/cgi/content/short/2021.05.18.21257396,A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program,Anurag Verma; Noah L. Tsao; Lauren O. Thomann; Yuk-Lam Ho; Sudha K. Iyengar; Shiuh-Wen Luoh; Rotonya Carr; Dana C. Crawford; Jimmy T. Efird; Giulio Genovese; Adriana Hung; Kerry L. Ivey; Michael G. Levin; Julie Lynch; Pradeep Natarajan; Saiju Pyarajan; Alexander Bick; Lauren Costa; Giulio Genovese; Richard Hauger; Ravi Madduri; Gita A. Pathak; Renato Polimanti; Benjamin F. Voight; Marijana Vujkovic; Maryam Zekavat; Hongyu Zhao; Marylyn Ritchie; Kyong-Mi Chang; Kelly Cho; Juan P Casas; Philip S Tsao; J. Michael Gaziano; Christopher O?Donnell; Scott M. Damrauer; Katherine P. Liao,"Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Departments of Population and Quantitative Health Sciences, Ophthalmology and Visual Sciences and Genetics and Genome Sciences, Case Western Reserve University,; VA Portland Health Care System, Portland OR, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA; Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, USA.; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Tennessee Valley Healthcare System (Nashville VA) , Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, USA.; Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.; VA Boston Healthcare System, Boston, Massachusetts, USA;Harvard Medical School, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA;Vanderbilt University, Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Department of Psychiatry, University of California, San Diego, La Jolla, CA; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, ; University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, USA;Data Science and Learning Division, Arg; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; VA Boston Healthcare System, Boston, Massachusetts, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Palo Alto Health Care System, Palo Alto, California, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts","The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n=35) or hospitalization (n=42) due to severe COVID-19 using genome-wide association summary from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828= 53 and nrs505922=59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p=1.32 x 10-199), and thrombosis ORrs505922 1.33, p=2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p=4.12 x 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p=2.26x 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p=6.48 x10-23, lupus OR 0.84, p=3.97 x 10-06. PheWAS stratified by genetic ancestry demonstrated differences in genotype-phenotype associations across ancestry. LMNA (rs581342) associated with neutropenia OR 1.29 p=4.1 x 10-13 among Veterans of African ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.",genetic and genomic medicine,fuzzy,91,92 medRxiv,10.1101/2021.05.13.21257161,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.13.21257161,"Occupation, Work-Related Contact, and SARS-CoV-2 Anti-Nucleocapsid Serological Status: Findings from the Virus Watch prospective cohort study",Sarah Beale; Parth Patel; Alison Rodger; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ,"BackgroundWorkers differ in their risk of acquiring SARS-CoV-2 infection according to their occupation; however, few studies have been able to control for multiple confounders or investigate the work-related factors that drive differences in occupational risk. Using data from the Virus Watch community cohort study in England and Wales, we set out to estimate the total effect of occupation on SARS-CoV-2 serological status, whether this is mediated by frequency of close contact within the workplace, and how exposure to poorly ventilated workplaces varied across occupations. MethodsWe used data from a sub-cohort (n =3761) of adults ([≥]18) tested for SARS-CoV-2 anti-nucleocapsid antibodies between 01 February-28 April 2021 and responded to a questionnaire about work during the pandemic. Anti-nucleocapsid antibodies were used as a proxy of prior natural infection with COVID-19. We used logistic decomposition to estimate the total and direct effect of occupation and indirect effect of workplace contact frequency on odds of seropositivity, adjusting for age, sex, household income and region. We investigated the relationship between occupation and exposure to poorly-ventilated workplace environments using ordinal logistic regression. @@ -3085,13 +3073,6 @@ MethodsWe report the most recent findings on community infections from the REal- ResultsBetween rounds 10 and 11, prevalence of swab-positivity dropped by 50% in England from 0.20% (0.17%, 0.23%) to 0.10% (0.08%, 0.13%), with a corresponding R estimate of 0.90 (0.87, 0.94). Rates of swab-positivity fell in the 55 to 64 year old group from 0.17% (0.12%, 0.25%) in round 10 to 0.06% (0.04%, 0.11%) in round 11. Prevalence in round 11 was higher in the 25 to 34 year old group at 0.21% (0.12%, 0.38%) than in the 55 to 64 year olds and also higher in participants of Asian ethnicity at 0.31% (0.16%, 0.60%) compared with white participants at 0.09% (0.07%, 0.11%). Based on sequence data for positive samples for which a lineage could be identified, we estimate that 92.3% (75.9%, 97.9%, n=24) of infections were from the B.1.1.7 lineage compared to 7.7% (2.1%, 24.1%, n=2) from the B.1.617.2 lineage. Both samples from the B.1.617.2 lineage were detected in London from participants not reporting travel in the previous two weeks. Also, allowing for suitable lag periods, the prior close alignment between prevalence of infections and hospitalisations and deaths nationally has diverged. DiscussionWe observed marked reductions in prevalence from March to April and early May 2021 in England reflecting the success of the vaccination programme and despite easing of restrictions during lockdown. However, there is potential upwards pressure on prevalence from the further easing of lockdown regulations and presence of the B.1.617.2 lineage. If prevalence rises in the coming weeks, policy-makers will need to assess the possible impact on hospitalisations and deaths. In addition, consideration should be given to other health and economic impacts if increased levels of community transmission occur.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.05.17.21257223,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.17.21257223,Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).,Cyril Roman Geismar; Ellen Fragaszy; Vincent Grigori Nguyen; Wing Lam Erica Fong; Madhumita Shrotri; Sarah Beale; Alison Rodger; Vasileios Lampos; Thomas Edward Byrne; Jana Kovar; Annalan Navaratnam; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ,"IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant. - -MethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks. - -ResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)). - -ConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.05.13.21257146,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.13.21257146,Sociodemographic inequality in COVID-19 vaccination coverage amongst elderly adults in England: a national linked data study,Vahe Nafilyan; Ted Dolby; Cameron Razieh; Charlotte Gaughan; Jasper Morgan; Daniel Ayoubkhani; Ann Sarah Walker; Kamlesh Khunti; Myer Glickman; Thomas Yates,"Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Diabetes Research Centre, University of Leicester; Office for National Statistics; Diabetes Research Centre, University of Leicester","ObjectiveTo examine inequalities in COVID-19 vaccination rates amongst elderly adults in England DesignCohort study @@ -3635,6 +3616,23 @@ FindingsBetween 28 May 2020 and 15 January 2021, 5795 patients were randomly all InterpretationAmong patients hospitalised with COVID-19, high-titre convalescent plasma did not improve survival or other prespecified clinical outcomes. FundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant refs: MC_PC_19056; COV19-RECPLA).",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.03.04.21252921,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.04.21252921,A systematic review and meta-analysis of longitudinal cohort studies comparing mental health before versus during the COVID-19 pandemic,Eric Robinson; Angelina R Sutin; Michael Daly; Andrew Jones,University of Liverpool; Florida State University; Maynooth University; University of Liverpool,"BackgroundIncreases in mental health problems have been observed in some studies during the COVID-19 pandemic. It is unclear whether changes have been large and experienced by most population sub-groups, persisted over time or been symptom specific. + +MethodsWe systematically reviewed and meta-analysed longitudinal cohort studies that examined changes in mental health among the same group of participants before and during the pandemic (PROSPERO: CRD42021231256). Searches for published and unpublished studies were conducted in January 2021. Changes in mental health (standardised mean change; SMC) were examined using meta-analyses. + +FindingsSixty-five studies were included. There was an overall increase in mental health symptoms that was most pronounced during March-April 2020 (SMC = .102 [95% CI: .026 to .192], p = 0.03) before significantly declining over time (May-July SMC = .067 [95% CI: -.022 to .157], p = .141). Compared to measures of anxiety (SMC = 0.13, p = 0.02) and general mental health (SMC = -.03, p = 0.65), increases in depression and mood disorder symptoms tended to be larger (SMC = 0.22, p < .001) and reductions over time appeared less pronounced. Increased mental health symptoms were observed across most population subgroups examined but there was no evidence of any change in symptoms among samples with a pre-existing mental health condition. + +InterpretationThere was a small increase in mental health symptoms soon after the outbreak of the COVID-19 pandemic that decreased and was comparable to pre-pandemic levels by mid-2020 among most population sub-groups and symptom types. + +FundingN/A + +Research in contextO_ST_ABSEvidence before this studyC_ST_ABSThere have been reported increases in mental health problems during the outbreak of the COVID-19 pandemic. However, it is unclear whether changes in mental health problems have been symptom specific, how changes have differed across populations and whether increased mental health problems have persisted over time. We systematically reviewed and meta-analysed longitudinal cohort studies that examined mental health among the same participants prior to and during the pandemic in 2020. This approach allowed us to quantify the mental health burden associated with the outbreak of the pandemic and how it has changed over time. We searched Pubmed, SCOPUS, Web of Science and PsychInfo from January 2020 to January 11, 2021 and identified eligible unpublished articles available on pre-print servers. + +Added value of this studyWe identified 65 eligible articles that reported 201 comparisons of mental health pre vs. post pandemic outbreak. Meta-analysis indicated that longitudinal cohort studies that examined mental health prior to and during the COVID-19 pandemic in 2020 showed a significant but statistically small increase in mental health symptoms. The overall increase in mental health symptoms was most pronounced during the early stages of the pandemic (March-April), before decreasing and being generally comparable to pre-pandemic levels by mid-2020. + +Compared to anxiety and general measures of mental health functioning, increases tended to be larger in depressive symptoms and although statistically small, remained elevated past the early stages of the pandemic. Increases in mental health symptoms were observed across most population sub-groups, but there was no evidence of a change in mental health symptoms among samples of participants with a pre-existing mental health condition. + +Implications of all the available evidenceFindings confirm that the initial outbreak of the pandemic was associated with a significant but statistically small increase in mental health symptoms. Given that small effects may have meaningful cumulative consequences at the population level, there is a need for continued mental health provision and monitoring particularly during periods of the pandemic when infection rates and deaths are high. Further into the pandemic, mental health problems decreased significantly, which indicated recovery and resilience in overall mental health. Contrary to predictions made early in the pandemic, there was also no evidence of a worsening of mental health symptoms among samples of participants with a pre-existing mental health condition. Overall the results of the present analyses suggest that the pandemic may not have caused an unprecedented and long lasting mental health crisis, instead there appears to have been resilience in mental health.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2021.03.04.21252918,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.04.21252918,An increase in willingness to vaccinate against COVID-19 in the US between October 2020 and February 2021: longitudinal evidence from the Understanding America Study,Michael Daly; Andrew Jones; Eric Robinson,Maynooth University; University of Liverpool; University of Liverpool,"BackgroundRecent evidence suggests that willingness to vaccinate against COVID-19 has been declining throughout the pandemic and is low among ethnic minority groups. MethodsObservational study using a nationally representative longitudinal sample (N =7,840) from the Understanding America Study (UAS). Changes in the percentage of respondents willing to vaccinate, undecided, or intending to refuse a COVID-19 vaccine were examined over 20 survey waves from April 1 2020 to February 15 2021. @@ -3661,6 +3659,15 @@ Main outcome measures(i) COVID-19 related death, (ii) COVID-19 related hospitali ResultsIn wave 1, of 14,301,415 included individuals aged 16 and over, 90,095 (0.63%) were identified as being on the LDR. 30,173 COVID-related hospital admissions, 13,919 COVID-19 related deaths and 69,803 non-COVID deaths occurred; of which 538 (1.8%), 221 (1.6%) and 596 (0.85%) were among individuals on the LDR, respectively. In wave 2, 27,611 COVID-related hospital admissions, 17,933 COVID-19 related deaths and 54,171 non-COVID deaths occurred; of which 383 (1.4%), 260 (1.4%) and 470 (0.87%) were among individuals on the LDR. Wave 1 hazard ratios for individuals on the LDR, adjusted for age, sex, ethnicity and geographical location, were 5.3 (95% confidence interval (CI) 4.9, 5.8) for COVID-19 related hospital admissions and 8.2 (95% CI: 7.1, 9.4) for COVID-19 related death. Wave 2 produced similar estimates. Associations were stronger among those classed as severe-profound and among those in residential care. Down syndrome and cerebral palsy were associated with increased hazard of both events in both waves; Down syndrome to a much greater extent. Hazards of non-COVID-19 related death followed similar patterns with weaker associations. ConclusionsPeople with learning disabilities have markedly increased risks of hospitalisation and mortality from COVID-19. This raised risk is over and above that seen for non-COVID causes of death. Ensuring prompt access to Covid-19 testing and health care and consideration of prioritisation for COVID-19 vaccination and other targeted preventive measures are warranted.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.03.03.21252856,2021-03-06,https://medrxiv.org/cgi/content/short/2021.03.03.21252856,REACT-1 round 9 final report: Continued but slowing decline of prevalence of SARS-CoV-2 during national lockdown in England in February 2021,Steven Riley; Caroline E. Walters; Haowei Wang; Oliver Eales; David Haw; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundEngland will start to exit its third national lockdown in response to the COVID-19 pandemic on 8th March 2021, with safe effective vaccines being rolled out rapidly against a background of emerging transmissible and immunologically novel variants of SARS-CoV-2. A subsequent increase in community prevalence of infection could delay further relaxation of lockdown if vaccine uptake and efficacy are not sufficiently high to prevent increased pressure on healthcare services. + +MethodsThe PCR self-swab arm of the REal-time Assessment of Community Transmission Study (REACT-1) estimates community prevalence of SARS-CoV-2 infection in England based on random cross-sections of the population ages five and over. Here, we present results from the complete round 9 of REACT-1 comprising round 9a in which swabs were collected from 4th to 12th February 2021 and round 9b from 13th to 23rd February 2021. We also compare the results of REACT-1 round 9 to round 8, in which swabs were collected mainly from 6th January to 22nd January 2021. + +ResultsOut of 165,456 results for round 9 overall, 689 were positive. Overall weighted prevalence of infection in the community in England was 0.49% (0.44%, 0.55%), representing a fall of over two thirds from round 8. However the rate of decline of the epidemic has slowed from 15 (13, 17) days, estimated for the period from the end of round 8 to the start of round 9, to 31 days estimated using data from round 9 alone (lower confidence limit 17 days). When comparing round 9a to 9b there were apparent falls in four regions, no apparent change in one region and apparent rises in four regions, including London where there was a suggestion of sub-regional heterogeneity in growth and decline. Smoothed prevalence maps suggest large contiguous areas of growth and decline that do not align with administrative regions. + +Prevalence fell by 50% or more across all age groups in round 9 compared to round 8, with prevalence (round 9) ranging from 0.21% in those aged 65 and over to 0.71% in those aged 13 to 17 years. Round 9 prevalence was highest among Pakistani participants at 2.1% compared to white participants at 0.45% and Black participants at 0.83%. There were higher adjusted odds of infection for healthcare and care home workers, for those working in public transport and those working in education, school, nursery or childcare and lower adjusted odds for those not required to work outside the home. + +ConclusionsCommunity prevalence of swab-positivity has declined markedly between January and February 2021 during lockdown in England, but remains high; the rate of decline has slowed in the most recent period, with a suggestion of pockets of growth. Continued adherence to social distancing and public health measures is required so that infection rates fall to much lower levels. This will help to ensure that the benefits of the vaccination roll-out programme in England are fully realised.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.02.21252444,2021-03-03,https://medrxiv.org/cgi/content/short/2021.03.02.21252444,An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis,Dominic Cushnan; Oscar Bennett; Rosalind Berka; Ottavia Bertolli; Ashwin Chopra; Samie Dorgham; Alberto Favaro; Tara Ganepola; Mark Halling-Brown; Gergely Imreh; Joseph Jacob; Emily Jefferson; François Lemarchand; Daniel Schofield; Jeremy C Wyatt; - NCCID Collaborative,"AI Lab, NHSX, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Scientific Computing, Royal Surrey NHS Foundation Trust, Guildford, UK; Faculty, London, UK; Centre for Medical Image Computing, University College London, London, UK; Health Informatics Centre (HIC), School of Medicine, University of Dundee, UK; AI Lab, NHSX, London, UK; AI Lab, NHSX, London, UK; University of Southampton, Southampton, UK; ","The National COVID-19 Chest Imaging Database (NCCID) is a centralised database containing chest X-rays, chest Computed Tomography (CT) scans and cardiac Magnetic Resonance Images (MRI) from patients across the UK, jointly established by NHSX, the British Society of Thoracic Imaging (BSTI), Royal Surrey NHS Foundation Trust (RSNFT) and Faculty. The objective of the initiative is to support a better understanding of the coronavirus SARS-CoV-2 disease (COVID-19) and development of machine learning (ML) technologies that will improve care for patients hospitalised with a severe COVID-19 infection. The NCCID is now accumulating data from 20 NHS Trusts and Health Boards across England and Wales, with a total contribution of approximately 25,000 imaging studies in the training set (at time of writing) and is actively being used as a research tool by several organisations. This paper introduces the training dataset, including a snapshot analysis performed by NHSX covering: the completeness of clinical data, the availability of image data for the various use-cases (diagnosis, prognosis and longitudinal risk) and potential model confounders within the imaging data. The aim is to inform both existing and potential data users of the NCCIDs suitability for developing diagnostic/prognostic models. In addition, a cohort analysis was performed to measure the representativeness of the NCCID to the wider COVID-19 affected population. Three major aspects were included: geographic, demographic and temporal coverage, revealing good alignment in some categories, e.g., sex and identifying areas for improvements to data collection methods, particularly with respect to geographic coverage. All analyses and discussions are focused on the implications for building ML tools that will generalise well to the clinical use cases.",radiology and imaging,fuzzy,100,100 medRxiv,10.1101/2021.03.02.21252734,2021-03-03,https://medrxiv.org/cgi/content/short/2021.03.02.21252734,Relation of severe COVID-19 in Scotland to transmission-related factors and risk conditions eligible for shielding support: REACT-SCOT case-control study,Paul M McKeigue; David McAllister; David Caldwell; Ciara Gribben; Jen Bishop; Stuart J McGurnaghan; Matthew Armstrong; Joke Delvaux; Sam Colville; Sharon Hutchinson; Chris Robertson; Nazir Lone; Jim McMenamin; David Goldberg; Helen M Colhoun,University of Edinburgh; University of Glasgow; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Edinburgh; Public Health Scotland; Public Health Scotland; Public Health Scotland; Glasgow Caledonian University; Public Health Scotland; Strathclyde University; Public Health Scotland; University of Edinburgh; Public Health Scotland; Public Health Scotland; University of Edinburgh,"BackgroundClinically vulnerable individuals have been advised to shield themselves during the COVID-19 epidemic. The objectives of this study were to investigate: (1) the risk of severe COVID-19 in those eligible for shielding, and (2) the relation of severe COVID-19 to transmission-related factors in those in shielding and the general population. @@ -3825,6 +3832,7 @@ Our results show that absences as a result of COVID-19 infection rose steadily f In December, we observed a large rise in the number of absences per school in secondary school settings in the South East and Greater London, but such rises were not observed in other regions or in primary school settings. We conjecture that the increased transmissibility of the new variant in these regions may have contributed to this rise in cases in secondary schools. Finally, we observe a positive correlation between cases in the community and cases in schools in most regions, with weak evidence suggesting that cases in schools lag behind cases in the surrounding community. We conclude that there is not significant evidence to suggest that schools are playing a significant role in driving spread in the community and that careful monitoring may be required as schools re-open to determine the effect associated with open schools upon community incidence.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.10.21251480,2021-02-12,https://medrxiv.org/cgi/content/short/2021.02.10.21251480,Symptom reporting in over 1 million people: community detection of COVID-19,Joshua Elliott; Matthew Whitaker; Barbara Bodinier; Steven Riley; Helen Ward; Graham Cooke; Ara Darzi; Marc Chadeau-Hyam; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London,,infectious diseases,fuzzy,96,100 +medRxiv,10.1101/2021.02.11.21251587,2021-02-12,https://medrxiv.org/cgi/content/short/2021.02.11.21251587,Assessing the impact of secondary school reopening strategies on within-school COVID-19 transmission and absences: a modelling study,Trystan Leng; Edward M Hill; Robin N Thompson; Michael J Tildesley; Matt J Keeling; Louise J Dyson,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,,infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.11.21249258,2021-02-11,https://medrxiv.org/cgi/content/short/2021.02.11.21249258,"Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): preliminary results of a randomised, controlled, open-label, platform trial",Peter W Horby; Mark Campbell; Natalie Staplin; Enti Spata; Jonathan R Emberson; Guilherme Pessoa-Amorim; Leon Peto; Christopher E Brightling; Rahuldeb Sarkar; Koshy Thomas; Vandana Jeebun; Abdul Ashish; Redmond Tully; David Chadwick; Muhammad Sharafat; Richard Stewart; Banu Rudran; J Kenneth Baillie; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Furst; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Medway Foundation NHS Trust, Gillingham, United Kingdom; King?s College London, London, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, United Kingdom; Royal Oldham Hospital, Northern Care Alliance, Oldham, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; Milton Keynes University Hospital, Milton Keynes, United Kingdom; Luton & Dunstable University Hospital, Luton, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, Kings College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","Findings: Between 23 April 2020 and 25 January 2021, 4116 adults were included in the assessment of tocilizumab, including 562 (14%) patients receiving invasive mechanical ventilation, 1686 (41%) receiving non-invasive respiratory support, and. 1868 (45%) receiving no respiratory support other than oxygen. Median CRP was 143 [IQR 107-205] mg/L and 3385 (82%) patients were receiving systemic corticosteroids at randomisation. Overall, 596 (29%) of the 2022 patients allocated tocilizumab and 694 (33%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0.86; 95% confidence interval [CI] 0.77-0.96; p=0.007). Consistent results were seen in all pre-specified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital alive within 28 days (54% vs. 47%; rate ratio 1.23; 95% CI 1.12-1.34; p<0.0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (33% vs. 38%; risk ratio 0.85; 95% CI 0.78-0.93; p=0.0005). Interpretation: In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes regardless of the level of respiratory support received and in addition to the use of systemic corticosteroids.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.08.21250525,2021-02-09,https://medrxiv.org/cgi/content/short/2021.02.08.21250525,"COVID-19 infection and outcomes in a population-based cohort of 17,173 adults with intellectual disabilities compared with the general population",Angela Henderson; Micheal Fleming; Sally-Ann Cooper; Jill Pell; Craig Melville; Daniel MacKay; Christopher Hatton; Deborah Kinnear,University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; Manchester Metropolitan University; University of Glasgow,"ObjectivesTo compare COVID-19 infection, severe infection, mortality, case-fatality, and excess deaths, among adults with intellectual disabilities and those without. @@ -4392,6 +4400,19 @@ ConclusionOlder adults living with younger people are at increased risk of COVID FundingThis research was funded by the Office for National Statistics.",epidemiology,fuzzy,100,100 bioRxiv,10.1101/2020.12.02.408047,2020-12-02,https://biorxiv.org/cgi/content/short/2020.12.02.408047,Effective in-vitro inactivation of SARS-CoV-2 by commercially available mouthwashes,Katherine Davies; Hubert Buczkowski; Stephen R Welch; Nicole Green; Damian Mawer; Neil Woodford; Allen D.G Roberts; Peter Nixon; David Seymour; Marian J Killip,Public Health England; Public Health England; Public Health England; Public Health England; York Hospitals NHS Foundation Trust; Public Health England; Public Health England; York Hospitals NHS Foundation Trust; York Hospitals NHS Foundation Trust; Public Health England,"Infectious SARS-CoV-2 can be recovered from the oral cavities and saliva of COVID-19 patients with potential implications for disease transmission. Reducing viral load in patient saliva using antiviral mouthwashes may therefore have a role as a control measure in limiting virus spread, particularly in dental settings. Here, the efficacy of SARS-CoV-2 inactivation by seven commercially available mouthwashes with a range of active ingredients were evaluated in vitro. We demonstrate [≥]4.1 to [≥]5.5 log10 reduction in SARS-CoV-2 titre following a one minute treatment with commercially available mouthwashes containing 0.01-0.02% stabilised hypochlorous acid or 0.58% povidone iodine, and non-specialist mouthwashes with both alcohol-based and alcohol-free formulations designed for home use. In contrast, products containing 1.5% hydrogen peroxide or 0.2% chlorhexidine gluconate were ineffective against SARS-CoV-2 in these tests. This study contributes to the growing body of evidence surrounding virucidal efficacy of mouthwashes/oral rinses against SARS-CoV-2, and has important applications in reducing risk associated with aerosol generating procedures in dentistry and potentially for infection control more widely.",microbiology,fuzzy,100,100 +medRxiv,10.1101/2020.11.27.20239087,2020-11-30,https://medrxiv.org/cgi/content/short/2020.11.27.20239087,Dietary supplements during the COVID-19 pandemic: insights from 1.4M users of the COVID Symptom Study app - a longitudinal app-based community survey,Panayiotis Louca; Benjamin Murray; Kerstin Klaser; Mark S Graham; Mohsen Mazidi; Emily R Leeming; Ellen J Thompson; Ruth Bowyer; David Alden Drew; Long Alden Nguyen; Jordi Merino; Maria F Gomez; Olatz Mompeo; Ricardo Costeira; Carole H Sudre; Rachel Gibson; Claire Steves; Jonathan Wolf; Paul W Franks; Sebastien Ourselin; Andrew T Chan; Sarah E Berry; Ana Valdes; Philip Calder; Tim D Spector; Cristina Menni,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Lund University; King's College London; King's College London; University College London; King's College London; King's College London; Zoe Global Limited; Lund University; King's College London; Massachusetts General Hospital and Harvard Medical School; King's College London; King's College London; University of Southampton; King's College London; King's College London,"ObjectivesDietary supplements may provide nutrients of relevance to ameliorate SARS-CoV-2 infection, although scientific evidence to support a role is lacking. We investigate whether the regular use of dietary supplements can reduce the risk of testing positive for SARS-CoV-2 infection in around 1.4M users of the COVID Symptom Study App who completed a supplement use questionnaire. + +DesignLongitudinal app-based community survey and nested case control study. + +SettingSubscribers to an app that was launched to enable self-reported information related to SARS-CoV-2 infection for use in the general population in three countries. + +Main ExposureSelf-reported regular dietary supplement usage since the beginning of the pandemic. + +Main Outcome MeasuresSARS-CoV-2 infection confirmed by viral RNA polymerase chain reaction test (RT-PCR) or serology test. A secondary outcome was new-onset anosmia. + +ResultsIn an analysis including 327,720 UK participants, the use of probiotics, omega-3 fatty acids, multivitamins or vitamin D was associated with a lower risk of SARS-CoV-2 infection by 14%(95%CI: [8%,19%]), 12%(95%CI: [8%,16%]), 13%(95%CI: [10%,16%]) and 9%(95%CI: [6%,12%]), respectively, after adjusting for potential confounders. No effect was observed for vitamin C, zinc or garlic supplements. When analyses were stratified by sex, age and body mass index (BMI), the protective associations for probiotics, omega-3 fatty acids, multivitamins and vitamin D were observed in females across all ages and BMI groups, but were not seen in men. The same overall pattern of association was observed in both the US and Swedish cohorts. Results were further confirmed in a sub-analysis of 993,365 regular app users who were not tested for SARS-CoV-2 with cases (n= 126,556) defined as those with new onset anosmia (the strongest COVID-19 predictor). + +ConclusionWe observed a modest but significant association between use of probiotics, omega-3 fatty acid, multivitamin or vitamin D supplements and lower risk of testing positive for SARS-CoV-2 in women. No clear benefits for men were observed nor any effect of vitamin C, garlic or zinc for men or women. Randomised controlled trials of selected supplements would be required to confirm these observational findings before any therapeutic recommendations can be made.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.11.25.20238600,2020-11-29,https://medrxiv.org/cgi/content/short/2020.11.25.20238600,Spatially resolved simulations of the spread of COVID-19 in European countries,Andrea Parisi; Samuel P C Brand; Joe Hilton; Rabia Aziza; Matt J Keeling; D. James Nokes,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; Kemri-Wellcome Trust,"We explore the spatial and temporal spread of the novel SARS-CoV-2 virus under containment measures in three European countries based on fits to data of the early outbreak. Using data from Spain and Italy, we estimate an age dependent infection fatality ratio for SARS-CoV-2, as well as risks of hospitalization and intensive care admission. We use them in a model that simulates the dynamics of the virus using an age structured, spatially detailed agent based approach, that explicitly incorporates governamental interventions, changes in mobility and contact patterns occurred during the COVID-19 outbreak in each country. Our simulations reproduce several of the features of its spatio-temporal spread in the three countries studied. They show that containment measures combined with high density are responsible for the containment of cases within densely populated areas, and that spread to less densely populated areas occurred during the late stages of the first wave. The capability to reproduce observed features of the spatio-temporal dynamics of SARS-CoV-2 makes this model a potential candidate for forecasting the dynamics of SARS-CoV-2 in other settings, and we recommend its application in low and lower-middle countries which remain understudied.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.11.23.20237313,2020-11-24,https://medrxiv.org/cgi/content/short/2020.11.23.20237313,"Identifying optimal combinations of symptoms to trigger diagnostic work-up of suspected COVID-19 cases in vaccine trials: analysis from a community-based, prospective, observational cohort",Michela Antonelli; Joan Capdevila; Amol Chaudhari; Julia Granerod; Liane S Canas; Mark S Graham; Kerstin Klaser; Marc Modat; Erika Molteni; Ben Murray; Carole H Sudre; Richard Davies; Anna May; Long H Nguyen; David A Drew; Amit Joshi; Andrew T Chan; Jakob Cramer; Tim Spector; Jonathan Wolf; Sebastien Ourselin; Claire J Steves; Alfred E Loeliger,King's College London; Zoe Global; Coalition for Epidemic Preparedness Innovations; Coalition for Epidemic Preparedness Innovations; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University College London; Zoe Global; Zoe Global; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Coalition for Epidemic Preparedness Innovations; King's College London; Zoe Global; King's College London; King's College London; Coalition for Epidemic Preparedness Innovations,"ObjectivesDiagnostic work-up following any COVID-19 associated symptom will lead to extensive testing, potentially overwhelming laboratory capacity whilst primarily yielding negative results. We aimed to identify optimal symptom combinations to capture most cases using fewer tests with implications for COVID-19 vaccine developers across different resource settings and public health. @@ -4406,14 +4427,8 @@ C_LIO_LIAdditional symptoms increased case finding to > 90% but tests needed dou C_LIO_LIOptimal symptom combinations maximise case capture considering available resources C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public health C_LI",health informatics,fuzzy,100,100 +medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.11.18.20233932,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20233932,REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundEngland is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020. - -MethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020. - -ResultsOverall weighted prevalence of infection in the community in England was 1.3% or 130 people per 10,000 infected, up from 60 people per 10,000 in the round 5 report (18th September to 5th October 2020), doubling every 24 days on average since the prior round. The corresponding R number was estimated to be 1.2. Prevalence of infection was highest in North West (2.4%, up from 1.2%), followed by Yorkshire and The Humber (2.3% up from 0.84%), West Midlands (1.6% up from 0.60%), North East (1.5% up from 1.1%), East Midlands (1.3% up from 0.56%), London (0.97%, up from 0.54%), South West (0.80% up from 0.33%), South East (0.69% up from 0.29%), and East of England (0.69% up from 0.30%). Rapid growth in the South observed in the first half of round 6 was no longer apparent in the second half of round 6. We also observed a decline in prevalence in Yorkshire and The Humber during this period. Comparing the first and second halves of round 6, there was a suggestion of decline in weighted prevalence in participants aged 5 to 12 years and in those aged 25 to 44 years. While prevalence remained high, in the second half of round 6 there was suggestion of a slight fall then rise that was seen nationally and also separately in both the North and the South. - -ConclusionThe impact of the second national lockdown in England is not yet known. We provide here a detailed description of swab-positivity patterns at national, regional and local scales for the period immediately preceding lockdown, against which future trends in prevalence can be evaluated.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.11.18.20230649,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20230649,A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2,Edward M Hill; Benjamin D Atkins; Matt J Keeling; Louise Dyson; Michael J Tildesley,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"BackgroundAs part of a concerted pandemic response to protect public health, businesses can enact non-pharmaceutical controls to minimise exposure to pathogens in workplaces and premises open to the public. Amendments to working practices can lead to the amount, duration and/or proximity of interactions being changed, ultimately altering the dynamics of disease spread. These modifications could be specific to the type of business being operated. MethodsWe use a data-driven approach to parameterise an individual-based network model for transmission of SARS-CoV-2 amongst the working population, stratified into work sectors. The network is comprised of layered contacts to consider the risk of spread in multiple encounter settings (workplaces, households, social and other). We analyse several interventions targeted towards working practices: mandating a fraction of the population to work from home; using temporally asynchronous work patterns; and introducing measures to create COVID-secure workplaces. We also assess the general role of adherence to (or effectiveness of) isolation and test and trace measures and demonstrate the impact of all these interventions across a variety of relevant metrics. @@ -4641,6 +4656,15 @@ Implications of all the available evidenceWe show that spatial mobility data ava Data SharingData used in this study are available from the Facebook Data for Good Partner Program by application. Code and supplementary information for this paper are available online (https://github.com/hamishgibbs/facebook_mobility_uk), alongside publication.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.10.26.20219642,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219642,A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events,Christopher J R Illingworth; William L Hamilton; Christopher H Jackson; Ashley Popay; Luke Meredith; Charlotte J Houldcroft; Myra Hosmillo; Aminu Jahun; Matthew Routledge; Ben Warne; Laura Caller; Sarah Caddy; Anna Yakovleva; Grant Hall; Fahad A Khokhar; Theresa Feltwell; Malte Pinckert; Iliana Georgana; Yasmin Chaudhry; Martin Curran; Surendra Parmar; Dominic Sparkes; Lucy Rivett; Nick K Jones; Sushmita Sridhar; Sally Forest; Tom Dymond; Kayleigh Grainger; Chris Workman; Effrossyni Gkrania-Klotsas; Nicholas M Brown; Michael Weekes; Stephen Baker; Sharon J Peacock; Theodore Gouliouris; Ian G. Goodfellow; Daniela de Angelis; M. Estee Torok,"MRC Biostatistics Unit, University of Cambridge; Department of Medicine, University of Cambridge; MRC Biostatistics Unit, University of Cambridge; Public Health England Field Epidemiology Unit, Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust, Cambridge; Department of Medicine, University of Cambridge; Francis Crick Institute; Cambridge Institute for Therapeutic Immunology and Infectious Disease; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Department of Medicine, University of Cambridge; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University; Cambridge University; Department of Medicine, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; MRC Biostatistics Unit, University of Cambridge; University of Cambridge","Identifying linked cases of infection is a key part of the public health response to viral infectious disease. Viral genome sequence data is of great value in this task, but requires careful analysis, and may need to be complemented by additional types of data. The Covid-19 pandemic has highlighted the urgent need for analytical methods which bring together sources of data to inform epidemiological investigations. We here describe A2B-COVID, an approach for the rapid identification of linked cases of coronavirus infection. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and novel approaches to genome sequence data to assess whether or not cases of infection are consistent or inconsistent with linkage via transmission. We apply our method to analyse and compare data collected from two wards at Cambridge University Hospitals, showing qualitatively different patterns of linkage between cases on designated Covid-19 and non-Covid-19 wards. Our method is suitable for the rapid analysis of data from clinical or other potential outbreak settings.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.10.26.20219725,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219725,"Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults",Helen Ward; Graham Cooke; Christina J Atchison; Matthew Whitaker; Joshua Elliott; Maya Moshe; Jonathan C Brown; Barney Flower; Anna Daunt; Kylie E. C. Ainslie; Deborah Ashby; Christl A. Donnelly; Steven Riley; Ara Darzi; Wendy Barclay; Paul Elliott,"Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London","BackgroundThe prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into its spread in the community, the likelihood of reinfection and potential for some level of population immunity. + +MethodsPrevalence of antibody positivity in England, UK (REACT2) with three cross-sectional surveys between late June and September 2020. 365104 adults used a self-administered lateral flow immunoassay (LFIA) test for IgG. A laboratory comparison of LFIA results to neutralization activity in panel of sera was performed. + +ResultsThere were 17,576 positive tests over the three rounds. Antibody prevalence, adjusted for test characteristics and weighted to the adult population of England, declined from 6.0% [5.8, 6.1], to 4.8% [4.7, 5.0] and 4.4% [4.3, 4.5], a fall of 26.5% [-29.0, -23.8] over the three months of the study. There was a decline between rounds 1 and 3 in all age groups, with the highest prevalence of a positive result and smallest overall decline in positivity in the youngest age group (18-24 years: -14.9% [-21.6, -8.1]), and lowest prevalence and largest decline in the oldest group (75+ years: -39.0% [-50.8, -27.2]); there was no change in antibody positivity between rounds 1 and 3 in healthcare workers (+3.45% [-5.7, +12.7]). + +The decline from rounds 1 to 3 was largest in those who did not report a history of COVID-19, (-64.0% [-75.6, -52.3]), compared to -22.3% ([-27.0, -17.7]) in those with SARS-CoV-2 infection confirmed on PCR. + +DiscussionThese findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.10.26.20219485,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219485,Predicting the impact of COVID-19 interruptions on transmission of gambiense human African trypanosomiasis in two health zones of the Democratic Republic of Congo,Maryam Aliee; Soledad Castano; Christopher Davis; Swati Patel; Erick Mwamba Miaka; Simon EF Spencer; Matt J Keeling; Nakul Chitnis; Kat S Rock,"University of Warwick; Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute; University of Warwick; University of Warwick; Programme National de Lutte contre la Trypanosomiase Humaine Africaine, Kinshasa, the Democratic Republic of the Congo; University of Warwick; University of Warwick; Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Warwick","Many control programmes against neglected tropical diseases have been interrupted due to COVID-19 pandemic, including those that rely on active case finding. In this study we focus on gambiense human African trypanosomiasis (gHAT), where active screening was suspended in the Democratic Republic of Congo (DRC) due to the pandemic. We use two independent mathematical models to predict the impact of COVID-19 interruptions on transmission and reporting, and the achievement of 2030 elimination of transmission (EOT) goal for gHAT in two moderate-risk regions of DRC. We consider different interruption scenarios, including reduced passive surveillance in fixed health facilities, and whether this suspension lasts until the end of 2020 or 2021. Our models predict an increase in the number of new infections in the interruption period only if both active screening and passive surveillance were suspended, and with slowed reduction - but no increase - if passive surveillance remains fully functional. In all scenarios, the EOT may be slightly pushed back if no mitigation such as increased screening coverage is put in place. However, we emphasise that the biggest challenge will remain in the higher prevalence regions where EOT is already predicted to be behind schedule without interruptions unless interventions are bolstered.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.10.19.20214494,2020-10-21,https://medrxiv.org/cgi/content/short/2020.10.19.20214494,Attributes and predictors of Long-COVID: analysis of COVID cases and their symptoms collected by the Covid Symptoms Study App,Carole H Sudre; Benjamin Murray; Thomas Varsavsky; Mark S Graham; Rose S Penfold; Ruth C.E Bowyer; Joan Capdevila Pujol; Kerstin Klaser; Michela Antonelli; Liane S Canas; Erika Molteni; Marc Modat; M. Jorge Cardoso; Anna May; Sajaysurya Ganesh; Richard Davies; Long H Nguyen; David Alden Drew; Christina M Astley; Amit D. Joshi; Jordi Merino; Neli Tsereteli; Tove Fall; Maria F Gomez; Emma Duncan; Christina Menni; Frances MK Williams; Paul W Franks; Andrew T Chan; Jonathan Wolf; Sebastien Ourselin; Timothy Spector; Claire J Steves,KCL; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital; Boston Children's Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Lund University; Uppsala University; Lund University; King's College London; King's College London; King's College London; Lund University; Massachusetts General Hospital; Zoe Global Limited; King's College London; King's College London; King's College London,"Reports of ""Long-COVID"", are rising but little is known about prevalence, risk factors, or whether it is possible to predict a protracted course early in the disease. We analysed data from 4182 incident cases of COVID-19 who logged their symptoms prospectively in the COVID Symptom Study app. 558 (13.3%) had symptoms lasting >=28 days, 189 (4.5%) for >=8 weeks and 95 (2.3%) for >=12 weeks. Long-COVID was characterised by symptoms of fatigue, headache, dyspnoea and anosmia and was more likely with increasing age, BMI and female sex. Experiencing more than five symptoms during the first week of illness was associated with Long-COVID, OR=3.53 [2.76;4.50]. A simple model to distinguish between short and long-COVID at 7 days, which gained a ROC-AUC of 76%, was replicated in an independent sample of 2472 antibody positive individuals. This model could be used to identify individuals for clinical trials to reduce long-term symptoms and target education and rehabilitation services.",infectious diseases,fuzzy,94,100 medRxiv,10.1101/2020.10.15.20213108,2020-10-20,https://medrxiv.org/cgi/content/short/2020.10.15.20213108,FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study,Samuel G Urwin; B Clare Lendrem; Jana Suklan; Kile Green; Sara Graziadio; Peter Buckle; Paul M Dark; Adam L Gordon; Daniel S Lasserson; Brian Nicholson; D Ashley Price; Charles Reynard; Mark H Wilcox; Gail Hayward; Graham Prestwich; Valerie Tate; Tristan W Clark; Raja V Reddy; Hamish Houston; Ankur Gupta-Wright; Laurence John; Richard Body; A Joy Allen,"NIHR Newcastle In Vitro Diagnostics Co-operative, Newcastle-upon-Tyne Hospitals Foundation Trust, Newcastle-upon-Tyne, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Newcastle-upon-Tyne Hospitals Foundation Trust, Newcastle-upon-Tyne, UK; Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, UK; Division of Infection, Immunity & Respiratory Medicine, University of Manchester, UK; School of Medicine, University of Nottingham, UK; NIHR Applied Research Collaboration East Midlands (ARC-EM), Nottingham, UK; NIHR Community Healthcare MedTech and In Vitro Diagnostics Cooperative, Oxford Health NHS Foundation Trust, Oxford, UK; Division of Health Sciences, University ; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Newcastle-upon-Tyne Hospitals Foundation Trust, Newcastle-upon-Tyne, UK; NIHR Doctoral Research Fellowship Programme, UK; Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK; Healthcare Associated Infections Research Group, NIHR Leeds In Vitro Diagnostics Co-operative, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds; NIHR Community Healthcare MedTech and In Vitro Diagnostics Co-operative, Oxford Health NHS Foundation Trust, Oxford, UK; Nuffield Department of Primary Care Hea; Yorkshire and Humber Academic Health Science Network, Wakefield, UK; Patient Public Involvement (PPI) Member, Precision Antimicrobial Prescribing PPI Group, NIHR Community Healthcare MedTech and In Vitro Diagnostics Cooperative, ; School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; Department of Infection, University Hospital Sout; Department of Respiratory Medicine, Kettering General Hospital NHS Foundation Trust, Kettering, UK; Northwick Park Hospital, London North West University Healthcare NHS Trust, Harrow, UK; Institute for Global Health, University College London, London, UK; Ealing Hospital, London North West University Healthcare NHS Trust, London, UK; Clinical Res; Northwick Park Hospital, London North West University Healthcare NHS Trust, Harrow, UK; Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK; Emergency Department, Manchester Royal Infirmary, Ma; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK","BackgroundWe conducted a systematic review and individual patient data (IPD) meta-analysis to evaluate the diagnostic accuracy of a commercial point-of-care test, the FebriDx lateral flow device (LFD), in adult patients with suspected COVID-19. The FebriDx LFD is designed to distinguish between viral and bacterial respiratory infection. @@ -4844,6 +4868,7 @@ The number of admissions due to psychiatric conditions and overdoses was higher There were no significant differences in non-COVID-related intensive care admissions or mortality between the same months in the two years. ConclusionIn this large, single-centre study, there was a change in hospitalised case-mix when comparing April 2019 with April 2020: an increase in conditions which potentially reflect social isolation (falls, drug and alcohol misuse and psychiatric illness) and a decrease in conditions which rarely require in-patient hospital treatment (musculoskeletal pain and non-cardiac chest pain) especially among younger adults. These results highlight two areas for further research; the impact of social isolation on health and whether younger adults could be offered alternative health services to avoid potentially unnecessary hospital assessment.",emergency medicine,fuzzy,100,100 +medRxiv,10.1101/2020.09.17.20196469,2020-09-18,https://medrxiv.org/cgi/content/short/2020.09.17.20196469,Renin-angiotensin system inhibitors and susceptibility to COVID-19 in patients with hypertension: a propensity score-matched cohort study in primary care,Shamil Haroon; Anuradhaa Subramanian; Jennifer Cooper; Astha Anand; Krishna Gokhale; Nathan Byne; Samir Dhalla; Dionisio Acosta-Mena; Thomas Taverner; Kelvin Okoth; Jingya Wang; Joht Singh Chandan; Christopher Sainsbury; Dawit Tefra Zemedikun; G Neil Thomas; Dhruv Parekh; Tom Marshall; Elizabeth Sapey; Nicola J Adderley; Krishnarajah Nirantharakumar,"University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Cegedim Health Data, Cegedim Rx, London, UK; Cegedim Health Data, Cegedim Rx, London, UK; Cegedim Health Data, Cegedim Rx, London, UK; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham and Department of Diabetes, Gartnavel General Hospital, NHS Greater Glasgow and Clyde, UK; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham","Introduction A significant proportion of patients with Coronavirus Disease-19 (COVID-19) have hypertension and are treated with renin-angiotensin system (RAS) inhibitors, namely angiotensin-converting enzyme I inhibitors (ACE inhibitors) or angiotensin II type-1 receptor blockers (ARBs). These medications have been postulated to influence susceptibility to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The objective of this study was to assess a possible association between prescription of RAS inhibitors and the incidence of COVID-19 and all-cause mortality. Methods We conducted a propensity-score matched cohort study to assess the incidence of COVID-19 among patients with hypertension who were prescribed ACE inhibitors or ARBs compared to patients treated with calcium channel blockers (CCBs) in a large UK-based primary care database (The Health Improvement Network). We estimated crude incidence rates for confirmed/suspected COVID-19 among those prescribed ACE inhibitors, ARBs and CCBs. We used a Cox proportional hazards model to produce adjusted hazard ratios for COVID-19 comparing patients prescribed ACE inhibitors or ARBs to those prescribed CCBs. We further assessed all-cause mortality as a secondary outcome and a composite of accidents, trauma or fractures as a negative control outcome to assess for residual confounding. Results In the propensity score matched analysis, 83 of 18,895 users (0.44%) of ACE inhibitors developed COVID-19 over 8,923 person-years, an incidence rate of 9.3 per 1000 person-years. 85 of 18,895 (0.45%) users of CCBs developed COVID-19 over 8,932 person-years, an incidence rate of 9.5 per 1000 person-years. The adjusted hazard ratio for suspected/confirmed COVID-19 for users of ACE inhibitors compared to CCBs was 0.92 (95% CI 0.68 to 1.26). 79 out of 10,623 users (0.74%) of ARBs developed COVID-19 over 5010 person-years, an incidence rate of 15.8 per 1000 person-years, compared to 11.6 per 1000 person-years among users of CCBs. The adjusted hazard ratio for suspected/confirmed COVID-19 for users of ARBs compared to CCBs was 1.38 (95% CI 0.98 to 1.95). There were no significant associations between use of ACE inhibitors or ARBs and all-cause mortality, compared to use of CCBs. We found no evidence of significant residual confounding with the negative control analysis. Conclusion Current use of ACE inhibitors was not associated with the risk of suspected or confirmed COVID-19 whereas use of ARBs was associated with a statistically non-significant 38% relative increase in risk compared to use of CCBs. However, no significant associations were observed between prescription of either ACE inhibitors or ARBs and all-cause mortality during the peak of the pandemic.",infectious diseases,fuzzy,100,100 bioRxiv,10.1101/2020.09.16.297945,2020-09-16,https://biorxiv.org/cgi/content/short/2020.09.16.297945,Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing,Bjoern Meyer; Jeanne Chiaravalli; Stacy Gellenoncourt; Philip Brownridge; Dominic P. Bryne; Leonard A. Daly; Arturas Grauslys; Marius Walter; Fabrice Agou; Lisa A. Chakrabarti; Charles S. Craik; Claire E. Eyers; Patrick A. Eyers; Yann Gambin; Andrew R Jones; Emma Sierecki; Eric Verdin; Marco Vignuzzi; Edward Emmott,Institut Pasteur; Institut Pasteur; Institut Pasteur; University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool; Buck Institute for Aging; Institut Pasteur; Institut Pasteur; UCSF; University of Liverpool; University of Liverpool; UNSW; University of Liverpool; UNSW; Buck Institute for Aging; Institut Pasteur; University of Liverpool,"SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, and responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication, and inhibitors targeting proteases have already shown success at inhibiting SARS-CoV-2 in cell culture models. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigenic proteins S and N, which are the main targets for vaccine and antibody testing efforts. We discovered significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases, validating a subset with in vitro assays. We showed that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, showed a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.",microbiology,fuzzy,100,100 medRxiv,10.1101/2020.09.12.20191973,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.12.20191973,Inequality in access to health and care services during lockdown - Findings from the COVID-19 survey in five UK national longitudinal studies,Constantin-Cristian Topriceanu; Andrew Wong; James C Moon; Alun Hughes; David Bann; Nishi Chaturvedi; Praveetha Patalay; Gabriella Conti; Gabriella Captur,University College London; UCL; UCL; UCL; University College London; UCL; University College London; UCL; University College London,"Background: Access to health services and adequate care is influenced by sex, ethnicity, socio-economic position (SEP) and burden of co-morbidities. However, it is unknown whether the COVID-19 pandemic further deepened these already existing health inequalities. Methods: Participants were from five longitudinal age-homogenous British cohorts (born in 2001, 1990, 1970, 1958 and 1946). A web and telephone-based survey provided data on cancelled surgical or medical appointments, and the number of care hours received during the UK COVID-19 national lockdown. Using binary or ordered logistic regression, we evaluated whether these outcomes differed by sex, ethnicity, SEP and having a chronic illness. Adjustment was made for study-design, non-response weights, psychological distress, presence of children or adolescents in the household, keyworker status, and whether participants had received a shielding letter. Meta-analyses were performed across the cohorts and meta-regression evaluated the effect of age as a moderator. Findings: 14891 participants were included. Females (OR 1.40, 95% confidence interval [1.27,1.55]) and those with a chronic illness (OR 1.84 [1.65-2.05]) experienced significantly more cancellations during lockdown (all p<0.0001). Ethnic minorities and those with a chronic illness required a higher number of care hours during the lockdown (both OR approx. 2.00, all p<0.002). Age was not independently associated with either outcome in meta-regression. SEP was not associated with cancellation or care hours. Interpretation: The UK government's lockdown approach during the COVID-19 pandemic appears to have deepened existing health inequalities, impacting predominantly females, ethnic-minorities and those with chronic illnesses. Public health authorities need to implement urgent policies to ensure equitable access to health and care for all in preparation for a second wave.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.09.13.20193730,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.13.20193730,Mental health service activity during COVID-19 lockdown among individuals with Personality Disorders: South London and Maudsley data on services and mortality from January to May 2020,Eleanor Nuzum; Evangelia Martin; Matthew Broadbent; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have a widespread impact on mental healthcare for both services themselves and the people accessing those services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to understand this further for specific groups, including those diagnosed with a personality disorder who might have particular vulnerabilities. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with personality disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st May 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with personality disorders. In addition, daily deaths are described for all current and previous SLaM service users with personality disorder over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. Liaison and Older Adult teams showed the largest drop in caseloads, whereas Early Intervention in Psychosis service caseloads remained the same. Reduced accepted referrals and inpatient admissions were observed and there was a 28% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March.",psychiatry and clinical psychology,fuzzy,100,100 @@ -4894,13 +4919,6 @@ At the recommended threshold, PMEWS and the WHO criteria showed good sensitivity ConclusionCURB-65, PMEWS and NEWS2 provide good but not excellent prediction for adverse outcome in suspected COVID-19, and predicted death without organ support better than receipt of organ support. PMEWS, the WHO criteria and NEWS2 (using a lower threshold than usually recommended) provide good sensitivity at the expense of specificity. RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,fuzzy,100,100 -medRxiv,10.1101/2020.09.03.20187377,2020-09-05,https://medrxiv.org/cgi/content/short/2020.09.03.20187377,Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study,Max T Eyre; Rachel Burns; Victoria Kirkby; Catherine Smith; Spiros Denaxas; Vincent Nguyen; Andrew Hayward; Laura Shallcross; Ellen Fragaszy; Robert W Aldridge,"Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK; Liverpool School of Tropical Med; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Health Data Research UK, London, NW1 2DA, UK; The Alan Turing Institute, London; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Epidemiology and Health Care; Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Faculty of Epidemiology and Population Health, London School of Hygiene and Tro; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK","BackgroundDiagnostic testing forms a major part of the UKs response to the current COVID-19 pandemic with tests offered to people with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK. - -MethodsIn this analysis of the Bug Watch prospective community cohort study, we estimated the incidence of cough or fever in England in 2018-2019. We then estimated the COVID-19 diagnostic testing rates required in the UK for baseline cough or fever cases for the period July 2020-June 2021. This was explored for different rates of the population requesting tests and four second wave scenarios and then compared to current national capacity. - -ResultsThe baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020. - -ConclusionsOur results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UKs response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.09.01.20185793,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.01.20185793,Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study,Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection. MethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. @@ -5166,6 +5184,11 @@ FindingsWe demonstrated a seroprevalence of 12% (51participants of 431). Of 48 s InterpretationSeroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response. FundingNIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC",epidemiology,fuzzy,92,100 +medRxiv,10.1101/2020.07.26.20161570,2020-07-28,https://medrxiv.org/cgi/content/short/2020.07.26.20161570,"Magnitude, demographics and dynamics of the impact of the first phase of the Covid-19 pandemic on all-cause mortality in 17 industrialised countries",Vasilis Kontis; James E Bennett; Theo Rashid; Robbie M Parks; Jonathan Pearson-Stuttard; Michel Guillot; Perviz Asaria; Bin Zhou; Marco Battaglini; Gianni Corsetti; Martin McKee; Mariachiara Di Cesare; Colin D Mathers; Majid Ezzati,Imperial College London; Imperial College London; Imperial College London; Columbia University; Imperial College London; University of Pennsylvania; Imperial College London; Imperial College London; Italian National Institute of Statistics; Italian National Institute of Statistics; London School of Hygiene & Tropical Medicine; Middlesex University London; Independent Researcher; Imperial College London,"The Covid-19 pandemic affects mortality directly through infection as well as through changes in the social, environmental and healthcare determinants of health1. The impacts on mortality are likely to vary across countries in magnitude, timing, and age and sex composition. Here, we applied an ensemble of 16 Bayesian probabilistic models to vital statistics data, by age group and sex, to consistently and comparably estimate the impacts of the first phase of the pandemic on all-cause mortality for 17 industrialised countries. The models accounted for factors that affect death rates including seasonality, temperature, and public holidays, as well as for medium-long-term secular trends and the dependency of death rates in each week on those in preceding week(s). From mid-February through the end of May 2020, an estimated 202,900 (95% credible interval 179,400-224,900) more people died in these 17 countries than would have had the pandemic not taken place. Nearly three quarters of these excess deaths occurred in England and Wales, Italy and Spain, where less than half of the total population of these countries live. When all-cause mortality is considered, the total number of deaths, deaths per 100,000 people, and relative increase in deaths were similar between men and women in most countries. Further, in many countries, the balance of excess deaths changed from male-dominated early in the pandemic to being equal or female-dominated later on. + +Taken over the entire first phase of the pandemic, there was no detectable rise in all-cause mortality in New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland and for women in Austria and Switzerland (posterior probability of an increase in deaths <90%). Women in Portugal and men in Austria experienced relatively small increases in all-cause mortality, with posterior probabilities of 90-99%. For men in Switzerland and Portugal, and both sexes in the Netherlands, France, Sweden, Belgium, Italy, Scotland, Spain and England and Wales, all-cause mortality increased as a result of the pandemic with a posterior probability >99%. After accounting for population size, England and Wales and Spain experienced the highest death toll, nearly 100 deaths per 100,000 people; they also had the largest relative (percent) increase in deaths (37% (95% credible interval 30-44) in England and Wales; 38% (31-44) in Spain). New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland experienced changes in deaths that ranged from possible slight declines to increases of no more than 5%. The large impact in England and Wales stems partly from having experienced (together with Spain) the highest weekly increases in deaths, more than doubling in some weeks, and having had (together with Sweden) the longest duration when deaths exceeded levels that would be expected in the absence of the pandemic. + +The heterogeneous magnitude and character of the excess deaths due to the Covid-19 pandemic reflect differences in how well countries have managed the pandemic (e.g., timing, extent and adherence to lockdowns and other social distancing measures; effectiveness of test, trace and isolate mechanisms), and the resilience and preparedness of the health and social care system (e.g., effective facility and community care pathways; minimising spread of infection within hospitals and care homes, and between them and the community).",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.07.23.20160747,2020-07-27,https://medrxiv.org/cgi/content/short/2020.07.23.20160747,Associations of severe COVID-19 with polypharmacy in the REACT-SCOT case-control study,Paul M McKeigue; Sharon Kennedy; Amanda Weir; Jen Bishop; Stuart J McGurnaghan; David McAllister; Chris Robertson; Rachael Wood; Nazir Lone; Janet Murray; Thomas M Caparrotta; Alison Smith-Palmer; David Goldberg; Jim McMenamin; Colin Ramsay; Bruce Guthrie; Sharon Hutchinson; Helen M Colhoun,University of Edinburgh; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Edinburgh; University of Glasgow; University of Strathclyde; NHS Information Services Division (Public Health Scotland); University of Edinburgh; Public Health Scotland; University of Edinburgh; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Edinburgh; Glasgow Caledonian University; University of Edinburgh,"ObjectivesTo investigate the relation of severe COVID-19 to prior drug prescribing. DesignMatched case-control study (REACT-SCOT) based on record linkage to hospital discharges since June 2015 and dispensed prescriptions issued in primary care during the last 240 days. @@ -5490,13 +5513,6 @@ FindingsIn ALSPAC-G1 there was evidence that anxiety and lower wellbeing, but no InterpretationThese results suggest increases in anxiety and lower wellbeing that may be related to the COVID-19 pandemic and/or its management, particularly in young people. This research highlights that specific groups may be disproportionally at risk of elevated levels of depression and anxiety during COVID-19 and supports recent calls for increasing funds for mental health services. FundingThe UK Medical Research Council (MRC), the Wellcome Trust and University of Bristol.",psychiatry and clinical psychology,fuzzy,100,100 -medRxiv,10.1101/2020.06.16.20133157,2020-06-18,https://medrxiv.org/cgi/content/short/2020.06.16.20133157,Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease.,Petra Mlcochova; Dami Collier; Allyson V Ritchie; Sonny M Assennato; Myra Hosmillo; Neha Goel; Bo Meng; Krishna Chatterji; Vivien Mendoza; Nigel Temperton; Leo Kiss; Katarzyna A Ciazyns; Xiaoli Xiong; John AG Briggs; James Nathan; Federica Mescia; Hongyi Zhang; Petros Barmpounakis; Nikos Demeris; Richard Skells; Paul Lyons; John Bradley; Stephen Baker; Jean Pierre Allain; Kenneth GC Smith; Ian Goodfellow; Ravindra K Gupta,"University of Cambridge; UCL; Diagnostics for the Real World Europe Ltd; DRW; University of Cambridge; University of Cambridge; University of Cambridge; NIHR Cambridge Clinical Research Facility; CUH NHS Trust; University of Kent; Medical Research Council Laboratory of Molecular Biology, Cambridge; Medical Research Council Laboratory of Molecular Biology, Cambridge; Medical Research Council Laboratory of Molecular Biology; Medical Research Council Laboratory of Molecular Biology; University of Cambridge; University of Cambridge; CUH NHS Trust; Athens University of Economics and Business; Cambridge Clinical Trials Unit-Cancer Theme; Cambridge Clinical Trials Unit-Cancer Theme; University of Cambridge; University of Cambridge; Cambridge University; Diagnostics for the Real World EU Ltd; University of Cambridge; ig299@cam.ac.uk; University of Cambridge","BackgroundRapid COVID-19 diagnosis in hospital is essential for patient management and identification of infectious patients to limit the potential for nosocomial transmission. The diagnosis of infection is complicated by 30-50% of COVID-19 hospital admissions with nose/throat swabs testing negative for SARS-CoV-2 nucleic acid, frequently after the first week of illness when SARS-CoV-2 antibody responses become detectable. We assessed the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease in the emergency department. - -MethodsWe developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike (S) protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and S proteins from SARS-CoV-2. We tested two lateral flow rapid fingerprick tests with bands for IgG and IgM. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid POC nucleic acid amplification (NAAT) test. Additionally, serum collected at admission was retrospectively tested by in vitro neutralisation, ELISA and the candidate POC antibody tests. We evaluated the performance of the individual and combined rapid POC diagnostic tests against a composite reference standard of neutralisation and standard laboratory based RT-PCR. - -Results45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Using the composite reference standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our reference standard and 63.0 (IQR 41.0-72.0) years in those without disease. The overall detection rate by rapid NAAT was 79.2% (95CI 57.8-92.9%), decreasing from 100% (95% CI 65.3-98.6%) in days 1-4 to 50.0% (95% CI 11.8-88.2) for days 9-28 post symptom onset. Correct identification of COVID-19 with combined rapid POC diagnostic tests was 100% (95CI 85.8-100%) with a false positive rate of 5.3-14.3%, driven by POC LFA antibody tests. - -ConclusionsCombined POC tests have the potential to transform our management of COVID-19, including inflammatory manifestations later in disease where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.06.15.20131722,2020-06-17,https://medrxiv.org/cgi/content/short/2020.06.15.20131722,"Delirium is a presenting symptom of COVID-19 in frail, older adults: a cohort study of 322 hospitalised and 535 community-based older adults",Maria Beatrice Zazzara; Rose S. Penfold; Amy L. Roberts; Karla Lee; Hannah Dooley; Carole H. Sudre; Carly Welch; Ruth C. E. Bowyer; Alessia Visconti; Massimo Mangino; Maxim B. Freydin; Julia S. El-Sayed Moustafa; Kerrin Small; Benjamin Murray; Marc Modat; Jonathan Wolf; Sebastien Ourselin; Finbarr C. Martin; Claire J. Steves; Mary Ni Lochlainn,"Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Gerontology, Neuroscience and O; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Institute of Inflammation and Ageing, University of Birmingham, B15 2TT; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; NIHR Biomedical Research Centre at Guy's and ; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Zoe Global Limited,164 Westminster Bridge Road, London SE1 7RW, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Population Health Sciences, King's College London, Westminster Bridge Road, SE17EH, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH; Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH","BackgroundFrailty, increased vulnerability to physiological stressors, is associated with adverse outcomes. COVID-19 exhibits a more severe disease course in older, co-morbid adults. Awareness of atypical presentations is critical to facilitate early identification. ObjectiveTo assess how frailty affects presenting COVID-19 symptoms in older adults. @@ -5618,6 +5634,13 @@ We compared eight strategies for reopening primary and secondary schools in Engl We predicted reopening schools with half-sized classes or focused on younger children was unlikely to push R above one. Older children generally have more social contacts, so reopening secondary schools results in more cases than reopening primary schools, while reopening both could have pushed R above one in some regions. Reductions in community social-distancing were found to outweigh and exacerbate any impacts of reopening. In particular, opening schools when the reproduction number R is already above one generates the largest increase in cases. Our work indicates that while any school reopening will result in increased mixing and infection amongst children and the wider population, reopening schools alone in June was unlikely to push R above one. Ultimately, reopening decisions are a difficult trade-off between epidemiological consequences and the emotional, educational and developmental needs of children. Into the future, there are difficult questions about what controls can be instigated such that schools can remain open if cases increase.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.06.04.20122069,2020-06-05,https://medrxiv.org/cgi/content/short/2020.06.04.20122069,Mechanical ventilation utilization in COVID-19: A systematic review and meta-analysis,Mohammed A Almeshari; Nowaf Y Alobaidi; Mansour Al Asmri; Eyas Alhuthail; Ziyad Alshehri; Farhan Alenezi; Elizabeth Sapey; Dhruv Parekh,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Taibah University; King Saud bin Abdulaziz University for Health Sciences; University of Birmingham; University of Birmingham,"BackgroundIn December 2019, SARS-CoV-2 caused a global pandemic with a viral infection called COVID-19. The disease usually causes respiratory symptoms but in a small proportion of patients can lead to a pneumonitis, Adult Respiratory Distress Syndrome and death. Invasive Mechanical Ventilation (IMV) is considered a life-saving treatment for COVID-19 patients and a huge demand for IMV devices was reported globally. This review aims to provide insight on the initial IMV practises for COVID-19 patients in the initial phase of the pandemic. + +MethodsElectronic databases (Embase and MEDLINE) were searched for applicable articles using relevant keywords. The references of included articles were hand searched. Articles that reported the use of IMV in adult COVID-19 patients were included in the review. The NIH quality assessment tool for cohort and cross-sectional studies was used to appraise studies. + +Results106 abstracts were identified from the databases search, of which 16 were included. 5 studies were included in the meta-analysis. In total, 9988 patients were included across all studies. The overall cases of COVID-19 requiring IMV ranged from 2-77%. Increased age and pre-existing comorbidities increased the likelihood of IMV requirement. The reported mortality rate in patients receiving IMV ranged between 50-100%. On average, IMV was required and initiated between 10-10.5 days from symptoms onset. When invasively ventilated, COVID-19 patients required IMV for a median of 10-17 days across studies. Little information was provided on ventilatory protocols or management strategies and were inconclusive. + +ConclusionIn these initial reporting studies for the first month of the pandemic, patients receiving IMV were older and had more pre-existing co-morbidities than those who did not require IMV. The mortality rate was high in COVID-19 patients who received IMV. Studies are needed to evaluate protocols and modalities of IMV to improve outcomes and identify the populations most likely to benefit from IMV.",intensive care and critical care medicine,fuzzy,100,100 medRxiv,10.1101/2020.06.01.20116608,2020-06-03,https://medrxiv.org/cgi/content/short/2020.06.01.20116608,Is death from Covid-19 a multistep process?,Neil Pearce; Giovenale Moirano; Milena Maule; Manolis Kogevinas; Xavier Rodo; Deborah Lawlor; Jan Vandenbroucke; Christina Vandenbroucke-Grauls; Fernando P Polack; Adnan Custovic,"London School of Hygiene and Tropical Medicine; University of Turin, Italy; University of Turin, Italy; ISGlobal; ISGlobal; University of Bristol; Leiden University Medical Center; Amsterdam UMC; Vanderbilt Unversity; Imperial College London","Covid-19 death has a different relationship with age than is the case for other severe respiratory pathogens. The Covid-19 death rate increases exponentially with age, and the main risk factors are age itself, as well as having underlying conditions such as hypertension, diabetes, cardiovascular disease, severe chronic respiratory disease and cancer. Furthermore, the almost complete lack of deaths in children suggests that infection alone is not sufficient to cause death; rather, one must have gone through a number of changes, either as a result of undefined aspects of aging, or as a result of chronic disease. These characteristics of Covid-19 death are consistent with the multistep model of disease, a model which has primarily been used for cancer, and more recently for amyotrophic lateral sclerosis (ALS). We applied the multi-step model to data on Covid-19 case fatality rates (CFRs) from China, South Korea, Italy, Spain and Japan. In all countries we found that a plot of ln (CFR) against ln (age) was approximately linear with a slope of about 5. As a comparison, we also conducted similar analyses for selected other respiratory diseases. SARS showed a similar log-log age-pattern to that of Covid-19, albeit with a lower slope, whereas seasonal and pandemic influenza showed quite different age-patterns. Thus, death from Covid-19 and SARS appears to follow a distinct age-pattern, consistent with a multistep model of disease that in the case of Covid-19 is probably defined by comorbidities and age producing immune-related susceptibility. Identification of these steps would be potentially important for prevention and therapy for SARS-COV-2 infection.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.06.01.20118943,2020-06-02,https://medrxiv.org/cgi/content/short/2020.06.01.20118943,"Greater risk of severe COVID-19 in non-White ethnicities is not explained by cardiometabolic, socioeconomic, or behavioural factors, or by 25(OH)-vitamin D status: study of 1,326 cases from the UK Biobank",Zahra Raisi-Estabragh; Celeste McCracken; Mae S Bethell; Jackie Cooper; Cyrus Cooper; Mark J Caulfield; Patricia B Munroe; Nicholas C Harvey; Steffen E Petersen,"William Harvey Research Institute; William Harvey Research Institute; North West Anglia NHS Foundation Trust; William Harvey Research Institute; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute; William Harvey Research Institute; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute","BackgroundWe examined whether the greater severity of coronavirus disease 2019 (COVID-19) amongst men and non-White ethnicities is explained by cardiometabolic, socio-economic, or behavioural factors. @@ -5750,15 +5773,6 @@ C_LI O_LSTHow might this impact on policy or clinical practice in the foreseeable future?C_LSTO_LIOur findings reinforce the need for adequate health and safety arrangements and provision of PPE, particularly in the health and social care sectors, and highlight the need for national and organizational policies and practices that protect and support workers with elevated risk of SARS-CoV-2 infection. C_LI",occupational and environmental health,fuzzy,100,100 -medRxiv,10.1101/2020.05.20.20108183,2020-05-23,https://medrxiv.org/cgi/content/short/2020.05.20.20108183,A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings,Sarah Beale; Andrew Hayward; Laura Shallcross; Robert W Aldridge; Ellen Fragaszy,University College London; University College London; University College London; University College London; University College London,"BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings. - -MethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis. - -FindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited. - -InterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted. - -FundingMedical Research Council",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.05.18.20086157,2020-05-22,https://medrxiv.org/cgi/content/short/2020.05.18.20086157,COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis,Nicola L Boddington; Andre Charlett; Suzanne Elgohari; Jemma L Walker; Helen Mcdonald; Chloe Byers; Laura Coughlan; Tatiana Garcia Vilaplana; Rosie Whillock; Mary Sinnathamby; Nikolaos Panagiotopoulos; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Joseph Shingleton; Emma Bennett; Daniel J Grint; Helen Strongman; Kathryn E Mansfield; Christopher Rentsch; Caroline Minassian; Ian J Douglas; Rohini Mathur; Maria Peppa; Simon Cottrell; Jim McMenamin; Maria Zambon; Mary Ramsay; Gavin Dabrera; Vanessa Saliba; Jamie Lopez Bernal,Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health Wales; Public Health Scotland; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England,"ObjectivesFollowing detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and underlying health conditions associated with infection of the first few hundred cases. MethodsInformation was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and underlying health conditions associated with infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented. @@ -5851,13 +5865,6 @@ Laura Bergamaschi, Ariana Betancourt, Georgie Bowyer, Aloka De Sa, Maddie Epping Epic team/other computing supportBarrie Bailey, Afzal Chaudhry, Rachel Doughton, Chris Workman Statistics/modellingRichard J. Samworth, Caroline Trotter",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.05.10.20096925,2020-05-15,https://medrxiv.org/cgi/content/short/2020.05.10.20096925,"NON-WHITE ETHNICITY, MALE SEX, AND HIGHER BODY MASS INDEX, BUT NOT MEDICATIONS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM ARE ASSOCIATED WITH CORONAVIRUS DISEASE 2019 (COVID-19) HOSPITALISATION: REVIEW OF THE FIRST 669 CASES FROM THE UK BIOBANK",Zahra Raisi-Estabragh; Celeste McCracken; Maddalena Ardissino; Mae S Bethell; Jackie Cooper; Cyrus Cooper; Nicholas C Harvey; Steffen E Petersen,"William Harvey Research Institute; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK; Sir Alexander Fleming Building, Imperial College London, London, UK; North West Anglia NHS Foundation Trust, Hinchingbrooke Hospital, Huntingdon, UK; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK","BackgroundCardiometabolic morbidity and medications, specifically Angiotensin Converting Enzyme inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs), have been linked with adverse outcomes from coronavirus disease 2019 (COVID-19). This study aims to investigate factors associated with COVID-19 positivity for the first 669 UK Biobank participants; compared with individuals who tested negative, and with the untested, presumed negative, rest of the population. - -MethodsWe studied 1,474 participants from the UK Biobank who had been tested for COVID-19. Given UK testing policy, this implies a hospital setting, suggesting at least moderate to severe symptoms. We considered the following exposures: age, sex, ethnicity, body mass index (BMI), diabetes, hypertension, hypercholesterolaemia, ACEi/ARB use, prior myocardial infarction (MI), and smoking. We undertook comparisons between: 1) COVID-19 positive and COVID-19 tested negative participants; and 2) COVID-19 tested positive and the remaining participants (tested negative plus untested, n=501,837). Logistic regression models were used to investigate univariate and mutually adjusted associations. - -ResultsAmong participants tested for COVID-19, non-white ethnicity, male sex, and greater BMI were independently associated with COVID-19 positive result. Non-white ethnicity, male sex, greater BMI, diabetes, hypertension, prior MI, and smoking were independently associated with COVID-19 positivity compared to the remining cohort (test negatives plus untested). However, similar associations were observed when comparing those who tested negative for COVID-19 with the untested cohort; suggesting that these factors associate with general hospitalisation rather than specifically with COVID-19. - -ConclusionsAmong participants tested for COVID-19 with presumed moderate to severe symptoms in a hospital setting, non-white ethnicity, male sex, and higher BMI are associated with a positive result. Other cardiometabolic morbidities confer increased risk of hospitalisation, without specificity for COVID-19. Notably, ACE/ARB use did not associate with COVID-19 status.",cardiovascular medicine,fuzzy,100,100 medRxiv,10.1101/2020.05.11.20096347,2020-05-15,https://medrxiv.org/cgi/content/short/2020.05.11.20096347,"The effects of ARBs, ACEIs and statins on clinical outcomes of COVID-19 infection among nursing home residents",Anton De Spiegeleer; Antoon Bronselaer; James T Teo; Geert Byttebier; Guy De Tre; Luc Belmans; Richard Dobson; Evelien Wynendaele; Christophe Van De Wiele; Filip Vandaele; Diemer Van Dijck; Daniel Bean; David Fedson; Bart De Spiegeleer,"Ghent University, Belgium; Ghent University, Belgium; Kings College Hospital NHS Foundation Trust, UK; Bioconstat BV, Belgium; Ghent University, Belgium; Ghent University, Belgium; Kings College London, UK; Ghent University, Belgium; Ghent University, Belgium; VZW Zorg-Saam Zusters Kindsheid Jesu, Belgium; Corilus Health IT Center, Belgium; King's College London, UK; Former University of Virginia, USA; Ghent University, Belgium","Background.COVID-19 infection has limited preventive or therapeutic drug options at this stage. Some of common existing drugs like angiotensin-converting enzyme inhibitors (ACEi), angiotensin II receptor blockers (ARB) and the HMG-CoA reductase inhibitors ( statins) have been hypothesised to impact on disease severity. However, up till now, no studies investigating this association were conducted in the most vulnerable and affected population groups, i.e. older people residing in nursing homes. The purpose of this study has been to explore the association of ACEi/ARB and/or statins with clinical manifestations in COVID-19 infected older people residing in nursing homes. Methods and Findings.We undertook a retrospective multi-centre cohort study in two Belgian nursing homes that experienced similar COVID-19 outbreaks. COVID-19 diagnoses were based on clinical suspicion and/or viral presence using PCR of nasopharyngeal samples. A total of 154 COVID-19 positive subjects was identified. The outcomes were 1) serious COVID-19 defined as a long-stay hospital admission (length of stay [≥] 7 days) or death (at hospital or nursing home) within 14 days of disease onset, and 2) asymptomatic, i.e. no disease symptoms in the whole study-period while still being PCR diagnosed. Disease symptoms were defined as any COVID-19-related clinical symptom (e.g. coughing, dyspnoea, sore throat) or sign (low oxygen saturation and fever) for [≥] 2 days out of 3 consecutive days. @@ -6031,13 +6038,6 @@ medRxiv,10.1101/2020.04.27.20081810,2020-05-03,https://medrxiv.org/cgi/content/s Highlights- A completely redesigned clinical proteomics platform increases throughput and precision while reducing costs. - 27 biomarkers are differentially expressed between WHO severity grades for COVID-19. - The study highlights potential therapeutic targets that include complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signalling both upstream and downstream of interleukin 6.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.04.27.20081711,2020-05-03,https://medrxiv.org/cgi/content/short/2020.04.27.20081711,Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study,Kevin van Zandvoort; Christopher I Jarvis; Carl Pearson; Nicholas G Davies; CMMID COVID-19 working group; Timothy W Russell; Adam J Kucharski; Mark J Jit; Stefan Flasche; Rosalind M Eggo; Francesco Checchi,London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; ; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundThe health impact of COVID-19 may differ in African settings as compared to countries in Europe or China due to demographic, epidemiological, environmental and socio-economic factors. We evaluated strategies to reduce SARS-CoV-2 burden in African countries, so as to support decisions that balance minimising mortality, protecting health services and safeguarding livelihoods. - -MethodsWe used a Susceptible-Exposed-Infectious-Recovered mathematical model, stratified by age, to predict the evolution of COVID-19 epidemics in three countries representing a range of age distributions in Africa (from oldest to youngest average age: Mauritius, Nigeria and Niger), under various effectiveness assumptions for combinations of different non-pharmaceutical interventions: self-isolation of symptomatic people, physical distancing, and shielding (physical isolation) of the high-risk population. We adapted model parameters to better represent uncertainty about what might be expected in African populations, in particular by shifting the distribution of severity risk towards younger ages and increasing the case-fatality ratio. - -ResultsWe predicted median clinical attack rates over the first 12 months of 17% (Niger) to 39% (Mauritius), peaking at 2-4 months, if epidemics were unmitigated. Self-isolation while symptomatic had a maximum impact of about 30% on reducing severe cases, while the impact of physical distancing varied widely depending on percent contact reduction and R0. The effect of shielding high-risk people, e.g. by rehousing them in physical isolation, was sensitive mainly to residual contact with low-risk people, and to a lesser extent to contact among shielded individuals. Response strategies incorporating self-isolation of symptomatic individuals, moderate physical distancing and high uptake of shielding reduced predicted peak bed demand by 46% to 54% and mortality by 60% to 75%. Lockdowns delayed epidemics by about 3 months. Estimates were sensitive to differences in age-specific social mixing patterns, as published in the literature. - -DiscussionIn African settings, as elsewhere, current evidence suggests large COVID-19 epidemics are expected. However, African countries have fewer means to suppress transmission and manage cases. We found that self-isolation of symptomatic persons and general physical distancing are unlikely to avert very large epidemics, unless distancing takes the form of stringent lockdown measures. However, both interventions help to mitigate the epidemic. Shielding of high-risk individuals can reduce health service demand and, even more markedly, mortality if it features high uptake and low contact of shielded and unshielded people, with no increase in contact among shielded people. Strategies combining self-isolation, moderate physical distancing and shielding will probably achieve substantial reductions in mortality in African countries. Temporary lockdowns, where socioeconomically acceptable, can help gain crucial time for planning and expanding health service capacity.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.04.28.20083295,2020-05-02,https://medrxiv.org/cgi/content/short/2020.04.28.20083295,Modifiable and non-modifiable risk factors for COVID-19: results from UK Biobank,Frederick K Ho; Carlos A Celis-Morales; Stuart R Gray; Srinivasa Vittal Katikireddi; Claire L Niedzwiedz; Claire Hastie; Donald M. Lyall; Lyn D. Ferguson; Colin Berry; Daniel F. Mackay; Jason M.R. Gill; Jill P. Pell; Naveed Sattar; Paul I Welsh,University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University Of Glasgow,"BackgroundInformation on risk factors for COVID-19 is sub-optimal. We investigated demographic, lifestyle, socioeconomic, and clinical risk factors, and compared them to risk factors for pneumonia and influenza in UK Biobank. MethodsUK Biobank recruited 37-70 year olds in 2006-2010 from the general population. The outcome of confirmed COVID-19 infection (positive SARS-CoV-2 test) was linked to baseline UK Biobank data. Incident influenza and pneumonia were obtained from primary care data. Poisson regression was used to study the association of exposure variables with outcomes. @@ -6076,6 +6076,15 @@ ResultsAmong 428,225 participants in England, 1,474 had been tested and 669 test ConclusionsSome minority ethnic groups have a higher risk of confirmed SARS-CoV-2 infection in the UK Biobank study which was not accounted for by differences in socioeconomic conditions, measured baseline health or behavioural risk factors. An urgent response to addressing these elevated risks is required.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.04.22.20072124,2020-04-24,https://medrxiv.org/cgi/content/short/2020.04.22.20072124,"Self-reported symptoms of covid-19 including symptoms most predictive of SARS-CoV-2 infection, are heritable",Frances MK Williams; Maxim Freydin; Massimo Mangino; Simon Couvreur; Alessia Visconti; Ruth CE Bowyer; Caroline I Le Roy; Mario Falchi; Carole Sudre; Richard Davies; Christopher Hammond; Cristina Menni; Claire Steves; Tim Spector,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Ltd; King's College London; King's College London; King's College London; King's College London,"Susceptibility to infection such as SARS-CoV-2 may be influenced by host genotype. TwinsUK volunteers (n=2633) completing the C-19 Covid symptom tracker app allowed classical twin studies of covid-19 symptoms including predicted covid-19, a symptom-based algorithm predicting true infection derived in app users tested for SARS-CoV-2. We found heritability for fever = 41 (95% confidence intervals 12-70)%; anosmia 47 (27-67)%; delirium 49 (24-75)%; and predicted covid-19 gave heritability = 50 (29-70)%.",genetic and genomic medicine,fuzzy,100,100 +medRxiv,10.1101/2020.04.21.20073049,2020-04-24,https://medrxiv.org/cgi/content/short/2020.04.21.20073049,What can trends in hospital deaths from COVID-19 tell us about the progress and peak of the pandemic? An analysis of death counts from England announced up to 20 April 2020,David A Leon; Christopher I Jarvis; Anne M Johnson; Liam Smeeth; Vladimir M Shkolnikov,London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; London School of Hygiene & Tropical Medicine; Max Planck Institute for Demographic Research,"BackgroundReporting of daily hospital COVID-19 deaths in the UK are promoted by the government and scientific advisers alike as a key metric for assessing the progress in the control of the epidemic. These data, however, have certain limitations, among which one of the most significant concerns the fact that the daily totals span deaths that have occurred between 1 and 10 days or more in the past. + +Data and methodsWe obtained daily data published published by NHS England up to and including April 25 in the form of Excel spreadsheets in which deaths counts are presented by date of death according to age and region. Simple descriptive analyses were conducted and presented in graphical and tabular form which were aimed at illustrating the biases inherent in focussing on daily counts regardless of when the deaths occurred. We then looked at how a less biased picture could be obtained by looking at trends in death counts stratifying by individual period of delay in days between occurrence of death and when the death was included in the daily announcement. + +FindingsThe number of hospital COVID-19 deaths announced daily overestimates the maximum number of deaths actually occurring so far in the epidemic in the UK, and also obscures the pattern of decline in deaths. Taking account of reporting delays suggests that for England as a whole a peak in hospital COVID-19 deaths may have been reached on April 8 with a subsequent gradual decline suggested. The same peak is also seen among those aged 60-79 and 80+, although there is slightly shallower decline in the oldest age group (80+ years). Among those aged 40-59 years a later peak on April 11 is evident. London shows a peak on April 8 and a clearer and steeper pattern of subsequent decline compared to England as a whole. + +InterpretationAnalyses of mortality trends must take account of delay, and in communication with the public more emphasis should be placed on looking at trends based on deaths that occurred 5 or more days prior to the announcement day. The slightly weaker decline seen at age 80+ may reflect increased hospitalisation of people from care homes, whereas the later peak under the age of 60 years may reflect the higher proportions at these younger ages being admitted to critical care resulting in an extension of life of several days. + +Competing interestsAll authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: no support from any organization for the submitted work; no financial relationships with any organizations that might have an interest in the submitted work in the previous three years other than LS who reported grants from Wellcome, MRC, NIHR, GSK, BHF, Diabetes UK all outside the submitted work; no other relationships or activities that could appear to have influenced the submitted work other than LS who is a Trustee of the British Heart Foundation and AJM who is a member of the Royal Society Delve Committee.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.04.18.20064774,2020-04-22,https://medrxiv.org/cgi/content/short/2020.04.18.20064774,"How many are at increased risk of severe COVID-19 disease? Rapid global, regional and national estimates for 2020",Andrew Clark; Mark Jit; Charlotte Warren-Gash; Bruce Guthrie; Harry HX Wang; Stewart W Mercer; Colin Sanderson; Martin McKee; Christopher Troeger; Kanyin I Ong; Francesco Checchi; Pablo Perel; Sarah Joseph; Hamish P Gibbs; Amitava Banerjee; LSHTM CMMID COVID-19 working group; Rosalind M Eggo,LSHTM; London School of Hygiene & Tropical Medicine; LSHTM; Edinburgh University; Sun Yat-Sen University; Edinburgh University; LSHTM; LSHTM; University of Washington; University of Washington; LSHTM; LSHTM; IAVI; LSHTM; UCL; ; London School of Hygiene & Tropical Medicine,"BackgroundThe risk of severe COVID-19 disease is known to be higher in older individuals and those with underlying health conditions. Understanding the number of individuals at increased risk of severe COVID-19 illness, and how this varies between countries may inform the design of possible strategies to shield those at highest risk. MethodsWe estimated the number of individuals at increased risk of severe COVID-19 disease by age (5-year age groups), sex and country (n=188) based on prevalence data from the Global Burden of Disease (GBD) study for 2017 and United Nations population estimates for 2020. We also calculated the number of individuals without an underlying condition that could be considered at-risk because of their age, using thresholds from 50-70 years. The list of underlying conditions relevant to COVID-19 disease was determined by mapping conditions listed in GBD to the guidelines published by WHO and public health agencies in the UK and US. We analysed data from two large multimorbidity studies to determine appropriate adjustment factors for clustering and multimorbidity. @@ -6128,29 +6137,6 @@ medRxiv,10.1101/2020.04.09.20059865,2020-04-14,https://medrxiv.org/cgi/content/s MethodsWe developed a modelling framework to simulate SARS-CoV-2 transmission in Kenya, KenyaCoV. KenyaCoV was used to simulate SARS-CoV-2 transmission both within, and between, different Kenyan regions and age groups. KenyaCoV was parameterized using a combination of human mobility data between the defined regions, the recent 2019 Kenyan census, and estimates of age group social interaction rates specific to Kenya. Key epidemiological characteristics such as the basic reproductive number and the age-specific rate of developing COVID-19 symptoms after infection with SARS-CoV-2, were adapted for the Kenyan setting from a combination of published estimates and analysis of the age distribution of cases observed in the Chinese outbreak. ResultsWe find that if person-to-person transmission becomes established within Kenya, identifying the role of subclinical, and therefore largely undetected, infected individuals is critical to predicting and containing a very significant epidemic. Depending on the transmission scenario our reproductive number estimates for Kenya range from 1.78 (95% CI 1.44 -2.14) to 3.46 (95% CI 2.81-4.17). In scenarios where asymptomatic infected individuals are transmitting significantly, we expect a rapidly growing epidemic which cannot be contained only by case isolation. In these scenarios, there is potential for a very high percentage of the population becoming infected (median estimates: >80% over six months), and a significant epidemic of symptomatic COVID-19 cases. Exceptional social distancing measures can slow transmission, flattening the epidemic curve, but the risk of epidemic rebound after lifting restrictions is predicted to be high.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.04.10.20059121,2020-04-14,https://medrxiv.org/cgi/content/short/2020.04.10.20059121,"ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study",Dipender Gill; Marios Arvanitis; Paul Carter; Ana I Hernandez Cordero; Brian Jo; Ville Karhunen; Susanna C Larsson; Xuan Li; Sam M Lockhart; Amy M Mason; Evanthia Pashos; Ashis Saha; Vanessa Tan; Verena Zuber; Yohan Bosse; Sarah Fahle; Ke Hao; Tao Jiang; Philippe Joubert; Alan C Lunt; Willem hendrik Ouwehand; David J Roberts; Wim Timens; Maarten van den Berge; Nicholas A Watkins; Alexis Battle; Adam S Butterworth; John Danesh; Barbara E Engelhard; James E Peters; Don Sin; Stephen Burgess,"Imperial College London; Johns Hopkins University; University of Cambridge; The University of British Columbia Center for Heart Lung Innovation; Lewis Sigler Institute for Integrative Biology; Imperial College London; Karolinska Institutet; The University of British Columbia Center for Heart Lung Innovation; University of Cambridge; University of Cambridge; Pfizer; Johns Hopkins University; University of Bristol; Imperial College London; Laval University, Quebec; University of Cambridge; School of Medicine at Mount Sinai; University of Cambridge; Laval University, Quebec; Imperial College London; University of Cambridge; University of Oxford; University of Groningen; University of Groningen; University of Cambridge; Johns Hopkins University; University of Cambridge; University of Cambridge; Princeton University; Imperial College London; University of British Columbia; University of Cambridge","ObjectivesTo use human genetic variants that proxy angiotensin-converting enzyme (ACE) inhibitor drug effects and cardiovascular risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 gene expression and circulating ACE2 levels. - -DesignTwo-sample Mendelian randomization (MR) analysis. - -SettingSummary-level genetic association data. - -ParticipantsParticipants were predominantly of European ancestry. Variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors (body mass index, chronic obstructive pulmonary disease, lifetime smoking index, low-density lipoprotein cholesterol, systolic blood pressure and type 2 diabetes mellitus) were selected from publicly available genome-wide association study data (sample sizes ranging from 188,577 to 898,130 participants). Genetic association estimates for lung expression of ACE2 and TMPRSS2 were obtained from the Gene-Tissue Expression (GTEx) project (515 participants) and the Lung eQTL Consortium (1,038 participants). Genetic association estimates for circulating plasma ACE2 levels were obtained from the INTERVAL study (4,947 participants). - -Main outcomes and measuresLung ACE2 and TMPRSS2 expression and plasma ACE2 levels. - -ResultsThere were no association of genetically proxied ACE inhibition with any of the outcomes considered here. There was evidence of a positive association of genetic liability to type 2 diabetes mellitus with lung ACE2 gene expression in GTEx (p = 4x10-4) and with circulating plasma ACE2 levels in INTERVAL (p = 0.03), but not with lung ACE2 expression in the Lung eQTL Consortium study (p = 0.68). There were no associations between genetically predicted levels of the other cardiometabolic traits with the outcomes. - -ConclusionsThis study does not provide evidence to support that ACE inhibitor antihypertensive drugs affect lung ACE2 and TMPRSS2 expression or plasma ACE2 levels. In the current COVID-19 pandemic, our findings do not support a change in ACE inhibitor medication use without clinical justification. - -Summary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current coronavirus disease 2019 (COVID-19) pandemic. -C_LIO_LISerine protease TMPRSS2 is involved in priming the SARS-CoV-2 spike protein for cellular entry through the angiotensin-converting enzyme 2 (ACE2) receptor. -C_LIO_LIExpression of ACE2 and TMPRSS2 in the lung epithelium might have implications for risk of SARS-CoV-2 infection and severity of COVID-19. -C_LI - -What this study addsO_LIWe used human genetic variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 expression and circulating ACE2 levels. -C_LIO_LIOur findings do not support the hypothesis that ACE inhibitors have effects on ACE2 expression. -C_LIO_LIWe found some support for an association of genetic liability to type 2 diabetes mellitus with higher lung ACE2 expression and plasma ACE2 levels, but evidence was inconsistent across studies. -C_LI",genetic and genomic medicine,fuzzy,100,100 medRxiv,10.1101/2020.04.07.20056788,2020-04-11,https://medrxiv.org/cgi/content/short/2020.04.07.20056788,Treatment with ACE-inhibitors is associated with less severe disease with SARS-Covid-19 infection in a multi-site UK acute Hospital Trust,Daniel Bean; Zeljko Kraljevic; Thomas Searle; Rebecca Bendayan; Andrew Pickles; Amos Folarin; Lukasz Roguski; Kawsar Noor; Anthony Shek; Rosita Zakeri; Ajay Shah; James Teo; Richard JB Dobson,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University College London; University College London; King's College London; King's College London; King's College London; King's College Hospital; Kings College London,"AimsThe SARS-Cov2 virus binds to the ACE2 receptor for cell entry. It has been suggested that ACE-inhibitors (ACEi) and Angiotensin-2 Blockers (ARB), which are commonly used in patients with hypertension or diabetes and may raise ACE2 levels, could increase the risk of severe COVID19 infection. Methods and ResultsWe evaluated this hypothesis in a consecutive cohort of 1200 acute inpatients with COVID19 at two hospitals with a multi-ethnic catchment population in London (UK). The mean age was 68{+/-}17 years (57% male) and 74% of patients had at least 1 comorbidity. 415 patients (34.6%) reached the primary endpoint of death or transfer to a critical care unit for organ support within 21-days of symptom onset. 399 patients (33.3 %) were taking ACEi or ARB. Patients on ACEi/ARB were significantly older and had more comorbidities. The odds ratio (OR) for the primary endpoint in patients on ACEi and ARB, after adjustment for age, sex and co-morbidities, was 0.63 (CI 0.47-0.84, p<0.01). @@ -6258,6 +6244,13 @@ MethodsWe adapted an existing national-scale metapopulation model to capture the ResultsWe predict that a CoVID-19 outbreak will peak 126 to 147 days ([~]4 months) after the start of person-to-person transmission in England and Wales in the absence of controls, assuming biological parameters remain unchanged. Therefore, if person-to-person transmission persists from February, we predict the epidemic peak would occur in June. The starting location has minimal impact on peak timing, and model stochasticity varies peak timing by 10 days. Incorporating realistic parameter uncertainty leads to estimates of peak time ranging from 78 days to 241 days after person-to-person transmission has been established. Seasonal changes in transmission rate substantially impact the timing and size of the epidemic peak, as well as the total attack rate. DiscussionWe provide initial estimates of the potential course of CoVID-19 in England and Wales in the absence of control measures. These results can be refined with improved estimates of epidemiological parameters, and permit investigation of control measures and cost effectiveness analyses. Seasonal changes in transmission rate could shift the timing of the peak into winter months, which will have important implications for health-care capacity planning.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.02.12.20022426,2020-02-13,https://medrxiv.org/cgi/content/short/2020.02.12.20022426,Interventions targeting air travellers early in the pandemic may delay local outbreaks of SARS-CoV-2,Samuel J Clifford; Carl A B Pearson; Petra Klepac; Kevin Van Zandvoort; Billy J Quilty; - CMMID COVID-19 working group; Rosalind M Eggo; Stefan Flasche,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; -; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine,"BackgroundWe evaluated if interventions aimed at air travellers can delay local SARS-CoV-2 community transmission in a previously unaffected country. + +MethodsWe simulated infected air travellers arriving into countries with no sustained SARS-CoV-2 transmission or other introduction routes from affected regions. We assessed the effectiveness of syndromic screening at departure and/or arrival & traveller sensitisation to the COVID-2019-like symptoms with the aim to trigger rapid self-isolation and reporting on symptom onset to enable contact tracing. We assumed that syndromic screening would reduce the number of infected arrivals and that traveller sensitisation reduces the average number of secondary cases. We use stochastic simulations to account for uncertainty in both arrival and secondary infections rates, and present sensitivity analyses on arrival rates of infected travellers and the effectiveness of traveller sensitisation. We report the median expected delay achievable in each scenario and an inner 50% interval. + +ResultsUnder baseline assumptions, introducing exit and entry screening in combination with traveller sensitisation can delay a local SARS-CoV-2 outbreak by 8 days (50% interval: 3-14 days) when the rate of importation is 1 infected traveller per week at time of introduction. The additional benefit of entry screening is small if exit screening is effective: the combination of only exit screening and traveller sensitisation can delay an outbreak by 7 days (50% interval: 2-13 days). In the absence of screening, with less effective sensitisation, or a higher rate of importation, these delays shrink rapidly to less than 4 days. + +ConclusionSyndromic screening and traveller sensitisation in combination may have marginally delayed SARS-CoV-2 outbreaks in unaffected countries.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.02.08.20021162,2020-02-11,https://medrxiv.org/cgi/content/short/2020.02.08.20021162,Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts,Joel Hellewell; Sam Abbott; Amy Gimma; Nikos I Bosse; Christopher I Jarvis; Timothy W Russell; James D Munday; Adam J Kucharski; W John Edmunds; CMMID nCoV working group; Sebastian Funk; Rosalind M Eggo,LSHTM; LSHTM; LSHTM; LSHTM; LSHTM; LSHTM; LSHTM; London School of Hygiene & Tropical Medicine; LSHTM; LSHTM; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundTo assess the viability of isolation and contact tracing to control onwards transmission from imported cases of 2019-nCoV. MethodsWe developed a stochastic transmission model, parameterised to the 2019-nCoV outbreak. We used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a 2019 nCoV-like pathogen. We considered scenarios that varied in: the number of initial cases; the basic reproduction number R0; the delay from symptom onset to isolation; the probability contacts were traced; the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. We assumed isolation prevented all further transmission in the model. Outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. We measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort. diff --git a/data/covid/preprints.exact.csv b/data/covid/preprints.exact.csv index d5014abb..0fdf9633 100644 --- a/data/covid/preprints.exact.csv +++ b/data/covid/preprints.exact.csv @@ -185,15 +185,6 @@ FindingsOverall, 276,840/800,000 (34.6%) of invited participants completed the q InterpretationAlthough COVID-19 is usually of short duration, some adults experience persistent and burdensome illness. FundingThis work is independent research funded by the National Institute for Health and Care Research (NIHR) (REACT Long COVID (REACT-LC) (COV-LT-0040)). This research is part of the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (UKRI) (MC_PC_20029). The views expressed in this publication are those of the author(s) and not necessarily those of NIHR or UKRI.",public and global health,exact,100,100 -medRxiv,10.1101/2023.03.24.23287700,2023-03-26,https://medrxiv.org/cgi/content/short/2023.03.24.23287700,The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey,Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes,University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester,"ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection. - -DesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups. - -Setting - -ResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage. - -ConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.",occupational and environmental health,exact,100,100 medRxiv,10.1101/2023.03.24.23287666,2023-03-24,https://medrxiv.org/cgi/content/short/2023.03.24.23287666,Occupational differences in the prevalence and severity of long-COVID: Analysis of the ONS Coronavirus (COVID-19) Infection Survey,Theocharis Kromydas; Evangelia Demou; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Neil Pearce; Martie van Tongeren; Jack Wilkinson; Sarah Rhodes,University of Glasgow; University of Glasgow; Lancaster University; University of Manchester; University of Glasgow; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester,"ObjectivesTo establish whether prevalence and severity of long-COVID symptoms vary by industry and occupation. MethodsWe utilised ONS Coronavirus Infection Survey (CIS) data (February 2021-April 2022) of working-age participants (16-65 years). Exposures were industrial sector, occupation and major Standard Occupational Classification (SOC) group. Outcomes were self-reported: (1) long-COVID symptoms; and (2) reduced function due to long-COVID. Binary (outcome 1) and ordered (outcome 2) logistic regression were used to estimate odds ratios (OR) and prevalence (marginal means) for all exposures. @@ -650,7 +641,6 @@ MethodsCOVIDENCE UK is a longitudinal population-based study that investigates r ResultsThe study was launched on 1st May 2020 and closed to recruitment on 6th October 2021. A total of 19,981 participants enrolled and consented to 5-year follow-up with medical record linkage. Their mean age was 59.1 years (range 16.0 to 94.4 years), 70.2% were female, and 93.7% identified their ethnic origin as White. Analyses conducted to date have provided key insights into risk factors for SARS-CoV-2 infection and COVID-19 disease, determinants of SARS-CoV-2 vaccine immunogenicity and efficacy, and impacts of COVID-19 on health economic outcomes. The cohort has also supported conduct of a Phase 3 randomised trial-within-cohort study (CORONAVIT) evaluating implementation of a test-and-treat approach to correcting sub-optimal vitamin D status on incidence and severity of acute respiratory infections, including COVID-19. ConclusionsThe COVIDENCE UK dataset represents a valuable resource containing granular information on factors influencing susceptibility to, and impacts of, COVID-19 in UK adults. Researchers wishing to access anonymised participant-level data should contacting the corresponding author for further information.",epidemiology,exact,100,100 -medRxiv,10.1101/2022.06.20.22275994,2022-06-20,https://medrxiv.org/cgi/content/short/2022.06.20.22275994,Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies,Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood,King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London,"Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.",epidemiology,exact,100,100 medRxiv,10.1101/2022.06.18.22276437,2022-06-19,https://medrxiv.org/cgi/content/short/2022.06.18.22276437,A patient-centric characterization of systemic recovery from SARS-CoV-2 infection,Hélène Ruffieux; Aimee Hanson; Samantha Lodge; Nathan Lawler; Luke Whiley; Nicola Gray; Tui Nolan; Laura Bergamaschi; Federica Mescia; - CITIID-NIHR COVID BioResource Collaboration; Nathalie Kingston; John Bradley; Elaine Holmes; Julien Wist; Jeremy Nicholson; Paul Lyons; Kenneth Smith; Sylvia Richardson; Glenn Bantug; Christoph Hess,University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; ; University of Cambridge; University of Cambridge; Murdoch University; Murdoch University; Murdoch University; University of Cambridge; University of Cambridge; University of Cambridge; University and University Hospital Basel; University of Cambridge,"The biology driving individual patient responses to SARS-CoV-2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data, covering a year post disease onset, from 215 SARS-CoV-2 infected subjects with differing disease severities. Our analyses revealed distinct ""systemic recovery"" profiles with specific progression and resolution of the inflammatory, immune, metabolic and clinical responses, over weeks to several months after infection. In particular, we found a strong intra-patient temporal covariation of innate immune cell numbers, kynurenine- and host lipid-metabolites, which suggested candidate immunometabolic pathways putatively influencing restoration of homeostasis, the risk of death and of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery on the patient level, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool http://shiny.mrc-bsu.cam.ac.uk/apps/covid-systemic-recovery-prediction-app, designed to test our findings prospectively. Graphical abstract @@ -672,6 +662,19 @@ HighlightsO_LIClinical frontline healthcare workers (HCWs) have been exposed to C_LIO_LIHCWs described the significant adverse impact of this exposure on their mental health, including increased anxiety and depression symptoms and sleep disturbance C_LIO_LIMost HCWs interviewed believed that organisational change within the NHS was necessary to prevent excess PMIE exposure and promote resolution of moral distress C_LI",psychiatry and clinical psychology,exact,100,100 +medRxiv,10.1101/2022.06.16.22276479,2022-06-16,https://medrxiv.org/cgi/content/short/2022.06.16.22276479,Mental health of healthcare workers in England during the COVID-19 pandemic: a longitudinal cohort study,Danielle Lamb; Rafael Gafoor; Hannah Scott; Ewan Carr; Sharon Stevelink; Rosalind Raine; Matthew Hotopf; Neil Greenberg; Siobhan Hegarty; Ira Madan; Paul Moran; Richard Morriss; Dominic Murphy; Anne Marie Rafferty; Scott Weich; Sarah Dorrington; Simon Wessely,UCL; University College London; King's College London; King's College London; King's College London; University College London; King's College London; King's College London; King's College London; Guy's and St Thomas' NHS Foundation Trust; University of Bristol; University of Nottingham; Combat Stress; King's College London; University of Sheffield; King's College London; King's College London,"ObjectiveTo examine variations in impact of the COVID-19 pandemic on the mental health of all types of healthcare workers (HCWs) in England over the first 17 months of the pandemic. + +MethodWe undertook a prospective cohort study of 22,501 HCWs from 18 English acute and mental health NHS Trusts, collecting online survey data on common mental disorders (CMDs), depression, anxiety, alcohol use, and PTSD, from April 2020 to August 2021. We analysed these data cross-sectionally by time period (corresponding to periods the NHS was under most pressure), and longitudinally. Data were weighted to better represent Trust population demographics. + +ResultsThe proportion of those with probable CMDs was greater during periods when the NHS was under most pressure (measured by average monthly deaths). For example, 55% (95%CI 53%, 58%) of participants reported symptoms of CMDs in April-June 2020 versus 47% (95%CI 46%, 48%) July-October 2020. Contrary to expectation, there were no major differences between professional groups (i.e. clinical and non-clinical staff). Younger, female, lower paid staff, who felt poorly supported by colleagues/managers, and who experienced potentially morally injurious events were most at risk of negative mental health outcomes. + +ConclusionAmong HCWs, the prevalence of probable CMDs increased during periods of escalating pressure on the NHS, suggesting staff support should be increased at such points in the future, and staff should be better prepared for such situations via training. All staff, regardless of role, experienced poorer mental health during these periods, suggesting that support should be provided for all staff groups. + +Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSExisting evidence about the mental health of healthcare workers (HCWs) through the COVID-19 pandemic comes mainly from cross-sectional studies using unrepresentative convenience samples, typically focussing on clinical staff rather than all HCWs. Such studies show high prevalence of symptoms of mental disorders, but the strength of this evidence is uncertain. + +What this study addsUsing a defined sampling frame, with longitudinal, weighted data, we show that during periods of greater pressure on the NHS (as indicated by average monthly national COVID-19 death rates), prevalence of mental disorder symptoms increased, and, importantly, that this effect was seen in non-clinical as well as clinical staff. + +How this study might affect research, practice or policyThese findings indicate that provision of support for HCWs should not only focus on those providing clinical care, but also on non-clinical staff such as porters, cleaners, and administrative staff, and additional support should be provided during higher pressure periods. Better preparation of staff for such situations is also suggested.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2022.06.16.22276487,2022-06-16,https://medrxiv.org/cgi/content/short/2022.06.16.22276487,"Capturing the experiences of UK healthcare workers during the COVID-19 pandemic: A structural topic modelling analysis of 7,412 free-text survey responses",Danielle Lamb; Liam Wright; Hannah Scott; Bethany Croak; Sam Gnanapragasam; Mary Jane Docherty; Neil Greenberg; Matthew Hotopf; Sharon Stevelink; Rosalind Raine; Simon Wessely,UCL; University College London; King's College London; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; University College London; King's College London,"BackgroundHealthcare workers (HCWs) have provided vital services during the COVID-19 pandemic, but existing research consists of quantitative surveys (lacking in depth or context) or qualitative interviews (with limited generalisability). Structural Topic Modelling (STM) of large-scale free-text survey data offers a way of capturing the perspectives of a wide range of HCWs in their own words about their experiences of the pandemic. MethodsIn an online survey distributed to all staff at 18 geographically dispersed NHS Trusts, we asked respondents, ""Is there anything else you think we should know about your experiences of the COVID-19 pandemic?"". We used STM on 7,412 responses to identify topics, and thematic analysis on the resultant topics and text excerpts. @@ -711,6 +714,7 @@ MethodsOn average, risk of infection is proportional to infection prevalence. Th ResultsFollowing an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was masked by the effects of vaccination and the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups. ConclusionHigh-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was highly effective at reducing risk of infection with school holidays/closures playing a significant part.",infectious diseases,exact,100,100 +medRxiv,10.1101/2022.05.23.22275458,2022-05-25,https://medrxiv.org/cgi/content/short/2022.05.23.22275458,Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States,Seth Flaxman; Charles Whittaker; Elizaveta Semenova; Theo Rashid; Robbie Parks; Alexandra Blenkinsop; H Juliette T Unwin; Swapnil Mishra; Samir Bhatt; Deepti Gurdasani; Oliver Ratmann,"Oxford; Imperial College London; AstraZeneca; Imperial College London; Columbia University; Imperial College London; Imperial College London; University of Copenhagen; University of Copenhagen, Imperial College London; Queen Mary University of London; Imperial College London","Covid-19 has caused more than 1 million deaths in the US, including at least 1,204 deaths among children and young people (CYP) aged 0-19 years, with 796 occurring in the one year period April 1, 2021 - March 31, 2022. Deaths among US CYP are rare in general, and so we argue here that the mortality burden of Covid-19 in CYP is best understood in the context of all other causes of CYP death. Using publicly available data from CDC WONDER on NCHSs 113 Selected Causes of Death, and comparing to mortality in 2019, the immediate pre-pandemic period, we find that Covid-19 mortality is among the 10 leading causes of death in CYP aged 0-19 years in the US, ranking 8th among all causes of deaths, 5th in disease-related causes of deaths (excluding accidents, assault and suicide), and 1st in deaths caused by infectious or respiratory diseases. Covid-19 deaths constitute 2.3% of the 10 leading causes of death in this age group. Covid-19 caused substantially more deaths in CYP than major vaccine-preventable diseases did historically in the period before vaccines became available. Various factors including underreporting and Covid-19s role as a contributing cause of death from other diseases mean that our estimates may understate the true mortality burden of Covid-19. Our findings underscore the public health relevance of Covid-19 to CYP. In the likely future context of sustained SARS-CoV-2 circulation, pharmaceutical and non-pharmaceutical interventions will continue to play an important role in limiting transmission of the virus in CYP and mitigating severe disease.",infectious diseases,exact,100,100 medRxiv,10.1101/2022.05.19.22275214,2022-05-22,https://medrxiv.org/cgi/content/short/2022.05.19.22275214,Antibody levels following vaccination against SARS-CoV-2: associations with post-vaccination infection and risk factors,Nathan J Cheetham; Milla Kibble; Andrew Wong; Richard J Silverwood; Anika Knuppel; Dylan M Williams; Olivia K L Hamilton; Paul H Lee; Charis Bridger Staatz; Giorgio Di Gessa; Jingmin Zhu; Srinivasa Vittal Katikireddi; George B Ploubidis; Ellen J Thompson; Ruth C E Bowyer; Xinyuan Zhang; Golboo Abbasian; Maria Paz Garcia; Deborah Hart; Jeffrew Seow; Carl Graham; Neophytos Kouphou; Sam Acors; Michael H Malim; Ruth E Mitchell; Kate Northstone; Daniel Major-Smith; Sarah Matthews; Thomas Breeze; Michael Crawford; Lynn Molloy; Alex Siu Fung Kwong; Katie J Doores; Nishi Chaturvedi; Emma L Duncan; Nicholas J Timpson; Claire J Steves,King's College London; University of Cambridge; University College London; University College London; University College London; University College London; University of Glasgow; University of Leicester; University College London; University College London; University College London; University of Glasgow; University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; King's College London; University College London; King's College London; University of Bristol; King's College London,"SARS-CoV-2 antibody levels can be used to assess humoral immune responses following SARS-CoV-2 infection or vaccination, and may predict risk of future infection. From cross-sectional antibody testing of 9,361 individuals from TwinsUK and ALSPAC UK population-based longitudinal studies (jointly in April-May 2021, and TwinsUK only in November 2021-January 2022), we tested associations between antibody levels following vaccination and: (1) SARS-CoV-2 infection following vaccination(s); (2) health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables. Within TwinsUK, single-vaccinated individuals with the lowest 20% of anti-Spike antibody levels at initial testing had 3-fold greater odds of SARS-CoV-2 infection over the next six to nine months, compared to the top 20%. In TwinsUK and ALSPAC, individuals identified as at increased risk of COVID-19 complication through the UK ""Shielded Patient List"" had consistently greater odds (2 to 4-fold) of having antibody levels in the lowest 10%. Third vaccination increased absolute antibody levels for almost all individuals, and reduced relative disparities compared with earlier vaccinations. @@ -1388,6 +1392,13 @@ MethodsDuring round 8 of REACT-1 from 6 January to 22 January 2021, of the 2,282 ResultsWe estimated the overall sensitivity of REACT-1 to detect virus on a single swab as 0.79 (0.77, 0.81) and median duration of positivity following a positive test as 9.7 (8.9, 10.6) days. We found greater median duration of positivity where there was a low N-gene Ct value, in those exhibiting symptoms, or for infection with the Alpha variant. The estimated proportion of positive individuals detected on first swab, P0, was found to be higher for those with an initially low N-gene Ct value and those who were pre-symptomatic. When compared to swab-positivity, estimates of infection incidence over the duration of REACT-1 included sharper features with evident transient increases around the time of key changes in social distancing measures. DiscussionHome self-swabbing for RT-PCR based on a single swab, as implemented in REACT-1, has high overall sensitivity. However, participants time-since-infection, symptom status and viral lineage affect the probability of detection and the duration of positivity. These results validate previous efforts to estimate incidence of SARS-CoV-2 from swab-positivity data, and provide a reliable means to obtain community infection estimates to inform policy response.",infectious diseases,exact,100,100 +medRxiv,10.1101/2021.08.05.21259863,2021-08-07,https://medrxiv.org/cgi/content/short/2021.08.05.21259863,Recording of 'COVID-19 vaccine declined' among vaccination priority groups: a cohort study on 57.9 million NHS patients' primary care records in situ using OpenSAFELY,Helen J Curtis; Peter Inglesby; Brian MacKenna; Richard Croker; William J Hulme; Christopher T Rentsch; Krishnan Bhaskaran; Alex J Walker; Caroline E Morton; David Evans; Amir Mehrkar; Sebastian CJ Bacon; Christopher Bates; George Hickman; Tom Ward; Jessica Morley; Jonathan Cockburn; Simon Davy; Anna Schultze; Elizabeth J Williamson; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; John Tazare; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundAll patients in England within vaccine priority groups were offered a COVID-19 vaccine by mid-April 2021. Clinical record systems contain codes to denote when such an offer has been declined by a patient (although these can in some cases be entered for a variety of other reasons including vaccination delay, or other administrative issues). We set out to describe the patterns of usage of codes for COVID-19 vaccines being declined. + +MethodsWith the approval of NHS England and using the full pseudonymised primary care records for 57.9 million NHS patients, we identified all patients in key vaccine priority groups: aged over 50, or over 16 and at increased risk from COVID-19 (Clinically Extremely Vulnerable [CEV] or otherwise ""at risk""). We describe the proportion of patients recorded as declining a COVID-19 vaccination for each priority group, and by other clinical and demographic factors; whether patients recorded as ""declined"" subsequently went on to receive a vaccination; and the distribution of code usage across GP practices. + +ResultsOf 24.5 million patients in priority groups as of May 25th 2021, 89.2% had received a vaccine, 8.8% had neither a vaccination nor a decline recorded, and 663,033 (2.7%) had a decline code recorded. Of patients with a recorded decline, 125,587 (18.9%) were subsequently vaccinated. Subsequent vaccination was slightly more common in the South Asian population than other ethnicities (e.g. 32.3% vs 22.8%, over 65s). The proportion of declining-unvaccinated patients varied strongly with ethnicity (Black 15.3%, South Asian 5.6%, White 1.5% in over 80s); and was higher in patients from more deprived areas. COVID-19 vaccine decline codes were present in almost all practices (98.8%), but with wide variation between practices in rates of usage. Among all priority groups, declining-unvaccinated status was most common in CEV (3.3%). + +ConclusionsClinical codes indicative of COVID-19 vaccinations being declined are widely used in English general practice. They are substantially more common among Black and South Asian patients, and patients from more deprived areas. There is a need for more detailed survey and/or qualitative research with patients and clinicians to determine the most common reasons for these recorded declines.",public and global health,exact,100,100 medRxiv,10.1101/2021.07.29.21261190,2021-07-31,https://medrxiv.org/cgi/content/short/2021.07.29.21261190,Right Ventricular Dysfunction in Ventilated Patients with COVID-19 (COVID-RV),Philip McCall; Jennifer Willder; Bethany Stanley; Claudia-Martina Messow; John Allan; Lisa Gemmell; Alex Puxty; Dominic Strachan; Colin Berry; Ben Shelley; - The COVID-RV investigators.,"Anaesthesia, Critical Care & Peri-operative Medicine Research Group, University of Glasgow, Glasgow, UK.; West of Scotland School of Anaesthesia, NHS Education for Scotland, Glasgow, UK.; Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK.; Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK.; Intensive Care Unit, University Hospital Crosshouse, Kilmarnock, UK.; Intensive Care Unit, Royal Alexandra Hospital, Paisley, UK.; Intensive Care Unit, Glasgow Royal Infirmary, Glasgow, UK.; Intensive Care Unit, University Hospital Wishaw, Wishaw, UK.; Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK.; Anaesthesia, Critical Care & Peri-operative Medicine Research Group, University of Glasgow, UK.; ","PurposeCOVID-19 is associated with cardiovascular complications, with right ventricular dysfunction (RVD) commonly reported. The combination of acute respiratory distress syndrome (ARDS), injurious invasive ventilation, micro/macro thrombi and the potential for direct myocardial injury create conditions where RVD is likely to occur. No study has prospectively explored the prevalence of RVD, and its association with mortality, in a cohort requiring mechanical ventilation. MethodsProspective, multi-centre, trans-thoracic echocardiographic, cohort study of ventilated patients with COVID-19 in Scottish intensive care units. RVD was defined as the presence of severe RV dilatation and interventricular septal flattening. To explore role of myocardial injury, high sensitivity troponin and N-terminal pro B-type natriuretic peptide (NT-proBNP) were measured in all patients. @@ -1513,6 +1524,9 @@ MethodsSamples: 6907 adults self-reporting COVID-19 infection from 48,901 partic ResultsIn LS, symptoms impacted normal functioning for 12+ weeks in 1.2% (mean age 20 years) to 4.8% (mean age 63 y) of COVID-19 cases. Between 7.8% (mean age 28 y) and 17% (mean age 58 y) reported any symptoms for 12+ weeks, and greater proportions for 4+ weeks. Age was associated with a linear increased risk in long COVID between 20 and 70 years. Being female (LS: OR=1.49; 95%CI:1.24-1.79; EHR: OR=1.51 [1.41-1.61]), having poor pre-pandemic mental health (LS: OR=1.46 [1.17-1.83]; EHR: OR=1.57 [1.47-1.68]) and poor general health (LS: OR=1.62 [1.25-2.09]; EHR: OR=1.26; [1.18-1.35]) were associated with higher risk of long COVID. Individuals with asthma (LS: OR=1.32 [1.07-1.62]; EHR: OR=1.56 [1.46-1.67]), and overweight or obesity (LS: OR=1.25 [1.01-1.55]; EHR: OR=1.31 [1.21-1.42]) also had higher risk. Non-white ethnic minority groups had lower risk (LS: OR=0.32 [0.22-0.47]), a finding consistent in EHR. . Few participants had been hospitalised (0.8-5.2%). ConclusionLong COVID is associated with sociodemographic and pre-existing health factors. Further investigations into causality should inform strategies to address long COVID in the population.",epidemiology,exact,100,100 +bioRxiv,10.1101/2021.06.21.449178,2021-06-21,https://biorxiv.org/cgi/content/short/2021.06.21.449178,Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune pathways related to tissue injury,Amy R Cross; Carlos de Andrea; Maria Villalba-Esparza; Manuel Landecho Acha; Lucia Cerundolo; Praveen Weeratunga; Rachel Etherington; Laura Denney; Graham Ogg; Ling-Pei Ho; Ian Roberts; Joanna Hester; Paul Klenerman; Ignacio Melero; Stephen Sansom; Fadi Issa,"University of Oxford; Universidad de Navarra; Department of Pathology, Clinica de la Universidad de Navarra, Pamplona, Spain; Clinica Universidad de Navarra; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Universidad de Navarra; University of Oxford; University of Oxford","Severe lung damage in COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways and genes present across the spectrum of histopathological damage in COVID-19 lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from areas of interest within well preserved post-mortem lung samples from three patients. Despite substantial inter-patient heterogeneity we discovered evidence for a common immune cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines including CXCL9, CXCL10 and CXCL11 which are known to promote the recruitment of CXCR3+ immune cells. The tumour necrosis factor (TNF) superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were found to be consistently upregulated in the areas with severe tissue damage. We used published spatial and single cell SARS-CoV-2 datasets to confirm our findings in the lung tissue from additional cohorts of COVID-19 patients. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies. + +One Sentence SummarySpatial analysis identifies IFN{gamma} response signatures as focal to severe alveolar damage in COVID-19 pneumonitis.",immunology,exact,100,100 medRxiv,10.1101/2021.06.08.21258551,2021-06-15,https://medrxiv.org/cgi/content/short/2021.06.08.21258551,NHS CHECK: protocol for a cohort study investigating the psychosocial impact of the COVID-19 pandemic on healthcare workers,Danielle Lamb; Neil Greenberg; Matthew Hotopf; Rosalind Raine; Reza Razavi; Rupa Bhundia; Hannah Scott; Ewan Carr; Rafael Gafoor; Ioannis Bakolis; Siobhan Hegarty; Emilia Souliou; Anne Marie Rafferty; Rebecca Rhead; Danny Weston; Sam Gnanapragasam; Sally Marlow; Simon Wessely; Sharon Stevelink,UCL; King's College London; King's College London; UCL; King's College London; King's College London; King's College London; King's College London; ICL; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London,"IntroductionThe COVID-19 pandemic has had profound effects on the working lives of healthcare workers (HCWs), but the extent to which their well-being and mental health have been affected remains unclear. This longitudinal cohort study aims to recruit a cohort of NHS healthcare workers, conducting surveys at regular intervals to provide evidence about the prevalence of symptoms of mental disorders, investigate associated factors such as occupational contexts and support interventions available. Methods and AnalysisAll staff, students, and volunteers working in each of the 18 participating NHS Trusts in England will be sent emails inviting them to complete a survey at baseline, with email invitations for the follow up surveys being sent 6 and 12 months later. Opening in late April 2020, the baseline survey collects data on demographics, occupational and organisational factors, experiences of COVID-19, a number of validated measures of symptoms of poor mental health (e.g. depression, anxiety, post-traumatic stress disorder; PTSD), and measures of constructs such as resilience and moral injury. These regular surveys will be complemented by in-depth psychiatric interviews with a select sample of healthcare workers. Qualitative interviews will also be conducted, to gain deeper understanding of the support programmes used or desired by staff, and facilitators and barriers to accessing such programmes. @@ -1590,13 +1604,6 @@ MethodsWe report the most recent findings on community infections from the REal- ResultsBetween rounds 10 and 11, prevalence of swab-positivity dropped by 50% in England from 0.20% (0.17%, 0.23%) to 0.10% (0.08%, 0.13%), with a corresponding R estimate of 0.90 (0.87, 0.94). Rates of swab-positivity fell in the 55 to 64 year old group from 0.17% (0.12%, 0.25%) in round 10 to 0.06% (0.04%, 0.11%) in round 11. Prevalence in round 11 was higher in the 25 to 34 year old group at 0.21% (0.12%, 0.38%) than in the 55 to 64 year olds and also higher in participants of Asian ethnicity at 0.31% (0.16%, 0.60%) compared with white participants at 0.09% (0.07%, 0.11%). Based on sequence data for positive samples for which a lineage could be identified, we estimate that 92.3% (75.9%, 97.9%, n=24) of infections were from the B.1.1.7 lineage compared to 7.7% (2.1%, 24.1%, n=2) from the B.1.617.2 lineage. Both samples from the B.1.617.2 lineage were detected in London from participants not reporting travel in the previous two weeks. Also, allowing for suitable lag periods, the prior close alignment between prevalence of infections and hospitalisations and deaths nationally has diverged. DiscussionWe observed marked reductions in prevalence from March to April and early May 2021 in England reflecting the success of the vaccination programme and despite easing of restrictions during lockdown. However, there is potential upwards pressure on prevalence from the further easing of lockdown regulations and presence of the B.1.617.2 lineage. If prevalence rises in the coming weeks, policy-makers will need to assess the possible impact on hospitalisations and deaths. In addition, consideration should be given to other health and economic impacts if increased levels of community transmission occur.",epidemiology,exact,100,100 -medRxiv,10.1101/2021.05.17.21257223,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.17.21257223,Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).,Cyril Roman Geismar; Ellen Fragaszy; Vincent Grigori Nguyen; Wing Lam Erica Fong; Madhumita Shrotri; Sarah Beale; Alison Rodger; Vasileios Lampos; Thomas Edward Byrne; Jana Kovar; Annalan Navaratnam; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ,"IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant. - -MethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks. - -ResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)). - -ConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.",epidemiology,exact,100,100 medRxiv,10.1101/2021.05.06.21256757,2021-05-14,https://medrxiv.org/cgi/content/short/2021.05.06.21256757,COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study,Yiqun Chen; Timothy Aldridge; - UK COVID-19 National Core Studies Consortium; Claire F Ferraro; Fu-Meng Khaw,"Health and Safety Executive, UK; Health and Safety Executive, UK; ; National Infection Service, Public Health England, UK; Public Health England, UK","BackgroundA large number of COVID-19 outbreaks/clusters have been reported in a variety of workplace settings since the start of the pandemic. However, information on the rate of outbreak occurrences which helps to identify the type of workplaces that are more likely to experience an outbreak, or infection attack rates which estimates the potential extent of the virus transmission in an outbreak, has not yet been available to inform intervention strategies to limit transmission. ObjectivesTo link datasets on workplace settings and COVID-19 workplace outbreaks in England in order to: identify the geographical areas and workplace sectors with a high rate of outbreaks; and compare infection attack rates by workplace size and sector. @@ -2131,6 +2138,7 @@ C_LIO_LIAdditional symptoms increased case finding to > 90% but tests needed dou C_LIO_LIOptimal symptom combinations maximise case capture considering available resources C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public health C_LI",health informatics,exact,100,100 +medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,exact,100,100 medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,exact,100,100 medRxiv,10.1101/2020.11.06.20227108,2020-11-07,https://medrxiv.org/cgi/content/short/2020.11.06.20227108,Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey,Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy,Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University,"School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.",public and global health,exact,100,100 medRxiv,10.1101/2020.11.03.20220699,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.03.20220699,A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital,Daniel J Cooper; Sara Lear; Laura Watson; Ashley Shaw; Mark Ferris; Rainer Doffinger; Rachel Bousfield; Katherine Sharrocks; Michael Weekes; Ben Warne; Dominic Sparkes; Nick K Jones; Lucy Rivett; Matthew Routledge; Afzal Chaudhry; Katherine Dempsey; Montgomery Matson; Adil Lakha; George Gathercole; Olivia O'Connor; Emily Wilson; Orthi Shahzad; Kieran Toms; Rachel Thompson; Ian Halsall; David Halsall; Sally Houghton; Sofia Papadia; Nathalie Kingston; Kathleen Stirrups; Barbara Graves; Neil Walker; Hannah Stark; - The CITIID-NIHR BioResource COVID-19 Collaboration; Daniela De Angelis; Shaun Seaman; John Bradley; M Estée Török; Ian G. Goodfellow; Stephen Baker,"Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility.; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust; ; MRC Biostatistics Unit, University of Cambridge; MRC Biostatistics Unit, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Department of pathology, Division of virology, University of Cambridge; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK","BackgroundThe COVID-19 pandemic continues to grow at an unprecedented rate. Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population but risk factors for HCW infection are not well described. @@ -2247,6 +2255,15 @@ Added value of this studyWe used daily mobility data aggregated from Facebook us Implications of all the available evidenceWe show that spatial mobility data available in near real-time can give information on connectivity that can be used to understand the impact of geographically-targeted interventions and in the future, to inform spatially-targeted intervention strategies. Data SharingData used in this study are available from the Facebook Data for Good Partner Program by application. Code and supplementary information for this paper are available online (https://github.com/hamishgibbs/facebook_mobility_uk), alongside publication.",epidemiology,exact,100,100 +medRxiv,10.1101/2020.10.26.20219725,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219725,"Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults",Helen Ward; Graham Cooke; Christina J Atchison; Matthew Whitaker; Joshua Elliott; Maya Moshe; Jonathan C Brown; Barney Flower; Anna Daunt; Kylie E. C. Ainslie; Deborah Ashby; Christl A. Donnelly; Steven Riley; Ara Darzi; Wendy Barclay; Paul Elliott,"Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London","BackgroundThe prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into its spread in the community, the likelihood of reinfection and potential for some level of population immunity. + +MethodsPrevalence of antibody positivity in England, UK (REACT2) with three cross-sectional surveys between late June and September 2020. 365104 adults used a self-administered lateral flow immunoassay (LFIA) test for IgG. A laboratory comparison of LFIA results to neutralization activity in panel of sera was performed. + +ResultsThere were 17,576 positive tests over the three rounds. Antibody prevalence, adjusted for test characteristics and weighted to the adult population of England, declined from 6.0% [5.8, 6.1], to 4.8% [4.7, 5.0] and 4.4% [4.3, 4.5], a fall of 26.5% [-29.0, -23.8] over the three months of the study. There was a decline between rounds 1 and 3 in all age groups, with the highest prevalence of a positive result and smallest overall decline in positivity in the youngest age group (18-24 years: -14.9% [-21.6, -8.1]), and lowest prevalence and largest decline in the oldest group (75+ years: -39.0% [-50.8, -27.2]); there was no change in antibody positivity between rounds 1 and 3 in healthcare workers (+3.45% [-5.7, +12.7]). + +The decline from rounds 1 to 3 was largest in those who did not report a history of COVID-19, (-64.0% [-75.6, -52.3]), compared to -22.3% ([-27.0, -17.7]) in those with SARS-CoV-2 infection confirmed on PCR. + +DiscussionThese findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.10.14.20212555,2020-10-16,https://medrxiv.org/cgi/content/short/2020.10.14.20212555,Multi-organ impairment in low-risk individuals with long COVID,Andrea Dennis; Malgorzata Wamil; Sandeep Kapur; Johann Alberts; Andrew Badley; Gustav Anton Decker; Stacey A Rizza; Rajarshi Banerjee; Amitava Banerjee,Perspectum; Great Western Hospitals NHS Foundation Trust; Mayo Clinic Healthcare; Alliance Medical; Mayo Clinic; Mayo Clinic International; Mayo Clinic; Perspectum; University College London,"BackgroundSevere acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection has disproportionately affected older individuals and those with underlying medical conditions. Research has focused on short-term outcomes in hospital, and single organ involvement. Consequently, impact of long COVID (persistent symptoms three months post-infection) across multiple organs in low-risk individuals is yet to be assessed. MethodsAn ongoing prospective, longitudinal, two-centre, observational study was performed in individuals symptomatic after recovery from acute SARS-CoV-2 infection. Symptoms and organ function (heart, lungs, kidneys, liver, pancreas, spleen) were assessed by standardised questionnaires (EQ-5D-5L, Dyspnoea-12), blood investigations and quantitative magnetic resonance imaging, defining single and multi-organ impairment by consensus definitions. @@ -2547,6 +2564,11 @@ Results30-day mortality peaked for people admitted to critical care in early Apr ConclusionsThere has been a substantial mortality improvement in people admitted to critical care with COVID-19 in England, with markedly lower mortality in people admitted in mid-April and May compared to earlier in the pandemic. This trend remains after adjustment for patient demographics and comorbidities suggesting this improvement is not due to changing patient characteristics. Possible causes include the introduction of effective treatments as part of clinical trials and a falling critical care burden.",health systems and quality improvement,exact,100,100 medRxiv,10.1101/2020.07.29.20164269,2020-07-30,https://medrxiv.org/cgi/content/short/2020.07.29.20164269,The potential health and economic impact of dexamethasone treatment for patients with COVID-19,RICARDO AGUAS; Adam Mahdi; RIMA SHRETTA; Peter Horby; Martin Landray; Lisa J White,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"Dexamethasone has been shown to reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment would be rolled out in the UK and globally, as well as its cost-effectiveness of implementing this intervention. We estimate that, for the UK, approximately 12,000 [4,250 - 27,000] lives could be saved by January 2021. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate into approximately 650,000 [240,000 - 1,400,000] lives saved globally. If dexamethasone acts differently in these settings, the impact could be less than half of this value. To estimate the full potential of dexamethasone in the global fight against COVID-19, it is essential to perform clinical research in settings with limited access to oxygen and/or ventilators, e.g. in low and middle-income countries.",epidemiology,exact,100,100 +medRxiv,10.1101/2020.07.26.20161570,2020-07-28,https://medrxiv.org/cgi/content/short/2020.07.26.20161570,"Magnitude, demographics and dynamics of the impact of the first phase of the Covid-19 pandemic on all-cause mortality in 17 industrialised countries",Vasilis Kontis; James E Bennett; Theo Rashid; Robbie M Parks; Jonathan Pearson-Stuttard; Michel Guillot; Perviz Asaria; Bin Zhou; Marco Battaglini; Gianni Corsetti; Martin McKee; Mariachiara Di Cesare; Colin D Mathers; Majid Ezzati,Imperial College London; Imperial College London; Imperial College London; Columbia University; Imperial College London; University of Pennsylvania; Imperial College London; Imperial College London; Italian National Institute of Statistics; Italian National Institute of Statistics; London School of Hygiene & Tropical Medicine; Middlesex University London; Independent Researcher; Imperial College London,"The Covid-19 pandemic affects mortality directly through infection as well as through changes in the social, environmental and healthcare determinants of health1. The impacts on mortality are likely to vary across countries in magnitude, timing, and age and sex composition. Here, we applied an ensemble of 16 Bayesian probabilistic models to vital statistics data, by age group and sex, to consistently and comparably estimate the impacts of the first phase of the pandemic on all-cause mortality for 17 industrialised countries. The models accounted for factors that affect death rates including seasonality, temperature, and public holidays, as well as for medium-long-term secular trends and the dependency of death rates in each week on those in preceding week(s). From mid-February through the end of May 2020, an estimated 202,900 (95% credible interval 179,400-224,900) more people died in these 17 countries than would have had the pandemic not taken place. Nearly three quarters of these excess deaths occurred in England and Wales, Italy and Spain, where less than half of the total population of these countries live. When all-cause mortality is considered, the total number of deaths, deaths per 100,000 people, and relative increase in deaths were similar between men and women in most countries. Further, in many countries, the balance of excess deaths changed from male-dominated early in the pandemic to being equal or female-dominated later on. + +Taken over the entire first phase of the pandemic, there was no detectable rise in all-cause mortality in New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland and for women in Austria and Switzerland (posterior probability of an increase in deaths <90%). Women in Portugal and men in Austria experienced relatively small increases in all-cause mortality, with posterior probabilities of 90-99%. For men in Switzerland and Portugal, and both sexes in the Netherlands, France, Sweden, Belgium, Italy, Scotland, Spain and England and Wales, all-cause mortality increased as a result of the pandemic with a posterior probability >99%. After accounting for population size, England and Wales and Spain experienced the highest death toll, nearly 100 deaths per 100,000 people; they also had the largest relative (percent) increase in deaths (37% (95% credible interval 30-44) in England and Wales; 38% (31-44) in Spain). New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland experienced changes in deaths that ranged from possible slight declines to increases of no more than 5%. The large impact in England and Wales stems partly from having experienced (together with Spain) the highest weekly increases in deaths, more than doubling in some weeks, and having had (together with Sweden) the longest duration when deaths exceeded levels that would be expected in the absence of the pandemic. + +The heterogeneous magnitude and character of the excess deaths due to the Covid-19 pandemic reflect differences in how well countries have managed the pandemic (e.g., timing, extent and adherence to lockdowns and other social distancing measures; effectiveness of test, trace and isolate mechanisms), and the resilience and preparedness of the health and social care system (e.g., effective facility and community care pathways; minimising spread of infection within hospitals and care homes, and between them and the community).",public and global health,exact,100,100 medRxiv,10.1101/2020.07.24.20149815,2020-07-26,https://medrxiv.org/cgi/content/short/2020.07.24.20149815,Systematic evaluation and external validation of 22 prognostic models among hospitalised adults with COVID-19: An observational cohort study,Rishi K Gupta; Michael Marks; Thomas H. A. Samuels; Akish Luintel; Tommy Rampling; Humayra Chowdhury; Matteo Quartagno; Arjun Nair; Marc Lipman; Ibrahim Abubakar; Maarten van Smeden; Wai Keong Wong; Bryan Williams; Mahdad Noursadeghi,"Institute for Global Health, University College London, London, UK; London School of Hygiene and Tropical Medicine; University College London Hospitals NHS Trust; University College London Hospitals NHS Trust; University College London Hospitals NHS Trust; University College London Hospitals NHS Trust; MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK; University College London Hospitals NHS Trust; UCL Respiratory, Division of Medicine, University College London, London, UK; Institute for Global Health, University College London, London, UK; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; University College London Hospitals NHS Trust; NIHR University College London Hospitals Biomedical Research Centre; Division of Infection & Immunity, University College London, UK","BackgroundThe number of proposed prognostic models for COVID-19, which aim to predict disease outcomes, is growing rapidly. It is not known whether any are suitable for widespread clinical implementation. We addressed this question by independent and systematic evaluation of their performance among hospitalised COVID-19 cases. MethodsWe conducted an observational cohort study to assess candidate prognostic models, identified through a living systematic review. We included consecutive adults admitted to a secondary care hospital with PCR-confirmed or clinically diagnosed community-acquired COVID-19 (1st February to 30th April 2020). We reconstructed candidate models as per their original descriptions and evaluated performance for their original intended outcomes (clinical deterioration or mortality) and time horizons. We assessed discrimination using the area under the receiver operating characteristic curve (AUROC), and calibration using calibration plots, slopes and calibration-in-the-large. We calculated net benefit compared to the default strategies of treating all and no patients, and against the most discriminating predictor in univariable analyses, based on a limited subset of a priori candidates. @@ -2807,15 +2829,6 @@ Key pointsO_ST_ABSQuestionC_ST_ABSWhat is the evidence on the susceptibility and FindingsIn this systematic review and meta-analysis, children and young people under 18-20 years had an 435 lower odds of secondary infection of with SARS-CoV-2 compared to adults 20 years plus, a significant difference. This finding was most marked in children under 12-14 years. Data were insufficient to conclude whether transmission of SARS-CoV-2 by children is lower than by adults. MeaningWe found preliminary evidence that children have a lower susceptibility for SARS-CoV-2 infection compared with adults, although data for adolescents is less clear. The role that children and young people play in transmission of this pandemic remains unclear.",public and global health,exact,100,100 -medRxiv,10.1101/2020.05.20.20108183,2020-05-23,https://medrxiv.org/cgi/content/short/2020.05.20.20108183,A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings,Sarah Beale; Andrew Hayward; Laura Shallcross; Robert W Aldridge; Ellen Fragaszy,University College London; University College London; University College London; University College London; University College London,"BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings. - -MethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis. - -FindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited. - -InterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted. - -FundingMedical Research Council",infectious diseases,exact,100,100 medRxiv,10.1101/2020.05.18.20086157,2020-05-22,https://medrxiv.org/cgi/content/short/2020.05.18.20086157,COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis,Nicola L Boddington; Andre Charlett; Suzanne Elgohari; Jemma L Walker; Helen Mcdonald; Chloe Byers; Laura Coughlan; Tatiana Garcia Vilaplana; Rosie Whillock; Mary Sinnathamby; Nikolaos Panagiotopoulos; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Joseph Shingleton; Emma Bennett; Daniel J Grint; Helen Strongman; Kathryn E Mansfield; Christopher Rentsch; Caroline Minassian; Ian J Douglas; Rohini Mathur; Maria Peppa; Simon Cottrell; Jim McMenamin; Maria Zambon; Mary Ramsay; Gavin Dabrera; Vanessa Saliba; Jamie Lopez Bernal,Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health Wales; Public Health Scotland; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England,"ObjectivesFollowing detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and underlying health conditions associated with infection of the first few hundred cases. MethodsInformation was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and underlying health conditions associated with infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented. @@ -2920,6 +2933,15 @@ ResultsWe used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity a ConclusionThe worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.",genomics,exact,100,100 medRxiv,10.1101/2020.04.22.20072124,2020-04-24,https://medrxiv.org/cgi/content/short/2020.04.22.20072124,"Self-reported symptoms of covid-19 including symptoms most predictive of SARS-CoV-2 infection, are heritable",Frances MK Williams; Maxim Freydin; Massimo Mangino; Simon Couvreur; Alessia Visconti; Ruth CE Bowyer; Caroline I Le Roy; Mario Falchi; Carole Sudre; Richard Davies; Christopher Hammond; Cristina Menni; Claire Steves; Tim Spector,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Ltd; King's College London; King's College London; King's College London; King's College London,"Susceptibility to infection such as SARS-CoV-2 may be influenced by host genotype. TwinsUK volunteers (n=2633) completing the C-19 Covid symptom tracker app allowed classical twin studies of covid-19 symptoms including predicted covid-19, a symptom-based algorithm predicting true infection derived in app users tested for SARS-CoV-2. We found heritability for fever = 41 (95% confidence intervals 12-70)%; anosmia 47 (27-67)%; delirium 49 (24-75)%; and predicted covid-19 gave heritability = 50 (29-70)%.",genetic and genomic medicine,exact,100,100 +medRxiv,10.1101/2020.04.21.20073049,2020-04-24,https://medrxiv.org/cgi/content/short/2020.04.21.20073049,What can trends in hospital deaths from COVID-19 tell us about the progress and peak of the pandemic? An analysis of death counts from England announced up to 20 April 2020,David A Leon; Christopher I Jarvis; Anne M Johnson; Liam Smeeth; Vladimir M Shkolnikov,London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; London School of Hygiene & Tropical Medicine; Max Planck Institute for Demographic Research,"BackgroundReporting of daily hospital COVID-19 deaths in the UK are promoted by the government and scientific advisers alike as a key metric for assessing the progress in the control of the epidemic. These data, however, have certain limitations, among which one of the most significant concerns the fact that the daily totals span deaths that have occurred between 1 and 10 days or more in the past. + +Data and methodsWe obtained daily data published published by NHS England up to and including April 25 in the form of Excel spreadsheets in which deaths counts are presented by date of death according to age and region. Simple descriptive analyses were conducted and presented in graphical and tabular form which were aimed at illustrating the biases inherent in focussing on daily counts regardless of when the deaths occurred. We then looked at how a less biased picture could be obtained by looking at trends in death counts stratifying by individual period of delay in days between occurrence of death and when the death was included in the daily announcement. + +FindingsThe number of hospital COVID-19 deaths announced daily overestimates the maximum number of deaths actually occurring so far in the epidemic in the UK, and also obscures the pattern of decline in deaths. Taking account of reporting delays suggests that for England as a whole a peak in hospital COVID-19 deaths may have been reached on April 8 with a subsequent gradual decline suggested. The same peak is also seen among those aged 60-79 and 80+, although there is slightly shallower decline in the oldest age group (80+ years). Among those aged 40-59 years a later peak on April 11 is evident. London shows a peak on April 8 and a clearer and steeper pattern of subsequent decline compared to England as a whole. + +InterpretationAnalyses of mortality trends must take account of delay, and in communication with the public more emphasis should be placed on looking at trends based on deaths that occurred 5 or more days prior to the announcement day. The slightly weaker decline seen at age 80+ may reflect increased hospitalisation of people from care homes, whereas the later peak under the age of 60 years may reflect the higher proportions at these younger ages being admitted to critical care resulting in an extension of life of several days. + +Competing interestsAll authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: no support from any organization for the submitted work; no financial relationships with any organizations that might have an interest in the submitted work in the previous three years other than LS who reported grants from Wellcome, MRC, NIHR, GSK, BHF, Diabetes UK all outside the submitted work; no other relationships or activities that could appear to have influenced the submitted work other than LS who is a Trustee of the British Heart Foundation and AJM who is a member of the Royal Society Delve Committee.",epidemiology,exact,100,100 medRxiv,10.1101/2020.04.18.20064774,2020-04-22,https://medrxiv.org/cgi/content/short/2020.04.18.20064774,"How many are at increased risk of severe COVID-19 disease? Rapid global, regional and national estimates for 2020",Andrew Clark; Mark Jit; Charlotte Warren-Gash; Bruce Guthrie; Harry HX Wang; Stewart W Mercer; Colin Sanderson; Martin McKee; Christopher Troeger; Kanyin I Ong; Francesco Checchi; Pablo Perel; Sarah Joseph; Hamish P Gibbs; Amitava Banerjee; LSHTM CMMID COVID-19 working group; Rosalind M Eggo,LSHTM; London School of Hygiene & Tropical Medicine; LSHTM; Edinburgh University; Sun Yat-Sen University; Edinburgh University; LSHTM; LSHTM; University of Washington; University of Washington; LSHTM; LSHTM; IAVI; LSHTM; UCL; ; London School of Hygiene & Tropical Medicine,"BackgroundThe risk of severe COVID-19 disease is known to be higher in older individuals and those with underlying health conditions. Understanding the number of individuals at increased risk of severe COVID-19 illness, and how this varies between countries may inform the design of possible strategies to shield those at highest risk. MethodsWe estimated the number of individuals at increased risk of severe COVID-19 disease by age (5-year age groups), sex and country (n=188) based on prevalence data from the Global Burden of Disease (GBD) study for 2017 and United Nations population estimates for 2020. We also calculated the number of individuals without an underlying condition that could be considered at-risk because of their age, using thresholds from 50-70 years. The list of underlying conditions relevant to COVID-19 disease was determined by mapping conditions listed in GBD to the guidelines published by WHO and public health agencies in the UK and US. We analysed data from two large multimorbidity studies to determine appropriate adjustment factors for clustering and multimorbidity. @@ -2945,29 +2967,6 @@ medRxiv,10.1101/2020.04.09.20059865,2020-04-14,https://medrxiv.org/cgi/content/s MethodsWe developed a modelling framework to simulate SARS-CoV-2 transmission in Kenya, KenyaCoV. KenyaCoV was used to simulate SARS-CoV-2 transmission both within, and between, different Kenyan regions and age groups. KenyaCoV was parameterized using a combination of human mobility data between the defined regions, the recent 2019 Kenyan census, and estimates of age group social interaction rates specific to Kenya. Key epidemiological characteristics such as the basic reproductive number and the age-specific rate of developing COVID-19 symptoms after infection with SARS-CoV-2, were adapted for the Kenyan setting from a combination of published estimates and analysis of the age distribution of cases observed in the Chinese outbreak. ResultsWe find that if person-to-person transmission becomes established within Kenya, identifying the role of subclinical, and therefore largely undetected, infected individuals is critical to predicting and containing a very significant epidemic. Depending on the transmission scenario our reproductive number estimates for Kenya range from 1.78 (95% CI 1.44 -2.14) to 3.46 (95% CI 2.81-4.17). In scenarios where asymptomatic infected individuals are transmitting significantly, we expect a rapidly growing epidemic which cannot be contained only by case isolation. In these scenarios, there is potential for a very high percentage of the population becoming infected (median estimates: >80% over six months), and a significant epidemic of symptomatic COVID-19 cases. Exceptional social distancing measures can slow transmission, flattening the epidemic curve, but the risk of epidemic rebound after lifting restrictions is predicted to be high.",infectious diseases,exact,100,100 -medRxiv,10.1101/2020.04.10.20059121,2020-04-14,https://medrxiv.org/cgi/content/short/2020.04.10.20059121,"ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study",Dipender Gill; Marios Arvanitis; Paul Carter; Ana I Hernandez Cordero; Brian Jo; Ville Karhunen; Susanna C Larsson; Xuan Li; Sam M Lockhart; Amy M Mason; Evanthia Pashos; Ashis Saha; Vanessa Tan; Verena Zuber; Yohan Bosse; Sarah Fahle; Ke Hao; Tao Jiang; Philippe Joubert; Alan C Lunt; Willem hendrik Ouwehand; David J Roberts; Wim Timens; Maarten van den Berge; Nicholas A Watkins; Alexis Battle; Adam S Butterworth; John Danesh; Barbara E Engelhard; James E Peters; Don Sin; Stephen Burgess,"Imperial College London; Johns Hopkins University; University of Cambridge; The University of British Columbia Center for Heart Lung Innovation; Lewis Sigler Institute for Integrative Biology; Imperial College London; Karolinska Institutet; The University of British Columbia Center for Heart Lung Innovation; University of Cambridge; University of Cambridge; Pfizer; Johns Hopkins University; University of Bristol; Imperial College London; Laval University, Quebec; University of Cambridge; School of Medicine at Mount Sinai; University of Cambridge; Laval University, Quebec; Imperial College London; University of Cambridge; University of Oxford; University of Groningen; University of Groningen; University of Cambridge; Johns Hopkins University; University of Cambridge; University of Cambridge; Princeton University; Imperial College London; University of British Columbia; University of Cambridge","ObjectivesTo use human genetic variants that proxy angiotensin-converting enzyme (ACE) inhibitor drug effects and cardiovascular risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 gene expression and circulating ACE2 levels. - -DesignTwo-sample Mendelian randomization (MR) analysis. - -SettingSummary-level genetic association data. - -ParticipantsParticipants were predominantly of European ancestry. Variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors (body mass index, chronic obstructive pulmonary disease, lifetime smoking index, low-density lipoprotein cholesterol, systolic blood pressure and type 2 diabetes mellitus) were selected from publicly available genome-wide association study data (sample sizes ranging from 188,577 to 898,130 participants). Genetic association estimates for lung expression of ACE2 and TMPRSS2 were obtained from the Gene-Tissue Expression (GTEx) project (515 participants) and the Lung eQTL Consortium (1,038 participants). Genetic association estimates for circulating plasma ACE2 levels were obtained from the INTERVAL study (4,947 participants). - -Main outcomes and measuresLung ACE2 and TMPRSS2 expression and plasma ACE2 levels. - -ResultsThere were no association of genetically proxied ACE inhibition with any of the outcomes considered here. There was evidence of a positive association of genetic liability to type 2 diabetes mellitus with lung ACE2 gene expression in GTEx (p = 4x10-4) and with circulating plasma ACE2 levels in INTERVAL (p = 0.03), but not with lung ACE2 expression in the Lung eQTL Consortium study (p = 0.68). There were no associations between genetically predicted levels of the other cardiometabolic traits with the outcomes. - -ConclusionsThis study does not provide evidence to support that ACE inhibitor antihypertensive drugs affect lung ACE2 and TMPRSS2 expression or plasma ACE2 levels. In the current COVID-19 pandemic, our findings do not support a change in ACE inhibitor medication use without clinical justification. - -Summary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current coronavirus disease 2019 (COVID-19) pandemic. -C_LIO_LISerine protease TMPRSS2 is involved in priming the SARS-CoV-2 spike protein for cellular entry through the angiotensin-converting enzyme 2 (ACE2) receptor. -C_LIO_LIExpression of ACE2 and TMPRSS2 in the lung epithelium might have implications for risk of SARS-CoV-2 infection and severity of COVID-19. -C_LI - -What this study addsO_LIWe used human genetic variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 expression and circulating ACE2 levels. -C_LIO_LIOur findings do not support the hypothesis that ACE inhibitors have effects on ACE2 expression. -C_LIO_LIWe found some support for an association of genetic liability to type 2 diabetes mellitus with higher lung ACE2 expression and plasma ACE2 levels, but evidence was inconsistent across studies. -C_LI",genetic and genomic medicine,exact,100,100 medRxiv,10.1101/2020.04.07.20056788,2020-04-11,https://medrxiv.org/cgi/content/short/2020.04.07.20056788,Treatment with ACE-inhibitors is associated with less severe disease with SARS-Covid-19 infection in a multi-site UK acute Hospital Trust,Daniel Bean; Zeljko Kraljevic; Thomas Searle; Rebecca Bendayan; Andrew Pickles; Amos Folarin; Lukasz Roguski; Kawsar Noor; Anthony Shek; Rosita Zakeri; Ajay Shah; James Teo; Richard JB Dobson,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University College London; University College London; King's College London; King's College London; King's College London; King's College Hospital; Kings College London,"AimsThe SARS-Cov2 virus binds to the ACE2 receptor for cell entry. It has been suggested that ACE-inhibitors (ACEi) and Angiotensin-2 Blockers (ARB), which are commonly used in patients with hypertension or diabetes and may raise ACE2 levels, could increase the risk of severe COVID19 infection. Methods and ResultsWe evaluated this hypothesis in a consecutive cohort of 1200 acute inpatients with COVID19 at two hospitals with a multi-ethnic catchment population in London (UK). The mean age was 68{+/-}17 years (57% male) and 74% of patients had at least 1 comorbidity. 415 patients (34.6%) reached the primary endpoint of death or transfer to a critical care unit for organ support within 21-days of symptom onset. 399 patients (33.3 %) were taking ACEi or ARB. Patients on ACEi/ARB were significantly older and had more comorbidities. The odds ratio (OR) for the primary endpoint in patients on ACEi and ARB, after adjustment for age, sex and co-morbidities, was 0.63 (CI 0.47-0.84, p<0.01). diff --git a/data/covid/preprints.exact.json b/data/covid/preprints.exact.json index 47f2de69..3d160eee 100644 --- a/data/covid/preprints.exact.json +++ b/data/covid/preprints.exact.json @@ -363,20 +363,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.03.24.23287700", - "date": "2023-03-26", - "link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287700", - "title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", - "authors": "Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes", - "affiliations": "University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester", - "abstract": "ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection.\n\nDesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups.\n\nSetting\n\nResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage.\n\nConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.", - "category": "occupational and environmental health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.03.24.23287666", @@ -965,20 +951,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.20.22275994", - "date": "2022-06-20", - "link": "https://medrxiv.org/cgi/content/short/2022.06.20.22275994", - "title": "Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies", - "authors": "Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood", - "affiliations": "King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London", - "abstract": "Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.18.22276437", @@ -1007,6 +979,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.06.16.22276479", + "date": "2022-06-16", + "link": "https://medrxiv.org/cgi/content/short/2022.06.16.22276479", + "title": "Mental health of healthcare workers in England during the COVID-19 pandemic: a longitudinal cohort study", + "authors": "Danielle Lamb; Rafael Gafoor; Hannah Scott; Ewan Carr; Sharon Stevelink; Rosalind Raine; Matthew Hotopf; Neil Greenberg; Siobhan Hegarty; Ira Madan; Paul Moran; Richard Morriss; Dominic Murphy; Anne Marie Rafferty; Scott Weich; Sarah Dorrington; Simon Wessely", + "affiliations": "UCL; University College London; King's College London; King's College London; King's College London; University College London; King's College London; King's College London; King's College London; Guy's and St Thomas' NHS Foundation Trust; University of Bristol; University of Nottingham; Combat Stress; King's College London; University of Sheffield; King's College London; King's College London", + "abstract": "ObjectiveTo examine variations in impact of the COVID-19 pandemic on the mental health of all types of healthcare workers (HCWs) in England over the first 17 months of the pandemic.\n\nMethodWe undertook a prospective cohort study of 22,501 HCWs from 18 English acute and mental health NHS Trusts, collecting online survey data on common mental disorders (CMDs), depression, anxiety, alcohol use, and PTSD, from April 2020 to August 2021. We analysed these data cross-sectionally by time period (corresponding to periods the NHS was under most pressure), and longitudinally. Data were weighted to better represent Trust population demographics.\n\nResultsThe proportion of those with probable CMDs was greater during periods when the NHS was under most pressure (measured by average monthly deaths). For example, 55% (95%CI 53%, 58%) of participants reported symptoms of CMDs in April-June 2020 versus 47% (95%CI 46%, 48%) July-October 2020. Contrary to expectation, there were no major differences between professional groups (i.e. clinical and non-clinical staff). Younger, female, lower paid staff, who felt poorly supported by colleagues/managers, and who experienced potentially morally injurious events were most at risk of negative mental health outcomes.\n\nConclusionAmong HCWs, the prevalence of probable CMDs increased during periods of escalating pressure on the NHS, suggesting staff support should be increased at such points in the future, and staff should be better prepared for such situations via training. All staff, regardless of role, experienced poorer mental health during these periods, suggesting that support should be provided for all staff groups.\n\nKey messagesO_ST_ABSWhat is already known on this topicC_ST_ABSExisting evidence about the mental health of healthcare workers (HCWs) through the COVID-19 pandemic comes mainly from cross-sectional studies using unrepresentative convenience samples, typically focussing on clinical staff rather than all HCWs. Such studies show high prevalence of symptoms of mental disorders, but the strength of this evidence is uncertain.\n\nWhat this study addsUsing a defined sampling frame, with longitudinal, weighted data, we show that during periods of greater pressure on the NHS (as indicated by average monthly national COVID-19 death rates), prevalence of mental disorder symptoms increased, and, importantly, that this effect was seen in non-clinical as well as clinical staff.\n\nHow this study might affect research, practice or policyThese findings indicate that provision of support for HCWs should not only focus on those providing clinical care, but also on non-clinical staff such as porters, cleaners, and administrative staff, and additional support should be provided during higher pressure periods. Better preparation of staff for such situations is also suggested.", + "category": "psychiatry and clinical psychology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.06.16.22276487", @@ -1077,6 +1063,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.05.23.22275458", + "date": "2022-05-25", + "link": "https://medrxiv.org/cgi/content/short/2022.05.23.22275458", + "title": "Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States", + "authors": "Seth Flaxman; Charles Whittaker; Elizaveta Semenova; Theo Rashid; Robbie Parks; Alexandra Blenkinsop; H Juliette T Unwin; Swapnil Mishra; Samir Bhatt; Deepti Gurdasani; Oliver Ratmann", + "affiliations": "Oxford; Imperial College London; AstraZeneca; Imperial College London; Columbia University; Imperial College London; Imperial College London; University of Copenhagen; University of Copenhagen, Imperial College London; Queen Mary University of London; Imperial College London", + "abstract": "Covid-19 has caused more than 1 million deaths in the US, including at least 1,204 deaths among children and young people (CYP) aged 0-19 years, with 796 occurring in the one year period April 1, 2021 - March 31, 2022. Deaths among US CYP are rare in general, and so we argue here that the mortality burden of Covid-19 in CYP is best understood in the context of all other causes of CYP death. Using publicly available data from CDC WONDER on NCHSs 113 Selected Causes of Death, and comparing to mortality in 2019, the immediate pre-pandemic period, we find that Covid-19 mortality is among the 10 leading causes of death in CYP aged 0-19 years in the US, ranking 8th among all causes of deaths, 5th in disease-related causes of deaths (excluding accidents, assault and suicide), and 1st in deaths caused by infectious or respiratory diseases. Covid-19 deaths constitute 2.3% of the 10 leading causes of death in this age group. Covid-19 caused substantially more deaths in CYP than major vaccine-preventable diseases did historically in the period before vaccines became available. Various factors including underreporting and Covid-19s role as a contributing cause of death from other diseases mean that our estimates may understate the true mortality burden of Covid-19. Our findings underscore the public health relevance of Covid-19 to CYP. In the likely future context of sustained SARS-CoV-2 circulation, pharmaceutical and non-pharmaceutical interventions will continue to play an important role in limiting transmission of the virus in CYP and mitigating severe disease.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.05.19.22275214", @@ -2141,6 +2141,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.08.05.21259863", + "date": "2021-08-07", + "link": "https://medrxiv.org/cgi/content/short/2021.08.05.21259863", + "title": "Recording of 'COVID-19 vaccine declined' among vaccination priority groups: a cohort study on 57.9 million NHS patients' primary care records in situ using OpenSAFELY", + "authors": "Helen J Curtis; Peter Inglesby; Brian MacKenna; Richard Croker; William J Hulme; Christopher T Rentsch; Krishnan Bhaskaran; Alex J Walker; Caroline E Morton; David Evans; Amir Mehrkar; Sebastian CJ Bacon; Christopher Bates; George Hickman; Tom Ward; Jessica Morley; Jonathan Cockburn; Simon Davy; Anna Schultze; Elizabeth J Williamson; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; John Tazare; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Ben Goldacre", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", + "abstract": "BackgroundAll patients in England within vaccine priority groups were offered a COVID-19 vaccine by mid-April 2021. Clinical record systems contain codes to denote when such an offer has been declined by a patient (although these can in some cases be entered for a variety of other reasons including vaccination delay, or other administrative issues). We set out to describe the patterns of usage of codes for COVID-19 vaccines being declined.\n\nMethodsWith the approval of NHS England and using the full pseudonymised primary care records for 57.9 million NHS patients, we identified all patients in key vaccine priority groups: aged over 50, or over 16 and at increased risk from COVID-19 (Clinically Extremely Vulnerable [CEV] or otherwise \"at risk\"). We describe the proportion of patients recorded as declining a COVID-19 vaccination for each priority group, and by other clinical and demographic factors; whether patients recorded as \"declined\" subsequently went on to receive a vaccination; and the distribution of code usage across GP practices.\n\nResultsOf 24.5 million patients in priority groups as of May 25th 2021, 89.2% had received a vaccine, 8.8% had neither a vaccination nor a decline recorded, and 663,033 (2.7%) had a decline code recorded. Of patients with a recorded decline, 125,587 (18.9%) were subsequently vaccinated. Subsequent vaccination was slightly more common in the South Asian population than other ethnicities (e.g. 32.3% vs 22.8%, over 65s). The proportion of declining-unvaccinated patients varied strongly with ethnicity (Black 15.3%, South Asian 5.6%, White 1.5% in over 80s); and was higher in patients from more deprived areas. COVID-19 vaccine decline codes were present in almost all practices (98.8%), but with wide variation between practices in rates of usage. Among all priority groups, declining-unvaccinated status was most common in CEV (3.3%).\n\nConclusionsClinical codes indicative of COVID-19 vaccinations being declined are widely used in English general practice. They are substantially more common among Black and South Asian patients, and patients from more deprived areas. There is a need for more detailed survey and/or qualitative research with patients and clinicians to determine the most common reasons for these recorded declines.", + "category": "public and global health", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.07.29.21261190", @@ -2351,6 +2365,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.06.21.449178", + "date": "2021-06-21", + "link": "https://biorxiv.org/cgi/content/short/2021.06.21.449178", + "title": "Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune pathways related to tissue injury", + "authors": "Amy R Cross; Carlos de Andrea; Maria Villalba-Esparza; Manuel Landecho Acha; Lucia Cerundolo; Praveen Weeratunga; Rachel Etherington; Laura Denney; Graham Ogg; Ling-Pei Ho; Ian Roberts; Joanna Hester; Paul Klenerman; Ignacio Melero; Stephen Sansom; Fadi Issa", + "affiliations": "University of Oxford; Universidad de Navarra; Department of Pathology, Clinica de la Universidad de Navarra, Pamplona, Spain; Clinica Universidad de Navarra; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Universidad de Navarra; University of Oxford; University of Oxford", + "abstract": "Severe lung damage in COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways and genes present across the spectrum of histopathological damage in COVID-19 lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from areas of interest within well preserved post-mortem lung samples from three patients. Despite substantial inter-patient heterogeneity we discovered evidence for a common immune cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines including CXCL9, CXCL10 and CXCL11 which are known to promote the recruitment of CXCR3+ immune cells. The tumour necrosis factor (TNF) superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were found to be consistently upregulated in the areas with severe tissue damage. We used published spatial and single cell SARS-CoV-2 datasets to confirm our findings in the lung tissue from additional cohorts of COVID-19 patients. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies.\n\nOne Sentence SummarySpatial analysis identifies IFN{gamma} response signatures as focal to severe alveolar damage in COVID-19 pneumonitis.", + "category": "immunology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.06.08.21258551", @@ -2477,20 +2505,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.17.21257223", - "date": "2021-05-17", - "link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257223", - "title": "Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).", - "authors": "Cyril Roman Geismar; Ellen Fragaszy; Vincent Grigori Nguyen; Wing Lam Erica Fong; Madhumita Shrotri; Sarah Beale; Alison Rodger; Vasileios Lampos; Thomas Edward Byrne; Jana Kovar; Annalan Navaratnam; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative", - "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", - "abstract": "IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant.\n\nMethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks.\n\nResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)).\n\nConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.06.21256757", @@ -3289,6 +3303,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.19.20234120", + "date": "2020-11-23", + "link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234120", + "title": "Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19", + "authors": "Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas", + "affiliations": "VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School", + "abstract": "Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.19.20234849", @@ -3457,6 +3485,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.10.26.20219725", + "date": "2020-10-27", + "link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219725", + "title": "Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults", + "authors": "Helen Ward; Graham Cooke; Christina J Atchison; Matthew Whitaker; Joshua Elliott; Maya Moshe; Jonathan C Brown; Barney Flower; Anna Daunt; Kylie E. C. Ainslie; Deborah Ashby; Christl A. Donnelly; Steven Riley; Ara Darzi; Wendy Barclay; Paul Elliott", + "affiliations": "Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London", + "abstract": "BackgroundThe prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into its spread in the community, the likelihood of reinfection and potential for some level of population immunity.\n\nMethodsPrevalence of antibody positivity in England, UK (REACT2) with three cross-sectional surveys between late June and September 2020. 365104 adults used a self-administered lateral flow immunoassay (LFIA) test for IgG. A laboratory comparison of LFIA results to neutralization activity in panel of sera was performed.\n\nResultsThere were 17,576 positive tests over the three rounds. Antibody prevalence, adjusted for test characteristics and weighted to the adult population of England, declined from 6.0% [5.8, 6.1], to 4.8% [4.7, 5.0] and 4.4% [4.3, 4.5], a fall of 26.5% [-29.0, -23.8] over the three months of the study. There was a decline between rounds 1 and 3 in all age groups, with the highest prevalence of a positive result and smallest overall decline in positivity in the youngest age group (18-24 years: -14.9% [-21.6, -8.1]), and lowest prevalence and largest decline in the oldest group (75+ years: -39.0% [-50.8, -27.2]); there was no change in antibody positivity between rounds 1 and 3 in healthcare workers (+3.45% [-5.7, +12.7]).\n\nThe decline from rounds 1 to 3 was largest in those who did not report a history of COVID-19, (-64.0% [-75.6, -52.3]), compared to -22.3% ([-27.0, -17.7]) in those with SARS-CoV-2 infection confirmed on PCR.\n\nDiscussionThese findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.10.14.20212555", @@ -4017,6 +4059,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.26.20161570", + "date": "2020-07-28", + "link": "https://medrxiv.org/cgi/content/short/2020.07.26.20161570", + "title": "Magnitude, demographics and dynamics of the impact of the first phase of the Covid-19 pandemic on all-cause mortality in 17 industrialised countries", + "authors": "Vasilis Kontis; James E Bennett; Theo Rashid; Robbie M Parks; Jonathan Pearson-Stuttard; Michel Guillot; Perviz Asaria; Bin Zhou; Marco Battaglini; Gianni Corsetti; Martin McKee; Mariachiara Di Cesare; Colin D Mathers; Majid Ezzati", + "affiliations": "Imperial College London; Imperial College London; Imperial College London; Columbia University; Imperial College London; University of Pennsylvania; Imperial College London; Imperial College London; Italian National Institute of Statistics; Italian National Institute of Statistics; London School of Hygiene & Tropical Medicine; Middlesex University London; Independent Researcher; Imperial College London", + "abstract": "The Covid-19 pandemic affects mortality directly through infection as well as through changes in the social, environmental and healthcare determinants of health1. The impacts on mortality are likely to vary across countries in magnitude, timing, and age and sex composition. Here, we applied an ensemble of 16 Bayesian probabilistic models to vital statistics data, by age group and sex, to consistently and comparably estimate the impacts of the first phase of the pandemic on all-cause mortality for 17 industrialised countries. The models accounted for factors that affect death rates including seasonality, temperature, and public holidays, as well as for medium-long-term secular trends and the dependency of death rates in each week on those in preceding week(s). From mid-February through the end of May 2020, an estimated 202,900 (95% credible interval 179,400-224,900) more people died in these 17 countries than would have had the pandemic not taken place. Nearly three quarters of these excess deaths occurred in England and Wales, Italy and Spain, where less than half of the total population of these countries live. When all-cause mortality is considered, the total number of deaths, deaths per 100,000 people, and relative increase in deaths were similar between men and women in most countries. Further, in many countries, the balance of excess deaths changed from male-dominated early in the pandemic to being equal or female-dominated later on.\n\nTaken over the entire first phase of the pandemic, there was no detectable rise in all-cause mortality in New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland and for women in Austria and Switzerland (posterior probability of an increase in deaths <90%). Women in Portugal and men in Austria experienced relatively small increases in all-cause mortality, with posterior probabilities of 90-99%. For men in Switzerland and Portugal, and both sexes in the Netherlands, France, Sweden, Belgium, Italy, Scotland, Spain and England and Wales, all-cause mortality increased as a result of the pandemic with a posterior probability >99%. After accounting for population size, England and Wales and Spain experienced the highest death toll, nearly 100 deaths per 100,000 people; they also had the largest relative (percent) increase in deaths (37% (95% credible interval 30-44) in England and Wales; 38% (31-44) in Spain). New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland experienced changes in deaths that ranged from possible slight declines to increases of no more than 5%. The large impact in England and Wales stems partly from having experienced (together with Spain) the highest weekly increases in deaths, more than doubling in some weeks, and having had (together with Sweden) the longest duration when deaths exceeded levels that would be expected in the absence of the pandemic.\n\nThe heterogeneous magnitude and character of the excess deaths due to the Covid-19 pandemic reflect differences in how well countries have managed the pandemic (e.g., timing, extent and adherence to lockdowns and other social distancing measures; effectiveness of test, trace and isolate mechanisms), and the resilience and preparedness of the health and social care system (e.g., effective facility and community care pathways; minimising spread of infection within hospitals and care homes, and between them and the community).", + "category": "public and global health", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.24.20149815", @@ -4437,20 +4493,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.20.20108183", - "date": "2020-05-23", - "link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108183", - "title": "A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings", - "authors": "Sarah Beale; Andrew Hayward; Laura Shallcross; Robert W Aldridge; Ellen Fragaszy", - "affiliations": "University College London; University College London; University College London; University College London; University College London", - "abstract": "BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings.\n\nMethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis.\n\nFindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited.\n\nInterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted.\n\nFundingMedical Research Council", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.18.20086157", @@ -4619,6 +4661,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.04.21.20073049", + "date": "2020-04-24", + "link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073049", + "title": "What can trends in hospital deaths from COVID-19 tell us about the progress and peak of the pandemic? An analysis of death counts from England announced up to 20 April 2020", + "authors": "David A Leon; Christopher I Jarvis; Anne M Johnson; Liam Smeeth; Vladimir M Shkolnikov", + "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; London School of Hygiene & Tropical Medicine; Max Planck Institute for Demographic Research", + "abstract": "BackgroundReporting of daily hospital COVID-19 deaths in the UK are promoted by the government and scientific advisers alike as a key metric for assessing the progress in the control of the epidemic. These data, however, have certain limitations, among which one of the most significant concerns the fact that the daily totals span deaths that have occurred between 1 and 10 days or more in the past.\n\nData and methodsWe obtained daily data published published by NHS England up to and including April 25 in the form of Excel spreadsheets in which deaths counts are presented by date of death according to age and region. Simple descriptive analyses were conducted and presented in graphical and tabular form which were aimed at illustrating the biases inherent in focussing on daily counts regardless of when the deaths occurred. We then looked at how a less biased picture could be obtained by looking at trends in death counts stratifying by individual period of delay in days between occurrence of death and when the death was included in the daily announcement.\n\nFindingsThe number of hospital COVID-19 deaths announced daily overestimates the maximum number of deaths actually occurring so far in the epidemic in the UK, and also obscures the pattern of decline in deaths. Taking account of reporting delays suggests that for England as a whole a peak in hospital COVID-19 deaths may have been reached on April 8 with a subsequent gradual decline suggested. The same peak is also seen among those aged 60-79 and 80+, although there is slightly shallower decline in the oldest age group (80+ years). Among those aged 40-59 years a later peak on April 11 is evident. London shows a peak on April 8 and a clearer and steeper pattern of subsequent decline compared to England as a whole.\n\nInterpretationAnalyses of mortality trends must take account of delay, and in communication with the public more emphasis should be placed on looking at trends based on deaths that occurred 5 or more days prior to the announcement day. The slightly weaker decline seen at age 80+ may reflect increased hospitalisation of people from care homes, whereas the later peak under the age of 60 years may reflect the higher proportions at these younger ages being admitted to critical care resulting in an extension of life of several days.\n\nCompeting interestsAll authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: no support from any organization for the submitted work; no financial relationships with any organizations that might have an interest in the submitted work in the previous three years other than LS who reported grants from Wellcome, MRC, NIHR, GSK, BHF, Diabetes UK all outside the submitted work; no other relationships or activities that could appear to have influenced the submitted work other than LS who is a Trustee of the British Heart Foundation and AJM who is a member of the Royal Society Delve Committee.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.04.18.20064774", @@ -4661,20 +4717,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.10.20059121", - "date": "2020-04-14", - "link": "https://medrxiv.org/cgi/content/short/2020.04.10.20059121", - "title": "ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study", - "authors": "Dipender Gill; Marios Arvanitis; Paul Carter; Ana I Hernandez Cordero; Brian Jo; Ville Karhunen; Susanna C Larsson; Xuan Li; Sam M Lockhart; Amy M Mason; Evanthia Pashos; Ashis Saha; Vanessa Tan; Verena Zuber; Yohan Bosse; Sarah Fahle; Ke Hao; Tao Jiang; Philippe Joubert; Alan C Lunt; Willem hendrik Ouwehand; David J Roberts; Wim Timens; Maarten van den Berge; Nicholas A Watkins; Alexis Battle; Adam S Butterworth; John Danesh; Barbara E Engelhard; James E Peters; Don Sin; Stephen Burgess", - "affiliations": "Imperial College London; Johns Hopkins University; University of Cambridge; The University of British Columbia Center for Heart Lung Innovation; Lewis Sigler Institute for Integrative Biology; Imperial College London; Karolinska Institutet; The University of British Columbia Center for Heart Lung Innovation; University of Cambridge; University of Cambridge; Pfizer; Johns Hopkins University; University of Bristol; Imperial College London; Laval University, Quebec; University of Cambridge; School of Medicine at Mount Sinai; University of Cambridge; Laval University, Quebec; Imperial College London; University of Cambridge; University of Oxford; University of Groningen; University of Groningen; University of Cambridge; Johns Hopkins University; University of Cambridge; University of Cambridge; Princeton University; Imperial College London; University of British Columbia; University of Cambridge", - "abstract": "ObjectivesTo use human genetic variants that proxy angiotensin-converting enzyme (ACE) inhibitor drug effects and cardiovascular risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 gene expression and circulating ACE2 levels.\n\nDesignTwo-sample Mendelian randomization (MR) analysis.\n\nSettingSummary-level genetic association data.\n\nParticipantsParticipants were predominantly of European ancestry. Variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors (body mass index, chronic obstructive pulmonary disease, lifetime smoking index, low-density lipoprotein cholesterol, systolic blood pressure and type 2 diabetes mellitus) were selected from publicly available genome-wide association study data (sample sizes ranging from 188,577 to 898,130 participants). Genetic association estimates for lung expression of ACE2 and TMPRSS2 were obtained from the Gene-Tissue Expression (GTEx) project (515 participants) and the Lung eQTL Consortium (1,038 participants). Genetic association estimates for circulating plasma ACE2 levels were obtained from the INTERVAL study (4,947 participants).\n\nMain outcomes and measuresLung ACE2 and TMPRSS2 expression and plasma ACE2 levels.\n\nResultsThere were no association of genetically proxied ACE inhibition with any of the outcomes considered here. There was evidence of a positive association of genetic liability to type 2 diabetes mellitus with lung ACE2 gene expression in GTEx (p = 4x10-4) and with circulating plasma ACE2 levels in INTERVAL (p = 0.03), but not with lung ACE2 expression in the Lung eQTL Consortium study (p = 0.68). There were no associations between genetically predicted levels of the other cardiometabolic traits with the outcomes.\n\nConclusionsThis study does not provide evidence to support that ACE inhibitor antihypertensive drugs affect lung ACE2 and TMPRSS2 expression or plasma ACE2 levels. In the current COVID-19 pandemic, our findings do not support a change in ACE inhibitor medication use without clinical justification.\n\nSummary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current coronavirus disease 2019 (COVID-19) pandemic.\nC_LIO_LISerine protease TMPRSS2 is involved in priming the SARS-CoV-2 spike protein for cellular entry through the angiotensin-converting enzyme 2 (ACE2) receptor.\nC_LIO_LIExpression of ACE2 and TMPRSS2 in the lung epithelium might have implications for risk of SARS-CoV-2 infection and severity of COVID-19.\nC_LI\n\nWhat this study addsO_LIWe used human genetic variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 expression and circulating ACE2 levels.\nC_LIO_LIOur findings do not support the hypothesis that ACE inhibitors have effects on ACE2 expression.\nC_LIO_LIWe found some support for an association of genetic liability to type 2 diabetes mellitus with higher lung ACE2 expression and plasma ACE2 levels, but evidence was inconsistent across studies.\nC_LI", - "category": "genetic and genomic medicine", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.07.20056788", diff --git a/data/covid/preprints.json b/data/covid/preprints.json index 38195e1e..130f3284 100644 --- a/data/covid/preprints.json +++ b/data/covid/preprints.json @@ -139,20 +139,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.12.04.23299364", - "date": "2023-12-04", - "link": "https://medrxiv.org/cgi/content/short/2023.12.04.23299364", - "title": "Clinical coding of long COVID in primary care 2020-2023 in a cohort of 19 million adults: an OpenSAFELY analysis", - "authors": "Alasdair D Henderson; Ben FC Butler-Cole; John Tazare; Laurie A Tomlinson; Michael Marks; Mark Jit; Andrew Briggs; Liang-Yu Lin; Oliver Carlile; Christopher Bates; John Parry; Sebastian CJ Bacon; Iain Dillingham; William A Dennison; Ruth E Costello; Yinghui Wei; Alex J Walker; William Hulme; Ben Goldacre; Amir Mehrkar; Brian MacKenna; The OpenSAFELY Collaborative; Emily Herrett; Rosalind M Eggo", - "affiliations": "London School of Hygiene & Tropical Medicine; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; TPP, TPP House, 129 Low Lane, Horsforth, Leeds; TPP, TPP House, 129 Low Lane, Horsforth, Leeds; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Patient and Public Involvement Steering Committee, London,; London School of Hygiene & Tropical Medicine; Centre for Mathematical Sciences, School of Engineering, Computing and Mathematics, University of Plymouth, Plymouth; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine", - "abstract": "BackgroundLong COVID is the patient-coined term for the persistent symptoms of COVID-19 illness for weeks, months or years following the acute infection. There is a large burden of long COVID globally from self-reported data, but the epidemiology, causes and treatments remain poorly understood. Primary care is used to help identify and treat patients with long COVID and therefore Electronic Health Records (EHRs) of past COVID-19 patients could be used to help fill these knowledge gaps. We aimed to describe those with long COVID in primary care records in England.\n\nMethodsWith the approval of NHS England we used routine clinical data from over 19 million adults in England linked to SARS-COV-2 test result, hospitalisation and vaccination data to describe trends in the recording of 16 clinical codes related to long COVID between November 2020 and January 2023. We calculated rates per 100,000 person-years and plotted how these changed over time. We compared crude and minimally adjusted rates of recorded long COVID in patient records between different key demographic and vaccination characteristics using negative binomial models.\n\nFindingsWe identified a total of 55,465 people recorded to have long COVID over the study period, with incidence of new long COVID records increasing steadily over 2021, and declining over 2022. The overall rate per 100,000 person-years was 177.5 cases in women (95% CI: 175.5-179) and 100.5 men (99.5-102). In terms of vaccination against COVID-19, the lowest rates were observed in those with 3+ vaccine doses (103.5 [95% CI: 101.5-105]). Finally, the majority of those with a long COVID record did not have a recorded positive SARS-COV-2 test 12 weeks before the long COVID record.\n\nInterpretationEHR recorded long COVID remains very low compared and incident records of long COVID declined over 2022. We found the lowest rates of recorded long COVID in people with 3 or more vaccine doses. We summarised several sources of possible bias for researchers using EHRs to study long COVID.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.11.30.23299229", @@ -237,20 +223,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "bioRxiv", - "doi": "10.1101/2023.10.22.563481", - "date": "2023-10-24", - "link": "https://biorxiv.org/cgi/content/short/2023.10.22.563481", - "title": "Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy", - "authors": "Ashley Priddey; Michael Xin Hua Chen-Xu; Daniel James Cooper; Serena MacMillan; Georg Meisl; Catherine K Xu; Myra Hosmillo; Ian G Goodfellow; Rafael Kollyfas; Rainer Doffinger; John R Bradley; Irina I Mohorianu; Rachel Jones; Tuomas P.J. Knowles; Rona Smith; Vasilis Kosmoliaptsis", - "affiliations": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D", - "abstract": "BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients.\n\nMethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30).\n\nResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination.\n\nDiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", - "category": "immunology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.10.12.23296948", @@ -573,6 +545,34 @@ "author_similarity": 100, "affiliation_similarity": 92 }, + { + "site": "bioRxiv", + "doi": "10.1101/2023.06.12.544667", + "date": "2023-06-12", + "link": "https://biorxiv.org/cgi/content/short/2023.06.12.544667", + "title": "Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic", + "authors": "Katharine Sherratt; Anna C Carnegie; Adam Kucharski; Anne Cori; Carl AB Pearson; Christopher I Jarvis; Christopher Overton; Dale Weston; Edward M Hill; Edward Knock; Elizabeth Fearon; Emily Nightingale; Joel Hellewell; W John Edmunds; Julian Villabona Arenas; Kiesha Prem; Li Pi; Marc Baguelin; Michelle Kendall; Neil Ferguson; Nicholas Davies; Rosalind M Eggo; Sabine van Elsland; Timothy Russell; Sebastian Funk; Yang Liu; Sam Abbott", + "affiliations": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & South African DSI-NRF Centre of Excellence in Epide; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; All Hazards Intelligence, Data Analytics and Surveillance, UK Health Security Agency, UK & Department of Mathematical Sciences, University of Liverpool, UK & De; Emergency Response Department Science & Technology Behavioural Science, UK Health Security Agency, UK; Warwick Mathematics Institute and The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, UK & Joint UNIvers; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK; Institute for Global Health, University College London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & Saw Swee Hock School of Public Health, National Uni; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & MRC Centre for Global Infectious Disease Analysis, ; Warwick Mathematics Institute and The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & European Molecular Biology Laboratory, European Bio; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK", + "abstract": "The COVID-19 pandemic both relied and placed significant burdens on the experts involved from research and public health sectors. The sustained high pressure of a pandemic on responders, such as healthcare workers, can lead to lasting psychological impacts including acute stress disorder, post-traumatic stress disorder, burnout, and moral injury, which can impact individual wellbeing and productivity. As members of the infectious disease modelling community, we convened a reflective workshop to understand the professional and personal impacts of response work on our community and to propose recommendations for future epidemic responses. The attendees represented a range of career stages, institutions, and disciplines. This piece was collectively produced by those present at the session based on our collective experiences. Key issues we identified at the workshop were lack of institutional support, insecure contracts, unequal credit and recognition, and mental health impacts. Our recommendations include rewarding impactful work, fostering academia-public health collaboration, decreasing dependence on key individuals by developing teams, increasing transparency in decision-making, and implementing sustainable work practices. Despite limitations in representation, this workshop provided valuable insights into the UK COVID-19 modelling experience and guidance for future public health crises. Recognising and addressing the issues highlighted is crucial, in our view, for ensuring the effectiveness of epidemic response work in the future.", + "category": "scientific communication and education", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, + { + "site": "medRxiv", + "doi": "10.1101/2023.05.31.23290774", + "date": "2023-06-05", + "link": "https://medrxiv.org/cgi/content/short/2023.05.31.23290774", + "title": "POST-COVID ORTHOPAEDIC ELECTIVE RESOURCE PLANNING USING SIMULATION MODELLING", + "authors": "Alison Harper; Thomas Monks; Rebecca Wilson; Maria Theresa Redaniel; Emily Eyles; Timothy Jones; Chris Penfold; Andrew Elliott; Tim Keen; Martin Pitt; Ashley Blom; Michael Whitehouse; Andrew Judge", + "affiliations": "University of Exeter; University of Exeter; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; North Bristol NHS Foundation Trust; North Bristol NHS Foundation Trust; University of Exeter; University of Sheffield; University of Bristol; University of Bristol", + "abstract": "ObjectivesTo develop a simulation model to support orthopaedic elective capacity planning.\n\nMethodsAn open-source, generalisable discrete-event simulation was developed, including a web-based application. The model used anonymised patient records between 2016-2019 of elective orthopaedic procedures from an NHS Trust in England. In this paper, it is used to investigate scenarios including resourcing (beds and theatres) and productivity (lengths-of-stay, delayed discharges, theatre activity) to support planning for meeting new NHS targets aimed at reducing elective orthopaedic surgical backlogs in a proposed ring fenced orthopaedic surgical facility. The simulation is interactive and intended for use by health service planners and clinicians.\n\nResultsA higher number of beds (65-70) than the proposed number (40 beds) will be required if lengths-of-stay and delayed discharge rates remain unchanged. Reducing lengths-of-stay in line with national benchmarks reduces bed utilisation to an estimated 60%, allowing for additional theatre activity such as weekend working. Further, reducing the proportion of patients with a delayed discharge by 75% reduces bed utilisation to below 40%, even with weekend working. A range of other scenarios can also be investigated directly by NHS planners using the interactive web app.\n\nConclusionsThe simulation model is intended to support capacity planning of orthopaedic elective services by identifying a balance of capacity across theatres and beds and predicting the impact of productivity measures on capacity requirements. It is applicable beyond the study site and can be adapted for other specialties.\n\nStrengths and Limitations of this studyO_LIThe simulation model provides rapid quantitative estimates to support post-COVID elective services recovery toward medium-term elective targets.\nC_LIO_LIParameter combinations include changes to both resourcing and productivity.\nC_LIO_LIThe interactive web app enables intuitive parameter changes by users while underlying source code can be adapted or re-used for similar applications.\nC_LIO_LIPatient attributes such as complexity are not included in the model but are reflected in variables such as length-of-stay and delayed discharge rates.\nC_LIO_LITheatre schedules are simplified, incorporating the five key orthopaedic elective surgical procedures.\nC_LI", + "category": "orthopedics", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.05.23.23290354", @@ -699,20 +699,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.03.24.23287700", - "date": "2023-03-26", - "link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287700", - "title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", - "authors": "Jack D Wilkinson; Evangelia Demou; Mark Cherrie; Rhiannon Edge; Matthew Gittins; Srinivasa Vittal Katikireddi; Theocharis Kromydas; WIll Mueller; Neil Pearce; Martie van Tongeren; Sarah Rhodes", - "affiliations": "University of Manchester; University of Glasgow; Institute of Occupational Medicine; University of Lancaster; University of Manchester; University of Glasgow; University of Glasgow; Institute for Occupational Medicine; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester", - "abstract": "ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection.\n\nDesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups.\n\nSetting\n\nResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage.\n\nConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.", - "category": "occupational and environmental health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.03.24.23287666", @@ -1735,20 +1721,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.20.22275994", - "date": "2022-06-20", - "link": "https://medrxiv.org/cgi/content/short/2022.06.20.22275994", - "title": "Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies", - "authors": "Ruth C E Bowyer; Charlotte Huggins; Renin Toms; Richard John Shaw; Bo Hou; Ellen J Thompson; Alex Siu Fung Kwong; Dylan M Williams; Milla Kibble; George B Ploubidis; Nicholas J Timpson; Jonathan A C Sterne; Nishi Chaturvedi; Claire J Steves; Kate Tilling; Richard J Silverwood", - "affiliations": "King's College London; University of Edinburgh; University of Bristol; University of Glasgow; Bradford Institute for Health Research; King's College London; University of Bristol; UCL; King's College London; University College London; University of Bristol; University of Bristol; University College London; King's College London; University of Bristol; University College London", - "abstract": "Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.18.22276437", @@ -1777,6 +1749,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.06.16.22276479", + "date": "2022-06-16", + "link": "https://medrxiv.org/cgi/content/short/2022.06.16.22276479", + "title": "Mental health of healthcare workers in England during the COVID-19 pandemic: a longitudinal cohort study", + "authors": "Danielle Lamb; Rafael Gafoor; Hannah Scott; Ewan Carr; Sharon Stevelink; Rosalind Raine; Matthew Hotopf; Neil Greenberg; Siobhan Hegarty; Ira Madan; Paul Moran; Richard Morriss; Dominic Murphy; Anne Marie Rafferty; Scott Weich; Sarah Dorrington; Simon Wessely", + "affiliations": "UCL; University College London; King's College London; King's College London; King's College London; University College London; King's College London; King's College London; King's College London; Guy's and St Thomas' NHS Foundation Trust; University of Bristol; University of Nottingham; Combat Stress; King's College London; University of Sheffield; King's College London; King's College London", + "abstract": "ObjectiveTo examine variations in impact of the COVID-19 pandemic on the mental health of all types of healthcare workers (HCWs) in England over the first 17 months of the pandemic.\n\nMethodWe undertook a prospective cohort study of 22,501 HCWs from 18 English acute and mental health NHS Trusts, collecting online survey data on common mental disorders (CMDs), depression, anxiety, alcohol use, and PTSD, from April 2020 to August 2021. We analysed these data cross-sectionally by time period (corresponding to periods the NHS was under most pressure), and longitudinally. Data were weighted to better represent Trust population demographics.\n\nResultsThe proportion of those with probable CMDs was greater during periods when the NHS was under most pressure (measured by average monthly deaths). For example, 55% (95%CI 53%, 58%) of participants reported symptoms of CMDs in April-June 2020 versus 47% (95%CI 46%, 48%) July-October 2020. Contrary to expectation, there were no major differences between professional groups (i.e. clinical and non-clinical staff). Younger, female, lower paid staff, who felt poorly supported by colleagues/managers, and who experienced potentially morally injurious events were most at risk of negative mental health outcomes.\n\nConclusionAmong HCWs, the prevalence of probable CMDs increased during periods of escalating pressure on the NHS, suggesting staff support should be increased at such points in the future, and staff should be better prepared for such situations via training. All staff, regardless of role, experienced poorer mental health during these periods, suggesting that support should be provided for all staff groups.\n\nKey messagesO_ST_ABSWhat is already known on this topicC_ST_ABSExisting evidence about the mental health of healthcare workers (HCWs) through the COVID-19 pandemic comes mainly from cross-sectional studies using unrepresentative convenience samples, typically focussing on clinical staff rather than all HCWs. Such studies show high prevalence of symptoms of mental disorders, but the strength of this evidence is uncertain.\n\nWhat this study addsUsing a defined sampling frame, with longitudinal, weighted data, we show that during periods of greater pressure on the NHS (as indicated by average monthly national COVID-19 death rates), prevalence of mental disorder symptoms increased, and, importantly, that this effect was seen in non-clinical as well as clinical staff.\n\nHow this study might affect research, practice or policyThese findings indicate that provision of support for HCWs should not only focus on those providing clinical care, but also on non-clinical staff such as porters, cleaners, and administrative staff, and additional support should be provided during higher pressure periods. Better preparation of staff for such situations is also suggested.", + "category": "psychiatry and clinical psychology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.06.16.22276487", @@ -1945,6 +1931,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.05.23.22275458", + "date": "2022-05-25", + "link": "https://medrxiv.org/cgi/content/short/2022.05.23.22275458", + "title": "Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States", + "authors": "Seth Flaxman; Charles Whittaker; Elizaveta Semenova; Theo Rashid; Robbie Parks; Alexandra Blenkinsop; H Juliette T Unwin; Swapnil Mishra; Samir Bhatt; Deepti Gurdasani; Oliver Ratmann", + "affiliations": "Oxford; Imperial College London; AstraZeneca; Imperial College London; Columbia University; Imperial College London; Imperial College London; University of Copenhagen; University of Copenhagen, Imperial College London; Queen Mary University of London; Imperial College London", + "abstract": "Covid-19 has caused more than 1 million deaths in the US, including at least 1,204 deaths among children and young people (CYP) aged 0-19 years, with 796 occurring in the one year period April 1, 2021 - March 31, 2022. Deaths among US CYP are rare in general, and so we argue here that the mortality burden of Covid-19 in CYP is best understood in the context of all other causes of CYP death. Using publicly available data from CDC WONDER on NCHSs 113 Selected Causes of Death, and comparing to mortality in 2019, the immediate pre-pandemic period, we find that Covid-19 mortality is among the 10 leading causes of death in CYP aged 0-19 years in the US, ranking 8th among all causes of deaths, 5th in disease-related causes of deaths (excluding accidents, assault and suicide), and 1st in deaths caused by infectious or respiratory diseases. Covid-19 deaths constitute 2.3% of the 10 leading causes of death in this age group. Covid-19 caused substantially more deaths in CYP than major vaccine-preventable diseases did historically in the period before vaccines became available. Various factors including underreporting and Covid-19s role as a contributing cause of death from other diseases mean that our estimates may understate the true mortality burden of Covid-19. Our findings underscore the public health relevance of Covid-19 to CYP. In the likely future context of sustained SARS-CoV-2 circulation, pharmaceutical and non-pharmaceutical interventions will continue to play an important role in limiting transmission of the virus in CYP and mitigating severe disease.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.05.22.22275417", @@ -1959,20 +1959,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.05.21.22275368", - "date": "2022-05-23", - "link": "https://medrxiv.org/cgi/content/short/2022.05.21.22275368", - "title": "Variant-specific symptoms of COVID-19 among 1,542,510 people in England", - "authors": "Matthew Whitaker; Joshua Elliott; Barbara Bodinier; Wendy S Barclay; Helen Ward; Graham Cooke; Christl A Donnelly; Marc Chadeau-Hyam; Paul Elliott", - "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health", - "abstract": "Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 96, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.05.19.22275214", @@ -2001,20 +1987,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.05.09.22274769", - "date": "2022-05-11", - "link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274769", - "title": "COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from the Born In Wales study", - "authors": "Mohamed Mhereeg; Hope Jones; Jonathan Kennedy; Michael Seaborne; Michael Parker; Natasha Kennedy; Sarah Beeson; Luisa Zuccolo; Alisha Davies; Sinead Brophy", - "affiliations": "Swansea University Medical School, Swansea, Wales, UK; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Swansea University Medical School, Swansea, Wales, UK.; Bristol Medical School, University of Bristol, Bristol, England, UK.; Public Health Wales, UK; Swansea University Medical School, Swansea, Wales, UK", - "abstract": "BackgroundVaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics.\n\nObjectivesThe aims of this study were to 1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health records (EHR) linkage, and 2) explore pregnant womens views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born in Wales Cohort).\n\nDesignA mixed methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) (Objective 1) and the Born In Wales Birth Cohort participants (Objective 2). SAIL combines data from general practice, hospital admissions, the national community child health dataset, maternal indicators dataset, and COVID-19 vaccination databases.\n\nSetting and participantsObjective 1) All women documented as being pregnant on or after 13th April 2021, aged 18 years or older, and eligible for COVID-19 vaccination were identified in routine health care. They were linked to the vaccination data up to and including 31st December 2021. Objective 2) Separately, a cross-section of pregnant women in Wales were invited to complete an online survey via social media advertising. The survey asked what their views were on having the COVID-19 vaccination during pregnancy, and if they had already received, or intended to receive, the COVID-19 vaccination during their pregnancies. They were also asked to give reasons for their decisions.\n\nOutcomes1 (a). Rate of vaccination uptake per month during pregnancy among women eligible for vaccination. 1 (b). Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnicity, and deprivation area was examined using hazard ratios (HR) from Cox regression. 2.Expectant mothers views of the COVID-19 vaccination during pregnancy.\n\nResults\n\nPopulation-level data linkage (objective 1)Within the population cohort, 32.7% (n = 8,203) were vaccinated (at least one dose of the vaccine) during pregnancy, 34.1% (n = 8,572) remained unvaccinated throughout follow-up period, and 33.2% (n = 8,336) received the vaccine postpartum. Younger women (<30 years) were less likely to have the vaccine and those living in areas of high deprivation were also less likely to have the vaccine (HR=0.88, 95% CI 0.82 to 0.95). Asian and other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared to women of White ethnicity (HR=1.12, 95% CI 1.00 to 1.25) and (HR=1.18, 95% CI 1.03 to 1.37) respectively.\n\nSurvey responses (objective 2)69% of participants stated that they would be happy to have the vaccine during pregnancy (n = 207). The remainder, 31%, indicated that they would not have the vaccine during pregnancy (n = 94). Reasons for having the vaccine related to protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy.\n\nConclusionPotentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and to decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation level areas.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "bioRxiv", "doi": "10.1101/2022.05.07.491004", @@ -2239,20 +2211,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.04.14.22272888", - "date": "2022-04-14", - "link": "https://medrxiv.org/cgi/content/short/2022.04.14.22272888", - "title": "Anti-inflammatory therapy with nebulised dornase alfa in patients with severe COVID-19 pneumonia", - "authors": "Joanna Porter; Jamie Inshaw; Vincente Joel Solis; Emma Denneny; Rebecca Evans; Mia I. Temkin; Nathalia De Vasconcelos; Iker Valle Aramburu; Dennis Hoving; Donna Basire; Tracey Crissell; Jesusa Guinto; Alison Webb; Hanif Esmail; Victoria Johnston; Anna Last; Thomas Rampling; Elisa Theresa Helbig; Lena Lippert; Florian Kurth; Bryan Williams; Aiden Flynn; Pauline Lukey; Veronique Birault; Venizelos Papayannopoulos", - "affiliations": "UCL Respiratory, University College London, UK; Exploristics, Belfast, N. Ireland; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; UCL Respiratory, University College London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Exploristics, Belfast, N. Ireland; Target to Treatment Consulting Ltd, Stevenage, UK; Translation, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK", - "abstract": "BackgroundCell-free (cf)-DNA, from cellular sources, including Neutrophil Extracellular Traps (NETs), is found in the circulation of COVID-19 patients and may contribute to immune dysregulation. This study determined whether pulmonary administration of the endonuclease, dornase alfa, reduced systemic inflammation by degrading local and systemic cf-DNA.\n\nMethodsEligible patients were randomized (3:1) to receive twice-daily nebulised dornase alfa in addition to best available care (BAC) or BAC alone for seven days or until discharge. A 2:1 ratio of matched contemporary controls (CC-BAC) provided additional comparators. The primary endpoint was improvement in C-reactive protein (CRP) over time, analysed using a repeated-measures mixed model, adjusted for baseline factors.\n\nResultsBetween June 2020-October 2021 we recruited 39 evaluable patients: 30 randomised to dornase alfa (R-BAC+DA); 9 randomised to BAC (R-BAC); with the addition of 60 CC-BAC participants. Dornase alfa was well tolerated and reduced CRP by 33% compared to combined BAC groups (T-BAC). Least squares (LS) mean post-dexamethasone CRP fell from 101.9mg/L to 23.23 mg/L in the BAC+ dornase alfa group versus a fall from 99.5mg/L to 34.82 mg/L in the T-BAC group at 7 days; P=0.01. This effect of dornase alfa on CRP was confirmed with subgroup and sensitivity analyses that mitigated potential biases associated with the use of the CC-BAC group. Dornase alfa increased the chance of live discharge by 63% (HR 1.63, 95% CI 1.01 to 2.61, P=0.03), increased lymphocyte counts (LS mean: 1.08 vs 0.87, P=0.02) and reduced circulating cf-DNA and the coagulopathy marker D-dimer (LS mean: 570.78 vs 1656.96 g/mL, P=0.004).\n\nConclusionWe provide proof-of-concept evidence that dornase alfa reduces pathogenic inflammation in hospitalised patients with COVID-19 pneumonia, suggesting that best available care can be improved by the inclusion of anti-inflammatory treatments that target damage-associated molecules.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.04.12.22273752", @@ -2897,20 +2855,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.01.16.22269146", - "date": "2022-01-17", - "link": "https://medrxiv.org/cgi/content/short/2022.01.16.22269146", - "title": "Development and validation of the Symptom Burden Questionnaire\u2122 for Long COVID: a Rasch analysis", - "authors": "Sarah E Hughes; Shamil Haroon; Anuradhaa Subramanian; Christel McMullan; Olalekan L Aiyegbusi; Grace M Turner; Louise Jackson; Elin Haf Davies; Chris Frost; Gary McNamara; Gary Price; Karen Matthews; Jennifer Camaradou; Jane Ormerod; Anita Walker; Melanie J Calvert", - "affiliations": "University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito Limited; Aparito Limited; Aparito Limited; University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham; University of Birmingham; University of BIrmingham", - "abstract": "ObjectiveTo describe the development and initial validation of a novel patient-reported outcome measure of Long COVID symptom burden, the Symptom-Burden Questionnaire for Long COVID (SBQ-LC).\n\nMethod and FindingsThis multi-phase, prospective mixed-methods study took place between April and August 2021 in the United Kingdom (UK). A conceptual framework and initial item pool were developed from published systematic reviews. Further concept elicitation and content validation was undertaken with adults with lived experience (n = 13) and clinicians (n = 10), and face validity was confirmed by the Therapies for Long COVID Study Patient and Public Involvement group (n = 25). The draft SBQ-LC was field tested by adults with self-reported Long COVID recruited via social media and international Long COVID support groups (n = 274). Thematic analysis of interview and survey transcripts established content validity and informed construction of the draft questionnaire. Rasch analysis of field test data guided item and scale refinement and provided evidence of the final SBQ-LCs measurement properties. The Rasch-derived SBQ-LC is composed of 17 independent scales with promising psychometric properties. Respondents rate symptom burden during the past 7-days using a dichotomous response or 4-point rating scale. Each scale provides coverage of a different symptom domain and returns a summed raw score that may be converted to a linear (0 - 100) score. Higher scores represent higher symptom burden.\n\nConclusionsThe SBQ-LC is a comprehensive patient-reported assessment of Long COVID symptom burden developed using modern psychometric methods. It measures symptoms of Long COVID important to individuals with lived experience and may be used to evaluate the impact of interventions and inform best practice in clinical management.", - "category": "health informatics", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.01.13.22268948", @@ -3149,6 +3093,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.14.21267806", + "date": "2021-12-16", + "link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267806", + "title": "REACT-1 round 15 final report: Increased breakthrough SARS-CoV-2 infections among adults who had received two doses of vaccine, but booster doses and first doses in children are providing important protection", + "authors": "Marc Chadeau-Hyam; Oliver Eales; Barbara Bodinier; Haowei Wang; David Haw; Matthew Whitaker; Caroline E. Walters; Jakob Jonnerby; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Deborah Ashby; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Christl A Donnelly; Paul Elliott", + "affiliations": "School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research", + "abstract": "BackgroundIt has been nearly a year since the first vaccinations against SARS-CoV-2 were delivered in England. The third wave of COVID-19 in England began in May 2021 as the Delta variant began to outcompete and largely replace other strains. The REal-time Assessment of Community Transmission-1 (REACT-1) series of community surveys for SARS-CoV-2 infection has provided insights into transmission dynamics since May 2020. Round 15 of the REACT-1 study was carried out from 19 October to 5 November 2021.\n\nMethodsWe estimated prevalence of SARS-CoV2 infection and used multiple logistic regression to analyse associations between SARS-CoV-2 infection in England and demographic and other risk factors, based on RT-PCR results from self-administered throat and nose swabs in over 100,000 participants. We estimated (single-dose) vaccine effectiveness among children aged 12 to 17 years, and among adults compared swab-positivity in people who had received a third (booster) dose with those who had received two vaccine doses. We used splines to analyse time trends in swab-positivity.\n\nResultsDuring mid-October to early-November 2021, weighted prevalence was 1.57% (1.48%, 1.66%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). Weighted prevalence increased between rounds 14 and 15 across most age groups (including older ages, 65 years and over) and regions, with average reproduction number across rounds of R=1.09 (1.08, 1.11). During round 15, there was a fall in prevalence from a maximum around 20-21 October, with an R of 0.76 (0.70, 0.83), reflecting falls in prevalence at ages 17 years and below and 18 to 54 years. School-aged children had the highest weighted prevalence of infection: 4.95% (4.39%, 5.58%) in those aged 5 to 12 years and 5.21% (4.61%, 5.87%) in those aged 13 to 17 years. In multiple logistic regression, age, sex, key worker status and presence of one or more children in the home were associated with swab positivity. There was evidence of heterogeneity between rounds in swab positivity rates among vaccinated individuals at ages 18 to 64 years, and differences in key demographic and other variables between vaccinated and unvaccinated adults at these ages. Vaccine effectiveness against infection in children was estimated to be 56.2% (41.3%, 67.4%) in rounds 13, 14 and 15 combined, adjusted for demographic factors, with a similar estimate obtained for round 15 only. Among adults we found that those who received a third dose of vaccine were less likely to test positive compared to those who received only two vaccine doses, with adjusted odds ratio (OR) =0.38 (0.26, 0.55).\n\nDiscussionSwab-positivity was very high at the start of round 15, reaching a maximum around 20 to 21 October 2021, and then falling through late October with an uncertain trend in the last few days of data collection. The observational nature of survey data and the relatively small proportion of unvaccinated adults call into question the comparability of vaccinated and unvaccinated groups at this relatively late stage in the vaccination programme. However, third vaccine doses for eligible adults and the vaccination of children aged 12 years and over are associated with lower infection risk and, thus, remain a high priority (with possible extension to children aged 5-12 years). These should help reduce SARS-CoV-2 transmission during the winter period when healthcare demands typically rise.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.16.21267906", @@ -4019,13 +3977,13 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.09.02.21262965", - "date": "2021-09-02", - "link": "https://medrxiv.org/cgi/content/short/2021.09.02.21262965", - "title": "Whole genome sequencing identifies multiple loci for critical illness caused by COVID-19", - "authors": "Athanasios Kousathanas; Erola Pairo-Castineira; Konrad Rawlik; Alex Stuckey; Christopher A Odhams; Susan Walker; Clark D Russell; Tomas Malinauskas; Jonathan Millar; Katherine S Elliott; Fiona Griffiths; Wilna Oosthuyzen; Kirstie Morrice; Sean Keating; Bo Wang; Daniel Rhodes; Lucija Klaric; Marie Zechner; Nick Parkinson; Andrew D. Bretherick; Afshan Siddiq; Peter Goddard; Sally Donovan; David Maslove; Alistair Nichol; Malcolm G Semple; Tala Zainy; Fiona Maleady-Crowe; Linda Todd; Shahla Salehi; Julian Knight; Greg Elgar; Georgia Chan; Prabhu Arumugam; Tom A Fowler; Augusto Rendon; Manu Shankar-Hari; Charlotte Summers; Charles Hinds; Peter Horby; Danny McAuley; Hugh Montgomery; Peter J.M. Openshaw; Yang Wu; Jian Yang; Paul Elliott; Timothy Walsh; - GenoMICC Investigators; - 23andMe Investigators; - Covid-19 Human Genetics Initiative; Angie Fawkes; Lee Murphy; Kathy Rowan; Chris P Ponting; Veronique Vitart; James F Wilson; Richard H Scott; Sara Clohisey; Loukas Moutsianas; Andy Law; Mark J Caulfield; J. Kenneth Baillie", - "affiliations": "Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, ON, Canada.; Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland.; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, L; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Genomics England, London UK; Department of Intensive Care Medicine, Guy's and St. Thomas NHS Foundation Trust, London, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK; UCL Centre for Human Health and Performance, London, W1T 7HA, UK.; National Heart and Lung Institute, Imperial College London, London, UK; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Imperial College, London; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; ; ; ; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Intensive Care National Audit & Research Centre, London, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England, London UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK", - "abstract": "Critical illness in COVID-19 is caused by inflammatory lung injury, mediated by the host immune system. We and others have shown that host genetic variation influences the development of illness requiring critical care1 or hospitalisation2;3;4 following SARS-Co-V2 infection. The GenOMICC (Genetics of Mortality in Critical Care) study recruits critically-ill cases and compares their genomes with population controls in order to find underlying disease mechanisms.\n\nHere, we use whole genome sequencing and statistical fine mapping in 7,491 critically-ill cases compared with 48,400 population controls to discover and replicate 22 independent variants that significantly predispose to life-threatening COVID-19. We identify 15 new independent associations with critical COVID-19, including variants within genes involved in interferon signalling (IL10RB, PLSCR1), leucocyte differentiation (BCL11A), and blood type antigen secretor status (FUT2). Using transcriptome-wide association and colocalisation to infer the effect of gene expression on disease severity, we find evidence implicating expression of multiple genes, including reduced expression of a membrane flippase (ATP11A), and increased mucin expression (MUC1), in critical disease.\n\nWe show that comparison between critically-ill cases and population controls is highly efficient for genetic association analysis and enables detection of therapeutically-relevant mechanisms of disease. Therapeutic predictions arising from these findings require testing in clinical trials.", + "doi": "10.1101/2021.08.26.21262523", + "date": "2021-08-28", + "link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262523", + "title": "Association between tocilizumab, sarilumab and all-cause mortality at 28 days in hospitalized patients with COVID-19: A network meta-analysis", + "authors": "Peter J Godolphin; David J Fisher; Lindsay R Berry; Lennie PG Derde; Janet V Diaz; Anthony C Gordon; Elizabeth Lorenzi; John C Marshall; Srinivas Murthy; Manu Shankar-Hari; Jonathan AC Sterne; Jayne F Tierney; Claire L Vale", + "affiliations": "University College London; University College London; Berry Consultants; University Medical Center Utrecht; World Health Organization; Imperial College London; Berry Consultants; University of Toronto; University of British Columbia; King's College London; University of Bristol; University College London; University College London", + "abstract": "ObjectiveTo estimate pairwise associations between administration of tocilizumab, sarilumab and usual care or placebo with 28-day mortality, in COVID-19 patients receiving concomitant corticosteroids and non-invasive or mechanical ventilation, based on all available direct and indirect evidence.\n\nMethodsEligible trials randomized hospitalized patients with COVID-19 that compared either interleukin-6 receptor antagonist with usual care or placebo in a recent prospective meta-analysis (27 trials, 10930 patients) or that directly compared tocilizumab with sarilumab. Data were restricted to patients receiving corticosteroids and either non-invasive or invasive ventilation at randomization.\n\nPairwise associations between tocilizumab, sarilumab and usual care or placebo for all-cause mortality 28 days after randomization were estimated using a frequentist contrast-based network meta-analysis of odds ratios (ORs), implementing multivariate fixed-effects models that assume consistency between the direct and indirect evidence.\n\nResultsOne trial (REMAP-CAP) was identified that directly compared tocilizumab with sarilumab and supplied results on all-cause mortality at 28-days. This network meta-analysis was based on 898 eligible patients (278 deaths) from REMAP-CAP and 3710 eligible patients from 18 trials (1278 deaths) from the prospective meta-analysis. Summary ORs were similar for tocilizumab [0.82 [0.71-0.95, P=0.008]] and sarilumab [0.80 [0.61-1.04, P=0.09]] compared with usual care or placebo. The summary OR for 28-day mortality comparing tocilizumab with sarilumab was 1.03 [95%CI 0.81-1.32, P=0.80]. The P value for the global test for inconsistency was 0.28.\n\nConclusionAdministration of either tocilizumab or sarilumab was associated with lower 28-day all-cause mortality compared with usual care or placebo. The association is not dependent on the choice of interleukin-6 receptor antagonist.", "category": "intensive care and critical care medicine", "match_type": "fuzzy", "author_similarity": 100, @@ -4185,6 +4143,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.08.05.21259863", + "date": "2021-08-07", + "link": "https://medrxiv.org/cgi/content/short/2021.08.05.21259863", + "title": "Recording of 'COVID-19 vaccine declined' among vaccination priority groups: a cohort study on 57.9 million NHS patients' primary care records in situ using OpenSAFELY", + "authors": "Helen J Curtis; Peter Inglesby; Brian MacKenna; Richard Croker; William J Hulme; Christopher T Rentsch; Krishnan Bhaskaran; Alex J Walker; Caroline E Morton; David Evans; Amir Mehrkar; Sebastian CJ Bacon; Christopher Bates; George Hickman; Tom Ward; Jessica Morley; Jonathan Cockburn; Simon Davy; Anna Schultze; Elizabeth J Williamson; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; John Tazare; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Ben Goldacre", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", + "abstract": "BackgroundAll patients in England within vaccine priority groups were offered a COVID-19 vaccine by mid-April 2021. Clinical record systems contain codes to denote when such an offer has been declined by a patient (although these can in some cases be entered for a variety of other reasons including vaccination delay, or other administrative issues). We set out to describe the patterns of usage of codes for COVID-19 vaccines being declined.\n\nMethodsWith the approval of NHS England and using the full pseudonymised primary care records for 57.9 million NHS patients, we identified all patients in key vaccine priority groups: aged over 50, or over 16 and at increased risk from COVID-19 (Clinically Extremely Vulnerable [CEV] or otherwise \"at risk\"). We describe the proportion of patients recorded as declining a COVID-19 vaccination for each priority group, and by other clinical and demographic factors; whether patients recorded as \"declined\" subsequently went on to receive a vaccination; and the distribution of code usage across GP practices.\n\nResultsOf 24.5 million patients in priority groups as of May 25th 2021, 89.2% had received a vaccine, 8.8% had neither a vaccination nor a decline recorded, and 663,033 (2.7%) had a decline code recorded. Of patients with a recorded decline, 125,587 (18.9%) were subsequently vaccinated. Subsequent vaccination was slightly more common in the South Asian population than other ethnicities (e.g. 32.3% vs 22.8%, over 65s). The proportion of declining-unvaccinated patients varied strongly with ethnicity (Black 15.3%, South Asian 5.6%, White 1.5% in over 80s); and was higher in patients from more deprived areas. COVID-19 vaccine decline codes were present in almost all practices (98.8%), but with wide variation between practices in rates of usage. Among all priority groups, declining-unvaccinated status was most common in CEV (3.3%).\n\nConclusionsClinical codes indicative of COVID-19 vaccinations being declined are widely used in English general practice. They are substantially more common among Black and South Asian patients, and patients from more deprived areas. There is a need for more detailed survey and/or qualitative research with patients and clinicians to determine the most common reasons for these recorded declines.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.07.29.21261190", @@ -4703,6 +4675,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.06.21.449178", + "date": "2021-06-21", + "link": "https://biorxiv.org/cgi/content/short/2021.06.21.449178", + "title": "Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune pathways related to tissue injury", + "authors": "Amy R Cross; Carlos de Andrea; Maria Villalba-Esparza; Manuel Landecho Acha; Lucia Cerundolo; Praveen Weeratunga; Rachel Etherington; Laura Denney; Graham Ogg; Ling-Pei Ho; Ian Roberts; Joanna Hester; Paul Klenerman; Ignacio Melero; Stephen Sansom; Fadi Issa", + "affiliations": "University of Oxford; Universidad de Navarra; Department of Pathology, Clinica de la Universidad de Navarra, Pamplona, Spain; Clinica Universidad de Navarra; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Universidad de Navarra; University of Oxford; University of Oxford", + "abstract": "Severe lung damage in COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways and genes present across the spectrum of histopathological damage in COVID-19 lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from areas of interest within well preserved post-mortem lung samples from three patients. Despite substantial inter-patient heterogeneity we discovered evidence for a common immune cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines including CXCL9, CXCL10 and CXCL11 which are known to promote the recruitment of CXCR3+ immune cells. The tumour necrosis factor (TNF) superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were found to be consistently upregulated in the areas with severe tissue damage. We used published spatial and single cell SARS-CoV-2 datasets to confirm our findings in the lung tissue from additional cohorts of COVID-19 patients. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies.\n\nOne Sentence SummarySpatial analysis identifies IFN{gamma} response signatures as focal to severe alveolar damage in COVID-19 pneumonitis.", + "category": "immunology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.06.17.21259100", @@ -4857,20 +4843,6 @@ "author_similarity": 100, "affiliation_similarity": 92 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.06.08.21258531", - "date": "2021-06-08", - "link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258531", - "title": "The UK Coronavirus Job Retention Scheme and changes in diet, physical activity and sleep during the COVID-19 pandemic: Evidence from eight longitudinal studies", - "authors": "Bozena Wielgoszewska; Jane Maddock; Michael J Green; Giorgio Di Gessa; Sam Parsons; Gareth J Griffith; Jazz Croft; Anna J Stevenson; Charlotte Booth; Richard J Silverwood; David Bann; Praveetha Patalay; Alun D Hughes; Nishi Chaturvedi; Laura D Howe; Emla Fitzsimons; Srinivasa Vittal Katikireddi; George B Ploubidis", - "affiliations": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Institute of Epidemiology and Health Care, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; UCL; MRC Unit for Lifelong Health and Ageing, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London", - "abstract": "BackgroundIn March 2020 the UK implemented the Coronavirus Job Retention Scheme (furlough) to minimize job losses. Our aim was to investigate associations between furlough and diet, physical activity, and sleep during the early stages of the COVID-19 pandemic.\n\nMethodsWe analysed data from 25,092 participants aged 16 to 66 years from eight UK longitudinal studies. Changes in employment (including being furloughed) were defined by comparing employment status pre- and during the first lockdown. Health behaviours included fruit and vegetable consumption, physical activity, and sleeping patterns. Study-specific estimates obtained using modified Poisson regression, adjusting for socio-demographic characteristics and pre-pandemic health and health behaviours, were statistically pooled using random effects meta-analysis. Associations were also stratified by sex, age, and education.\n\nResultsAcross studies, between 8 and 25% of participants were furloughed. Compared to those who remained working, furloughed workers were slightly less likely to be physically inactive (RR:0.85, [0.75-0.97], I2=59%) and did not differ in diet and sleep behaviours, although findings for sleep were heterogenous (I2=85%). In stratified analyses, furlough was associated with low fruit and vegetable consumption among males (RR=1.11; 95%CI: 1.01-1.22; I2: 0%) but not females (RR=0.84; 95%CI: 0.68-1.04; I2: 65%). Considering change in these health behaviours, furloughed workers were more likely than those who remained working to report increased fruit and vegetable consumption, exercise, and hours of sleep.\n\nConclusionsThose furloughed exhibited broadly similar levels of health behaviours to those who remained in employment during the initial stages of the pandemic. There was little evidence to suggest that such social protection policies if used in the post-pandemic recovery period and during future economic crises would have adverse impacts on population health behaviours.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.06.08.21258132", @@ -4983,20 +4955,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.18.21257396", - "date": "2021-05-23", - "link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257396", - "title": "A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program", - "authors": "Anurag Verma; Noah L. Tsao; Lauren O. Thomann; Yuk-Lam Ho; Sudha K. Iyengar; Shiuh-Wen Luoh; Rotonya Carr; Dana C. Crawford; Jimmy T. Efird; Giulio Genovese; Adriana Hung; Kerry L. Ivey; Michael G. Levin; Julie Lynch; Pradeep Natarajan; Saiju Pyarajan; Alexander Bick; Lauren Costa; Giulio Genovese; Richard Hauger; Ravi Madduri; Gita A. Pathak; Renato Polimanti; Benjamin F. Voight; Marijana Vujkovic; Maryam Zekavat; Hongyu Zhao; Marylyn Ritchie; Kyong-Mi Chang; Kelly Cho; Juan P Casas; Philip S Tsao; J. Michael Gaziano; Christopher O?Donnell; Scott M. Damrauer; Katherine P. Liao", - "affiliations": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Departments of Population and Quantitative Health Sciences, Ophthalmology and Visual Sciences and Genetics and Genome Sciences, Case Western Reserve University,; VA Portland Health Care System, Portland OR, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA; Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, USA.; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Tennessee Valley Healthcare System (Nashville VA) , Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, USA.; Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.; VA Boston Healthcare System, Boston, Massachusetts, USA;Harvard Medical School, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA;Vanderbilt University, Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Department of Psychiatry, University of California, San Diego, La Jolla, CA; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, ; University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, USA;Data Science and Learning Division, Arg; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; VA Boston Healthcare System, Boston, Massachusetts, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Palo Alto Health Care System, Palo Alto, California, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts", - "abstract": "The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n=35) or hospitalization (n=42) due to severe COVID-19 using genome-wide association summary from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828= 53 and nrs505922=59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p=1.32 x 10-199), and thrombosis ORrs505922 1.33, p=2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p=4.12 x 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p=2.26x 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p=6.48 x10-23, lupus OR 0.84, p=3.97 x 10-06. PheWAS stratified by genetic ancestry demonstrated differences in genotype-phenotype associations across ancestry. LMNA (rs581342) associated with neutropenia OR 1.29 p=4.1 x 10-13 among Veterans of African ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.", - "category": "genetic and genomic medicine", - "match_type": "fuzzy", - "author_similarity": 91, - "affiliation_similarity": 92 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.13.21257161", @@ -5095,20 +5053,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.17.21257223", - "date": "2021-05-17", - "link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257223", - "title": "Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).", - "authors": "Cyril Roman Geismar; Ellen Fragaszy; Vincent Grigori Nguyen; Wing Lam Erica Fong; Madhumita Shrotri; Sarah Beale; Alison Rodger; Vasileios Lampos; Thomas Edward Byrne; Jana Kovar; Annalan Navaratnam; Parth Patel; Robert W Aldridge; Andrew Hayward; - Virus Watch Collaborative", - "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", - "abstract": "IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant.\n\nMethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks.\n\nResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)).\n\nConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.13.21257146", @@ -5935,6 +5879,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.04.21252921", + "date": "2021-03-08", + "link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252921", + "title": "A systematic review and meta-analysis of longitudinal cohort studies comparing mental health before versus during the COVID-19 pandemic", + "authors": "Eric Robinson; Angelina R Sutin; Michael Daly; Andrew Jones", + "affiliations": "University of Liverpool; Florida State University; Maynooth University; University of Liverpool", + "abstract": "BackgroundIncreases in mental health problems have been observed in some studies during the COVID-19 pandemic. It is unclear whether changes have been large and experienced by most population sub-groups, persisted over time or been symptom specific.\n\nMethodsWe systematically reviewed and meta-analysed longitudinal cohort studies that examined changes in mental health among the same group of participants before and during the pandemic (PROSPERO: CRD42021231256). Searches for published and unpublished studies were conducted in January 2021. Changes in mental health (standardised mean change; SMC) were examined using meta-analyses.\n\nFindingsSixty-five studies were included. There was an overall increase in mental health symptoms that was most pronounced during March-April 2020 (SMC = .102 [95% CI: .026 to .192], p = 0.03) before significantly declining over time (May-July SMC = .067 [95% CI: -.022 to .157], p = .141). Compared to measures of anxiety (SMC = 0.13, p = 0.02) and general mental health (SMC = -.03, p = 0.65), increases in depression and mood disorder symptoms tended to be larger (SMC = 0.22, p < .001) and reductions over time appeared less pronounced. Increased mental health symptoms were observed across most population subgroups examined but there was no evidence of any change in symptoms among samples with a pre-existing mental health condition.\n\nInterpretationThere was a small increase in mental health symptoms soon after the outbreak of the COVID-19 pandemic that decreased and was comparable to pre-pandemic levels by mid-2020 among most population sub-groups and symptom types.\n\nFundingN/A\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThere have been reported increases in mental health problems during the outbreak of the COVID-19 pandemic. However, it is unclear whether changes in mental health problems have been symptom specific, how changes have differed across populations and whether increased mental health problems have persisted over time. We systematically reviewed and meta-analysed longitudinal cohort studies that examined mental health among the same participants prior to and during the pandemic in 2020. This approach allowed us to quantify the mental health burden associated with the outbreak of the pandemic and how it has changed over time. We searched Pubmed, SCOPUS, Web of Science and PsychInfo from January 2020 to January 11, 2021 and identified eligible unpublished articles available on pre-print servers.\n\nAdded value of this studyWe identified 65 eligible articles that reported 201 comparisons of mental health pre vs. post pandemic outbreak. Meta-analysis indicated that longitudinal cohort studies that examined mental health prior to and during the COVID-19 pandemic in 2020 showed a significant but statistically small increase in mental health symptoms. The overall increase in mental health symptoms was most pronounced during the early stages of the pandemic (March-April), before decreasing and being generally comparable to pre-pandemic levels by mid-2020.\n\nCompared to anxiety and general measures of mental health functioning, increases tended to be larger in depressive symptoms and although statistically small, remained elevated past the early stages of the pandemic. Increases in mental health symptoms were observed across most population sub-groups, but there was no evidence of a change in mental health symptoms among samples of participants with a pre-existing mental health condition.\n\nImplications of all the available evidenceFindings confirm that the initial outbreak of the pandemic was associated with a significant but statistically small increase in mental health symptoms. Given that small effects may have meaningful cumulative consequences at the population level, there is a need for continued mental health provision and monitoring particularly during periods of the pandemic when infection rates and deaths are high. Further into the pandemic, mental health problems decreased significantly, which indicated recovery and resilience in overall mental health. Contrary to predictions made early in the pandemic, there was also no evidence of a worsening of mental health symptoms among samples of participants with a pre-existing mental health condition. Overall the results of the present analyses suggest that the pandemic may not have caused an unprecedented and long lasting mental health crisis, instead there appears to have been resilience in mental health.", + "category": "psychiatry and clinical psychology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.04.21252918", @@ -5991,6 +5949,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.03.21252856", + "date": "2021-03-06", + "link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252856", + "title": "REACT-1 round 9 final report: Continued but slowing decline of prevalence of SARS-CoV-2 during national lockdown in England in February 2021", + "authors": "Steven Riley; Caroline E. Walters; Haowei Wang; Oliver Eales; David Haw; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", + "affiliations": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear", + "abstract": "BackgroundEngland will start to exit its third national lockdown in response to the COVID-19 pandemic on 8th March 2021, with safe effective vaccines being rolled out rapidly against a background of emerging transmissible and immunologically novel variants of SARS-CoV-2. A subsequent increase in community prevalence of infection could delay further relaxation of lockdown if vaccine uptake and efficacy are not sufficiently high to prevent increased pressure on healthcare services.\n\nMethodsThe PCR self-swab arm of the REal-time Assessment of Community Transmission Study (REACT-1) estimates community prevalence of SARS-CoV-2 infection in England based on random cross-sections of the population ages five and over. Here, we present results from the complete round 9 of REACT-1 comprising round 9a in which swabs were collected from 4th to 12th February 2021 and round 9b from 13th to 23rd February 2021. We also compare the results of REACT-1 round 9 to round 8, in which swabs were collected mainly from 6th January to 22nd January 2021.\n\nResultsOut of 165,456 results for round 9 overall, 689 were positive. Overall weighted prevalence of infection in the community in England was 0.49% (0.44%, 0.55%), representing a fall of over two thirds from round 8. However the rate of decline of the epidemic has slowed from 15 (13, 17) days, estimated for the period from the end of round 8 to the start of round 9, to 31 days estimated using data from round 9 alone (lower confidence limit 17 days). When comparing round 9a to 9b there were apparent falls in four regions, no apparent change in one region and apparent rises in four regions, including London where there was a suggestion of sub-regional heterogeneity in growth and decline. Smoothed prevalence maps suggest large contiguous areas of growth and decline that do not align with administrative regions.\n\nPrevalence fell by 50% or more across all age groups in round 9 compared to round 8, with prevalence (round 9) ranging from 0.21% in those aged 65 and over to 0.71% in those aged 13 to 17 years. Round 9 prevalence was highest among Pakistani participants at 2.1% compared to white participants at 0.45% and Black participants at 0.83%. There were higher adjusted odds of infection for healthcare and care home workers, for those working in public transport and those working in education, school, nursery or childcare and lower adjusted odds for those not required to work outside the home.\n\nConclusionsCommunity prevalence of swab-positivity has declined markedly between January and February 2021 during lockdown in England, but remains high; the rate of decline has slowed in the most recent period, with a suggestion of pockets of growth. Continued adherence to social distancing and public health measures is required so that infection rates fall to much lower levels. This will help to ensure that the benefits of the vaccination roll-out programme in England are fully realised.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.02.21252444", @@ -6215,6 +6187,20 @@ "author_similarity": 96, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.02.11.21251587", + "date": "2021-02-12", + "link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251587", + "title": "Assessing the impact of secondary school reopening strategies on within-school COVID-19 transmission and absences: a modelling study", + "authors": "Trystan Leng; Edward M Hill; Robin N Thompson; Michael J Tildesley; Matt J Keeling; Louise J Dyson", + "affiliations": "University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick", + "abstract": "", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.02.11.21249258", @@ -7027,6 +7013,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.27.20239087", + "date": "2020-11-30", + "link": "https://medrxiv.org/cgi/content/short/2020.11.27.20239087", + "title": "Dietary supplements during the COVID-19 pandemic: insights from 1.4M users of the COVID Symptom Study app - a longitudinal app-based community survey", + "authors": "Panayiotis Louca; Benjamin Murray; Kerstin Klaser; Mark S Graham; Mohsen Mazidi; Emily R Leeming; Ellen J Thompson; Ruth Bowyer; David Alden Drew; Long Alden Nguyen; Jordi Merino; Maria F Gomez; Olatz Mompeo; Ricardo Costeira; Carole H Sudre; Rachel Gibson; Claire Steves; Jonathan Wolf; Paul W Franks; Sebastien Ourselin; Andrew T Chan; Sarah E Berry; Ana Valdes; Philip Calder; Tim D Spector; Cristina Menni", + "affiliations": "King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Lund University; King's College London; King's College London; University College London; King's College London; King's College London; Zoe Global Limited; Lund University; King's College London; Massachusetts General Hospital and Harvard Medical School; King's College London; King's College London; University of Southampton; King's College London; King's College London", + "abstract": "ObjectivesDietary supplements may provide nutrients of relevance to ameliorate SARS-CoV-2 infection, although scientific evidence to support a role is lacking. We investigate whether the regular use of dietary supplements can reduce the risk of testing positive for SARS-CoV-2 infection in around 1.4M users of the COVID Symptom Study App who completed a supplement use questionnaire.\n\nDesignLongitudinal app-based community survey and nested case control study.\n\nSettingSubscribers to an app that was launched to enable self-reported information related to SARS-CoV-2 infection for use in the general population in three countries.\n\nMain ExposureSelf-reported regular dietary supplement usage since the beginning of the pandemic.\n\nMain Outcome MeasuresSARS-CoV-2 infection confirmed by viral RNA polymerase chain reaction test (RT-PCR) or serology test. A secondary outcome was new-onset anosmia.\n\nResultsIn an analysis including 327,720 UK participants, the use of probiotics, omega-3 fatty acids, multivitamins or vitamin D was associated with a lower risk of SARS-CoV-2 infection by 14%(95%CI: [8%,19%]), 12%(95%CI: [8%,16%]), 13%(95%CI: [10%,16%]) and 9%(95%CI: [6%,12%]), respectively, after adjusting for potential confounders. No effect was observed for vitamin C, zinc or garlic supplements. When analyses were stratified by sex, age and body mass index (BMI), the protective associations for probiotics, omega-3 fatty acids, multivitamins and vitamin D were observed in females across all ages and BMI groups, but were not seen in men. The same overall pattern of association was observed in both the US and Swedish cohorts. Results were further confirmed in a sub-analysis of 993,365 regular app users who were not tested for SARS-CoV-2 with cases (n= 126,556) defined as those with new onset anosmia (the strongest COVID-19 predictor).\n\nConclusionWe observed a modest but significant association between use of probiotics, omega-3 fatty acid, multivitamin or vitamin D supplements and lower risk of testing positive for SARS-CoV-2 in women. No clear benefits for men were observed nor any effect of vitamin C, garlic or zinc for men or women. Randomised controlled trials of selected supplements would be required to confirm these observational findings before any therapeutic recommendations can be made.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.25.20238600", @@ -7055,6 +7055,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.19.20234120", + "date": "2020-11-23", + "link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234120", + "title": "Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19", + "authors": "Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas", + "affiliations": "VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School", + "abstract": "Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.19.20234849", @@ -7069,20 +7083,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.11.18.20233932", - "date": "2020-11-20", - "link": "https://medrxiv.org/cgi/content/short/2020.11.18.20233932", - "title": "REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020", - "authors": "Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott", - "affiliations": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear", - "abstract": "BackgroundEngland is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020.\n\nMethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020.\n\nResultsOverall weighted prevalence of infection in the community in England was 1.3% or 130 people per 10,000 infected, up from 60 people per 10,000 in the round 5 report (18th September to 5th October 2020), doubling every 24 days on average since the prior round. The corresponding R number was estimated to be 1.2. Prevalence of infection was highest in North West (2.4%, up from 1.2%), followed by Yorkshire and The Humber (2.3% up from 0.84%), West Midlands (1.6% up from 0.60%), North East (1.5% up from 1.1%), East Midlands (1.3% up from 0.56%), London (0.97%, up from 0.54%), South West (0.80% up from 0.33%), South East (0.69% up from 0.29%), and East of England (0.69% up from 0.30%). Rapid growth in the South observed in the first half of round 6 was no longer apparent in the second half of round 6. We also observed a decline in prevalence in Yorkshire and The Humber during this period. Comparing the first and second halves of round 6, there was a suggestion of decline in weighted prevalence in participants aged 5 to 12 years and in those aged 25 to 44 years. While prevalence remained high, in the second half of round 6 there was suggestion of a slight fall then rise that was seen nationally and also separately in both the North and the South.\n\nConclusionThe impact of the second national lockdown in England is not yet known. We provide here a detailed description of swab-positivity patterns at national, regional and local scales for the period immediately preceding lockdown, against which future trends in prevalence can be evaluated.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.11.18.20230649", @@ -7517,6 +7517,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.10.26.20219725", + "date": "2020-10-27", + "link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219725", + "title": "Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults", + "authors": "Helen Ward; Graham Cooke; Christina J Atchison; Matthew Whitaker; Joshua Elliott; Maya Moshe; Jonathan C Brown; Barney Flower; Anna Daunt; Kylie E. C. Ainslie; Deborah Ashby; Christl A. Donnelly; Steven Riley; Ara Darzi; Wendy Barclay; Paul Elliott", + "affiliations": "Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London", + "abstract": "BackgroundThe prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into its spread in the community, the likelihood of reinfection and potential for some level of population immunity.\n\nMethodsPrevalence of antibody positivity in England, UK (REACT2) with three cross-sectional surveys between late June and September 2020. 365104 adults used a self-administered lateral flow immunoassay (LFIA) test for IgG. A laboratory comparison of LFIA results to neutralization activity in panel of sera was performed.\n\nResultsThere were 17,576 positive tests over the three rounds. Antibody prevalence, adjusted for test characteristics and weighted to the adult population of England, declined from 6.0% [5.8, 6.1], to 4.8% [4.7, 5.0] and 4.4% [4.3, 4.5], a fall of 26.5% [-29.0, -23.8] over the three months of the study. There was a decline between rounds 1 and 3 in all age groups, with the highest prevalence of a positive result and smallest overall decline in positivity in the youngest age group (18-24 years: -14.9% [-21.6, -8.1]), and lowest prevalence and largest decline in the oldest group (75+ years: -39.0% [-50.8, -27.2]); there was no change in antibody positivity between rounds 1 and 3 in healthcare workers (+3.45% [-5.7, +12.7]).\n\nThe decline from rounds 1 to 3 was largest in those who did not report a history of COVID-19, (-64.0% [-75.6, -52.3]), compared to -22.3% ([-27.0, -17.7]) in those with SARS-CoV-2 infection confirmed on PCR.\n\nDiscussionThese findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.10.26.20219485", @@ -7951,6 +7965,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.17.20196469", + "date": "2020-09-18", + "link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196469", + "title": "Renin-angiotensin system inhibitors and susceptibility to COVID-19 in patients with hypertension: a propensity score-matched cohort study in primary care", + "authors": "Shamil Haroon; Anuradhaa Subramanian; Jennifer Cooper; Astha Anand; Krishna Gokhale; Nathan Byne; Samir Dhalla; Dionisio Acosta-Mena; Thomas Taverner; Kelvin Okoth; Jingya Wang; Joht Singh Chandan; Christopher Sainsbury; Dawit Tefra Zemedikun; G Neil Thomas; Dhruv Parekh; Tom Marshall; Elizabeth Sapey; Nicola J Adderley; Krishnarajah Nirantharakumar", + "affiliations": "University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Cegedim Health Data, Cegedim Rx, London, UK; Cegedim Health Data, Cegedim Rx, London, UK; Cegedim Health Data, Cegedim Rx, London, UK; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham and Department of Diabetes, Gartnavel General Hospital, NHS Greater Glasgow and Clyde, UK; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham", + "abstract": "Introduction A significant proportion of patients with Coronavirus Disease-19 (COVID-19) have hypertension and are treated with renin-angiotensin system (RAS) inhibitors, namely angiotensin-converting enzyme I inhibitors (ACE inhibitors) or angiotensin II type-1 receptor blockers (ARBs). These medications have been postulated to influence susceptibility to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The objective of this study was to assess a possible association between prescription of RAS inhibitors and the incidence of COVID-19 and all-cause mortality. Methods We conducted a propensity-score matched cohort study to assess the incidence of COVID-19 among patients with hypertension who were prescribed ACE inhibitors or ARBs compared to patients treated with calcium channel blockers (CCBs) in a large UK-based primary care database (The Health Improvement Network). We estimated crude incidence rates for confirmed/suspected COVID-19 among those prescribed ACE inhibitors, ARBs and CCBs. We used a Cox proportional hazards model to produce adjusted hazard ratios for COVID-19 comparing patients prescribed ACE inhibitors or ARBs to those prescribed CCBs. We further assessed all-cause mortality as a secondary outcome and a composite of accidents, trauma or fractures as a negative control outcome to assess for residual confounding. Results In the propensity score matched analysis, 83 of 18,895 users (0.44%) of ACE inhibitors developed COVID-19 over 8,923 person-years, an incidence rate of 9.3 per 1000 person-years. 85 of 18,895 (0.45%) users of CCBs developed COVID-19 over 8,932 person-years, an incidence rate of 9.5 per 1000 person-years. The adjusted hazard ratio for suspected/confirmed COVID-19 for users of ACE inhibitors compared to CCBs was 0.92 (95% CI 0.68 to 1.26). 79 out of 10,623 users (0.74%) of ARBs developed COVID-19 over 5010 person-years, an incidence rate of 15.8 per 1000 person-years, compared to 11.6 per 1000 person-years among users of CCBs. The adjusted hazard ratio for suspected/confirmed COVID-19 for users of ARBs compared to CCBs was 1.38 (95% CI 0.98 to 1.95). There were no significant associations between use of ACE inhibitors or ARBs and all-cause mortality, compared to use of CCBs. We found no evidence of significant residual confounding with the negative control analysis. Conclusion Current use of ACE inhibitors was not associated with the risk of suspected or confirmed COVID-19 whereas use of ARBs was associated with a statistically non-significant 38% relative increase in risk compared to use of CCBs. However, no significant associations were observed between prescription of either ACE inhibitors or ARBs and all-cause mortality during the peak of the pandemic.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "bioRxiv", "doi": "10.1101/2020.09.16.297945", @@ -8063,20 +8091,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.09.03.20187377", - "date": "2020-09-05", - "link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187377", - "title": "Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study", - "authors": "Max T Eyre; Rachel Burns; Victoria Kirkby; Catherine Smith; Spiros Denaxas; Vincent Nguyen; Andrew Hayward; Laura Shallcross; Ellen Fragaszy; Robert W Aldridge", - "affiliations": "Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK; Liverpool School of Tropical Med; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Health Data Research UK, London, NW1 2DA, UK; The Alan Turing Institute, London; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Epidemiology and Health Care; Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Health Informatics, University College London, London, NW1 2DA, UK; Faculty of Epidemiology and Population Health, London School of Hygiene and Tro; Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK", - "abstract": "BackgroundDiagnostic testing forms a major part of the UKs response to the current COVID-19 pandemic with tests offered to people with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK.\n\nMethodsIn this analysis of the Bug Watch prospective community cohort study, we estimated the incidence of cough or fever in England in 2018-2019. We then estimated the COVID-19 diagnostic testing rates required in the UK for baseline cough or fever cases for the period July 2020-June 2021. This was explored for different rates of the population requesting tests and four second wave scenarios and then compared to current national capacity.\n\nResultsThe baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020.\n\nConclusionsOur results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UKs response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.09.01.20185793", @@ -8567,6 +8581,20 @@ "author_similarity": 92, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.07.26.20161570", + "date": "2020-07-28", + "link": "https://medrxiv.org/cgi/content/short/2020.07.26.20161570", + "title": "Magnitude, demographics and dynamics of the impact of the first phase of the Covid-19 pandemic on all-cause mortality in 17 industrialised countries", + "authors": "Vasilis Kontis; James E Bennett; Theo Rashid; Robbie M Parks; Jonathan Pearson-Stuttard; Michel Guillot; Perviz Asaria; Bin Zhou; Marco Battaglini; Gianni Corsetti; Martin McKee; Mariachiara Di Cesare; Colin D Mathers; Majid Ezzati", + "affiliations": "Imperial College London; Imperial College London; Imperial College London; Columbia University; Imperial College London; University of Pennsylvania; Imperial College London; Imperial College London; Italian National Institute of Statistics; Italian National Institute of Statistics; London School of Hygiene & Tropical Medicine; Middlesex University London; Independent Researcher; Imperial College London", + "abstract": "The Covid-19 pandemic affects mortality directly through infection as well as through changes in the social, environmental and healthcare determinants of health1. The impacts on mortality are likely to vary across countries in magnitude, timing, and age and sex composition. Here, we applied an ensemble of 16 Bayesian probabilistic models to vital statistics data, by age group and sex, to consistently and comparably estimate the impacts of the first phase of the pandemic on all-cause mortality for 17 industrialised countries. The models accounted for factors that affect death rates including seasonality, temperature, and public holidays, as well as for medium-long-term secular trends and the dependency of death rates in each week on those in preceding week(s). From mid-February through the end of May 2020, an estimated 202,900 (95% credible interval 179,400-224,900) more people died in these 17 countries than would have had the pandemic not taken place. Nearly three quarters of these excess deaths occurred in England and Wales, Italy and Spain, where less than half of the total population of these countries live. When all-cause mortality is considered, the total number of deaths, deaths per 100,000 people, and relative increase in deaths were similar between men and women in most countries. Further, in many countries, the balance of excess deaths changed from male-dominated early in the pandemic to being equal or female-dominated later on.\n\nTaken over the entire first phase of the pandemic, there was no detectable rise in all-cause mortality in New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland and for women in Austria and Switzerland (posterior probability of an increase in deaths <90%). Women in Portugal and men in Austria experienced relatively small increases in all-cause mortality, with posterior probabilities of 90-99%. For men in Switzerland and Portugal, and both sexes in the Netherlands, France, Sweden, Belgium, Italy, Scotland, Spain and England and Wales, all-cause mortality increased as a result of the pandemic with a posterior probability >99%. After accounting for population size, England and Wales and Spain experienced the highest death toll, nearly 100 deaths per 100,000 people; they also had the largest relative (percent) increase in deaths (37% (95% credible interval 30-44) in England and Wales; 38% (31-44) in Spain). New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland experienced changes in deaths that ranged from possible slight declines to increases of no more than 5%. The large impact in England and Wales stems partly from having experienced (together with Spain) the highest weekly increases in deaths, more than doubling in some weeks, and having had (together with Sweden) the longest duration when deaths exceeded levels that would be expected in the absence of the pandemic.\n\nThe heterogeneous magnitude and character of the excess deaths due to the Covid-19 pandemic reflect differences in how well countries have managed the pandemic (e.g., timing, extent and adherence to lockdowns and other social distancing measures; effectiveness of test, trace and isolate mechanisms), and the resilience and preparedness of the health and social care system (e.g., effective facility and community care pathways; minimising spread of infection within hospitals and care homes, and between them and the community).", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.23.20160747", @@ -9099,20 +9127,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.06.16.20133157", - "date": "2020-06-18", - "link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133157", - "title": "Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease.", - "authors": "Petra Mlcochova; Dami Collier; Allyson V Ritchie; Sonny M Assennato; Myra Hosmillo; Neha Goel; Bo Meng; Krishna Chatterji; Vivien Mendoza; Nigel Temperton; Leo Kiss; Katarzyna A Ciazyns; Xiaoli Xiong; John AG Briggs; James Nathan; Federica Mescia; Hongyi Zhang; Petros Barmpounakis; Nikos Demeris; Richard Skells; Paul Lyons; John Bradley; Stephen Baker; Jean Pierre Allain; Kenneth GC Smith; Ian Goodfellow; Ravindra K Gupta", - "affiliations": "University of Cambridge; UCL; Diagnostics for the Real World Europe Ltd; DRW; University of Cambridge; University of Cambridge; University of Cambridge; NIHR Cambridge Clinical Research Facility; CUH NHS Trust; University of Kent; Medical Research Council Laboratory of Molecular Biology, Cambridge; Medical Research Council Laboratory of Molecular Biology, Cambridge; Medical Research Council Laboratory of Molecular Biology; Medical Research Council Laboratory of Molecular Biology; University of Cambridge; University of Cambridge; CUH NHS Trust; Athens University of Economics and Business; Cambridge Clinical Trials Unit-Cancer Theme; Cambridge Clinical Trials Unit-Cancer Theme; University of Cambridge; University of Cambridge; Cambridge University; Diagnostics for the Real World EU Ltd; University of Cambridge; ig299@cam.ac.uk; University of Cambridge", - "abstract": "BackgroundRapid COVID-19 diagnosis in hospital is essential for patient management and identification of infectious patients to limit the potential for nosocomial transmission. The diagnosis of infection is complicated by 30-50% of COVID-19 hospital admissions with nose/throat swabs testing negative for SARS-CoV-2 nucleic acid, frequently after the first week of illness when SARS-CoV-2 antibody responses become detectable. We assessed the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease in the emergency department.\n\nMethodsWe developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike (S) protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and S proteins from SARS-CoV-2. We tested two lateral flow rapid fingerprick tests with bands for IgG and IgM. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid POC nucleic acid amplification (NAAT) test. Additionally, serum collected at admission was retrospectively tested by in vitro neutralisation, ELISA and the candidate POC antibody tests. We evaluated the performance of the individual and combined rapid POC diagnostic tests against a composite reference standard of neutralisation and standard laboratory based RT-PCR.\n\nResults45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Using the composite reference standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our reference standard and 63.0 (IQR 41.0-72.0) years in those without disease. The overall detection rate by rapid NAAT was 79.2% (95CI 57.8-92.9%), decreasing from 100% (95% CI 65.3-98.6%) in days 1-4 to 50.0% (95% CI 11.8-88.2) for days 9-28 post symptom onset. Correct identification of COVID-19 with combined rapid POC diagnostic tests was 100% (95CI 85.8-100%) with a false positive rate of 5.3-14.3%, driven by POC LFA antibody tests.\n\nConclusionsCombined POC tests have the potential to transform our management of COVID-19, including inflammatory manifestations later in disease where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.06.15.20131722", @@ -9337,6 +9351,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.06.04.20122069", + "date": "2020-06-05", + "link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122069", + "title": "Mechanical ventilation utilization in COVID-19: A systematic review and meta-analysis", + "authors": "Mohammed A Almeshari; Nowaf Y Alobaidi; Mansour Al Asmri; Eyas Alhuthail; Ziyad Alshehri; Farhan Alenezi; Elizabeth Sapey; Dhruv Parekh", + "affiliations": "University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Taibah University; King Saud bin Abdulaziz University for Health Sciences; University of Birmingham; University of Birmingham", + "abstract": "BackgroundIn December 2019, SARS-CoV-2 caused a global pandemic with a viral infection called COVID-19. The disease usually causes respiratory symptoms but in a small proportion of patients can lead to a pneumonitis, Adult Respiratory Distress Syndrome and death. Invasive Mechanical Ventilation (IMV) is considered a life-saving treatment for COVID-19 patients and a huge demand for IMV devices was reported globally. This review aims to provide insight on the initial IMV practises for COVID-19 patients in the initial phase of the pandemic.\n\nMethodsElectronic databases (Embase and MEDLINE) were searched for applicable articles using relevant keywords. The references of included articles were hand searched. Articles that reported the use of IMV in adult COVID-19 patients were included in the review. The NIH quality assessment tool for cohort and cross-sectional studies was used to appraise studies.\n\nResults106 abstracts were identified from the databases search, of which 16 were included. 5 studies were included in the meta-analysis. In total, 9988 patients were included across all studies. The overall cases of COVID-19 requiring IMV ranged from 2-77%. Increased age and pre-existing comorbidities increased the likelihood of IMV requirement. The reported mortality rate in patients receiving IMV ranged between 50-100%. On average, IMV was required and initiated between 10-10.5 days from symptoms onset. When invasively ventilated, COVID-19 patients required IMV for a median of 10-17 days across studies. Little information was provided on ventilatory protocols or management strategies and were inconclusive.\n\nConclusionIn these initial reporting studies for the first month of the pandemic, patients receiving IMV were older and had more pre-existing co-morbidities than those who did not require IMV. The mortality rate was high in COVID-19 patients who received IMV. Studies are needed to evaluate protocols and modalities of IMV to improve outcomes and identify the populations most likely to benefit from IMV.", + "category": "intensive care and critical care medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.06.01.20116608", @@ -9533,20 +9561,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.20.20108183", - "date": "2020-05-23", - "link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108183", - "title": "A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings", - "authors": "Sarah Beale; Andrew Hayward; Laura Shallcross; Robert W Aldridge; Ellen Fragaszy", - "affiliations": "University College London; University College London; University College London; University College London; University College London", - "abstract": "BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings.\n\nMethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis.\n\nFindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited.\n\nInterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted.\n\nFundingMedical Research Council", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.18.20086157", @@ -9631,20 +9645,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.10.20096925", - "date": "2020-05-15", - "link": "https://medrxiv.org/cgi/content/short/2020.05.10.20096925", - "title": "NON-WHITE ETHNICITY, MALE SEX, AND HIGHER BODY MASS INDEX, BUT NOT MEDICATIONS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM ARE ASSOCIATED WITH CORONAVIRUS DISEASE 2019 (COVID-19) HOSPITALISATION: REVIEW OF THE FIRST 669 CASES FROM THE UK BIOBANK", - "authors": "Zahra Raisi-Estabragh; Celeste McCracken; Maddalena Ardissino; Mae S Bethell; Jackie Cooper; Cyrus Cooper; Nicholas C Harvey; Steffen E Petersen", - "affiliations": "William Harvey Research Institute; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK; Sir Alexander Fleming Building, Imperial College London, London, UK; North West Anglia NHS Foundation Trust, Hinchingbrooke Hospital, Huntingdon, UK; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK", - "abstract": "BackgroundCardiometabolic morbidity and medications, specifically Angiotensin Converting Enzyme inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs), have been linked with adverse outcomes from coronavirus disease 2019 (COVID-19). This study aims to investigate factors associated with COVID-19 positivity for the first 669 UK Biobank participants; compared with individuals who tested negative, and with the untested, presumed negative, rest of the population.\n\nMethodsWe studied 1,474 participants from the UK Biobank who had been tested for COVID-19. Given UK testing policy, this implies a hospital setting, suggesting at least moderate to severe symptoms. We considered the following exposures: age, sex, ethnicity, body mass index (BMI), diabetes, hypertension, hypercholesterolaemia, ACEi/ARB use, prior myocardial infarction (MI), and smoking. We undertook comparisons between: 1) COVID-19 positive and COVID-19 tested negative participants; and 2) COVID-19 tested positive and the remaining participants (tested negative plus untested, n=501,837). Logistic regression models were used to investigate univariate and mutually adjusted associations.\n\nResultsAmong participants tested for COVID-19, non-white ethnicity, male sex, and greater BMI were independently associated with COVID-19 positive result. Non-white ethnicity, male sex, greater BMI, diabetes, hypertension, prior MI, and smoking were independently associated with COVID-19 positivity compared to the remining cohort (test negatives plus untested). However, similar associations were observed when comparing those who tested negative for COVID-19 with the untested cohort; suggesting that these factors associate with general hospitalisation rather than specifically with COVID-19.\n\nConclusionsAmong participants tested for COVID-19 with presumed moderate to severe symptoms in a hospital setting, non-white ethnicity, male sex, and higher BMI are associated with a positive result. Other cardiometabolic morbidities confer increased risk of hospitalisation, without specificity for COVID-19. Notably, ACE/ARB use did not associate with COVID-19 status.", - "category": "cardiovascular medicine", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.11.20096347", @@ -9911,20 +9911,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.27.20081711", - "date": "2020-05-03", - "link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081711", - "title": "Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study", - "authors": "Kevin van Zandvoort; Christopher I Jarvis; Carl Pearson; Nicholas G Davies; CMMID COVID-19 working group; Timothy W Russell; Adam J Kucharski; Mark J Jit; Stefan Flasche; Rosalind M Eggo; Francesco Checchi", - "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; ; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine", - "abstract": "BackgroundThe health impact of COVID-19 may differ in African settings as compared to countries in Europe or China due to demographic, epidemiological, environmental and socio-economic factors. We evaluated strategies to reduce SARS-CoV-2 burden in African countries, so as to support decisions that balance minimising mortality, protecting health services and safeguarding livelihoods.\n\nMethodsWe used a Susceptible-Exposed-Infectious-Recovered mathematical model, stratified by age, to predict the evolution of COVID-19 epidemics in three countries representing a range of age distributions in Africa (from oldest to youngest average age: Mauritius, Nigeria and Niger), under various effectiveness assumptions for combinations of different non-pharmaceutical interventions: self-isolation of symptomatic people, physical distancing, and shielding (physical isolation) of the high-risk population. We adapted model parameters to better represent uncertainty about what might be expected in African populations, in particular by shifting the distribution of severity risk towards younger ages and increasing the case-fatality ratio.\n\nResultsWe predicted median clinical attack rates over the first 12 months of 17% (Niger) to 39% (Mauritius), peaking at 2-4 months, if epidemics were unmitigated. Self-isolation while symptomatic had a maximum impact of about 30% on reducing severe cases, while the impact of physical distancing varied widely depending on percent contact reduction and R0. The effect of shielding high-risk people, e.g. by rehousing them in physical isolation, was sensitive mainly to residual contact with low-risk people, and to a lesser extent to contact among shielded individuals. Response strategies incorporating self-isolation of symptomatic individuals, moderate physical distancing and high uptake of shielding reduced predicted peak bed demand by 46% to 54% and mortality by 60% to 75%. Lockdowns delayed epidemics by about 3 months. Estimates were sensitive to differences in age-specific social mixing patterns, as published in the literature.\n\nDiscussionIn African settings, as elsewhere, current evidence suggests large COVID-19 epidemics are expected. However, African countries have fewer means to suppress transmission and manage cases. We found that self-isolation of symptomatic persons and general physical distancing are unlikely to avert very large epidemics, unless distancing takes the form of stringent lockdown measures. However, both interventions help to mitigate the epidemic. Shielding of high-risk individuals can reduce health service demand and, even more markedly, mortality if it features high uptake and low contact of shielded and unshielded people, with no increase in contact among shielded people. Strategies combining self-isolation, moderate physical distancing and shielding will probably achieve substantial reductions in mortality in African countries. Temporary lockdowns, where socioeconomically acceptable, can help gain crucial time for planning and expanding health service capacity.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.28.20083295", @@ -10009,6 +9995,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.04.21.20073049", + "date": "2020-04-24", + "link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073049", + "title": "What can trends in hospital deaths from COVID-19 tell us about the progress and peak of the pandemic? An analysis of death counts from England announced up to 20 April 2020", + "authors": "David A Leon; Christopher I Jarvis; Anne M Johnson; Liam Smeeth; Vladimir M Shkolnikov", + "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; London School of Hygiene & Tropical Medicine; Max Planck Institute for Demographic Research", + "abstract": "BackgroundReporting of daily hospital COVID-19 deaths in the UK are promoted by the government and scientific advisers alike as a key metric for assessing the progress in the control of the epidemic. These data, however, have certain limitations, among which one of the most significant concerns the fact that the daily totals span deaths that have occurred between 1 and 10 days or more in the past.\n\nData and methodsWe obtained daily data published published by NHS England up to and including April 25 in the form of Excel spreadsheets in which deaths counts are presented by date of death according to age and region. Simple descriptive analyses were conducted and presented in graphical and tabular form which were aimed at illustrating the biases inherent in focussing on daily counts regardless of when the deaths occurred. We then looked at how a less biased picture could be obtained by looking at trends in death counts stratifying by individual period of delay in days between occurrence of death and when the death was included in the daily announcement.\n\nFindingsThe number of hospital COVID-19 deaths announced daily overestimates the maximum number of deaths actually occurring so far in the epidemic in the UK, and also obscures the pattern of decline in deaths. Taking account of reporting delays suggests that for England as a whole a peak in hospital COVID-19 deaths may have been reached on April 8 with a subsequent gradual decline suggested. The same peak is also seen among those aged 60-79 and 80+, although there is slightly shallower decline in the oldest age group (80+ years). Among those aged 40-59 years a later peak on April 11 is evident. London shows a peak on April 8 and a clearer and steeper pattern of subsequent decline compared to England as a whole.\n\nInterpretationAnalyses of mortality trends must take account of delay, and in communication with the public more emphasis should be placed on looking at trends based on deaths that occurred 5 or more days prior to the announcement day. The slightly weaker decline seen at age 80+ may reflect increased hospitalisation of people from care homes, whereas the later peak under the age of 60 years may reflect the higher proportions at these younger ages being admitted to critical care resulting in an extension of life of several days.\n\nCompeting interestsAll authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: no support from any organization for the submitted work; no financial relationships with any organizations that might have an interest in the submitted work in the previous three years other than LS who reported grants from Wellcome, MRC, NIHR, GSK, BHF, Diabetes UK all outside the submitted work; no other relationships or activities that could appear to have influenced the submitted work other than LS who is a Trustee of the British Heart Foundation and AJM who is a member of the Royal Society Delve Committee.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.04.18.20064774", @@ -10093,20 +10093,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.10.20059121", - "date": "2020-04-14", - "link": "https://medrxiv.org/cgi/content/short/2020.04.10.20059121", - "title": "ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study", - "authors": "Dipender Gill; Marios Arvanitis; Paul Carter; Ana I Hernandez Cordero; Brian Jo; Ville Karhunen; Susanna C Larsson; Xuan Li; Sam M Lockhart; Amy M Mason; Evanthia Pashos; Ashis Saha; Vanessa Tan; Verena Zuber; Yohan Bosse; Sarah Fahle; Ke Hao; Tao Jiang; Philippe Joubert; Alan C Lunt; Willem hendrik Ouwehand; David J Roberts; Wim Timens; Maarten van den Berge; Nicholas A Watkins; Alexis Battle; Adam S Butterworth; John Danesh; Barbara E Engelhard; James E Peters; Don Sin; Stephen Burgess", - "affiliations": "Imperial College London; Johns Hopkins University; University of Cambridge; The University of British Columbia Center for Heart Lung Innovation; Lewis Sigler Institute for Integrative Biology; Imperial College London; Karolinska Institutet; The University of British Columbia Center for Heart Lung Innovation; University of Cambridge; University of Cambridge; Pfizer; Johns Hopkins University; University of Bristol; Imperial College London; Laval University, Quebec; University of Cambridge; School of Medicine at Mount Sinai; University of Cambridge; Laval University, Quebec; Imperial College London; University of Cambridge; University of Oxford; University of Groningen; University of Groningen; University of Cambridge; Johns Hopkins University; University of Cambridge; University of Cambridge; Princeton University; Imperial College London; University of British Columbia; University of Cambridge", - "abstract": "ObjectivesTo use human genetic variants that proxy angiotensin-converting enzyme (ACE) inhibitor drug effects and cardiovascular risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 gene expression and circulating ACE2 levels.\n\nDesignTwo-sample Mendelian randomization (MR) analysis.\n\nSettingSummary-level genetic association data.\n\nParticipantsParticipants were predominantly of European ancestry. Variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors (body mass index, chronic obstructive pulmonary disease, lifetime smoking index, low-density lipoprotein cholesterol, systolic blood pressure and type 2 diabetes mellitus) were selected from publicly available genome-wide association study data (sample sizes ranging from 188,577 to 898,130 participants). Genetic association estimates for lung expression of ACE2 and TMPRSS2 were obtained from the Gene-Tissue Expression (GTEx) project (515 participants) and the Lung eQTL Consortium (1,038 participants). Genetic association estimates for circulating plasma ACE2 levels were obtained from the INTERVAL study (4,947 participants).\n\nMain outcomes and measuresLung ACE2 and TMPRSS2 expression and plasma ACE2 levels.\n\nResultsThere were no association of genetically proxied ACE inhibition with any of the outcomes considered here. There was evidence of a positive association of genetic liability to type 2 diabetes mellitus with lung ACE2 gene expression in GTEx (p = 4x10-4) and with circulating plasma ACE2 levels in INTERVAL (p = 0.03), but not with lung ACE2 expression in the Lung eQTL Consortium study (p = 0.68). There were no associations between genetically predicted levels of the other cardiometabolic traits with the outcomes.\n\nConclusionsThis study does not provide evidence to support that ACE inhibitor antihypertensive drugs affect lung ACE2 and TMPRSS2 expression or plasma ACE2 levels. In the current COVID-19 pandemic, our findings do not support a change in ACE inhibitor medication use without clinical justification.\n\nSummary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current coronavirus disease 2019 (COVID-19) pandemic.\nC_LIO_LISerine protease TMPRSS2 is involved in priming the SARS-CoV-2 spike protein for cellular entry through the angiotensin-converting enzyme 2 (ACE2) receptor.\nC_LIO_LIExpression of ACE2 and TMPRSS2 in the lung epithelium might have implications for risk of SARS-CoV-2 infection and severity of COVID-19.\nC_LI\n\nWhat this study addsO_LIWe used human genetic variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 expression and circulating ACE2 levels.\nC_LIO_LIOur findings do not support the hypothesis that ACE inhibitors have effects on ACE2 expression.\nC_LIO_LIWe found some support for an association of genetic liability to type 2 diabetes mellitus with higher lung ACE2 expression and plasma ACE2 levels, but evidence was inconsistent across studies.\nC_LI", - "category": "genetic and genomic medicine", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.07.20056788", @@ -10345,6 +10331,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.02.12.20022426", + "date": "2020-02-13", + "link": "https://medrxiv.org/cgi/content/short/2020.02.12.20022426", + "title": "Interventions targeting air travellers early in the pandemic may delay local outbreaks of SARS-CoV-2", + "authors": "Samuel J Clifford; Carl A B Pearson; Petra Klepac; Kevin Van Zandvoort; Billy J Quilty; - CMMID COVID-19 working group; Rosalind M Eggo; Stefan Flasche", + "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; -; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine", + "abstract": "BackgroundWe evaluated if interventions aimed at air travellers can delay local SARS-CoV-2 community transmission in a previously unaffected country.\n\nMethodsWe simulated infected air travellers arriving into countries with no sustained SARS-CoV-2 transmission or other introduction routes from affected regions. We assessed the effectiveness of syndromic screening at departure and/or arrival & traveller sensitisation to the COVID-2019-like symptoms with the aim to trigger rapid self-isolation and reporting on symptom onset to enable contact tracing. We assumed that syndromic screening would reduce the number of infected arrivals and that traveller sensitisation reduces the average number of secondary cases. We use stochastic simulations to account for uncertainty in both arrival and secondary infections rates, and present sensitivity analyses on arrival rates of infected travellers and the effectiveness of traveller sensitisation. We report the median expected delay achievable in each scenario and an inner 50% interval.\n\nResultsUnder baseline assumptions, introducing exit and entry screening in combination with traveller sensitisation can delay a local SARS-CoV-2 outbreak by 8 days (50% interval: 3-14 days) when the rate of importation is 1 infected traveller per week at time of introduction. The additional benefit of entry screening is small if exit screening is effective: the combination of only exit screening and traveller sensitisation can delay an outbreak by 7 days (50% interval: 2-13 days). In the absence of screening, with less effective sensitisation, or a higher rate of importation, these delays shrink rapidly to less than 4 days.\n\nConclusionSyndromic screening and traveller sensitisation in combination may have marginally delayed SARS-CoV-2 outbreaks in unaffected countries.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.02.08.20021162", diff --git a/data/covid/raw-preprints.json b/data/covid/raw-preprints.json index 3bf6535b..6622b2c2 100644 --- a/data/covid/raw-preprints.json +++ b/data/covid/raw-preprints.json @@ -1,4 +1,186 @@ [ + { + "rel_doi": "10.1101/2024.01.24.577015", + "rel_title": "Interferon-\u03b3 as a Potential Inhibitor of SARS-CoV-2 ORF6 Accessory Protein", + "rel_date": "2024-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.24.577015", + "rel_abs": "ORF6 protein of the SARS-CoV-2 virus plays a crucial role in blocking the innate immune response of the infected cells by inhibiting interferon pathways. Additionally, it binds and immobilises the RAE1 protein onto the cytoplasmic membranes, thereby blocking the transport of mRNA from the nucleus to the cytoplasm. In all these cases the host cell proteins are tethered by the flexible C-terminus of ORF6. A possible strategy to inhibit the biological activity of ORF6 is to bind its C-terminus with suitable ligands. Our in silico experiments suggest that hIFN{gamma} binds the ORF6 protein with high affinity, thus impairing its interactions with RAE1 and, consequently, its activity in viral invasion. The here reported in vitro studies reveal a shift of the localization of RAE1 in ORF6 overexpressing cells upon treatment with hIFN{gamma} from predominantly cytoplasmic to mainly nuclear, resulting in restoration of the export of mRNA from the nucleus. We also explored the expression of GFP in transfected with ORF6 cells by means of fluorescence microscopy and qRT-PCR, finding that treatment with hIFN{gamma} unblocks the mRNA trafficking and reinstates the GFP expression level. The ability of the cytokine to block ORF6 is also reflected in minimising its negative effects on DNA replication by reducing accumulated RNA-DNA hybrids. Our results, therefore, suggest hIFN{gamma} as a promising inhibitor of the most toxic SARS-CoV-2 protein.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "new results", + "category": "molecular biology" + }, + { + "rel_doi": "10.1101/2024.01.24.576385", + "rel_title": "Investigating Sensitivity, Specificity and Accuracy of Variant Calling Pipelines for Analyzing SARS-CoV-2 Data", + "rel_date": "2024-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.24.576385", + "rel_abs": "The rapidly increasing popularity of Next Generation Sequencing and analysis methods in clinical and research settings necessitates an understanding of ideal combinations in identifying genomic variants. Especially with the importance of detecting accurate variants for the development of targeted SARS-CoV-2 vaccines. This research compares the results of two \\'Mapping Algorithms\\', BWA-MEM and Bowtie2, and two \\'Variant Calling Algorithms\\', LoFreq and FreeBayes, and their combinatory Variant Calling Pipelines on the analyses of Next Generation Sequencing (NGS) data of five SARS-CoV-2 samples collected from patients in the USA, India, Italy, and Malawi and sourced for this research from the publicly available NCBI SRA database. Our analysis of mapping algorithms found that BWA-MEM likely has higher sensitivity and specificity than Bowtie2 for mapping reads, and their specificity and sensitivity vary with read length. Furthermore, the accuracy of variant calling algorithms increases with the number of reads, while higher read length possibly leads to divergence in accuracy and sensitivity. Overall, FreeBayes was found to likely be more sensitive to detecting variants when used with Bowtie2 rather than BWA-MEM for analyzing SARS-CoV-2 data.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "new results", + "category": "bioinformatics" + }, + { + "rel_doi": "10.1101/2024.01.23.575696", + "rel_title": "Adaptive advantage of deletion repair in the N terminal domain of the SARS-CoV-2 spike protein in variants of concern", + "rel_date": "2024-01-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.23.575696", + "rel_abs": "Mutations within the N-terminal domain (NTD) of the spike (S) protein play a pivotal role in the emergence of successful SARS-CoV-2 viral lineages. This study investigates the influence of novel combinations of NTD lineage-defining mutations found in the Alpha, Delta, and Omicron variants on viral success. We performed comparative genomics of more than 10 million public SARS-CoV-2 samples to decipher the transmission success of different NTD markers. Additionally, we characterized the viral phenotype of such markers in a surrogate in vitro system. We found that viruses bearing repaired deletions SDeltaH69/V70 and SDeltaY144 in Alpha background were associated with increased transmission rates. After the emergence of the Omicron BA.1 lineage, Alpha viruses harbouring both repaired deletions still showed increased transmission compared to their BA.1 counterparts. Remarkably, Alpha viruses with the SDeltaH69/V70 repair displayed the highest emergence rate, while those in BA.1 exhibited the lowest. Moreover, repaired deletions were more frequently observed among older individuals infected with Alpha, but not with BA.1. In vitro biological characterization of Omicron BA.1 spike deletion repair patterns revealed substantial differences with Alpha. In BA.1, SDeltaV143/Y145 repair enhanced fusogenicity and susceptibility to neutralization by vaccinated individuals' sera. In contrast, the SDeltaH69/V70 repair did not significantly alter these traits but reduced viral infectivity. Simultaneous repair of both deletions led to lower fusogenicity. These findings highlight the intricate genotype-phenotype landscape of the spike NTD in SARS-CoV-2, which impacts viral biology, transmission efficiency, and susceptibility to neutralization. Overall, this study advances our comprehension of SARS-CoV-2 evolution, carrying implications for public health and future research.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Miguel Alvarez-Herrera", + "author_inst": "Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), FISABIO Joint Research Unit \"Infection and Public Health\", Paterna, Spain" + }, + { + "author_name": "Paula Ruiz-Rodriguez", + "author_inst": "Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), FISABIO Joint Research Unit \"Infection and Public Health\", Paterna, Spain" + }, + { + "author_name": "Beatriz Navarro-Dominguez", + "author_inst": "Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), FISABIO Joint Research Unit \"Infection and Public Health\", Paterna, Spain; Un" + }, + { + "author_name": "Joao Zulaica", + "author_inst": "Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), FISABIO Joint Research Unit \"Infection and Public Health\", Paterna, Spain" + }, + { + "author_name": "Brayan Grau", + "author_inst": "Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), FISABIO Joint Research Unit \"Infection and Public Health\", Paterna, Spain" + }, + { + "author_name": "Maria Alma Bracho", + "author_inst": "Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), FISABIO Joint Research Unit \"Infection and Public Health\", Paterna, Spain; CI" + }, + { + "author_name": "Manuel Guerreiro", + "author_inst": "Haematology Department, La Fe University and Polytechnic Hospital, Valencia, Spain; La Fe Health Research Institute (IIS-La Fe), Valencia, Spain" + }, + { + "author_name": "Cristobal Aguilar-Gallardo", + "author_inst": "La Fe Health Research Institute (IIS-La Fe), Valencia, Spain" + }, + { + "author_name": "Fernando Gonzalez-Candelas", + "author_inst": "Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), FISABIO Joint Research Unit \"Infection and Public Health\", Paterna, Spain; CI" + }, + { + "author_name": "Inaki Comas", + "author_inst": "Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain" + }, + { + "author_name": "Ron Geller", + "author_inst": "Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), FISABIO Joint Research Unit \"Infection and Public Health\", Paterna, Spain" + }, + { + "author_name": "Mireia Coscolla", + "author_inst": "Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC), FISABIO Joint Research Unit \"Infection and Public Health\", Paterna, Spain" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "evolutionary biology" + }, + { + "rel_doi": "10.1101/2024.01.23.576505", + "rel_title": "CD4+ and CD8+ T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment", + "rel_date": "2024-01-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.23.576505", + "rel_abs": "SARS-CoV-2 is the causative agent of COVID-19 and continues to pose a significant public health threat throughout the world. Following SARS-CoV-2 infection, virus-specific CD4+ and CD8+ T cells are rapidly generated to form effector and memory cells and persist in the blood for several months. However, the contribution of T cells in controlling SARS-CoV-2 infection within the respiratory tract are not well understood. Using C57BL/6 mice infected with a naturally occurring SARS-CoV-2 variant (B.1.351), we evaluated the role of T cells in the upper and lower respiratory tract. Following infection, SARS-CoV-2-specific CD4+ and CD8+ T cells are recruited to the respiratory tract and a vast proportion secrete the cytotoxic molecule Granzyme B. Using antibodies to deplete T cells prior to infection, we found that CD4+ and CD8+ T cells play distinct roles in the upper and lower respiratory tract. In the lungs, T cells play a minimal role in viral control with viral clearance occurring in the absence of both CD4+ and CD8+ T cells through 28 days post-infection. In the nasal compartment, depletion of both CD4+ and CD8+ T cells, but not individually, results in persistent and culturable virus replicating in the nasal compartment through 28 days post-infection. Using in situ hybridization, we found that SARS-CoV-2 infection persisted in the nasal epithelial layer of tandem CD4+ and CD8+ T cell-depleted mice. Sequence analysis of virus isolates from persistently infected mice revealed mutations spanning across the genome, including a deletion in ORF6. Overall, our findings highlight the importance of T cells in controlling virus replication within the respiratory tract during SARS-CoV-2 infection.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Meenakshi Kar", + "author_inst": "Emory University" + }, + { + "author_name": "Katherine E. E. Johnson", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Abigail Vanderheiden", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Elizabeth J. Elrod", + "author_inst": "Emory University" + }, + { + "author_name": "Katharine Floyd", + "author_inst": "Emory University" + }, + { + "author_name": "Elizabeth Geerling", + "author_inst": "St. Louis University School of Medicine" + }, + { + "author_name": "E. Taylor Stone", + "author_inst": "St. Louis University School of Medicine" + }, + { + "author_name": "Eduardo Salinas", + "author_inst": "Emory University" + }, + { + "author_name": "Stephanie Banakis", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Wei Wang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Shruti Sathish", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Swathi Shrihari", + "author_inst": "Emory University" + }, + { + "author_name": "Meredith E. Davis-Gardner", + "author_inst": "Emory University" + }, + { + "author_name": "Jacob Kohlmeier", + "author_inst": "Emory University" + }, + { + "author_name": "Amelia Pinto", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Robyn Klein", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Arash Grakoui", + "author_inst": "Emory University" + }, + { + "author_name": "Elodie Ghedin", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Mehul S. Suthar", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2024.01.20.576353", "rel_title": "Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission", @@ -165,6 +347,168 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2024.01.22.576742", + "rel_title": "Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination", + "rel_date": "2024-01-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.22.576742", + "rel_abs": "We used plasma IgG proteomics to study the molecular composition and temporal durability of polyclonal IgG antibodies triggered by ancestral SARS-CoV-2 infection, vaccination, or their combination (\"hybrid immunity\"). Infection, whether primary or post-vaccination, mainly triggered an anti-spike antibody response to the S2 domain, while vaccination predominantly induced anti-RBD antibodies. Immunological imprinting persisted after a secondary (hybrid) exposure, with >60% of the ensuing serological response originating from the initial antibodies generated during the first exposure. We highlight one instance where hybrid immunity arising from breakthrough infection resulted in a marked increase in the breadth and affinity of a highly abundant vaccination-elicited plasma IgG antibody, SC27. With an intrinsic binding affinity surpassing a theoretical maximum (KD < 5 pM), SC27 demonstrated potent neutralization of various SARS-CoV-2 variants and SARS-like zoonotic viruses (IC50 ~0.1-1.75 nM) and provided robust protection in vivo. Cryo-EM structural analysis unveiled that SC27 binds to the RBD class 1/4 epitope, with both VH and VL significantly contributing to the binding interface. These findings suggest that exceptionally broad and potent antibodies can be prevalent in plasma and can largely dictate the nature of serological neutralization.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "William N Voss", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Michael A. Mallory", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Patrick O. Byrne", + "author_inst": "GSK Vaccines Institute for Global Health" + }, + { + "author_name": "Jeffrey M. Marchioni", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Sean A. Knudson", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "John M. Powers", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Sarah R. Leist", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Bernadeta Dadonaite", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Douglas R. Townsend", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Jessica Kain", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Yimin Huang", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Ed Satterwhite", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Izabella N. Castillo", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Melissa Mattocks", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Chelsea Paresi", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Jennifer E. Munt", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Trevor Scobey", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Allison Seeger", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Lakshmanane Premkumar", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Jesse D. Bloom", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "George Georgiou", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Jason S. McLellan", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Jason J. Lavinder", + "author_inst": "The University of Texas at Austin" + }, + { + "author_name": "Gregory C. Ippolito", + "author_inst": "The University of Texas at Austin" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2024.01.23.24301661", + "rel_title": "Patients with end-stage kidney disease and COVID-19 are commonly hospitalized early during COVID-19 illness: an opportunity for early intervention", + "rel_date": "2024-01-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.23.24301661", + "rel_abs": "Antiviral medications such as remdesivir, molnupiravir, and nirmatrelvir/ritonavir are most effective when used early in the course of coronavirus disease 2019 (COVID-19). These medications are mainly authorized for outpatient use in high risk populations. End-stage kidney disease (ESKD) is among the strongest risk factors for mortality from COVID-19, however, therapeutic options have been lacking in this patient population given exclusion of ESKD in the registrational trials of antiviral therapy leading to limited FDA approval. In our retrospective study of patients with ESKD on dialysis admitted for symptomatic COVID-19 from March 2020 to January 2020, we found that majority of patients (>80%) were admitted to the hospital early during their disease course (within 5 days of symptom onset). Despite this pattern of early admission, there was a high risk of respiratory failure within 90 days since admission (30%) among this population. We argue that this unique pattern of early presentation and high risk of progression to respiratory failure of the ESKD patients suggests an opportunity for further research to determine if outpatient antiviral therapies should be expanded to patients with ESKD to address the huge unmet need of therapeutic intervention in this vulnerable population.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Rituvanthikaa Seethapathy", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Qiyu Wang", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Nurit Katz-Agranov", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Ian A Strohbehn", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Daiana Moreno", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Destiny Harden", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Roby Paul Bhattacharyya", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Meghan E Sise", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2024.01.21.24301574", "rel_title": "Pandemic-Related Post-traumatic Stress Symptomatology in COVID-19 Patients with and without Post-COVID Conditions", @@ -321,7 +665,7 @@ "rel_date": "2024-01-22", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.21.24301572", - "rel_abs": "OBJECTIVE At the beginning of 2020, hydroxychloroquine showed promising in vitro activity for Covid-19 and several studies were oriented to assess its safety and efficacy. However, after a few months, hydroxychloroquine has proved ineffective. The randomized controlled trials (RCTs) developed quickly and in different settings represent the scientific community capacity to assess drug repositioning effectiveness during a sanitary crisis. Therefore, a critical evaluation of the evidence generated can guide future efforts in analogous situations. We aimed to analyze the RCTs assessing the efficacy of hydroxychloroquine in treating Covid-19, describe their internal validity and power, and evaluate their contribution to the precision of the combined evidence for assessing the mortality outcome. STUDY DESIGN AND SETTINGS This meta-research included RCTs assessing hydroxychloroquine to treat patients diagnosed with Covid-19. It was part of an umbrella systematic review of methods/meta-research (PROSPERO: CRD42022360331) that included a comprehensive search in MEDLINE, EMBASE, Cochrane Library, and the Latin America Database - Lilacs. We retrieved studies published until January 10th, 2022. The risk of bias was assessed using Cochrane Risk of Bias (RoB) 2.0. We analyzed methodology of the studies, precision and random error change through time from pooled evidence, study comparators, patient important outcome, power in different magnitude of effects proxy. RESULTS A total of 22 RCT were included, from that 17 (77%) assessed hospitalized patients and five (23%) outpatients setting. Mortality was related as primary endpoint in only four studies, however half of the studies included composite endpoints including mortality as a component. The internal validity analysis using RoB2 found that eight studies (36%) had a high risk of bias. Only one study had sufficient power to evaluate a moderate magnitude of effect (RR = 0,7 on mortality). The standard error to evaluate efficacy on mortality did not change appreciably after October 2020. From Oct 2020 to Dec 2021, 18 additional studies were published with 2,429 patients recruited. CONCLUSION This meta-research highlights the impact that collaborative, and network scientific research have on informing clinical decision-making. Duplicate efforts create research waste as precision analysis shows that after October 2020, there was not appreciably changes in the precision of the pooled RCT evidence to estimate the hydroxychloroquine effect on mortality.", + "rel_abs": "OBJECTIVEAt the beginning of 2020, hydroxychloroquine showed promising in vitro activity for Covid-19 and several studies were oriented to assess its safety and efficacy. However, after a few months, hydroxychloroquine has proved ineffective. The randomized controlled trials (RCTs) developed quickly and in different settings represent the scientific communitys capacity to assess drug repositioning effectiveness during a sanitary crisis. Therefore, a critical evaluation of the evidence generated can guide future efforts in analogous situations. We aimed to analyze the RCTs assessing the efficacy of hydroxychloroquine in treating Covid-19, describe their internal validity and power, and evaluate their contribution to the precision of the combined evidence for assessing the mortality outcome.\n\nSTUDY DESIGN AND SETTINGSThis meta-research included RCTs assessing hydroxychloroquine to treat patients diagnosed with Covid-19. It was part of an umbrella systematic review of methods/meta-research (PROSPERO: CRD42022360331) that included a comprehensive search in MEDLINE, EMBASE, Cochrane Library, and the Latin America Database - Lilacs. We retrieved studies published until January 10th, 2022. The risk of bias was assessed using Risk of Bias (RoB) 2.0. We analyzed methodology of the studies, precision and random error change through time from pooled evidence, study comparators, patient important outcome, power in different magnitude of effects proxy.\n\nRESULTSA total of 22 RCT were included, from that 17 (77%) assessed hospitalized patients and five (23%) outpatients setting. Mortality was related as primary endpoint in only 4 studies, however half of the studies included composite endpoints including mortality as a component. The internal validity analysis using RoB2 found that eight studies (36%) had a high risk of bias. Only one study had sufficient power to evaluate a moderate magnitude of effect (RR = 0,7 on mortality). The standard error to evaluate efficacy on mortality did not change appreciably after October 2020. From Oct 2020 to Dec 2021, 18 additional studies were published with 2,429 patients recruited.\n\nCONCLUSIONThis meta-research highlights the impact that collaborative, and network scientific research have on informing clinical decision-making. Duplicate efforts create research waste as precision analysis shows that after October 2020, there was not appreciably changes in the precision of the pooled RCT evidence to estimate the hydroxychloroquine effect on mortality.\n\nWhat is new?O_LIAfter Oct2020, grouped RCT on the use of hydroxychloroquine in Covid-19 showed that precision estimate has not been appreciably modified in subsequent studies.\nC_LIO_LIAt least 18 RCT (n=2,429) could potentially be saved through collaborative work.\nC_LIO_LIMost individual studies did not have sufficient power to assess the size of moderate effect size on mortality.\nC_LIO_LIStrengthening cooperation and integrating research centers can decrease research waste.\nC_LI", "rel_num_authors": 4, "rel_authors": [ { @@ -352,7 +696,7 @@ "rel_date": "2024-01-22", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.21.24301582", - "rel_abs": "Objective: To investigate the relationship between vaccination rates and excess mortality during distinct waves of SARS-CoV-2 variant-specific infections, while considering a state's GDP per capita. Methods: We ranked U.S. states by vaccination rates and GDP and employed the CDC's excess mortality model for regression and odds ratio analysis. Results: Regression analysis reveals that both vaccination and GDP are significant factors related to mortality when considering the entire U.S. population. Notably, in wealthier states (with GDP above $65,000), excess mortality is primarily driven by slow vaccination rates, while in less affluent states, low GDP plays a major role. Odds ratio analysis demonstrates an almost twofold increase in mortality linked to the Delta and Omicron BA.1 virus variants in states with the slowest vaccination rates compared to those with the fastest (OR 1.8, 95% CI 1.7-1.9, p < 0.01). However, this gap disappeared in the post-Omicron BA.1 period. Conclusion: The interplay between slow vaccination and low GDP per capita drives high mortality.", + "rel_abs": "ObjectiveTo investigate the relationship between vaccination rates and excess mortality during distinct waves of SARS-CoV-2 variant-specific infections, while considering a states GDP per capita.\n\nMethodsWe ranked U.S. states by vaccination rates and GDP and employed the CDCs excess mortality model for regression and odds ratio analysis.\n\nResultsRegression analysis reveals that both vaccination and GDP are significant factors related to mortality when considering the entire U.S. population. Notably, in wealthier states (with GDP above $65,000), excess mortality is primarily driven by slow vaccination rates, while in less affluent states, low GDP plays a major role. Odds ratio analysis demonstrates an almost twofold increase in mortality linked to the Delta and Omicron BA.1 virus variants in states with the slowest vaccination rates compared to those with the fastest (OR 1.8, 95% CI 1.7-1.9, p < 0.01). However, this gap disappeared in the post-Omicron BA.1 period.\n\nConclusionThe interplay between slow vaccination and low GDP per capita drives high mortality.", "rel_num_authors": 3, "rel_authors": [ { @@ -379,7 +723,7 @@ "rel_date": "2024-01-22", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.18.24301504", - "rel_abs": "South America suffered large SARS-CoV-2 epidemics between 2020 and 2022 caused by multiple variants of interest and concern, some causing substantial morbidity and mortality. However, their transmission dynamics are poorly characterised. The epidemic situation in Chile enables us to investigate differences in the distribution and spread of variants Alpha, Gamma, Lambda, Mu and Delta. Chile implemented non-pharmaceutical interventions and an integrated genomic and epidemiological surveillance system that included airport and community surveillance to track SARS-CoV-2 variants. Here we combine viral genomic data and anonymised human mobility data from mobile phones to characterise the routes of importation of different variants into Chile, the relative contributions of airport-based importations to viral diversity versus land border crossings and test the impact of the mobility network on the diffusion of viral lineages within the country. We find that Alpha, Lambda and Mu were identified in Chile via airport surveillance six, four and five weeks ahead of their detection via community surveillance, respectively. Further, some variants that originated in South America were imported into Chile via land rather than international air travel, most notably Gamma. Different variants exhibited similar trends of viral dissemination throughout the country following their importation, and we show that the mobility network predicts the time of arrival of imported lineages to different Chilean comunas. Higher stringency of local NPIs was also associated with fewer domestic viral importations. Our results show how genomic surveillance combined with high resolution mobility data can help predict the multi-scale geographic expansion of emerging infectious diseases.", + "rel_abs": "South America suffered large SARS-CoV-2 epidemics between 2020 and 2022 caused by multiple variants of interest and concern, some causing substantial morbidity and mortality. However, their transmission dynamics are poorly characterised. The epidemic situation in Chile enables us to investigate differences in the distribution and spread of variants Alpha, Gamma, Lambda, Mu and Delta. Chile implemented non-pharmaceutical interventions and an integrated genomic and epidemiological surveillance system that included airport and community surveillance to track SARS-CoV-2 variants. Here we combine viral genomic data and anonymised human mobility data from mobile phones to characterise the routes of importation of different variants into Chile, the relative contributions of airport-based importations to viral diversity versus land border crossings and test the impact of the mobility network on the diffusion of viral lineages within the country. We find that Alpha, Lambda and Mu were identified in Chile via airport surveillance six, four and five weeks ahead of their detection via community surveillance, respectively. Further, some variants that originated in South America were imported into Chile via land rather than international air travel, most notably Gamma. Different variants exhibited similar trends of viral dissemination throughout the country following their importation, and we show that the mobility network predicts the time of arrival of imported lineages to different Chilean comunas. Higher stringency of local NPIs was also associated with fewer domestic viral importations. Our results show how genomic surveillance combined with high resolution mobility data can help predict the multi-scale geographic expansion of emerging infectious diseases.\n\nSignificance statementGlobal preparedness for pandemic threats requires an understanding of the global variations of spatiotemporal transmission dynamics. Regional differences are important because the local context sets the conditions for the unfolding of local epidemics, which in turn affect transmission dynamics at a broader scale. Knowledge gaps from the SARS-CoV-2 pandemic remain for regions like South America, where distinct sets of viral variants emerged and spread from late 2020 onwards, and where changes in human behaviour resulted in epidemics which differed from those observed in other regions. Our interdisciplinary analysis of the SARS-CoV-2 epidemic in Chile provides insights into the spatiotemporal trends of viral diffusion in the region which shed light on the drivers that can influence future epidemic waves and pandemics.", "rel_num_authors": 19, "rel_authors": [ { @@ -718,7 +1062,7 @@ "rel_date": "2024-01-20", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.18.576147", - "rel_abs": "Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls retrieved from public databases. nf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Documentation and example results are available at https://nf-co.re/airrflow.", + "rel_abs": "MotivationAdaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures.\n\nResultsTo address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls retrieved from public databases.\n\nAvailability and implementationnf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Documentation and example results are available at https://nf-co.re/airrflow.\n\nVisual abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC=\"FIGDIR/small/576147v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (24K):\norg.highwire.dtl.DTLVardef@1021bd5org.highwire.dtl.DTLVardef@1715616org.highwire.dtl.DTLVardef@1cabf17org.highwire.dtl.DTLVardef@1c79b9e_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 16, "rel_authors": [ { @@ -1599,41 +1943,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2024.01.17.24301436", - "rel_title": "Predicting COVID-19 Infection Among Older Syrian Refugees in Lebanon: A Multi-Wave Survey", - "rel_date": "2024-01-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.17.24301436", - "rel_abs": "BackgroundOlder refugees, exposed to a cluster of biological and social vulnerabilities, are more susceptible to COVID-19 infection and its complications. This study developed and internally validated a predictive model estimating COVID-19 infection risk among older Syrian refugees in Lebanon. Additionally, it described the barriers to PCR testing among those who reported a COVID-19 infection.\n\nMethodsThis was a cross-sectional analysis of a five-wave longitudinal study conducted between September 2020 and March 2022. Syrian refugees aged 50 years or older living in households that received assistance from a humanitarian organization were interviewed by phone. Self-reported COVID-19 infection was the outcome of interest. The predictors were identified using adaptive LASSO regression. The model performance and discrimination were presented using the calibration slope and the Area Under the Curve.\n\nFindingsOf 2,886 participants (median [IQR] age: 56[52-62]; 52.9% males), 283 individuals (9.8%) reported a COVID-19 infection at least once. Six predictors for COVID-19 infection were identified: living outside informal tented settlements, having elementary and preparatory education or above, having chronic conditions, not receiving cash assistance, being water insecure and having unmet waste management needs. The model had moderate discrimination and good calibration. Nearly half of the cases were diagnosed through PCR testing. The main reasons for not testing were perception that the tests were unnecessary (n=91[63.6%]) or inability to afford them (n=46[32.2%]).\n\nInterpretationHigh-risk individuals should be targeted based on predictive models incorporating social determinants. Implementing awareness campaigns, screening measures, and cash assistance may reduce vulnerability in future pandemics.\n\nFundingELRHAs Research for Health in Humanitarian Crisis Programme and AUB University Research Board.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSA literature search was conducted in the databases PubMed and Google Scholar for studies published between February 1, 2020, and June 14, 2022, with the objective of developing a predictive model or examining the associated factors of COVID-19 infection among older adults or refugees. Different combinations of the following keywords were used in our research: \"COVID-19 infection\", \"SARS-CoV-2\", \"Coronavirus\", \"predictors\", \"risk factors\", \"refugees\", \"migrants\", and \"Syrian\". Previous evidence has shown that displaced populations are considered vulnerable groups highly susceptible to the impacts of COVID-19, due to their exposure to a combination of biological and psychosocial vulnerabilities. In Lebanon, Syrian refugees face an elevated risk of infection and its complications, mainly due to the deterioration of their living conditions resulting from the multiple crises burdening the country. The literature search featured the following potential predictors: age, gender, educational attainment, marital status, housing conditions, socioeconomic status, and presence of chronic illnesses. However, to date, no studies have developed predictive models of COVID-19 infection focusing on Syrian refugees in the MENA region. Additionally, there has been a scarcity of predictive models incorporating social determinants to assess the risk of infection among refugees or older adults in this context. Hence, identifying individuals who are highly susceptible to COVID-19 infection and its severity amongst vulnerable populations is important to inform better targeting of assistance in future outbreaks and to reduce the risk of infection and its complications.\n\nAdded value of the studyTo the best of our knowledge, this is the first study that exclusively incorporates social determinants into a prediction model of COVID-19 infection among older Syrian refugees. Out of 2,886 participants, 283 individuals (9.8%) reported experiencing COVID-19 infection at least once. Six predictors of COVID-19 infection among older Syrian refugees were identified: living outside informal tented settlements, having elementary and preparatory education or above, having chronic conditions, not receiving cash assistance, being water insecure and having unmet waste management needs. Despite the efforts and the collaboration between UNHCR, several NGOs and the Lebanese Ministry of Public Health to cover the cost of COVID-19 testing and to raise awareness about COVID-19 symptoms and the necessity of testing, only half of the cases were diagnosed through PCR or lateral flow tests. The main reasons for not testing were perceptions that it was unnecessary or inability to afford the tests.\n\nImplications of all the available evidenceThe predictors identified in this study could be used to inform targeting efforts by humanitarian organizations to provide assistance to Syrian refugees at higher risk of COVID-19 infection or infections in future pandemics. In addition, it will be important for humanitarian organisations to continue outreach efforts outside of informal tented settlements into the community to reach the most vulnerable to COVID infection with interventions. Furthermore, intensifying awareness campaigns among Syrian refugees about testing availability and the importance of visiting a healthcare professional, and considering the implementation of free testing in primary healthcare centers and pharmacies will be essential to control infectious diseases in future pandemics.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Berthe Abi Zeid", - "author_inst": "Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Lebanon" - }, - { - "author_name": "Tanya El Khoury", - "author_inst": "Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Lebanon" - }, - { - "author_name": "Sawsan R Abdulrahim", - "author_inst": "Department of Health Promotion and Community Health, Faculty of Health Sciences, American University of Beirut, Lebanon" - }, - { - "author_name": "Hala Ghattas", - "author_inst": "Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Lebanon" - }, - { - "author_name": "Stephen J McCall", - "author_inst": "Center for Research on Population and Health, Faculty of Health Sciences, American University of Beirut, Lebanon" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2024.01.17.24301326", "rel_title": "Why did people not get vaccinated against COVID-19? Results from a nationwide survey among Mexican adults", @@ -1718,7 +2027,7 @@ "rel_date": "2024-01-16", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.15.575706", - "rel_abs": "Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of receptor-binding domain (RBD) mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native-biological interfaces, specifically the ACE2 receptor. Notably, we identify a twofold increase in structural deformations for the proteins receptor binding motif onto the inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of amino acids (landing-footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, with the WT RBD adsorbed more strongly to than the delta or omicron RBDs. In contrast, the adsorption of delta and omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces could lead current experimental efforts in the design of virucidal surfaces.", + "rel_abs": "Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of receptor-binding domain (RBD) mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native-biological interfaces, specifically the ACE2 receptor. Notably, we identify a twofold increase in structural deformations for the proteins receptor binding motif onto the inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of amino acids (landing-footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, with the WT RBD adsorbed more strongly than the delta or omicron RBDs. In contrast, the adsorption of delta and omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces could lead current experimental efforts in the design of virucidal surfaces.", "rel_num_authors": 3, "rel_authors": [ { @@ -1949,6 +2258,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2024.01.14.24301291", + "rel_title": "Heterogeneity in deaths of despair: excess mortality in the US during the Covid-19 pandemic", + "rel_date": "2024-01-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.14.24301291", + "rel_abs": "The impact of Covid-19 on mortality includes both direct effects of the virus and indirect effects mediated through other causal pathways. In the United States, the indirect effects, particularly from suicides, overdoses and alcohol-induced causes (i.e. deaths of despair) (1) are understudied. Here, we estimated excess non-Covid deaths and deaths of despair, in the US overall, in each state and in 72 demographic strata. Nationally, 114,230 (127,597) excess non-Covid deaths, 19,074 (33,559) excess poisoning deaths and 8,746 (13,771) excess alcohol-induced deaths were estimated during 2020 (2021). Excess poisoning and alcohol-induced mortality were highest among the 35-44 and the 55-64 year groups, respectively. The Black and the American Indian/Alaskan Native populations had the highest excess poisoning and alcohol-induced mortality, respectively. Fewer suicides than expected occurred nationally, but excess suicides were estimated among Black youth. These findings suggest that additional resources need to be mobilized to limit increases in deaths of despair.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sasikiran Kandula", + "author_inst": "Columbia University" + }, + { + "author_name": "Katherine M Keyes", + "author_inst": "Columbia University" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Columbia University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2024.01.14.23300571", "rel_title": "Pre-event psychiatric states predict trajectories of post-traumatic stress symptoms during the COVID-19 pandemic", @@ -3829,65 +4165,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2024.01.10.574975", - "rel_title": "Effective assessment of CD4+ T cell Immunodominance patterns: impact of antigen processing and HLA restriction", - "rel_date": "2024-01-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.10.574975", - "rel_abs": "Identifying T cell epitopes is essential for studying and potentially tuning immune responses to pathogens. The polymorphic nature of major histocompatibility complex of class II (MHCII)-genes, and the complexity of the antigen processing mechanisms hinders the effective prediction of immunodominant patterns in humans, specially at the population level. Here, we combined the output of a reconstituted antigen processing system and of in silico prediction tools for SARS-CoV-2 antigens considering a broad-population coverage DRB1* panel to gain insights on immunodominance patterns. The two methods complement each other, and the resulting model improves upon single positive predictive values (PPV) from each of them to explain known epitopes. This model was used to design a minimalistic peptide pool (59 peptides) matching the performance reported for large overlapping peptide pools (> 500 peptides). Furthermore, almost 70 % of the candidates (23 peptides) selected for a frequent HLA background (DRB1*03:01/*07:01) feature immunodominant responses ex vivo, validating our platform for accessing T cell epitopes at the population level. The analysis of the impact of processing constraints reveals distinct impact of proteolysis and solvent accessible surface area on epitope selection depending on the antigen. Thus, considering these properties for antigens in question should improve available epitope prediction tools.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Miguel Alvaro-Benito", - "author_inst": "Freie Universitaet Berlin" - }, - { - "author_name": "Esam T Abualrous", - "author_inst": "Freie Universitaet Berlin" - }, - { - "author_name": "Holger Lingel", - "author_inst": "Otto-von-Gericke-University" - }, - { - "author_name": "Stefan Meltendorf", - "author_inst": "Otto-von-Gericke-University" - }, - { - "author_name": "Jakob Holzapfel", - "author_inst": "Freie Universitaet Berlin" - }, - { - "author_name": "Jana Sticht", - "author_inst": "Freie Universitaet Berlin" - }, - { - "author_name": "Benno Kuropka", - "author_inst": "Freie Universitaet Berlin" - }, - { - "author_name": "Cecilia Clementi", - "author_inst": "Freie Universitaet Berlin" - }, - { - "author_name": "Frank Kuppler", - "author_inst": "Freie Universitaet Berlin" - }, - { - "author_name": "Monika C Brunner-Weinzierl", - "author_inst": "Otto-von-Gericke-University" - }, - { - "author_name": "Christian Freund", - "author_inst": "Freie Universitaet Berlin" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2024.01.10.574981", "rel_title": "Variant-specific interactions at the plasma membrane: Heparan sulfate's impact on SARS-CoV-2 binding kinetics", @@ -4119,6 +4396,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2024.01.08.574531", + "rel_title": "Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins in Escherichia coli", + "rel_date": "2024-01-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.08.574531", + "rel_abs": "The fundamental biology of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (Ncap), its use in diagnostic assays and its potential application as a vaccine component have received considerable attention since the outbreak of the Covid19 pandemic in late 2019. Here we report the scalable expression and purification of soluble, immunologically active, SARS-CoV-2 Ncap in Escherichia coli. Codon-optimised synthetic genes encoding the original Ncap sequence and four common variants with an N-terminal 6His affinity tag (sequence MHHHHHHG) were cloned into an inducible expression vector carrying a regulated bacteriophage T5 synthetic promoter controlled by lac operator binding sites. The constructs were used to express Ncap proteins and protocols developed which allow efficient production of purified Ncap with yields of over 200 mg per litre of culture media. These proteins were deployed in ELISA assays to allow comparison of their responses to human sera. Our results suggest that there was no detectable difference between the 6His-tagged and untagged original Ncap proteins but there may be a slight loss of sensitivity of sera to other Ncap isolates.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Emma L Brudenell", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Manoj B Pohare", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Domen Zafred", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Janine Phipps", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Hailey R Hornsby", + "author_inst": "University of Sheffield" + }, + { + "author_name": "John Darby", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Junxiao Dai", + "author_inst": "The University of Manchester" + }, + { + "author_name": "Ellen Liggett", + "author_inst": "The University of Manchester" + }, + { + "author_name": "Kathleen Cain", + "author_inst": "The University of Manchester" + }, + { + "author_name": "Perdita E Barran", + "author_inst": "The University of Manchester" + }, + { + "author_name": "Thushan I de Silva", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Jon R Sayers", + "author_inst": "University of Sheffield" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2024.01.08.574642", "rel_title": "Preferential apical infection of intestinal cell monolayers by SARS-CoV-2 is associated with damage to cellular barrier integrity: Implications for the physiopathology of COVID-19", @@ -5611,37 +5951,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2024.01.03.24300755", - "rel_title": "Quantifying the impact of social activities on SARS-CoV-2 transmission using Google mobility reports", - "rel_date": "2024-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.03.24300755", - "rel_abs": "We developed a state-space model to investigate which social behaviours had biggest impact on the spread of SARS-CoV-2. The analyses were based on reported hospitalizations, together with information on vaccinations, weather data, virus strains and, most importantly, Google mobility reports on 4 different types of social activities. While our new approach is general, we studied Sweden and Norway on a regional level over 75 weeks, and the major regions of Berlin and Bavaria in Germany over 10 months. Most results are shared for all three countries: Activity in four social settings explain between 40-60% of all infections; Public transport appears as an important setting for infections in all countries; and the transmission potential drops by 40-50% during the summer as compared to the winter peak. However, the analyses for Germany differ in that Retail and recreation is the other setting dominating transmission whereas it is contacts at the Workplace in Norway and Sweden, showing how our model is able to adapt to specific cases. Transmissions not captured by the Google data may happen in other settings, in particular in households. The statistical model has a deterministic time and region specific transmission rate with an additive component for the four Google settings, and a multiplicative part taking seasonality and circulating virus strains into account. Inference is performed in a Bayesian setting using Stan.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Felix G\u00fcnther", - "author_inst": "Department of Mathematics, Stockholm University" - }, - { - "author_name": "Hilde Kjelgaard Brustad", - "author_inst": "Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo University Hospital" - }, - { - "author_name": "Arnoldo Frigessi", - "author_inst": "Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo University Hospital" - }, - { - "author_name": "Tom Britton", - "author_inst": "Department of Mathematics, Stockholm University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2024.01.03.574018", "rel_title": "Prototype mRNA vaccines imprint broadly neutralizing human serum antibodies after Omicron variant-matched boosting", @@ -5953,6 +6262,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2024.01.03.574082", + "rel_title": "Mutation of highly conserved residues in loop 2 of the coronavirus macrodomain demonstrates that enhanced ADP-ribose binding is detrimental to infection", + "rel_date": "2024-01-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.03.574082", + "rel_abs": "All coronaviruses (CoVs) encode for a conserved macrodomain (Mac1) located in nonstructural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that binds and hydrolyzes mono-ADP-ribose from target proteins. Previous work has shown that Mac1 is important for virus replication and pathogenesis. Within Mac1, there are several regions that are highly conserved across CoVs, including the GIF (glycine-isoleucine-phenylalanine) motif. To determine how the biochemical activities of these residues impact CoV replication, the isoleucine and the phenylalanine residues were mutated to alanine (I-A/F-A) in both recombinant Mac1 proteins and recombinant CoVs, including murine hepatitis virus (MHV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The F-A mutant proteins had ADP-ribose binding and/or hydrolysis defects that led to attenuated replication and pathogenesis in cell culture and mice. In contrast, the I-A mutations had normal enzyme activity and enhanced ADP-ribose binding. Despite increased ADP-ribose binding, I-A mutant MERS-CoV and SARS-CoV-2 were highly attenuated in both cell culture and mice, indicating that this isoleucine residue acts as a gate that controls ADP-ribose binding for efficient virus replication. These results highlight the function of this highly conserved residue and provide unique insight into how macrodomains control ADP-ribose binding and hydrolysis to promote viral replication and pathogenesis.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Catherine M Kerr", + "author_inst": "University of Kansas" + }, + { + "author_name": "Jessica J Pfannenstiel", + "author_inst": "University of Kansas" + }, + { + "author_name": "Yousef M Alhammad", + "author_inst": "University of Kansas" + }, + { + "author_name": "Anuradha Roy", + "author_inst": "University of Kansas" + }, + { + "author_name": "Joseph J O'Connor", + "author_inst": "University of Kansas" + }, + { + "author_name": "Roshan Ghimire", + "author_inst": "Oklahoma State University" + }, + { + "author_name": "Reem Khattabi", + "author_inst": "University of Kansas" + }, + { + "author_name": "Rakshya Shrestha", + "author_inst": "Oklahoma State University" + }, + { + "author_name": "Peter R McDonald", + "author_inst": "University of Kansas" + }, + { + "author_name": "Philip Gao", + "author_inst": "University of Kansas" + }, + { + "author_name": "David K Johnson", + "author_inst": "University of Kansas" + }, + { + "author_name": "Sunil More", + "author_inst": "Oklahoma State University" + }, + { + "author_name": "Rudragouda Channappanavar", + "author_inst": "Oklahoma State University" + }, + { + "author_name": "Anthony R Fehr", + "author_inst": "University of Kansas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2024.01.04.24300836", "rel_title": "Automated Classification of At-home SARS-CoV-2 Lateral Flow Assay Test Results using Image Matching and Transfer Learning: multiple-pipeline study", @@ -7421,25 +7801,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2023.12.26.572282", - "rel_title": "Synthesis and Assembly of mRNA-Bifunctional Lipid Nanoparticle (BLNP) for Selective Delivery of mRNA Vaccines to Dendritic Cells", - "rel_date": "2023-12-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.26.572282", - "rel_abs": "The fight against COVID-19 pandemic has gained a strong consensus about the importance of developing mRNA vaccines to rapidly respond to an outbreak. Several studies have shown that mRNA vaccines formulated as mRNA-lipid nanoparticles (LNPs) for vaccination can elicit a robust and efficient immune response. In this study, we report the preparation of mRNA-bifunctional lipid nanoparticles (mRNA-BLNPs) as vaccines for targeted delivery to dendritic cells (DCs) to improve safety and enhance immune response. Using this DC-targeted delivery system, mice immunized with SARS-CoV-2 spike mRNA-BLNP vaccine elicited a stronger immune response with higher titer of neutralizing IgG antibody response than the LNPformulated vaccine against SARS-CoV-2. In addition, the spike mRNA-BLNP vaccine with deletion of glycosites in the stem elicited a broadly protective immune response against SARS-CoV2 and variants. These findings suggest the importance and potential of developing DC-targeted mRNA vaccines to elicit broadly protective immune responses against human viruses.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Chi-Huey Wong", - "author_inst": "Department of Chemistry, The Scripps Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.12.22.23300471", "rel_title": "Nowcasting Reported COVID-19 Hospitalizations Using De-Identified, Aggregated Medical Insurance Claims Data", @@ -7731,6 +8092,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.12.21.23300355", + "rel_title": "Assessing Sociodemographic Factors Associated with Household Hardships during the COVID-19 Pandemic in Manhica, Mozambique using Data Collected between April 2021 and February 2022", + "rel_date": "2023-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.21.23300355", + "rel_abs": "BackgroundCOVID-19 resulted in vast disruption to life in the 21st century. To quell the disease spread, national governments implemented several containment measures like state of emergency, curfews, and lockdowns that likely created hardships for households. To improve knowledge of the negative consequences of these lockdowns, we examine the extent to which the pandemic period was associated with hardships at the household level and assess factors associated with household vulnerability to these hardships.\n\nMethodsWe conducted a cross-sectional survey between April 2021 and February 2022 among households residing in the district of Manhica through a survey questionnaire fielded in the Health and Demographic Surveillance System (HDSS) operating in Manhica, Mozambique. Logistic regression was used to analyze associations between the head of household and household characteristics with specific household hardships (business closure, food price increase, household member detained, input inflation, job loss).\n\nResultsHouseholds headed by individuals with lower education and employed in non-agricultural occupations as well as households that were larger in size or poorer in asset ownership compared to other households were generally at greater risk of experiencing a larger variety of hardships. Conversely, households that owned \"distance demolishing technologies\" such as motorcycles were less likely to experience these hardships, presumably as they were able to transcend local conditions.\n\nConclusionsThese results identify at-risk groups according to a social determinants of vulnerability framework and will help inform future policies and practices that aim to mitigate the negative consequences of COVID-19 as well as future disease outbreaks.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Ariel Q. Nhacolo", + "author_inst": "Centro de Investigacao em Saude de Manhica, Maputo, Mozambique" + }, + { + "author_name": "Jonathan A Muir", + "author_inst": "Emory University, Atlanta, GA, United States" + }, + { + "author_name": "Zachary J. Madewell", + "author_inst": "Center for Global Health, US Centers for Disease Control and Prevention" + }, + { + "author_name": "Fatima Kheiri", + "author_inst": "Emory University, Atlanta, GA, United States" + }, + { + "author_name": "Charfudin N Sacoor", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Edgar L Jamisse", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Elisio G Xerinda", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Teodimiro Matsena", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Aura M Hunguana", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Quique Bassat", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Cynthia G Whitney", + "author_inst": "Emory University, Atlanta, GA, United States" + }, + { + "author_name": "Inacio M Mandomando", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Solveig A Cunningham", + "author_inst": "Emory University, Atlanta, GA, United States" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.12.20.23300299", "rel_title": "COVID-19 pandemic re-shaped the global dispersal of seasonal influenza viruses", @@ -9107,53 +9535,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.12.20.572504", - "rel_title": "Cell type-specific adaptation of the SARS-CoV-2 spike", - "rel_date": "2023-12-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.20.572504", - "rel_abs": "SARS-CoV-2 can infect various human tissues and cell types, principally via interaction with its cognate receptor ACE2. However, how the virus evolves in different cellular environments is poorly understood. Here, we used experimental evolution to study the adaptation of the SARS-CoV-2 spike to four human cell lines expressing different levels of key entry factors. After 20 passages, cell type-specific phenotypic changes were observed. Selected spike mutations were identified and functionally characterized in terms of entry efficiency, ACE2 affinity, spike processing, TMPRSS2 usage, entry pathway and syncytia formation. We found that the effects of these mutations varied across cell types. Interestingly, two spike mutations (L48S and A372T) that emerged in cells expressing low ACE2 levels increased receptor affinity, syncytia induction, and entry efficiency under low-ACE2 conditions. Our results demonstrate specific adaptation of the SARS-CoV-2 spike to different cell types and have implications for understanding SARS-CoV-2 tissue tropism and evolution.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Marc Carrascosa-Saez", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "Maria-Carmen Marques", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "- The IBV-COVID19-Pipeline", - "author_inst": "-" - }, - { - "author_name": "Ron Geller", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "Santiago F. Elena", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "Amal Rahmeh", - "author_inst": "Universitat Pompeu Fabra" - }, - { - "author_name": "Jeremy Dufloo", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - }, - { - "author_name": "Rafael Sanjuan", - "author_inst": "Instituto de Biologia Integrativa de Sistemas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.12.20.572494", "rel_title": "Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19", @@ -9553,6 +9934,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.12.18.572126", + "rel_title": "Multi-target mode of action of Sulfodyne(R), a stabilized Sulforaphane, against pathogenic effects of SARS-CoV-2 infection", + "rel_date": "2023-12-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.18.572126", + "rel_abs": "The coronavirus disease 2019 (COVID-19) due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown that, except vaccination, few therapeutics options for its treatment or prevention are available. Among the pathways that can be targeted for COVID-19 treatment, the Keap1/Nrf2 pathway seems of high interest as it regulates redox homeostasis and inflammation that are altered during SARS-CoV-2 infection. Here, we use three potent activators of the Keap1/Nrf2 pathway and showed that Sulfodyne(R), a stabilized natural Sulforaphane preparation with optimal bioavailability, had the highest antiviral activity in pulmonary or colonic epithelial cell lines even when added late after SARS-CoV-2 infection. This antiviral activity was not dependent on NRF2 activity but associated with action on ER stress and mTOR signaling that are activated during SARS-CoV-2 infection. Sulfodyne(R) also decreased the inflammatory response of epithelial cell lines infected by SARS-CoV-2 independently of SARS-CoV-2 replication and reduced the activation of human monocytes that are recruited after infection of epithelial cells by SARS-CoV-2. Administration of Sulfodyne(R) had little effects on SARS-CoV-2 replication in mice and hamsters infected with SARS-CoV-2 but significantly reduced weight loss and disease severity. Altogether, these results pinpoint the natural compound Sulfodyne(R) as a potent therapeutic agent of COVID-19 symptomatology.\n\nAuthor SummaryAccumulating evidence shows that oxidative stress coupled with the systemic inflammation contribute to COVID-19 pathogenesis. As the Keap1/Nrf2 pathway is the major regulator of redox homeostasis and promotes resolution of inflammation and as lung biopsies from COVID-19 patients showed a decreased NRF2 target gene signature, pharmacological agents that are known to activate NRF2 are good candidates for COVID-19 treatment. We show herein that Sulfodyne(R), an NRF2 activator that consists in a stabilized Sulforaphane preparation with optimal bioavailability, impairs SARS-CoV-2 replication in colonic or pulmonary epithelial cells. We show that this antiviral activity of Sulfodyne(R) is not dependent of NRF2 activation, characterize the pathways associated with the Sulfodyne(R) antiviral activity and show that Sulfodyne(R) displays multiple actions that result in a decrease of the inflammation associated with SARS-CoV-2 infection. Finally, we show that Sulfodyne(R) decreases the pathogenesis of mice or hamster infected with SARS-CoV-2. Overall, this study provides mechanistic explanations of the action of Sulfodyne(R) during SARS-CoV-2 infection and suggests that Sulfodyne(R) is a potential therapeutic agent of COVID-19 pathogenesis.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Paul-Henri Romeo", + "author_inst": "CEA" + }, + { + "author_name": "Laurine Conquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sebastien Messiaen", + "author_inst": "CEA" + }, + { + "author_name": "Quentin Pascal", + "author_inst": "CEA" + }, + { + "author_name": "Stephanie G Moreno", + "author_inst": "CEA" + }, + { + "author_name": "Anne Bravard", + "author_inst": "CEA" + }, + { + "author_name": "Jacqueline Bernardino-Sgherri", + "author_inst": "CEA" + }, + { + "author_name": "Nathalie Dereuddre-Bosquet", + "author_inst": "CEA" + }, + { + "author_name": "Xavier Montagutelli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Roger Le Grand", + "author_inst": "CEA" + }, + { + "author_name": "Vanessa Petit", + "author_inst": "CEA" + }, + { + "author_name": "Federica Ferri", + "author_inst": "CEA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2023.12.18.572191", "rel_title": "Broadly neutralizing antibody induction by non-stabilized SARS-CoV-2 Spike mRNA vaccination in nonhuman primates", @@ -11129,37 +11573,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.12.10.23299100", - "rel_title": "Protect or prevent? A practicable framework for the dilemmas of COVID-19 vaccine prioritization", - "rel_date": "2023-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.10.23299100", - "rel_abs": "Determining COVID-19 vaccination strategies presents many challenges in light of limited vaccination capacity and the heterogeneity of affected communities. Who should be prioritized for early vaccination when different groups manifest different levels of risks and contact rates? Answering such questions often becomes computationally intractable given that network size can exceed millions. We obtain a framework to compute the optimal vaccination strategy within seconds to minutes from among all strategies, including highly dynamic ones that adjust vaccine allocation as often as required, and even with modest computation resources. We then determine the optimal strategy for a large range of parameter values representative of various US states, countries, and case studies including retirement homes and prisons. The optimal is almost always one of a few candidate strategies, and, even when not, the suboptimality of the best among these candidates is minimal. Further, we find that many commonly deployed vaccination strategies, such as vaccinating the high risk group first, or administering second doses without delay, can often incur higher death rates, hospitalizations, and symptomatic counts. Our framework can be easily adapted to future variants or pandemics through appropriate choice of the compartments of the disease and parameters.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Raghu Arghal", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Harvey Rubin", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Shirin Saeedi Bidokhti", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Saswati Sarkar", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.12.14.23299967", "rel_title": "Diagnostic Accuracy of the Abbot BinaxNOW COVID-19 Antigen Card Test, Puerto Rico", @@ -11583,6 +11996,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2023.12.13.23299903", + "rel_title": "Expected and observed deaths in France from 2020 to 2022: accurately assessing the excess mortality during the COVID-19 pandemic period.", + "rel_date": "2023-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.13.23299903", + "rel_abs": "BackgroundExcess mortality has been used worldwide for summarizing the COVID-19 pandemic-related burden. In France, the reported estimates for years 2020 and 2021 vary by a factor of three, and reported evolving trends for year 2022 are discordant.\n\nObjectivesWe aimed at selecting the most appropriate modelling approach enabling an accurate estimation of the excess mortality in France during the 2020-2022 pandemic years.\n\nMethodBased on the 18,646,089 deaths that occurred In France between 1990 and 2023, the natural trend of age-and gender-specific death rates over time was considered according to three models which performances were compared for accurately predicting mortality data in the absence of pandemic perturbations. The best modelling approach was then used for estimating age-and gender-specific excess deaths and corresponding expected years of life lost in the individuals deceased in 2020, 2021, and 2022.\n\nResultsA quadratic model trained with years 2010-2019 estimated that 49,352 [40,257; 58,165] (mean [95% confidence interval]), 43,028 [29,071; 56,381], and 54,373 [34,696; 73,187] excess deaths occurred in France in 2020, 2021 and 2022, respectively. Corresponding years of life lost rose over time with 503,289 [446,347; 561,415], 581,495 [493,911; 671,162], and 667,439 [544,196; 794,225] years of life lost for the individuals deceased in 2020, 2021, and 2022, respectively.\n\nConclusionThe study proposes a reliable method for accurately estimating excess mortality. Applying this method to the 2020-2022 years of the COVID-19 pandemic in France yielded estimates of excess mortality that peaked in year 2022.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Paul Moulaire", + "author_inst": "INSERM" + }, + { + "author_name": "Gilles Hejblum", + "author_inst": "INSERM" + }, + { + "author_name": "Nathanael Lapidus", + "author_inst": "INSERM" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.12.13.571479", "rel_title": "A distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia", @@ -12871,45 +13311,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2023.12.08.23299736", - "rel_title": "Spatial and Temporal Patterns of SARS-CoV-2 transmission in uMgungundlovu, Kwa-Zulu Natal, South Africa", - "rel_date": "2023-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.08.23299736", - "rel_abs": "BackgroundInvestigating the spatial distribution of SARS-CoV-2 at a local level and describing the pattern of disease occurrence can be used as the basis for efficient prevention and control measures. This research project aims to utilize geospatial analysis to understand the distribution patterns of SARS-CoV-2 and its relationship with certain co-existing factors.\n\nMethodsSpatial characteristics of SARS-CoV-2 were investigated over the first four waves of transmission using ESRI ArcGISPro v2.0, including Local Indicators of Spatial Association (LISA) with Morans \"I\" as the measure of spatial autocorrelation; and Kernel Density Estimation (KDE). In implementing temporal analysis, time series analysis using the Python Seaborn library was used, with separate modelling carried out for each wave.\n\nResultsStatistically significant SARS-CoV-2 incidences were noted across age groups with p-values consistently < 0.001. The central region of the district experienced a higher level of clusters indicated by the LISA (Morans I: wave 1 - 0.22, wave 2 - 0.2, wave 3 - 0.11, wave 4 - 0.13) and the KDE (Highest density of cases: wave 1: 25.1-50, wave 2: 101-150, wave 3: 101-150, wave 4: 50.1-100). Temporal analysis showed more fluctuation at the beginning of each wave with less fluctuation in identified cases within the middle to end of each wave.\n\nConclusionA Geospatial approach of analysing infectious disease transmission is proposed to guide control efforts (e.g., testing/tracing and vaccine rollout) for populations at higher vulnerability. Additionally, the nature and configuration of the social and built environment may be associated with increased transmission. However, locally specific empirical research is required to assess other relevant factors associated with increased transmission.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Radiya Gangat", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Veranyuy Ngah", - "author_inst": "Stellenbosch University Faculty of Medicine and Health Sciences" - }, - { - "author_name": "Justine Blanford", - "author_inst": "University of Twente Faculty of Geo-Information Science and Earth Observation: Universiteit Twente Faculteit Geo-Informatie Wetenschappen en Aardobservatie" - }, - { - "author_name": "Rushambwa Tawonga", - "author_inst": "University of KwaZulu-Natal School of Development Studies: University of KwaZulu-Natal School of Built Environment and Development Studies" - }, - { - "author_name": "Jabulani Ronnie Ncayiyana", - "author_inst": "University of Kwazulu-Natal" - }, - { - "author_name": "Peter S. Nyasulu", - "author_inst": "Stellenbosch University - Tygerberg Campus: Stellenbosch University Faculty of Medicine and Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.12.07.23299429", "rel_title": "Mechanisms underlying exercise intolerance in Long COVID: an accumulation of multi-system dysfunction", @@ -13221,6 +13622,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.12.06.23299623", + "rel_title": "Lack of association between HLA and asymptomatic SARS-CoV-2 infection", + "rel_date": "2023-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.06.23299623", + "rel_abs": "Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B*15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B*15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the US (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B*15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified. These findings suggest that memory T-cell immunity to seasonal coronaviruses does not strongly influence the outcome of SARS-CoV-2 infection in unvaccinated individuals.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Astrid Marchal", + "author_inst": "Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU" + }, + { + "author_name": "Elizabeth T Cirulli", + "author_inst": "Helix, San Mateo, CA, USA" + }, + { + "author_name": "Iva Neveux", + "author_inst": "Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA" + }, + { + "author_name": "Evangelos Bellos", + "author_inst": "Department of Infectious Diseases, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Ryan S Thwaites", + "author_inst": "National Heart and Lung Institute, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Kelly M Schiabor Barrett", + "author_inst": "Helix, San Mateo, CA, USA" + }, + { + "author_name": "Yu Zhang", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA" + }, + { + "author_name": "Ivana Nemes-Bokun", + "author_inst": "Department of Infectious Diseases, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Mariya Kalinova", + "author_inst": "hVIVO Services Ltd., London, UK" + }, + { + "author_name": "Andrew Catchpole", + "author_inst": "hVIVO Services Ltd., London, UK" + }, + { + "author_name": "Stuart G Tangye", + "author_inst": "Garvan Institute of Medical Research, Darlinghurst, NSW, Australia" + }, + { + "author_name": "Andras N Spaan", + "author_inst": "St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA" + }, + { + "author_name": "Justin B Lack", + "author_inst": "NIAID Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA" + }, + { + "author_name": "Jade Ghosn", + "author_inst": "Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU" + }, + { + "author_name": "Charles Burdet", + "author_inst": "Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU" + }, + { + "author_name": "Guy Gorochov", + "author_inst": "Sorbonne Universite, Paris, France, EU" + }, + { + "author_name": "Florence Tubach", + "author_inst": "Sorbonne Universite, Paris, France, EU" + }, + { + "author_name": "Pierre Hausfater", + "author_inst": "Emergency Department, Hopital Pitie-Salpetriere, APHP-Sorbonne Universite, Paris, France, EU" + }, + { + "author_name": "- COVID Human Genetic Effort", + "author_inst": "-" + }, + { + "author_name": "- COVIDeF Study Group", + "author_inst": "-" + }, + { + "author_name": "- French COVID Cohort Study Group", + "author_inst": "-" + }, + { + "author_name": "- CoV-Contact Cohort", + "author_inst": "-" + }, + { + "author_name": "- COVID-STORM Clinicians", + "author_inst": "-" + }, + { + "author_name": "- COVID Clinicians", + "author_inst": "-" + }, + { + "author_name": "- Orchestra Working Group", + "author_inst": "-" + }, + { + "author_name": "- Amsterdam UMC Covid-19 Biobank", + "author_inst": "-" + }, + { + "author_name": "- NIAID-USUHS COVID Study Group", + "author_inst": "-" + }, + { + "author_name": "Clifton L Dalgard", + "author_inst": "Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA" + }, + { + "author_name": "Shen-Ying Zhang", + "author_inst": "St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA" + }, + { + "author_name": "Qian Zhang", + "author_inst": "St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA" + }, + { + "author_name": "Christopher Chiu", + "author_inst": "Department of Infectious Diseases, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Jacques Fellay", + "author_inst": "School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland" + }, + { + "author_name": "Joseph J Grzymski", + "author_inst": "Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA" + }, + { + "author_name": "Vanessa Sancho-Shimizu", + "author_inst": "Department of Infectious Diseases, Imperial College London, London, United Kingdom" + }, + { + "author_name": "Laurent Abel", + "author_inst": "Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU" + }, + { + "author_name": "Jean-Laurent Casanova", + "author_inst": "St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA" + }, + { + "author_name": "Aurelie Cobat", + "author_inst": "Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU" + }, + { + "author_name": "Alexandre Bolze", + "author_inst": "Helix" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.12.05.570216", "rel_title": "Algorithm for selecting potential SARS-CoV-2 dominant variants based on POS-NT frequency", @@ -14549,117 +15117,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.12.04.23299364", - "rel_title": "Clinical coding of long COVID in primary care 2020-2023 in a cohort of 19 million adults: an OpenSAFELY analysis", - "rel_date": "2023-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.04.23299364", - "rel_abs": "BackgroundLong COVID is the patient-coined term for the persistent symptoms of COVID-19 illness for weeks, months or years following the acute infection. There is a large burden of long COVID globally from self-reported data, but the epidemiology, causes and treatments remain poorly understood. Primary care is used to help identify and treat patients with long COVID and therefore Electronic Health Records (EHRs) of past COVID-19 patients could be used to help fill these knowledge gaps. We aimed to describe those with long COVID in primary care records in England.\n\nMethodsWith the approval of NHS England we used routine clinical data from over 19 million adults in England linked to SARS-COV-2 test result, hospitalisation and vaccination data to describe trends in the recording of 16 clinical codes related to long COVID between November 2020 and January 2023. We calculated rates per 100,000 person-years and plotted how these changed over time. We compared crude and minimally adjusted rates of recorded long COVID in patient records between different key demographic and vaccination characteristics using negative binomial models.\n\nFindingsWe identified a total of 55,465 people recorded to have long COVID over the study period, with incidence of new long COVID records increasing steadily over 2021, and declining over 2022. The overall rate per 100,000 person-years was 177.5 cases in women (95% CI: 175.5-179) and 100.5 men (99.5-102). In terms of vaccination against COVID-19, the lowest rates were observed in those with 3+ vaccine doses (103.5 [95% CI: 101.5-105]). Finally, the majority of those with a long COVID record did not have a recorded positive SARS-COV-2 test 12 weeks before the long COVID record.\n\nInterpretationEHR recorded long COVID remains very low compared and incident records of long COVID declined over 2022. We found the lowest rates of recorded long COVID in people with 3 or more vaccine doses. We summarised several sources of possible bias for researchers using EHRs to study long COVID.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Alasdair D Henderson", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Ben FC Butler-Cole", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "John Tazare", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Laurie A Tomlinson", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Michael Marks", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Mark Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Andrew Briggs", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Liang-Yu Lin", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Oliver Carlile", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Christopher Bates", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds" - }, - { - "author_name": "John Parry", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds" - }, - { - "author_name": "Sebastian CJ Bacon", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "William A Dennison", - "author_inst": "Patient and Public Involvement Steering Committee, London," - }, - { - "author_name": "Ruth E Costello", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Yinghui Wei", - "author_inst": "Centre for Mathematical Sciences, School of Engineering, Computing and Mathematics, University of Plymouth, Plymouth" - }, - { - "author_name": "Alex J Walker", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "William Hulme", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "The OpenSAFELY Collaborative", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" - }, - { - "author_name": "Emily Herrett", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.12.04.23299370", "rel_title": "Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 and BA.5 subvariant predominance: a systematic literature review", @@ -14935,6 +15392,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.12.03.23299339", + "rel_title": "Expression profile analysis of COVID-19 patients", + "rel_date": "2023-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.03.23299339", + "rel_abs": "The course of COVID-19 is determined by various factors. Studies worldwide have shown a correlation between changes in the expression profile and the severity of the disease. Thus, an in-depth study of differentially expressed genes will allow a more detailed investigation of the metabolic changes occurring in the background of coronavirus infection. The technique of RNA sequencing and subsequent bioinformatics analysis is suitable for such research tasks. In our study, we compared groups of samples from patients with mild and severe disease course and identified a number of differentially expressed genes. These genes are involved in metabolic pathways responsible for immune response, signaling, intercellular communication, metabolism of various compounds etc. We then identified master regulators whose function and role in pathways enriched by differentially expressed genes makes them potential targets for biochemical and meta-studies.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Valentin S Shimansky", + "author_inst": "St. Petersburg State Health Care Institution \"City Hospital No. 40\"" + }, + { + "author_name": "Oleg S Popov", + "author_inst": "St. Petersburg State Health Care Institution \"City Hospital No. 40\"" + }, + { + "author_name": "Tatiana G Klochkova", + "author_inst": "St. Petersburg State Health Care Institution \"City Hospital No. 40\"" + }, + { + "author_name": "Svetlana V Apalko", + "author_inst": "St. Petersburg State Health Care Institution \"City Hospital No. 40\"" + }, + { + "author_name": "Natalya N Sushentseva", + "author_inst": "St. Petersburg State Health Care Institution \"City Hospital No. 40\"" + }, + { + "author_name": "Anna Yu Anisenkova", + "author_inst": "St. Petersburg State Health Care Institution \"City Hospital No. 40\"" + }, + { + "author_name": "Sergey V Mosenko", + "author_inst": "St. Petersburg State Health Care Institution \"City Hospital No. 40\"" + }, + { + "author_name": "Sergey G Shcherbak", + "author_inst": "St. Petersburg State Health Care Institution \"City Hospital No. 40\"" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2023.12.01.569046", "rel_title": "Substrate recognition and selectivity in SARS-CoV-2 main protease: Unveiling the role of subsite interactions through dynamical nonequilibrium molecular dynamics simulations", @@ -16263,53 +16767,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.11.29.23299183", - "rel_title": "Diagnostic Performance of Rapid Antigen Testing for SARS-CoV-2: The COVid-19 AntiGen (COVAG) Extension study", - "rel_date": "2023-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.29.23299183", - "rel_abs": "BackgroundRapid antigen tests (RATs) for SARS-CoV-2 have been used to combat the still ongoing Covid-19 pandemic. This study is the extension of the COVAG study originally performed from February 1 to March 31, 2021. We compared two RATs, the Panbio COVID-19 Ag Rapid Test (Abbott) and the SD Biosensor Q SARS-CoV-2 Rapid Antigen Test (Roche), against RT-PCR on the foil of new variants.\n\nMethodsWe included 888 all-comers at a diagnostic center between October 20, 2021, and March 18, 2022. RT-PCR-positive samples with a Ct value [≤] 32 were examined for SARS-CoV-2 variants.\n\nFindingsThe sensitivity of the Abbott-RAT and Roche-RAT were 65% and 67%, respectively. For both RATs, lower Ct values were significantly correlated with higher sensitivity. For samples with Ct values [≤] 25, the sensitivities of the Roche-RAT and of the Abbott-RAT were 96% and 95%, for Ct values 25-30 both were 19%, and for Ct values [≥] 30 they were 6% and 2%, respectively. The RATs had substantially higher sensitivities in symptomatic than asymptomatic participants (76, 77%, vs. 29, 31%, for Abbott-RAT, Roche-RAT, respectively) and in participants referred to testing by their primary care physician (84%, 85%) compared to participants who sought testing due to referral by the health department (55%, 58%) or a warning by the Corona-Warn-App (49%, 49%). In persons with self-reported previous Covid-19 sensitivities were markedly lower than in patients without previous Covid-19: 27% vs. 75% for Roche-RAT and 27% vs. 73% for Abbott-RAT. Depending on the vaccination status, the sensitivity of the RATs is 67.6%, 61.5% and 70.6% for non-vaccinated, vaccinated and boostered participants, respectively. For the considered subpopulation of 888 participants, we find no significant correlation between vaccination status and sensitivity.\n\nThe Omicron variant was detected with a sensitivity of 94% and 92%, the delta variant with a sensitivity of 80% and 80% for Abbott-RAT and Roche-RAT, respectively. This difference is attributable to the lower Ct values of the Omicron samples compared to the Delta samples. When adjusted for the Ct value, a multivariate logistic regression did not show a significant difference between Omicron and Delta. In terms of sensitivity, we found no significant difference between the wild-type and the Omicron and Delta variants, but a significantly lower sensitivity to the alpha variant compared to the other variants.\n\nFor a Ct value [≤] 25 the sensitivities were 95.2% and 96.0% for the Abbott-RAT and the Roche-RAT, respectively (Table 4). For a Ct value of 25-30 both RATs had a sensitivity of 18.8%. For a Ct value of 30-32, the sensitivities were 0.0% and 7.1% respectively, for Ct values [≥]32 the sensitivities were 3.0% and 6.0% for Abbott-RAT and Roche-RAT, respectively.\n\nThe specificities were >99% overall.\n\nInterpretation: The sensitivity of the RATs for asymptomatic carriers is unsatisfactory questioning their use for screening. When used in symptomatic patients or when requested by a primary care physician the sensitivities were higher. Our study does not suggest that the vaccination status influences the sensitivity of RATs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Christoph Wertenauer", - "author_inst": "Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany" - }, - { - "author_name": "Alexander Dressel", - "author_inst": "Dr. Dressel Consulting, Mannheim, Germany" - }, - { - "author_name": "Eberhard Wieland", - "author_inst": "SYNLAB Medical Care Center Leinfelden-Echterdingen GmbH, Leinfelden-Echterdingen, Germany" - }, - { - "author_name": "Hans-Joerg Wertenauer", - "author_inst": "Hausaerzte am Schillerplatz, Stuttgart, Germany" - }, - { - "author_name": "Helmine Braitmaier", - "author_inst": "SYNLAB Medical Care Center Leinfelden-Echterdingen GmbH, Leinfelden-Echterdingen, Germany" - }, - { - "author_name": "Anna Straub", - "author_inst": "SYNLAB Medical Care Center Leinfelden-Echterdingen GmbH, Leinfelden-Echterdingen, Germany" - }, - { - "author_name": "Nicolas Luetzner", - "author_inst": "SYNLAB Medical Care Center Leinfelden-Echterdingen GmbH, Leinfelden-Echterdingen, Germany" - }, - { - "author_name": "Winfried Maerz", - "author_inst": "SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.11.28.23298927", "rel_title": "Social determinants of adult COVID-19 vaccine acceptance and uptake in a Brazilian urban informal community: a longitudinal time-to-event study", @@ -16513,6 +16970,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.11.25.568642", + "rel_title": "Safe plant Hsp90 adjuvants elicit an effective immune response against SARS-CoV2 derived RBD antigen", + "rel_date": "2023-11-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.25.568642", + "rel_abs": "To better understand the role of pHsp90 adjuvant in immune response modulation, we proposed the use of the Receptor Binding Domain (RBD) of the Spike protein of SARS-CoV2, the principal candidate in the design of subunit vaccines. We evaluated the humoral and cellular immune responses against RBD through the strategy \"protein mixture\" (Adjuvant + Antigen). The rRBD adjuvanted with rAtHsp81.2 group showed a higher increase of the anti-rRBD IgG1, while the rRBD adjuvanted with rNbHsp90.3 group showed a significant increase of anti-rRBD IgG2b/2a. These results were consistent with the cellular immune response analysis. Spleen cell cultures from rRBD+rNbHsp90.3-immunized mice showed significantly increased IFN-{gamma} production. In contrast, spleen cell cultures from rRBD+rAtHsp81.2-immunized mice showed significant increased IL-4 levels. Finally, vaccines adjuvanted with rNbHsp90.3 induced higher neutralizing antibody responses compared to those adjuvanted with rAtHsp81.2. To know whether both chaperones must form complexes to generate an effective immune response, we performed co-immunoprecipitation (co-IP) assays. The results indicated that the greater neutralizing capacity observed in the rRBD adjuvanted with rNbHsp90.3 group would be given by the rRBD-rNbHsp90.3 interaction rather than by the quality of the immune response triggered by the adjuvants. These results, together with our previous results, provide a comparative benchmark of these two novel and safe vaccine adjuvants for their capacity to stimulate immunity to a subunit vaccine, demonstrating the capacity of adjuvanted SARS-CoV2 subunit vaccines. Furthermore, these results revealed differences in the ability to modulate the immune response between these two pHsp90s, highlighting the importance of adjuvant selection for future rational vaccine and adjuvant design.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Victor A Ramos-Duarte", + "author_inst": "INTECH" + }, + { + "author_name": "Alejandro Orlowski", + "author_inst": "UNLP" + }, + { + "author_name": "Carolina Jaquenod de Giusti", + "author_inst": "UNLP" + }, + { + "author_name": "Mariana G Corigliano", + "author_inst": "INTECH" + }, + { + "author_name": "Ariel Legarralde", + "author_inst": "INTECH" + }, + { + "author_name": "Luisa F Mendoza-Morales", + "author_inst": "INTECH" + }, + { + "author_name": "Agustin Atela", + "author_inst": "INTECH" + }, + { + "author_name": "Manuel A Sanchez", + "author_inst": "INTECH" + }, + { + "author_name": "Valeria A Sander", + "author_inst": "INTECH" + }, + { + "author_name": "Sergio O Angel", + "author_inst": "INTECH" + }, + { + "author_name": "Marina Clemente", + "author_inst": "INTECH" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2023.11.25.568670", "rel_title": "Identification of the host reservoir of SARS-CoV-2 and determining when it spilled over into humans", @@ -18133,25 +18649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.11.22.23298917", - "rel_title": "Assessment of the effectiveness of required weekly COVID-19 surveillance antigen testing at a university", - "rel_date": "2023-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.22.23298917", - "rel_abs": "ObjectivesTo mitigate the COVID-19 pandemic, many institutions implemented a regimen of periodic required testing, irrespective of symptoms. The effectiveness of this\"surveillance testing\" requires assessment.\n\nMethodsI fit a zero-inflated negative binomial model to COVID-19 testing and case investigation data between 1 November 2020 and 15 May 2021, from young adult subjects in one community. I compared the duration of symptoms at time of specimen collection in those diagnosed via (1) surveillance testing at a university, (2) the same universitys student health services, and (3) all other testing venues.\n\nResultsThe data comprised 2926 records: 393 from surveillance testing, 493 from student health service, and 2040 from other venues. About 65% of people with COVID-19 detected via surveillance testing were already symptomatic at time of specimen collection.\n\nPredicted mean duration of pre-testing symptoms was 1.7 days (95% CI 1.59 to 1.84) for the community, 1.81 days (95% CI 1.62 to 1.99) for surveillance, and 2 days (95% CI 1.83 to 2.16) for student health service. The modelled \"inflated\" proportions of asymptomatic subjects from the surveillance stream and the other/community stream were comparable (odds ratio 0.95, p = 0.7709). Comparing surveillance testing with the student health service, the proportion of \"excess\" zero symptom durations was signficantly higher in the former (Chi-square = 12.08, p = 0.0005)\n\nConclusionsSurveillance testing at a university detected 393 people with COVID-19, but no earlier in their trajectory than similar-aged people detected in the broader community. This casts some doubt on the public health value of such programs, which tend to be labor-intensive and expensive.\n\n2 Three-question summary boxO_ST_ABSWhat is the current understanding of this subject?C_ST_ABSAssessments of long-term operational effectiveness of COVID-19 \"surveillance testing\" have not been published.\n\nWhat does this report add to the literature?During the 2020-2021 academic year at one university, people with COVID-19 detected via compulsory weekly surveillance antigen testing were equally likely to be symptomatic at time of detection, and for just as long, as similar-aged people detected via testing venues in the community.\n\nWhat are the implications for public health practice?Surveillance testing programs during the pandemic consumed a large amount of time, money, and effort. In future respiratory pandemics, resources might be better devoted to other mitigation measures.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Christopher W Ryan", - "author_inst": "SUNY Upstate Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.11.22.23298899", "rel_title": "Quantitative susceptibility mapping at 7 Tesla in COVID-19: mechanistic and outcome associations", @@ -18467,6 +18964,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.11.22.23298846", + "rel_title": "Recovery of Neurophysiological Measures in Post-COVID Fatigue - a 12-month Longitudinal Follow-up Study", + "rel_date": "2023-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.22.23298846", + "rel_abs": "One of the major consequences of the COVID-19 pandemic has been the significant incidence of persistent fatigue following resolution of an acute infection (i.e. post-COVID fatigue). We have shown previously that, in comparison to healthy controls, those suffering from post-COVID fatigue exhibit changes in muscle physiology, cortical circuitry, and autonomic function. Whether these changes preceded infection, potentially predisposing people to developing post-COVID fatigue, or whether the changes were a consequence of infection was unclear. Here we present results of a 12-month longitudinal study of 18 participants from the same cohort of post-COVID fatigue sufferers to investigate these correlates of fatigue over time. We report improvements in self-perception of fatigue via questionnaires, as well as significant improvements in objective measures of peripheral muscle fatigue and autonomic function, bringing them closer to healthy controls. Additionally, we found reductions in muscle twitch tension rise times, becoming faster than controls, suggesting that the improvement in muscle fatigability might be due to a process of adaptation rather than simply a return to baseline function.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Natalie J Maffitt", + "author_inst": "Newcastle University" + }, + { + "author_name": "Maria Germann", + "author_inst": "Newcastle University" + }, + { + "author_name": "Anne ME Baker", + "author_inst": "Newcastle University" + }, + { + "author_name": "Mark R Baker", + "author_inst": "Newcastle University" + }, + { + "author_name": "Stuart N Baker", + "author_inst": "Newcastle University" + }, + { + "author_name": "Demetris S Soteropoulos", + "author_inst": "Newcastle University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2023.11.22.23298807", "rel_title": "CLUSTER ANALYSIS IDENTIFIES LONG COVID SUBTYPES IN BELGIAN PATIENTS", @@ -18731,7 +19267,7 @@ "rel_date": "2023-11-22", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.13.23298435", - "rel_abs": "ImportanceEvidence regarding audiovestibular adverse events post COVID-19 vaccination to date has been inconclusive regarding a potential etiological association. This study used a multi-data source approach to assess incidence of these events following COVID-19 vaccination.\n\nObjectiveTo determine if there was an increase in audiovestibular adverse events following COVID-19 vaccination in South-eastern Australia during January 2021 - March 2023.\n\nDesignRetrospective observational analysis of spontaneous reports of audiovestibular events to a statewide vaccine safety surveillance service, SAEFVIC, as well as accompanying self-controlled case series (SCCS) analysis using general practice data collected via the POpulation Level Analysis and Reporting (POLAR) tool with permission from Primary Health Networks (PHNs) as the de-identified dataset owners in Victoria and New South Wales.\n\nSettingVictoria and New South Wales (NSW), Australia.\n\nParticipantsVictorians who spontaneously reported an audiovestibular-related symptom or diagnosis to SAEFVIC, and people in Victoria and NSW who presented to a POLAR GP registered practice with a new audiovestibular diagnosis.\n\nExposuresCOVID-19 vaccination with adenovirus vector, mRNA or protein-subunit vaccine.\n\nOutcomes and MeasuresIn SAEFVIC, audiovestibular events of interest were ascertained through searching key words in the vaccine safety database. Reporting rates were calculated and compared per 100,000 COVID-19 vaccine doses administered and recorded in the Australian Immunisation Register (AIR). Audiovestibular presentations of interest were isolated from the general practice dataset aggregated by POLAR, by searching for relevant SNOMED CT codes. Similarly, relative incidence (RI) was calculated for all COVID-19 vaccine types.\n\nResultsThis study demonstrates an increase in general practice presentations of vertigo following mRNA vaccines (RI= 1.40 P <.001), and tinnitus following both the adenovirus vector and mRNA vaccines (RI= 2.25, P <.001 and 1.53, P <.001 respectively). There was no increase in hearing loss following any COVID-19 vaccinations.\n\nConclusions and RelevanceThis is the first study that demonstrates an increase in audiovestibular presentations following COVID-19 vaccination, in particular, vertigo and tinnitus. Healthcare providers and vaccinees should be alert to potential audiovestibular complaints after COVID-19 vaccination. Our analysis highlights the importance of using large real-world datasets to gather reliable evidence for public health decision making.\n\nKEY POINTSQuestion: Is there an increase in audiovestibular adverse events after COVID-19 vaccination (adenovirus vector [AstraZenecas Vaxzervria(R) ChadOx1-S], mRNA [Pfizer-BioNTechs Comirnaty(R) BNT162b2 and Modernas Spikevax(R)] or protein-subunit [Novavaxs Nuvaxovid(R)])?\n\nFindings: This Australian study using spontaneous surveillance reports and large-scale general practice data, found an increase in incidence related to vertigo following mRNA vaccines (Relative Incidence = 1.40, P <.001), and tinnitus following both adenovirus vector and mRNA vaccines (Relative Incidence = 2.25, P <.001 and 1.53,P <.001 respectively). No increase in hearing loss following vaccination was observed.\n\nMeaning: Healthcare providers and vaccinees should be alert to potential audiovestibular complaints following COVID-19 vaccination.", + "rel_abs": "ImportanceEvidence regarding audiovestibular adverse events post COVID-19 vaccination to date has been inconclusive regarding a potential etiological association. This study used a multi-data source approach to assess incidence of these events following COVID-19 vaccination.\n\nObjectiveTo determine if there was an increase in audiovestibular adverse events following COVID-19 vaccination in South-eastern Australia during January 2021 - March 2023.\n\nDesignRetrospective observational analysis of spontaneous reports of audiovestibular events to a statewide vaccine safety surveillance service, SAEFVIC, as well as accompanying self-controlled case series (SCCS) analysis using general practice data collected via the POpulation Level Analysis and Reporting (POLAR) tool with permission from Primary Health Networks (PHNs) as the de-identified dataset owners in Victoria and New South Wales.\n\nSettingVictoria and New South Wales (NSW), Australia.\n\nParticipantsVictorians who spontaneously reported an audiovestibular-related symptom or diagnosis to SAEFVIC, and people in Victoria and NSW who presented to a POLAR GP registered practice with a new audiovestibular diagnosis.\n\nExposuresCOVID-19 vaccination with adenovirus vector, mRNA or protein-subunit vaccine.\n\nOutcomes and MeasuresIn SAEFVIC, audiovestibular events of interest were ascertained through searching key words in the vaccine safety database. Reporting rates were calculated and compared per 100,000 COVID-19 vaccine doses administered and recorded in the Australian Immunisation Register (AIR). Audiovestibular presentations of interest were isolated from the general practice dataset aggregated by POLAR, by searching for relevant SNOMED CT codes. Similarly, relative incidence (RI) was calculated for all COVID-19 vaccine types.\n\nResultsThis study demonstrates an increase in general practice presentations of vertigo following mRNA vaccines (RI= 1.40 P <.001), and tinnitus following both the adenovirus vector and mRNA vaccines (RI= 2.25, P <.001 and 1.53, P <.001 respectively). There was no increase in hearing loss following any COVID-19 vaccinations.\n\nConclusions and RelevanceThis is the first study that demonstrates an increase in audiovestibular presentations following COVID-19 vaccination, in particular, vertigo and tinnitus. Healthcare providers and vaccinees should be alert to potential audiovestibular complaints after COVID-19 vaccination. Our analysis highlights the importance of using large real-world datasets to gather reliable evidence for public health decision making.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSIs there an increase in audiovestibular adverse events after COVID-19 vaccination (adenovirus vector [AstraZenecas Vaxzervria(R) ChadOx1-S], mRNA [Pfizer-BioNTechs Comirnaty(R) BNT162b2 and Modernas Spikevax(R)] or protein-subunit [Novavaxs Nuvaxovid(R)])?\n\nFindingsThis Australian study using spontaneous surveillance reports and large-scale general practice data, found an increase in incidence related to vertigo following mRNA vaccines (Relative Incidence = 1.40, P <.001), and tinnitus following both adenovirus vector and mRNA vaccines (Relative Incidence = 2.25, P <.001 and 1.53, P <.001 respectively). No increase in hearing loss following vaccination was observed.\n\nMeaningHealthcare providers and vaccinees should be alert to potential audiovestibular complaints following COVID-19 vaccination.", "rel_num_authors": 9, "rel_authors": [ { @@ -19927,65 +20463,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.11.20.23298784", - "rel_title": "Assessment of the Usability of SARS-CoV-2 Self Tests in a Peer-Assisted Model among Factory Workers in Bengaluru, India", - "rel_date": "2023-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.20.23298784", - "rel_abs": "In order to mitigate the inequities in health outcomes and healthcare access for vulnerable populations during the COVID-19 pandemic, the government of India introduced antigen-based SARS-CoV-2 self-testing kits for self-administered use. In this study, we aimed to determine the usability of these nasal-sampling-based self-tests in a peer-assisted model among factory workers in Bengaluru. The mixed-method cross-sectional study was conducted with 106 factory workers, spanning two sites from February to March 2022 in Bengaluru, India. Panbio COVID-19 Antigen Self-Test kit and the mobile application NAVICA for self-reporting results were used. A peer assistant distributed test kits, guided participants on conducting tests and using the app, and offered demonstrations with their own kit, ensuring no contact with the participants kits. Findings were encapsulated by an observer, who used standardized product-specific usability checklists and pictures of contrived results to assess the usability of the kit and mobile application, result interpretation, and the efficiency of peer instruction/demonstration. Additionally, a post-test survey and focus group discussions with selected participants and peer assistants were conducted to understand user perceptions of the facilitators and barriers to usability. Study findings show that the overall usability score of the test kit with peer assistance was 75.9%, rising to 80.7% for critical steps and 33.8% for all critical steps in uploading results through NAVICA. Additionally, it was seen that peer assistants provided accurate instructions and support for 93.4% of the tests. Among the critical steps in test kit use, maximum errors were made in sample collection and using the correct amount of buffer solution. Concordance between the participant and observer/NAVICA was 97.9%. 62.0% and 56.6% of the participants reported confidence in a) performing and interpreting the test and b) capturing and uploading their results using the mobile application with the assistance of a peer, respectively. Less than half the participants reported confidence in performing these steps independently. The study indicates that the COVID-19 nasal self-testing kit has good usability in factories peer-assisted workplace testing model. Such models can empower vulnerable worker groups to access early detection and self-care tools equitably.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Meghana Ratna Pydi", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Petra Stankard", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Neha Parikh", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Purnima Ranawat", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Ravneet Kaur", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Shankar AG", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Angela Chaudhuri", - "author_inst": "Swasti - The Health Catalyst" - }, - { - "author_name": "Sonjelle Shilton", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Aditi Srinivasan", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Joyita Chowdhury", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - }, - { - "author_name": "Elena Ivanova Reipold", - "author_inst": "Foundation for Innovative New Diagnostics: FIND" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.11.20.23298741", "rel_title": "Increased Severity of New-onset Type 1 Diabetes in Children and Adolescents during the COVID-19 Pandemic: Experience from a Tertiary Care Center in Serbia", @@ -20257,6 +20734,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2023.11.17.23298700", + "rel_title": "Antibody response to symptomatic infection with SARS-CoV-2 Omicron variant viruses, December 2021 to June 2022", + "rel_date": "2023-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.17.23298700", + "rel_abs": "To describe humoral immune responses to symptomatic SARS-CoV-2 infection, we assessed immunoglobulin G binding antibody levels using a commercial multiplex bead assay against SARS-CoV-2 ancestral spike protein receptor binding domain (RBD) and nucleocapsid protein (N). We measured binding antibody units per mL (BAU/mL) during acute illness within 5 days of illness onset and during convalescence in 105 ambulatory patients with laboratory-confirmed SARS-CoV-2 infection with Omicron variant viruses. Comparing acute- to convalescent phase antibody concentrations, geometric mean anti-N antibody concentrations increased 47-fold from 5.5 to 259 BAU/mL. Anti-RBD antibody concentrations increased 2.5-fold from 1258 to 3189 BAU/mL.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Ryan Sandford", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Ruchi L Yadav", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Emma K Noble", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Kelsey M Sumner", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Devyani J Joshi", + "author_inst": "Emory University" + }, + { + "author_name": "Sara Y Tartof", + "author_inst": "Kaiser Permanente Southern California, Department of Research & Evaluation" + }, + { + "author_name": "Karen J Wernli", + "author_inst": "Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA" + }, + { + "author_name": "Emily T Martin", + "author_inst": "University of Michigan School of Public Health, Ann Arbor, MI, USA" + }, + { + "author_name": "Manjusha Gaglani", + "author_inst": "Baylor Scott & White Health, Temple, TX, USA" + }, + { + "author_name": "Richard Zimmerman", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "H Keipp Talbot", + "author_inst": "Vanderbilt University Medical Center, Nashville, TN, USA" + }, + { + "author_name": "Carlos G Grijalva", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Edward A Belongia", + "author_inst": "Marshfield Clinic Research Institute, Marshfield, WI, USA" + }, + { + "author_name": "Christina Carlson", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Melissa Coughlin", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Brendan M Flannery", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + }, + { + "author_name": "Brad Pearce", + "author_inst": "Rollins School of Public Health, Emory University, Atlanta, GA, USA" + }, + { + "author_name": "Eric Rogier", + "author_inst": "Centers for Disease Control and Prevention, Atlanta, GA, USA" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.11.18.23297862", "rel_title": "BFCI at #SMM4H 2023: Integration of Machine Learning and TF-IDF for Covid-19 Tweets Analysis", @@ -21733,49 +22297,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.11.13.23298480", - "rel_title": "Integrating stimulus-organism-response model and theory of planned behavior to explore athletes intention to receive the COVID-19 vaccine booster - A moderated mediation model", - "rel_date": "2023-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.13.23298480", - "rel_abs": "This study aims to investigate the factors influencing athletes intention to receive the COVID-19 vaccine booster in Mainland China by integrating the stimulus-organization-response (SOR) model and theory of planned behavior (TPB) as the theoretical framework. Purposive sampling was used to select respondents from the National Games of the Peoples Republic of China. Hard-copy questionnaires were utilized to collect data, resulting in 981 valid responses. Descriptive analysis and partial least squares structural equation modeling were used to analyze the data. The findings reveal that athletes subjective norm and knowledge significantly influence attitude, commitment, and perceived behavioral control. Attitude, commitment, and perceived behavioral control are verified as full mediators between subjective norm, knowledge, and intention to receive the COVID-19 vaccine booster. Knowledge to commitment is the most powerful path to predict athletes intention to receive the COVID-19 vaccine booster. Motivation moderates the relationships between knowledge, attitude, commitment, and perceived behavioral control. The integrating models explanatory power is 83.2%. Athletes knowledge is crucial in shaping a positive attitude, commitment, and perceived control, enhancing their intention to get the COVID-19 vaccine booster.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Wenpeng Zhan", - "author_inst": "Lingnan Normal University" - }, - { - "author_name": "Qianting Deng", - "author_inst": "South China Normal University" - }, - { - "author_name": "Van Bac Nguyen", - "author_inst": "National Taiwan University of Sport" - }, - { - "author_name": "Tran Phan Duc Anh", - "author_inst": "National Taiwan University of Sport" - }, - { - "author_name": "Phan Danh Na", - "author_inst": "National Taiwan University of Sport" - }, - { - "author_name": "An-Shin Shia", - "author_inst": "Lingnan Normal University" - }, - { - "author_name": "Gordon Chih Ming Ku", - "author_inst": "National Taiwan University of Sport" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.11.13.23298463", "rel_title": "A SOLUTION TO THE KERMACK AND MCKENDRICK INTEGRO-DIFFERENTIAL EQUATIONS WHICH ACCURATELY PROJECTS COVID-19 CASE DATA USING GOOGLE MOBILITY DATA AS AN INPUT", @@ -21959,6 +22480,85 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2023.11.10.566497", + "rel_title": "Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury", + "rel_date": "2023-11-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.10.566497", + "rel_abs": "Acute kidney injury (AKI) in COVID-19 patients is associated with high mortality and morbidity. Critically ill COVID-19 patients are at twice the risk of in-hospital mortality compared to non-COVID AKI patients. We know little about the cell-specific mechanism in the kidney that contributes to worse clinical outcomes in these patients. New generation single cell technologies have the potential to provide insights into physiological states and molecular mechanisms in COVID-AKI. One of the key limitations is that these patients are severely ill posing significant risks in procuring additional biopsy tissue. We recently generated single nucleus RNA-sequencing data using COVID-AKI patient biopsy tissue as part of the human kidney atlas. Here we describe this approach in detail and report deeper comparative analysis of snRNAseq of 4 COVID-AKI, 4 reference, and 6 non-COVID-AKI biopsies. We also generated and analyzed urine transcriptomics data to find overlapping COVID-AKI-enriched genes and their corresponding cell types in the kidney from snRNA-seq data. We identified all major and minor cell types and states by using by using less than a few cubic millimeters of leftover tissue after pathological workup in our approach. Differential expression analysis of COVID-AKI biopsies showed pathways enriched in viral response, WNT signaling, kidney development, and cytokines in several nephron epithelial cells. COVID-AKI profiles showed a much higher proportion of altered TAL cells than non-COVID AKI and the reference samples. In addition to kidney injury and fibrosis markers indicating robust remodeling we found that, 17 genes overlap between urine cell COVID-AKI transcriptome and the snRNA-seq data from COVID-AKI biopsies. A key feature was that several of the distal nephron and collecting system cell types express these markers. Some of these markers have been previously observed in COVID-19 studies suggesting a common mechanism of injury and potentially the kidney as one of the sources of soluble factors with a potential role in disease progression.\n\nTranslational StatementThe manuscript describes innovation, application and discovery that impact clinical care in kidney disease. First, the approach to maximize use of remnant frozen clinical biopsies to inform on clinically relevant molecular features can augment existing pathological workflow for any frozen tissue without much change in the protocol. Second, this approach is transformational in medical crises such as pandemics where mechanistic insights are needed to evaluate organ injury, targets for drug therapy and diagnostic and prognostic markers. Third, the cell type specific and soluble markers identified and validated can be used for diagnoses or prognoses in AKI due to different etiologies and in multiorgan injury.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Reetika Ghag", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Madhurima Kaushal", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Gerald Nwanne", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Amanda Knoten", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Krzysztof Kiryluk", + "author_inst": "Columbia University" + }, + { + "author_name": "Avi Rosenberg", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Steven Menez", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Serena M Bagnasco", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "C John Sperati", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Mohamed G Atta", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Joseph P Gaut", + "author_inst": "Washington University St. Louis" + }, + { + "author_name": "James C Williams Jr.", + "author_inst": "Indiana University" + }, + { + "author_name": "Tarek M El-Achkar", + "author_inst": "Indiana University" + }, + { + "author_name": "Lois J Arend", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Chirag R Parikh", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Sanjay Jain", + "author_inst": "Washington University in St Louis" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2023.11.12.23298174", "rel_title": "Application of the Fluctuation Test to the data of Morbidity and Mortality by COVID-19 in China 2020-2023", @@ -23695,81 +24295,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.11.06.565781", - "rel_title": "The \u03b1-dystroglycan N-terminus is a broad-spectrum antiviral agent against SARS-CoV-2 and enveloped viruses", - "rel_date": "2023-11-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.06.565781", - "rel_abs": "The COVID-19 pandemic has shown the need to develop effective therapeutics in preparedness for further epidemics of virus infections that pose a significant threat to human health. As a natural compound antiviral candidate, we focused on -dystroglycan, a highly glycosylated basement membrane protein that links the extracellular matrix to the intracellular cytoskeleton. Here we show that the N-terminal fragment of -dystroglycan (-DGN), as produced in E. coli in the absence of post-translational modifications, blocks infection of SARS-CoV-2 in cell culture, human primary gut organoids and the lungs of transgenic mice expressing the human receptor angiotensin I-converting enzyme 2 (hACE2). Prophylactic and therapeutic administration of -DGN reduced SARS-CoV-2 lung titres and protected the mice from respiratory symptoms and death. Recombinant -DGN also blocked infection of a wide range of enveloped viruses including the four Dengue virus serotypes, influenza A virus, respiratory syncytial virus, tick-borne encephalitis virus, but not human adenovirus, a non-enveloped virus in vitro. This study establishes soluble recombinant -DGN as a broad-band, natural compound candidate therapeutic against enveloped viruses.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Martia Giulia Bigotti", - "author_inst": "University of Bristol" - }, - { - "author_name": "Katja Klein", - "author_inst": "University of Bristol" - }, - { - "author_name": "Esther S Gan", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Maria Anastasina", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Simon Andersson", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Olli Vapalahti", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Pekka Katajisto", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Maximilian Erdmann", - "author_inst": "University of Bristol" - }, - { - "author_name": "Andrew D. Davidson", - "author_inst": "University of Bristol" - }, - { - "author_name": "Sarah Jane Butcher", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Ian Collinson", - "author_inst": "University of Bristol" - }, - { - "author_name": "Eng Eong Ooi", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Giuseppe Balistreri", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Andrea Brancaccio", - "author_inst": "CNR Rome and University of Bristol" - }, - { - "author_name": "Yohei Yamauchi", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.11.06.565757", "rel_title": "Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike", @@ -24037,6 +24562,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2023.11.06.23298096", + "rel_title": "Exploring the perceptions and experiences of community rehabilitation for Long COVID from the perspectives of Scottish General Practitioners and people living with Long COVID: a qualitative study", + "rel_date": "2023-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.06.23298096", + "rel_abs": "ObjectivesTo explore the experience of accessing Long COVID community rehabilitation from the perspectives of people with Long COVID and General Practitioners (GPs).\n\nDesignQualitative descriptive study employing one-to-one semi-structured virtual interviews analysed using the framework method.\n\nSettingFour NHS Scotland territorial health boards.\n\nParticipantsEleven people with Long COVID (1 male, 10 female; aged 40-65 [mean 53], and 13 GPs (5 male, 8 female).\n\nResultsFour key themes were identified: i) The lived experience of Long COVID; ii) The challenges of an emergent and complex chronic condition; iii) Systemic challenges for Long COVID service delivery, and iv) Perceptions and experiences of Long COVID and its management, including rehabilitation.\n\nConclusionsThere are several patient, GP, and service-level barriers to accessing community rehabilitation for Long COVID. There is a need for greater understanding by the public, GPs, and other potential referrers of the role of community rehabilitation professionals in the management of Long COVID. There is also a need for community rehabilitation services to be well promoted and accessible to the people with Long COVID for whom they may be appropriate. Service providers need to consider availability and accessibility of Long COVID rehabilitation and ensure adequate interprofessional communication and collaboration to enhance the experience for people with Long COVID.\n\nStrengths and limitations of this studyO_LIThis is the first study to explore the issue of accessing Long COVID community rehabilitation from the perspectives of potential service users and referrers in the Scottish context.\nC_LIO_LIOne researcher conducted all interviews, ensuring consistency in their conduct\nC_LIO_LIData were analysed and interpreted by multiple researchers, including people with Long COVID\nC_LIO_LIThe small sample size, largely drawn from health boards with a similar approach to Long COVID rehabilitation, limits generalisability\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Kay Cooper", + "author_inst": "Robert Gordon University" + }, + { + "author_name": "Edward Duncan", + "author_inst": "University of Stirling" + }, + { + "author_name": "Erin Hart-Winks", + "author_inst": "Robert Gordon University" + }, + { + "author_name": "Julie Cowie", + "author_inst": "Glasgow Caledonian University" + }, + { + "author_name": "Joanna Shim", + "author_inst": "Robert Gordon University" + }, + { + "author_name": "Emma Stage", + "author_inst": "Robert Gordon University" + }, + { + "author_name": "Tricia Tooman", + "author_inst": "University of Stirling" + }, + { + "author_name": "Lyndsay Alexander", + "author_inst": "Robert Gordon University" + }, + { + "author_name": "Alison Love", + "author_inst": "Long COVID Scotland" + }, + { + "author_name": "Jacqui Morris", + "author_inst": "University of Dundee" + }, + { + "author_name": "Jane Ormerod", + "author_inst": "Long COVID Scotland" + }, + { + "author_name": "Jenny Preston", + "author_inst": "Douglas Grant Rehabilitation Centre, Ayrshire Central Hospital" + }, + { + "author_name": "Paul Alan Swinton", + "author_inst": "Robert Gordon University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "rehabilitation medicine and physical therapy" + }, { "rel_doi": "10.1101/2023.11.03.23298048", "rel_title": "Family, community, institutional and policy factors on COVID-19 vaccine perceptions among urban poor adolescents in seven countries: qualitative cross-site analysis.", @@ -25549,53 +26141,6 @@ "type": "new results", "category": "developmental biology" }, - { - "rel_doi": "10.1101/2023.10.30.564067", - "rel_title": "Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds", - "rel_date": "2023-11-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.30.564067", - "rel_abs": "Protein homeostasis is tightly regulated, with damaged or misfolded proteins quickly eliminated by the proteasome and autophagosome pathways. By co-opting these processes, targeted protein degradation technologies enable pharmacological manipulation of protein abundance. Recently, cysteine-reactive molecules have been added to the degrader toolbox, which offer the benefit of unlocking the therapeutic potential of undruggable protein targets. The proteome-wide impact of these molecules remains to be fully understood and given the general reactivity of many classes of cysteine-reactive electrophiles, on- and off-target effects are likely. Using chemical proteomics, we identified a cysteine-reactive small molecule degrader of the SARS-CoV-2 non- structural protein 14 (nsp14), which effects degradation through direct modification of cysteines in both nsp14 and in host chaperones together with activation of global cell stress response pathways. We find that cysteine-reactive electrophiles increase global protein ubiquitylation, trigger proteasome activation, and result in widespread aggregation and depletion of host proteins, including components of the nuclear pore complex. Formation of stress granules was also found to be a remarkably ubiquitous cellular response to nearly all cysteine-reactive compounds and degraders. Collectively, our study sheds light on complexities of covalent target protein degradation and highlights untapped opportunities in manipulating and characterizing proteostasis processes via deciphering the cysteine-centric regulation of stress response pathways.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ashley R Julio", - "author_inst": "UNIVERSITY OF CALIFORNIA LOS ANGELES" - }, - { - "author_name": "Flowreen Shikwana", - "author_inst": "UNIVERSITY OF CALIFORNIA LOS ANGELES" - }, - { - "author_name": "Cindy Truong", - "author_inst": "UCLA" - }, - { - "author_name": "Nikolas R Burton", - "author_inst": "UNIVERSITY OF CALIFORNIA LOS ANGELES" - }, - { - "author_name": "Emil Dominguez", - "author_inst": "UCLA" - }, - { - "author_name": "Alexandra Turmon", - "author_inst": "UCLA" - }, - { - "author_name": "Jian Cao", - "author_inst": "UCLA" - }, - { - "author_name": "Keriann Backus", - "author_inst": "UNIVERSITY OF CALIFORNIA LOS ANGELES" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.10.31.565042", "rel_title": "SARS-CoV-2 infection leads to sustained testicular injury and functional impairments in K18 hACE2 mice", @@ -25899,6 +26444,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.10.30.23297772", + "rel_title": "Two-years mothering into the pandemic: Impact of the three COVID-19 waves in the Argentinian postpartum womens mental health", + "rel_date": "2023-10-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.30.23297772", + "rel_abs": "The COVID-19 pandemic disproportionately affects certain vulnerable groups, including postpartum women. Thus, this work aimed to analyze the mental health evolution in Argentinian postpartum women during the first three waves of COVID-19 and its determinants. In this repeated cross-sectional study, data were collected during the three waves of COVID-19: May-July/2020 (n=319), April-August/2021 (n=340), and December/2021-March/2022 (n=341). Postpartum depression (PDSS-SF), insomnia (ISI), and perceived stress symptoms (PSS-C) were used. Statistical analyses included multivariate logistic regression, analysis of variance, and structural equation modeling to test for temporal trends in mental health indicators during the pandemic and to identify their determinants. The prevalence rates of postpartum depression and insomnia rose from 37% to 60% and 46% to 62%, respectively. In contrast, pandemic-related stress decreased. Certain factors increased maternal risk of mental symptoms: unemployment status, no medical support, reduced family size, remote working, advanced maternal age, late postpartum, multiparity, and living in the least developed region of Argentina. Structural equation modeling confirmed a process of pandemic-stress adaptation, although there is a persistent increment of postpartum depression and consequent increased insomnia. Postpartum womens mental health was worsened during the COVID-19 pandemic. Although women have become more able to cope and perceive less pandemic-related stress, its social and economic impact still persists and puts them at higher psychological risk. Thus, health systems must ensure the womens well-being to deal with current and future consequences of this epidemiological scenario.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Agustin Ramiro Miranda", + "author_inst": "IRD: Institut de recherche pour le developpement" + }, + { + "author_name": "Ana Veronica Scotta", + "author_inst": "CONICET: Consejo Nacional de Investigaciones Cientificas y Tecnicas" + }, + { + "author_name": "Mariela Valentina Cortez", + "author_inst": "CONICET Cordoba" + }, + { + "author_name": "Elio Andr\u00e9s Soria", + "author_inst": "CONICET Cordoba" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.10.30.23297774", "rel_title": "Systematic SARS-CoV-2 S Gene Sequencing in Wastewater Samples Enables Early Lineage Detection and Uncovers Rare Mutations in Portugal", @@ -27159,33 +27735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.10.25.23297548", - "rel_title": "The experiences and impact of the COVID-19 pandemic on Young Carers: practice implications and planning for future health emergencies", - "rel_date": "2023-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297548", - "rel_abs": "BackgroundYoung Carers faced significant challenges brought on by the COVID-19 pandemic. We explored the impact of the pandemic and associated restrictions on mental health, wellbeing and access to support in Young Carers in the United Kingdom (UK) to understand how to improve services, as well as support this population in future health emergencies.\n\nMethodWe conducted 22 qualitative semi-structured interviews from May to November 2021, with 14 Young Carers and 8 staff working in organisations that supported them. Interviews took place remotely over video or telephone call, discussing topics such as experiences of the pandemic on their health, wellbeing and caring responsibilities. We used reflexive thematic analysis to analyse interview transcripts.\n\nResultsWe identified 4 overarching themes pertaining to the impact of the pandemic and associated restrictions on mental health, wellbeing, and access to support in Young Carers in the UK: 1) challenges to following the guidelines, 2) changes to and loss of routine, 3) changes in provision of informal and formal support and 4) better understanding of inner resilience and goals. Many participants struggled with their mental health and wellbeing as a result of pandemic related restrictions, impacting on support structures for themselves, as well as the individual cared for. However, positive impacts pertained to additional support from local authority and third sector organisations.\n\nConclusionsOur findings highlight some of the changes that affected Young Carers during the COVID-19 pandemic. The impact of changes to routine and a reduction in pre-pandemic support were the greatest concerns reported by participants in this study. The additional support provided by local authority and third sector organisations during social restrictions suggests such organisations could play a greater role in supporting this population going forward, and that schools and Governments may wish to put in additional strategies and provisions to protect this population in the future.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Dan Hayes", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Alexandra Burton", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.10.25.563967", "rel_title": "Discovery of a novel inhibitor of macropinocytosis with antiviral activity", @@ -27541,6 +28090,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.10.26.23297635", + "rel_title": "Online trend estimation and detection of trend deviations in sub-sewershed time series of SARS-CoV-2 RNA measured in wastewater.", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297635", + "rel_abs": "Wastewater surveillance has proven a key public health tool to understand a wide range of community health diseases and has proven to be especially critical to health departments throughout the SARS CoV-2 pandemic. The size of the population served by a wastewater treatment plant (WWTP) may limit the targeted insight about community disease dynamics. To investigate this concern, samples of wastewater were obtained at lift stations upstream of WWTPs within the sewer network. First, an online, semi-automatic time series model is fitted to the weekly measurements of WWTP samples to estimate the viral trend for the community and compared to the time series observations from the lift stations. Second, deviations from the WWTP trend are identified using an Exponentially Weighted Moving Average (EWMA) control chart. The analysis reveals that the lift stations display slightly different dynamics than the larger WWTP, highlighting the more granular insight gleaned from sampling sites which represent smaller populations. Discussion focuses on the use of our methods to support rapid public health decision-making based on additional, targeted samples in times of concern.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Katherine B Ensor", + "author_inst": "Rice University" + }, + { + "author_name": "Julia C Schedler", + "author_inst": "Rice University" + }, + { + "author_name": "Thomas Sun", + "author_inst": "Rice University" + }, + { + "author_name": "Rebecca Schneider", + "author_inst": "Houston Health Department" + }, + { + "author_name": "Anthony Mulenga", + "author_inst": "Houston Health Department" + }, + { + "author_name": "Jingjing Wu", + "author_inst": "Rice University" + }, + { + "author_name": "Lauren Stadler", + "author_inst": "Rice University" + }, + { + "author_name": "Loren Hopkins", + "author_inst": "Rice University and Houston Health Department" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.10.26.23297626", "rel_title": "Comparative Organ Disease Burden and Sequelae of Influenza and SARS-CoV-2 Infection: An Observational Study Using Real-World Data", @@ -29213,7 +29809,7 @@ "rel_date": "2023-10-24", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563669", - "rel_abs": "COVID-19 can result in neurological symptoms such as fever, headache, dizziness, and nausea. However, neurological signs of SARS-CoV-2 infection have been hardly assessed in mouse models. Here, we infected two commonly used wildtype mice lines (C57BL/6 and 129S) with mouse-adapted SARS-CoV-2 and demonstrated neurological signs including motion-related dizziness. We then evaluated whether the Calcitonin Gene-Related Peptide (CGRP) receptor antagonist, olcegepant, used in migraine treatment could mitigate acute neuroinflammatory and neurological responses to SARS-COV-2 infection. We infected wildtype C57BL/6J and 129/SvEv mice, and a 129 CGRP-null mouse line with a mouse-adapted SARS-CoV-2 virus, and evaluated the effect of CGRP receptor antagonism on the outcome of that infection. First, we determined that CGRP receptor antagonism provided protection from permanent weight loss in older (>12 m) C57BL/6J and 129 SvEv mice. We also observed acute fever and motion-induced dizziness in all older mice, regardless of treatment. However, in both wildtype mouse lines, CGRP antagonism reduced acute interleukin 6 (IL-6) levels by half, with virtually no IL-6 release in mice lacking CGRP. These findings suggest that migraine inhibitors such as those blocking CGRP signaling protect against acute IL-6 release and subsequent inflammatory events after SARS-CoV-2 infection, which may have repercussions for related pandemic and/or endemic coronaviruses.", + "rel_abs": "COVID-19 can result in neurological symptoms such as fever, headache, dizziness, and nausea. However, neurological signs of SARS-CoV-2 infection have been hardly assessed in mouse models. Here, we infected two commonly used wildtype mice lines (C57BL/6 and 129S) with mouse-adapted SARS-CoV-2 and demonstrated neurological signs including motion- related dizziness. We then evaluated whether the Calcitonin Gene-Related Peptide (CGRP) receptor antagonist, olcegepant, used in migraine treatment could mitigate acute neuroinflammatory and neurological responses to SARS-COV-2 infection. We infected wildtype C57BL/6J and 129/SvEv mice, and a 129 CGRP-null mouse line with a mouse-adapted SARS- CoV-2 virus, and evaluated the effect of CGRP receptor antagonism on the outcome of that infection. First, we determined that CGRP receptor antagonism provided protection from permanent weight loss in older (>12 m) C57BL/6J and 129 SvEv mice. We also observed acute fever and motion-induced dizziness in all older mice, regardless of treatment. However, in both wildtype mouse lines, CGRP antagonism reduced acute interleukin 6 (IL-6) levels by half, with virtually no IL-6 release in mice lacking CGRP. These findings suggest that migraine inhibitors such as those blocking CGRP signaling protect against acute IL-6 release and subsequent inflammatory events after SARS-CoV-2 infection, which may have repercussions for related pandemic and/or endemic coronaviruses.\n\nImportanceCOVID-19 can cause neurological symptoms such as fever, headache, dizziness, and nausea. However, such neurological symptoms of SARS-CoV-2 infection have been hardly assessed in mouse models. Here, we first infected two commonly used wildtype mice lines (C57BL/6 and 129S) with mouse-adapted SARS-CoV-2 and demonstrated neurological signs including motion-related dizziness. Further, we showed that migraine treatment drug olcegepant could reduce long-term weight loss and IL-6 release associated with SARS-CoV-2 infection. These findings suggest that a migraine blocker can be protective for at least some acute SARS-CoV-2 infection signs and raise the possibility that it may also impact long-term outcomes of infection.", "rel_num_authors": 10, "rel_authors": [ { @@ -29317,85 +29913,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.10.22.563481", - "rel_title": "Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy", - "rel_date": "2023-10-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.22.563481", - "rel_abs": "BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients.\n\nMethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30).\n\nResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination.\n\nDiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ashley Priddey", - "author_inst": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK" - }, - { - "author_name": "Michael Xin Hua Chen-Xu", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Daniel James Cooper", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Serena MacMillan", - "author_inst": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK" - }, - { - "author_name": "Georg Meisl", - "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK" - }, - { - "author_name": "Catherine K Xu", - "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK" - }, - { - "author_name": "Myra Hosmillo", - "author_inst": "Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Ian G Goodfellow", - "author_inst": "Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Rafael Kollyfas", - "author_inst": "Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK" - }, - { - "author_name": "Rainer Doffinger", - "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK" - }, - { - "author_name": "John R Bradley", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Irina I Mohorianu", - "author_inst": "Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK" - }, - { - "author_name": "Rachel Jones", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Tuomas P.J. Knowles", - "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK" - }, - { - "author_name": "Rona Smith", - "author_inst": "Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U" - }, - { - "author_name": "Vasilis Kosmoliaptsis", - "author_inst": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.10.23.563088", "rel_title": "Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2 in vitro activity", @@ -29671,6 +30188,29 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2023.10.21.563433", + "rel_title": "Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages", + "rel_date": "2023-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.21.563433", + "rel_abs": "MotivationCharged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus evolution.\n\nResultsWe analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2000 SARS-CoV-2 lineages that have emerged over the span of the pandemic. Our results show that the previously observed trend toward an increase in the positive charge on the spike protein of SARS-CoV-2 variants of concern has essentially stopped with the emergence of the early omicron variants. Furthermore, recently emerged lineages show a greater diversity in terms of their composition of ionizable amino acids. We also demonstrate that the patterns of change in the number of ionizable amino acids on the spike protein are characteristic of related lineages within the broader clade division of the SARS-CoV-2 phylogenetic tree. Due to the ubiquity of electrostatic interactions in the biological environment, our findings are relevant for a broad range of studies dealing with the structural stability of SARS-CoV-2 and its interactions with the environment.\n\nAvailabilityThe data underlying the article are available in the online Supplementary Material.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Anze Bozic", + "author_inst": "Jozef Stefan Institute" + }, + { + "author_name": "Rudolf Podgornik", + "author_inst": "UCAS" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.10.20.563308", "rel_title": "Assessing nanobody interaction with SARS-CoV-2 Nsp9", @@ -31203,41 +31743,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.18.23297204", - "rel_title": "Excess deaths in China during SARS-CoV-2 viral waves in 2022-2023", - "rel_date": "2023-10-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.18.23297204", - "rel_abs": "BackgroundThe extent to which the Omicron variant of SARS-CoV-2 raised death rates in China during its viral wave of December 2022-January 2023 remains undocumented.\n\nMethodsWe worked with an established national survey organization to survey 8,004 adults in all 31 administrative areas of China to ask about deaths in families since January 2020. We examined agespecific death rates, focusing on deaths above age 60 years, and at 15-59 years. We compared these to the United Nations (UN) estimates of age-specific mortality in 2019.\n\nFindingsThe survey participants were broadly similar to the 2020 census and other national surveys in age, sex, region, and smoking status, but had lower SARS-CoV-2 vaccination rates and higher education levels. There were no differences between reporting of deaths during the Omicron period versus earlier. The survey captured 456 deaths, of which 329 occurred at ages 60+ years and 212 were women. At ages 60+ years, death rates per 1000 rose 242% (95%CI 128-398%) during December 2022-January 2023. Deaths at ages 15-59 years did not rise appreciably. The UN estimates approximately 675,000 deaths per month at ages 60+ years in 2019. If rates doubled nationally as in our survey, China had approximately 1{middle dot}35 million excess deaths over the two months.\n\nInterpretationChina experienced a sharp but short increase in excess deaths among its elderly during the Omicron wave. If death registry data corroborate our estimates of substantial excess deaths in China, the worldwide estimates of excess deaths to 2023 may need upward adjustment.\n\nFundingCanadian Institutes of Health Research", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Prabhat Jha", - "author_inst": "University of Toronto" - }, - { - "author_name": "Patrick E Brown", - "author_inst": "University of Toronto" - }, - { - "author_name": "Teresa Lam", - "author_inst": "Angus Reid Institute" - }, - { - "author_name": "Ed Morawski", - "author_inst": "Angus Reid Institute" - }, - { - "author_name": "Angus Reid", - "author_inst": "Angus Reid Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.10.17.23297174", "rel_title": "Persistent high mortality rates for Diabetes Mellitus and Hypertension after excluding deaths associated with COVID-19 in Brazil, 2020-2022", @@ -31465,6 +31970,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.10.17.23297138", + "rel_title": "Forecasting regional-level COVID-19 hospitalisation in England as an ordinal variable using the machine learning method", + "rel_date": "2023-10-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.17.23297138", + "rel_abs": "BackgroundCOVID-19 causes substantial pressure on healthcare, with many healthcare systems now needing to prepare for and mitigate the consequences of surges in demand caused by multiple overlapping waves of infections. Therefore, public health agencies and health system managers also now benefit from short-term forecasts for respiratory infections that allow them to manage services better. However, the availability of easily implemented effective tools for generating precise forecasts at the individual regional level still needs to be improved.\n\nMethodsWe extended prior work on influenza to forecast regional COVID-19 hospitalisations in England for the period from 19th March 2020 to 31st December 2022, treating the number of hospital admissions in each region as an ordinal variable. We further developed the XGBoost model used previously to forecast influenza to enable it to exploit the ordering information in ordinal hospital admission levels. We incorporated different types of data as predictors: epidemiological data including weekly region COVID-19 cases and hospital admissions, weather conditions and mobility data for multiple categories of locations (e.g., parks, workplaces, etc). The impact of different discretisation methods and the number of ordinal levels was also considered.\n\nResultsWe find that the inclusion of weather data consistently increases the accuracy of our forecasts compared with models that rely only on the intrinsic epidemiological data, but only by a small amount. Mobility data brings about a more substantial increase in our forecasts. When both weather and mobility data are used in addition to the epidemiological data, the results are very similar to the model with only epidemiological data and mobility data.\n\nConclusionAccurate ordinal forecasts of COVID-19 hospitalisations can be obtained using XGBoost and mobility data. While uniform ordinal levels show higher apparent accuracy, we recommend N-tile ordinal levels which contain far richer information.\n\nAuthor SummaryAt the regional level, we address the pressing need for precise short-term forecasts of respiratory infections, particularly COVID-19. We focus on the specific context of England and cover the period from January 1 to December 31, 2022. We introduced an enhanced XGBoost model that leverages the ordinal nature of hospital admission data, utilising a combination of predictors, including epidemiological data, weather conditions, and mobility data across various location categories. Our findings indicate that the inclusion of weather data marginally improves forecasting accuracy, while mobility data yields more significant enhancements. This research contributes valuable insights for public health agencies and healthcare system managers in their ongoing efforts to manage and respond to the complexities of the COVID-19 pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Haowei Wang", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Steven Riley", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Kin O Kwok", + "author_inst": "Chinese University of Hong Kong" + }, + { + "author_name": "Ruiyun Li", + "author_inst": "Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.10.17.23297134", "rel_title": "Socioeconomic inequalities in COVID-19 infection and vaccine uptake among children and adolescents in Catalonia, Spain", @@ -33041,37 +33577,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2023.10.12.23296938", - "rel_title": "The impact of COVID-19 on non-communicable disease patients in sub-Saharan African countries: systematic review", - "rel_date": "2023-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.12.23296938", - "rel_abs": "BackgroundCOVID-19 and its prevention measures have had a significant impact on patients with non-communicable diseases (NCDs) by disrupting routine healthcare service and increasing risk factors. These challenges were expected to be more severe in sub-Saharan Africa due to the lack of physical infrastructure and inadequate resources. The quantity of studies conducted was limited, and there was a lack of published systematic reviews in the specified region. This systematic review aimed to comprehensively assess the impact of COVID-19 on NCD patients in sub-Saharan Countries.\n\nMethodThis systematic review adheres to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines and is registered with PROSPERO (ID CRD42023387755). Extensive searches were conducted in MEDLINE, EMBASE, and CINAHL databases in November 2022, supplemented by a manual search of references, grey literature, and the WHO COVID-19 database. Inclusion criteria encompassed studies that reported on the impact of COVID-19 on NCD patients in sub-Saharan African countries, focusing on access to care, health outcomes, and factors related to NCDs. Critical appraisal of study quality was performed using the Joanna Briggs Institute (JBI) analytical cross-sectional studies critical appraisal tool. Data were extracted and synthesized, highlighting the main findings and relevant limitations.\n\nFindingsThis review included 26 primary studies with a cumulative sample size of 15,722 participants, conducted in six sub-Saharan African countries. Findings of these studies identified that the COVID-19 pandemic caused a disruption of 76% to 80% of regular NCDs patient care provision. The studies also identified a reduction in patient health-seeking behavior and reduced medication adherence (39.0%-63%), leading to poor treatment outcome (35.66%-55.8%). Furthermore, the pandemic and related lockdowns have been implicated in the increased prevalence of substance use, decreased physical exercise, and increased mental health problems.\n\nConclusionThis systematic review identified the complex challenges faced by NCD patients in sub-Saharan Africa during the COVID-19 pandemic. It also underlines the need to consider the indirect impact on vulnerable populations while developing pandemic prevention and control strategies for the future. The current NCD management strategies should prioritize the restoration of access to essential healthcare services while considering the multifaceted risks posed by decreased physical activity, poor dietary practices, and increased substance use.\n\nThe main limitation of this review was the study design and setting. All of the studies included in this review employed a cross-sectional design, which may result in a low quality of evidence. This study identified research conducted in only six countries among the 46 UN-classified sub-Saharan nations, which may impair the generalizability of the result.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Muluken Bafa Basa", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - }, - { - "author_name": "Jan De Vries", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - }, - { - "author_name": "David McDonagh", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - }, - { - "author_name": "Catherine Comiskey", - "author_inst": "Trinity College Dublin: The University of Dublin Trinity College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.10.11.23296808", "rel_title": "Safety of SARS-CoV-2 test-to-stay in daycare: a regression discontinuity in time analysis", @@ -33423,6 +33928,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2023.10.10.561643", + "rel_title": "Snapshots from Cryo-ET of active SARS-CoV-2 virions", + "rel_date": "2023-10-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.10.561643", + "rel_abs": "Understanding the molecular properties of SARS-CoV-2 is crucial to tackle future outbreaks. Current knowledge of the trimeric spike protein relies on truncated recombinant proteins and inactivated full-length forms, which may suffer from overstabilization. Here, we apply cryo-electron tomography (cryo-ET) at a Biosafety level 3 facility to study the virus structure in its native, active state. The virus particles show variable shapes with diffusible spikes, with the majority in typical prefusion conformations. Notably, we also identified unprecedented, atypical open-trimer prefusion states, revealing hidden flexibility. The sub-tomogram averaged structure suggests a loosely packed trimer. The observed dynamics uncover conserved cryptic regions that can be targeted for broadly effective vaccines. Structural analysis of active viruses will have implications on understanding overlooked fusion mechanism and vaccine, antibody/drug design. (124 words)\n\nOne-Sentence SummaryThe BSL3 cryo-electron microscopy uncovered significant flexibility of the spike protein on active viruses, which will facilitate the design of broadly effective vaccines and drugs.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hideo Fukuhara", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Hisham M. Dokainish", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Shunsuke Kita", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Koshiro Tabata", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Akira Takasu", + "author_inst": "KEK (High Energy Accelerator Research Organization)" + }, + { + "author_name": "Juha T. Huiskonen", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Yuki Anraku", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Toshiya Senda", + "author_inst": "KEK (High Energy Accelerator Research Organization" + }, + { + "author_name": "David I. Stuart", + "author_inst": "University of Oxford" + }, + { + "author_name": "Michihito Sasaki", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Yasuko Orba", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Yasuhiko Suzuki", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Hirofumi Sawa", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Katsumi Maenaka", + "author_inst": "Hokkaido University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.10.07.23296699", "rel_title": "A phase I/II clinical trial of intradermal, controllable self-replicating RNA vaccine EXG 5003 against SARS-CoV-2", @@ -34983,105 +35559,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.04.560875", - "rel_title": "Unveiling the antiviral capabilities of targeting Human Dihydroorotate Dehydrogenase against SARS-CoV-2", - "rel_date": "2023-10-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.04.560875", - "rel_abs": "The urgent need for effective treatments against emerging viral diseases, driven by drug-resistant strains and new viral variants, remains critical. We focus on inhibiting the human dihydroorotate dehydrogenase (HsDHODH), one of the enzymes in charge of pyrimidine nucleotide synthesis. This strategy could impede viral replication without provoking resistance. We evaluated quinone-based compounds, discovering potent HsDHODH inhibition (low nanomolar IC50) and promising in vitro anti-SARS-CoV-2 activity (low micromolar EC50). These compounds exhibited low toxicity, indicating potential for further development. Additionally, we employed computational tools like molecular docking and QSAR models to analyze protein-ligand interactions. These findings represent a significant step forward in the search for effective antiviral treatments and have great potential to impact the development of new broad-spectrum antiviral drugs.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Aline Purificacao", - "author_inst": "(a) Protein Crystallography Laboratory, Department of Biomolecular Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Paulo, Ribei" - }, - { - "author_name": "Sabrina Silva-Mendonca", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Luiza Cruz", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Carolina Sacramento", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Jairo Temerozo", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Natalia Fintelman-Rodrigues", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Caroline Freitas", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Bruna Godoi", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Miguel Vaidergorn", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Juliana Leite", - "author_inst": "(h) Laboratory of Tropical Diseases, Dep. Genetics, Evolution, Microbiology and Immunology, Institute of Biology, Unicamp, Campinas, SP, Brazil." - }, - { - "author_name": "Luis Alvarez", - "author_inst": "(h) Laboratory of Tropical Diseases, Dep. Genetics, Evolution, Microbiology and Immunology, Institute of Biology, Unicamp, Campinas, SP, Brazil." - }, - { - "author_name": "Murillo Freitas", - "author_inst": "(c) Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goias, Goiania, 74605-170, GO, Brazil." - }, - { - "author_name": "Meryck Silva", - "author_inst": "(c) Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goias, Goiania, 74605-170, GO, Brazil." - }, - { - "author_name": "Bianca Martin", - "author_inst": "(i) Innovation Center in nanostructured systems and topical administration (NanoTop), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Pau" - }, - { - "author_name": "Renata Lopez", - "author_inst": "(i) Innovation Center in nanostructured systems and topical administration (NanoTop), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Pau" - }, - { - "author_name": "Bruno Neves", - "author_inst": "(c) Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goias, Goiania, 74605-170, GO, Brazil." - }, - { - "author_name": "Fabio Costa", - "author_inst": "h) Laboratory of Tropical Diseases, Dep. Genetics, Evolution, Microbiology and Immunology, Institute of Biology, Unicamp, Campinas, SP, Brazil." - }, - { - "author_name": "Thiago Souza", - "author_inst": "(d) Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil (e) National Institute for Science and Technology on Innovatio" - }, - { - "author_name": "Flavio Emery", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Carolina Andrade", - "author_inst": "(b) Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao P" - }, - { - "author_name": "Cristina Nonato", - "author_inst": "(a) Protein Crystallography Laboratory, Department of Biomolecular Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of Sao Paulo, Ribei" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.10.05.561047", "rel_title": "Fourth dose of Microneedle Array Patch of SARS-CoV-2 S1 Protein Subunit Vaccine Elicits Robust Long-lasting Humoral Responses in mice", @@ -35365,6 +35842,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2023.10.05.23296586", + "rel_title": "Modelling the impact of population mobility, post-infection immunity and vaccination on SARS-CoV-2 transmission in the Dominican Republic", + "rel_date": "2023-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.05.23296586", + "rel_abs": "COVID-19 epidemic dynamics are driven by a complex interplay of factors including population behaviour, government interventions, new variants, vaccination campaigns and immunity from prior infections. We aimed to quantify the epidemic drivers of SARS-CoV-2 dynamics in the Dominican Republic, an upper-middle income country of 10.8 million people, and assess the impact of the vaccination campaign implemented in February 2021 in saving lives and averting hospitalisations.\n\nWe used an age-structured, multi-variant transmission dynamic model to characterise epidemic drivers in the Dominican Republic and explore counterfactual scenarios around vaccination coverage and population mobility. We fit the model to reported deaths, hospital bed occupancy, ICU bed occupancy and seroprevalence data until December 2021 and simulated epidemic trajectories under different counterfactual vaccination scenarios.\n\nWe estimate that vaccination averted 5040 hospital admissions (95% CrI: 4750 - 5350), 1500 ICU admissions (95% CrI: 1420 - 1590) and 544 deaths (95% CrI: 488 - 606) in the first 6 months of the campaign. We also found that early vaccination with Sinovac-CoronaVac was preferable to delayed vaccination using a product with higher efficacy. We investigated the trade-off between changes in vaccination coverage and population mobility to understand how much relaxation of social distancing measures vaccination was able to buy in the later stages of a pandemic. We found that if no vaccination had occurred, an additional decrease of 10-20% in population mobility would have been required to maintain the same death and hospitalisation outcomes. We found SARS-CoV-2 transmission dynamics in the Dominican Republic were driven by substantial accumulation of immunity during the first two years of the pandemic but that, despite this, vaccination was essential in enabling a return to pre-pandemic mobility levels without incurring considerable additional morbidity and mortality.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Emilie Finch", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Eric J Nilles", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Cecilia Then Paulino", + "author_inst": "Ministerio de Salud Publica y Asistencia Social, Dominican Republic" + }, + { + "author_name": "Ronald Skewes-Ramm", + "author_inst": "Ministerio de Salud Publica y Asistencia Social, Dominican Republic" + }, + { + "author_name": "Colleen Lau", + "author_inst": "University of Queensland" + }, + { + "author_name": "Rachel Lowe", + "author_inst": "Barcelona Supercomputing Center: Centro Nacional de Supercomputacion" + }, + { + "author_name": "Adam J Kucharski", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.10.04.23296518", "rel_title": "COVID-19 and Influenza Infection Prevention and Control Measures in U.S. Jails, Prisons, and Detention Centers: A Scoping Review", @@ -36849,33 +37369,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.10.01.560357", - "rel_title": "The TMPRSS2 non-protease domains regulating SARS-CoV-2 Spike in mediated virus entry", - "rel_date": "2023-10-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.01.560357", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters cells by binding to the angiotensin-converting enzyme 2 (hACE2) receptor. This process is aided by the transmembrane protease serine 2 (TMPRSS2), which enhances entry efficiency and infectiousness by cleaving the SARS-CoV-2 surface glycoprotein (Spike). The cleavage primes the Spike protein, promoting membrane fusion instead of receptor-mediated endocytosis. Despite the pivotal role played by TMPRSS2, our understanding of its non-protease distinct domains remains limited. In this report, we present evidence indicating the potential phosphorylation of a minimum of six tyrosine residues within the cytosolic tail (CT) of TMPRSS2. Through the use of TMPRSS2 CT phospho-mimetic mutants, we observed a reduction in TMPRSS2 protease activity, accompanied by a decrease in SARS-CoV-2 pseudovirus infection, which was found to occur mainly via the endosomal pathway. We expanded our investigation beyond TMPRSS2 CT and discovered the involvement of other non-protease domains in regulating infection. Our co-immunoprecipitation experiments demonstrated a strong interaction between TMPRSS2 and Spike. We revealed a 21 amino acid long TMPRSS2-Spike-binding region (TSBR) within the TMPRSS2 scavenger receptor cysteine-rich (SRCR) domain that contributes to this interaction. Our study sheds light on novel functionalities associated with TMPRSS2s cytosolic tail and SRCR region. Both of these regions have the capability to regulate SARS-CoV-2 entry pathways. These findings contribute to a deeper understanding of the complex interplay between viral entry and host factors, opening new avenues for potential therapeutic interventions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Romano Strobelt", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Julia Adler", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Yosef Shaul", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.10.01.560365", "rel_title": "Neutralisation of SARS-CoV-2 Omicron subvariants BA.2.86 and EG.5.1 by antibodies induced by earlier infection or vaccination", @@ -37155,6 +37648,73 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.09.29.560163", + "rel_title": "Discovery of First-in-Class PROTAC Degraders of SARS-CoV-2 Main Protease", + "rel_date": "2023-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.29.560163", + "rel_abs": "We have witnessed three coronavirus (CoV) outbreaks in the past two decades, including the COVID-19 pandemic caused by SARS-CoV-2. Main protease (MPro) is a highly conserved and essential protease that plays key roles in viral replication and pathogenesis among various CoVs, representing one of the most attractive drug targets for antiviral drug development. Traditional antiviral drug development strategies focus on the pursuit of high-affinity binding inhibitors against MPro. However, this approach often suffers from issues such as toxicity, drug resistance, and a lack of broad-spectrum efficacy. Targeted protein degradation represents a promising strategy for developing next-generation antiviral drugs to combat infectious diseases. Here we leverage the proteolysis targeting chimera (PROTAC) technology to develop a new class of small-molecule antivirals that induce the degradation of SARS-CoV-2 MPro. Our previously developed MPro inhibitors MPI8 and MPI29 were used as MPro ligands to conjugate a CRBN E3 ligand, leading to compounds that can both inhibit and degrade SARS-CoV-2 MPro. Among them, MDP2 was demonstrated to effectively reduce MPro protein levels in 293T cells (DC50 = 296 nM), relying on a time-dependent, CRBN-mediated, and proteasome-driven mechanism. Furthermore, MPD2 exhibited remarkable efficacy in diminishing MPro protein levels in SARS-CoV-2-infected A549-ACE2 cells, concurrently demonstrating potent anti-SARS-CoV-2 activity (EC50 = 492 nM). This proof-of-concept study highlights the potential of PROTAC-mediated targeted protein degradation of MPro as an innovative and promising approach for COVID-19 drug discovery.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Yugendar R Alugubelli", + "author_inst": "Texas AM University" + }, + { + "author_name": "Jing Xiao", + "author_inst": "Texas AM University" + }, + { + "author_name": "Kaustav Khatua", + "author_inst": "Texas AM University" + }, + { + "author_name": "Sathish Kumar", + "author_inst": "Texas AM University" + }, + { + "author_name": "Yuying Ma", + "author_inst": "Texas AM University" + }, + { + "author_name": "Xinyu Ma", + "author_inst": "Texas AM University" + }, + { + "author_name": "Veerabhadra Reddy Vulupala", + "author_inst": "Texas AM University" + }, + { + "author_name": "Sandeep Atla", + "author_inst": "Texas AM University" + }, + { + "author_name": "Lauren Blankenship", + "author_inst": "Texas AM University" + }, + { + "author_name": "Demonta Coleman", + "author_inst": "Texas AM University" + }, + { + "author_name": "Benjamin W Neuman", + "author_inst": "Texas AM University" + }, + { + "author_name": "Wenshe Liu", + "author_inst": "Texas AM University" + }, + { + "author_name": "Shiqing Xu", + "author_inst": "Texas AM University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.09.28.560057", "rel_title": "The Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13", @@ -38431,29 +38991,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2023.09.26.23295911", - "rel_title": "Analysis of Potential Risk Factors of COVID-19 Based on Variants: Omicron, Delta, and Alpha", - "rel_date": "2023-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.26.23295911", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has changed which affects the risk of COVID-19 infection for specific subgroups. We focused on the subgroups based on the factors (sex, age, and vaccination) and COVID-19 strains (Alpha, Delta, and Omicron). Past studies focused on analyzing these factors based on one geographic region or one COVID-19 strain. Therefore, there is a need to understand these factors association with risk of COVID-19 infection through analyzing data from various geographic regions and strains. The association between COVID-19 strains and the factors was assessed through chi-square test and odds ratio tests. Sex, vaccination, age had a significant association with testing positive for the COVID-19 strains of interest in most geographies. The biggest difference was unvaccinated individuals have 3.14 higher odds of getting Alpha than vaccinated individuals in Canada. These findings provide insights into the groups that are more susceptible to contracting specific strains of COVID-19.\n\nSummaryThis manuscript offers a broad examination of key factors that may impact the risk of COVID-19 infection across various geographic regions. Results provide evidence about potential risk factors for COVID-19 infection around the world for certain sub-groups as COVID-19 mutates.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dharshini Kannan", - "author_inst": "Innovation Academy" - }, - { - "author_name": "Sreenidhi Muppiri", - "author_inst": "Cambridge High School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.09.25.23289158", "rel_title": "Recruitment, Consent and DNA Sample Acquisition in a U.S. Precision Health Cohort During the COVID-19 Pandemic", @@ -38821,6 +39358,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.09.25.558837", + "rel_title": "Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain", + "rel_date": "2023-09-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.25.558837", + "rel_abs": "The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N-terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5-cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here we determine high-resolution cryo-electron microscopy structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Gabriel I Small", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Olga Federova", + "author_inst": "Yale University" + }, + { + "author_name": "Paul Dominic B Olinares", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Joshua Chandanani", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Anoosha Banerjee", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Young Joo Choi", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Henrik Molina", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Brian Chait", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Seth A Darst", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Elizabeth A Campbell", + "author_inst": "The Rockefeller Univeristy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.09.25.23295828", "rel_title": "Evaluation of computer vision syndrome in the sample of students from the College of Medicine/University of Kerbala result of online learning with the isolation of COVID-19", @@ -39593,7 +40185,7 @@ "rel_date": "2023-09-25", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.22.23295541", - "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@18f48b8org.highwire.dtl.DTLVardef@1ef29dborg.highwire.dtl.DTLVardef@a50380org.highwire.dtl.DTLVardef@188d62a_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@146130corg.highwire.dtl.DTLVardef@18caab8org.highwire.dtl.DTLVardef@1c36a0org.highwire.dtl.DTLVardef@4658ff_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 22, "rel_authors": [ { @@ -40305,61 +40897,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.09.20.23295832", - "rel_title": "Targeted MRM-analysis of plasma proteins in frozen whole blood samples from patients with COVID-19", - "rel_date": "2023-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.20.23295832", - "rel_abs": "The COVID-19 pandemic has exposed a number of key challenges that need to be urgently addressed. In particular, rapid identification and validation of prognostic markers is required. Mass spectrometric studies of blood plasma proteomics provide a deep understanding of the relationship between the severe course of infection and activation of specific pathophysiological pathways. Analysis of plasma proteins in whole blood may also be relevant for the pandemic as it requires minimal sample preparation. Here, for the first time, frozen whole blood samples were used to analyze 189 plasma proteins using multiple reaction monitoring (MRM) mass spectrometry and stable isotope-labeled peptide standards (SIS). A total of 128 samples (FRCC, Russia) from patients with mild (n=40), moderate (n=36) and severe (n=19) COVID-19 infection and healthy controls (n=33) were analyzed. Levels of 114 proteins were quantified and compared. Significant differences between all of the groups were revealed for 61 proteins. Changes in the levels of 30 reproducible COVID-19 markers (SERPING1, CRP, C9, ORM1, APOA1, SAA1/SAA2, LBP, AFM, IGFALS, etc.) were consistent with studies performed with serum/plasma samples. Levels of 70 proteins correlated between whole blood and plasma samples. The best-performing classifier built with 13 significantly different proteins achieved the best combination of ROC-AUC (0.93-0.95) and accuracy (0.87-0.93) metrics and distinguished patients from controls, as well as patients by severity and risk of mortality. Overall, the results support the use of frozen whole blood for MRM analysis of plasma proteins and assessment of the status of patients with COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Anna E. Bugrova", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Polina A. Strelnikova", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - }, - { - "author_name": "Alexey S. Kononikhin", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - }, - { - "author_name": "Natalia V. Zakharova", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Elizaveta O. Diyachkova", - "author_inst": "Pulmonology Scientific and Research Institute, Federal Medical and Biological Agency, 115682 Moscow, Russia" - }, - { - "author_name": "Alexander G. Brzhozovskiy", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - }, - { - "author_name": "Maria I. Indeykina", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Ilya N. Kurochkin", - "author_inst": "Emanuel Institute of Biochemical Physics, Russian Academy of Science, 119334 Moscow, Russia" - }, - { - "author_name": "Alexander V. Averyanov", - "author_inst": "Pulmonology Scientific and Research Institute, Federal Medical and Biological Agency, 115682 Moscow, Russia" - }, - { - "author_name": "Evgeny N. Nikolaev", - "author_inst": "Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.09.19.23295768", "rel_title": "COVID-19 VACCINE ACCEPTANCE AND HESITANCY IN GHANA: A SYSTEMATIC REVIEW", @@ -40639,6 +41176,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.09.19.23295797", + "rel_title": "Automatic Population of the Case Report Forms for an International Multifactorial Adaptive Platform Trial Amid the COVID-19 Pandemic", + "rel_date": "2023-09-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.19.23295797", + "rel_abs": "ObjectivesTo automatically populate the case report forms (CRFs) for an international, pragmatic, multifactorial, response-adaptive, Bayesian COVID-19 platform trial.\n\nMethodsThe locations of focus included 27 hospitals and 2 large electronic health record (EHR) instances (1 Cerner Millennium and 1 Epic) that are part of the same health system in the United States. This paper describes our efforts to use EHR data to automatically populate four of the trials forms: baseline, daily, discharge, and response-adaptive randomization.\n\nResultsBetween April 2020 and May 2022, 417 patients from the UPMC health system were enrolled in the trial. A MySQL-based extract, transform, and load pipeline automatically populated 499 of 526 CRF variables. The populated forms were statistically and manually reviewed and then reported to the trials international data coordinating center.\n\nConclusionsWe accomplished automatic population of CRFs in a large platform trial and made recommendations for improving this process for future trials.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Andrew J King", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Lisa Higgins", + "author_inst": "Monash University" + }, + { + "author_name": "Carly Au", + "author_inst": "Intensive Care National Audit & Research Centre" + }, + { + "author_name": "Salim Malakouti", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Edvin Music", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Kyle Kalchthaler", + "author_inst": "UPMC Department of Clinical Analytics" + }, + { + "author_name": "Gilles Clermont", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "William Garrard", + "author_inst": "UPMC Department of Clinical Analytics" + }, + { + "author_name": "David T Huang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Bryan J McVerry", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Christopher W Seymour", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Kelsey Linstrum", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Amanda McNamara", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Cameron Green", + "author_inst": "Monash University" + }, + { + "author_name": "India D Loar", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Tracey Roberts", + "author_inst": "Global Coalition for Adaptive Research" + }, + { + "author_name": "Oscar Marroquin", + "author_inst": "UPMC Department of Clinical Analytics" + }, + { + "author_name": "Derek C Angus", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Christopher M Horvat", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2023.09.19.23295789", "rel_title": "Adapting COVID-19 research infrastructure to capture Influenza and Respiratory Syncytial Virus alongside SARS-CoV-2 in UK healthcare workers Winter 2022/23 and beyond: protocol for a pragmatic sub-study", @@ -42027,61 +42655,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.09.13.23295114", - "rel_title": "Assessing the impact of the Gamma variant on COVID-19 Patient admissions in a Southern Brazilian tertiary hospital - A comparison of dual pandemic phases", - "rel_date": "2023-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.13.23295114", - "rel_abs": "Since the first case of COVID-19, Brazil has undergone infection waves with distinct characteristics. The description of new variants has alerted the emergence of more contagious or virulent viruses. The variant of concern Gamma emerged in Brazil and caused an epidemic wave, but its spread outside the country was limited. We report the clinical-epidemiological profile of hospitalized patients with COVID-19 by comparing two periods. A retrospective cohort study was performed. The primary outcome was to assess individuals with COVID-19 admitted in wards and intensive care units at CHC-UFPR between March 2020 and July 2021, correlating demographic, clinical-epidemiologic, and survival data with the most prevalent viral variant found in each period. We used Kaplan-Meier analysis to estimate the probability of survival and receiver operating characteristic curves to evaluate laboratory tests to find a cutoff point for poor outcomes. Data from 2,887 individuals were analyzed, 1,495 and 1,392 from the first and second periods, respectively. Hospitalization predominated among males in both periods, and the median age was significantly lower in the second one. The frequency of comorbidities was similar. Various demographic factors, clinical assessments, and laboratory tests were examined in relation to greater severity. When comparing the two studied periods, we observed predominance of the Wild virus during the first wave and the Gamma variant during the second, with no significant difference in outcomes. The findings suggest that despite the association of many factors with increased severity, the temporal variation between the two periods did not result in a notable divergence in the measured outcomes. The COVID-19 pandemic has lasted for a long time, with periods marked by peaks of cases, often caused by the emergence of viral variants, resulting in higher infection rates and rapid dissemination but, for variant Gamma, no apparent greater virulence.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Natalia R Domino", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Bruna A Lapinscki", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Felipe Zhen", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Guilherme Yamaguto", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Emmanueli C S Costa", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Vitor L Moriya", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Luciane A Pereira", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Ricardo Petterle", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Meri B Nogueira", - "author_inst": "Universidade Federal do Paran\u00e1: Universidade Federal do Parana" - }, - { - "author_name": "Sonia M Raboni", - "author_inst": "Universidade Federal do Parana Setor de Ciencias da Saude" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.12.23294140", "rel_title": "Effectiveness of Canadian travel restrictions in reducing burden of SARS-CoV-2 variants of concern", @@ -42353,6 +42926,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2023.09.14.23295425", + "rel_title": "Estimating the population effectiveness of interventions against COVID-19 in France: a modelling study", + "rel_date": "2023-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.14.23295425", + "rel_abs": "BackgroundNon-pharmaceutical interventions (NPIs) and vaccines have been widely used to manage the COVID-19 pandemic. However, uncertainty persists regarding the effectiveness of these interventions due to data quality issues, methodological challenges, and differing contextual factors. Accurate estimation of their effects is crucial for future epidemic preparedness.\n\nMethodsTo address this, we developed a population-based mechanistic model that includes the impact of NPIs and vaccines on SARS-CoV-2 transmission and hospitalization rates. Our statistical approach estimated all parameters in one step, accurately propagating uncertainty. We fitted the model to comprehensive epidemiological data in France from March 2020 to October 2021. With the same model, we simulated scenarios of vaccine rollout.\n\nResultsThe first lockdown was the most effective, reducing transmission by 84% (95% confidence interval (CI) 83-85). Subsequent lockdowns had diminished effectiveness (reduction of 74% (69-77) and 11% (9-18), respectively). A 6pm curfew was more effective than one at 8 pm (68% (66-69) vs. 48% (45-49) reduction), while school closures reduced transmission by 15% (12-18). In a scenario without vaccines before November 2021, we predicted 159,000 or 194% (95% prediction interval (PI) 74-424) more deaths and 1,488,000 or 340% (136-689) more hospitalizations. If a vaccine had been available after 100 days, over 71,000 deaths (16,507-204,249) and 384,000 (88,579-1,020,386) hospitalizations could have been averted.\n\nConclusionOur results highlight the substantial impact of NPIs, including lockdowns and curfews, in controlling the COVID-19 pandemic. We also demonstrate the value of the 100 days objective of the CEPI initiative for vaccine availability.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Iris Ganser", + "author_inst": "Univ. Bordeaux - INRIA - Inserm U1219 - SISTM Team; McGill University" + }, + { + "author_name": "David L Buckeridge", + "author_inst": "McGill University" + }, + { + "author_name": "Jane M Heffernan", + "author_inst": "York University" + }, + { + "author_name": "Melanie Prague", + "author_inst": "Univ. Bordeaux - INRIA - Inserm U1219 - SISTM Team" + }, + { + "author_name": "Rodolphe Thi\u00e9baut", + "author_inst": "Univ. Bordeaux - INRIA - Inserm U1219 - SISTM Team" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.09.14.23295563", "rel_title": "The impact of the COVID-19 pandemic on short-term cancer survival in the United Kingdom: a cohort analysis", @@ -43453,89 +44061,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.09.12.23295441", - "rel_title": "Validation of Real-World Case Definitions for COVID-19 Diagnosis and Severe COVID-19 Illness Among Patients Infected with SARS-CoV-2: Translation of Clinical Trial Definitions to Real-World Settings", - "rel_date": "2023-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.12.23295441", - "rel_abs": "PurposeThis study assessed the performance of International Classification of Diseases 10th Revision, Clinical Modification (ICD-10-CM) coronavirus disease 2019 (COVID-19) diagnostic code U07.1 against polymerase chain reaction (PCR) test results (Objective 1), and electronic medical record (EMR)-based codified algorithm for severe COVID-19 illness based on endpoints used in the Pfizer-BioNTech COVID-19 vaccine trial against chart review (Objective 2).\n\nMethodsThis retrospective, longitudinal cohort study used EMR data from the Mass General Brigham COVID-19 Data Mart (3/1/2020-11/19/2020) for adult patients with [≥]1 PCR test, antigen test, or code U07.1 (Objective 1) and adult patients with a positive PCR test hospitalized with COVID-19 (Objective 2).\n\nResultsAmong 354,124 patients in Objective 1, 96% had [≥]1 PCR test (including 6% with [≥]1 positive PCR test; 11% with [≥]1 code U07.1). Code U07.1 had low sensitivity (54%) and positive predictive value (PPV; 63%) but high specificity (97%) against the PCR test. Among 300 patients hospitalized for COVID-19 randomly sampled for chart review in Objective 2, the EMR-based case definition for severe COVID-19 illness had high PPV (>95%), showing better performance than severe/critical COVID-19 endpoints defined by the World Health Organization (PPV: 79%).\n\nConclusionsCOVID-19 diagnosis based on ICD-10-CM code U07.1 had inadequate sensitivity and requires confirmation by PCR testing. The EMR-based case definition showed high PPV and can be used to identify cases of severe COVID-19 illness in real-world datasets. These findings highlight the importance of validating outcomes in real-world data, and can guide researchers analyzing COVID-19 data when PCR tests are not readily available.\n\nKEY POINTSO_LIThis study evaluated the performance of International Classification of Diseases 10th Revision, Clinical Modification (ICD-10-CM) codes and an electronic medical record (EMR)-based algorithm for identifying coronavirus disease 2019 (COVID-19) diagnosis and severe COVID-19 illness in real-world data.\nC_LIO_LIICD-10-CM code U07.1 for COVID-19 had low sensitivity and positive predictive value (PPV) against PCR tests.\nC_LIO_LIThe EMR-based algorithm for severe COVID-19 illness developed from the Pfizer- BioNTech COVID-19 vaccine trial had high PPV against chart review, and may be used to identify severe cases in real-world data.\nC_LIO_LIThese results highlight the importance of validating outcomes when conducting analyses of real-world datasets.\nC_LI\n\nPLAIN LANGUAGE SUMMARYAs polymerase chain reaction (PCR) tests for coronavirus disease 2019 (COVID-19) diagnosis are becoming less frequently used and there is no standard definition of severe COVID-19 illness, it is important to have a way of correctly identifying COVID-19 diagnosis or severe COVID-19 illness in real-world data (e.g., electronic medical records [EMRs]). This study examined: 1) how a diagnosis code for COVID-19 used in EMRs (i.e., U07.1) compares to PCR test results in terms of accurately identifying patients with COVID-19; and 2) whether a definition for severe COVID-19 illness developed based on the Pfizer-BioNTech COVID-19 vaccine trial and a definition used by the World Health Organization [WHO]) can be used to accurately identify patients with severe COVID-19 illness in EMRs. The results showed that code U07.1 was not very accurate in identifying patients with COVID-19. On the other hand, the developed definition for severe COVID-19 illness was more accurate than the WHO definition and was able to identify most patients with severe COVID-19 illness in real-world data.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Mei Sheng Duh", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Catherine Nguyen", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Heather Rubino", - "author_inst": "Pfizer, Inc." - }, - { - "author_name": "Christopher Herrick", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Rose Chang", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Maral DerSarkissian", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Yichuan Grace Hsieh", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Azeem Banatwala", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Louise H. Yu", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Gregory Belsky", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Marykate E. Murphy", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Janet Boyle-Kelly", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Andrew Cagan", - "author_inst": "Mass General Brigham" - }, - { - "author_name": "Bruce E. Stangle", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Pierre Y. Cremieux", - "author_inst": "Analysis Group, Inc." - }, - { - "author_name": "Francesca Kolitsopoulos", - "author_inst": "Pfizer, Inc." - }, - { - "author_name": "Shawn N. Murphy", - "author_inst": "Mass General Brigham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.12.23295384", "rel_title": "Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections", @@ -43935,6 +44460,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.09.11.23295344", + "rel_title": "Safety and immunogenicity of SW-BIC-213, a modified COVID-19 Lipo-Polyplex mRNA vaccine, in Laotian healthy adults aged 18 years and above: a Phase 1/2 trial", + "rel_date": "2023-09-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.11.23295344", + "rel_abs": "BackgroundThe mRNA vaccine against SARS-CoV-2 has demonstrated remarkable efficacy in protecting against coronavirus disease 2019 (COVID-19), including providing high protection against severe disease during the emergence of variant waves. In this study, we aimed to investigate the safety and immunogenicity of a 2-dose regimen of the LPP-based mRNA vaccine, SW-BIC-213, in Laos.\n\nMethodsFor this phase 1/2 clinical trial, we recruited healthy adults aged 18-60 years (phase 1) or [≥]18 years (phase 2) from Mahosot Hospital (Vientiane) and Champhone District Hospital (Savannakhet). Participants with SARS-CoV-2 infection, previous COVID-19 vaccination, known allergies to any vaccine component, or pregnancy were excluded. In the phase 1 trial, 41 eligible participants were sequentially assigned to either the 25 g dose group (25 g) or the 45 g dose group (45 g) in accordance with their enrollment order, with 21 participants in 45 g dose group and 20 participants in 25 g dose group. In the phase 2 trial, 480 participants were randomly allocated (2:2:1 ratio) to either the 25 g dose group, 45 g dose group, or placebo group.\n\nThe primary endpoints for the phase 1 trial were the incidence of local/systemic solicited adverse reactions/events (0-6 days after each vaccination dose), unsolicited adverse events (0-21 days and 0-28 days after the first and second dose of immunization, respectively), and serious adverse events from the first dose of vaccination to 28 days after completing the full course of immunization. In the phase 2 trial, the primary endpoints were the seroconversion rate and geometric mean titer (GMT) of SARS-CoV-2 S-protein specific IgG antibodies and neutralizing antibodies 14 days after the second dose in participants. As for neutralizing antibodies, we detected pseudo-virus neutralizing antibody against wild type (WT), Delta, BA.1 and BA.2. We also detected live viral neutralizing antibody against WT strain 14 days after the second dose. Furthermore, the safety endpoints were also measured during the trial.\n\nThis seamless phase 1/2 trial was registered with ClinicalTrials.gov under the identifier NCT05144139.\n\nResultsBetween December 3, 2021, and March 31, 2022, a total of 41 participants were recruited in the phase 1 trial, while the phase 2 trial enrolled 480 participants from January 20 to July 6, 2022. In the phase 1 trial, a total of 32 subjects (80.0%) reported 103 cases of adverse reactions. All adverse reactions were limited to Grade 1-2. In the phase 2 trial, a total of 479 subjects, 372 subjects (77.7%) reported 929 cases of adverse reactions. All adverse reactions in severity of Grade 3 were manifested as fever (3.4%, 2.1% and 2.9% in 45 g dose, 25 g dose and placebo group respectively, only observed in adults), except which all other reactions were limited to Grade 1-2. All adverse reactions noted during the study were tolerable, predominantly transient, and resolved spontaneously. No serious adverse events (SAEs) related to vaccination were observed.\n\nIn Phase 2 study, SW-BIC-213 could elicit a high level of seroconversion rate of pseudo-virus neutralizing antibody against WT (100.0% in 25 g dose group, 99.3% in 45 g dose group), Delta (99.2% in 25 g dose group, 98.0% in 45 g dose group), Omicron BA.1 (84.1% in 25 g dose group, 84.7% in 45 g dose group) and Omicron BA.2 (96.0% in 25 g dose group, 88.8% in 45 g dose group) at 14 days after the second dose. The pseudo-virus neutralizing antibody titer against WT, Delta, BA.1 and BA.2 was all significant higher (P<0.0001) in both 45 g dose group (1175.02, 620.62, 72.39 and 172.80) and 25 g dose group (885.80, 579.40, 47.24 and 101.96) compared with the placebo group (9.67, 10.66, 13.99 and 29.53) at 14 days after the second dose. As for live viral neutralizing antibodies against WT strain, the seroconversion rate could reach more than 94% at 14 days after second dose. The neutralizing antibody titer against WT strain was significantly higher (P<0.0001) in both 45 g dose group (315.00) and 25 g dose group (323.18) compared with the placebo group (8.51) at 14 days after second dose.\n\nConclusionCOVID-19 mRNA vaccine SW-BIC-213 manifests a favorable safety profile and is highly immunogenic in eligible subjects aged [≥]18 years.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "yujie chen", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "jingxin li", + "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China" + }, + { + "author_name": "Davone Duangdany", + "author_inst": "Food and Drug Department, Ministry of Health, Vientiane, Laos" + }, + { + "author_name": "Chanthala Phamisith", + "author_inst": "Savannakhet Province Hospital, Savannakhet, Laos" + }, + { + "author_name": "yu bo", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "shengke lan", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "Lairun Jin", + "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China" + }, + { + "author_name": "Dawei Lv", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "yang li", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "bin luo", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "peng han", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "jinyan wu", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "yuzhu wang", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "congcong xu", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "mingyun shen", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "fanfan zhao", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "peipei liu", + "author_inst": "Chinese center for disease control and prevention, China" + }, + { + "author_name": "rongjuan pei", + "author_inst": "Wuhan Institute of Virology, Wuhan, China" + }, + { + "author_name": "Haifa shen", + "author_inst": "StemiRNA Therapeutics" + }, + { + "author_name": "wuxiang guan", + "author_inst": "Wuhan Institute of Virology, Wuhan, China" + }, + { + "author_name": "hangwen li", + "author_inst": "Stemirna Therapeutics" + }, + { + "author_name": "Mayfong Mayxay", + "author_inst": "Institute of Research and Education Development, University of Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.09.10.23295343", "rel_title": "Navigating the Neurological Aftermath of COVID-19: An In-Depth Exploration", @@ -45503,105 +46131,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2023.09.06.23294696", - "rel_title": "Predictors of SARS-CoV-2 anti-Spike IgG antibody levels following two COVID-19 vaccine doses among children and adults in the Canadian CHILD Cohort", - "rel_date": "2023-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.06.23294696", - "rel_abs": "BackgroundVaccination helps prevent SARS-CoV-2 infection and severe COVID-19. However, vaccine-induced humoral immune responses vary among individuals and wane over time. We aimed to describe the SARS-CoV-2 anti-spike IgG antibody response to vaccination and identify health and demographic factors associated with this response among children and adults.\n\nMethodsWe studied a subset of double-vaccinated children (n= 151; mean age: 12 {+/-}1.5 years, 46% female) and adults (n= 995; 44 {+/-}6.0 years, 60% female) from the Canadian CHILD Cohort. Dried blood spots were collected over two time periods (March 2021 to September 2021; October 2021 to January 2022). Antibody levels were quantified using automated chemiluminescent ELISAs. Demographic, vaccination, and health data were collected via online questionnaires. Associations were determined using multivariable regression.\n\nResultsOur cohort had SARS-CoV-2 anti-spike seropositivity rate of 97% following two COVID-19 vaccine doses. In both children and adults, the highest antibody levels were observed around three months post-vaccination and did not differ by biological sex. Higher antibody levels were associated with: prior SARS-CoV-2 infection ({beta}=0.15 scaled luminescence units, 95%CI, 0.06-0.24), age <18 years ({beta}=0.15, 95%CI 0.05-0.26) and receiving the Moderna mRNA ({beta}=0.23, 95%CI 0.11-0.34) or Pfizer-BioNTech mRNA vaccines ({beta}= 0.10, 95%CI, 0.02-0.18) vs. a combination of mRNA and Oxford-AstraZeneca viral vector vaccines. There were no differences in antibody levels when comparing a 3-8 vs. 9-16-week interval between vaccine doses.\n\nInterpretationWe identified key factors associated with post-vaccination antibody responses in children and adults, which could help improve future vaccine development and deployment among different population subgroups.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Rilwan Azeez", - "author_inst": "Department of Immunology, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Larisa Lotoski", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Geoffery L. Winsor", - "author_inst": "Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Corey R. Arnold", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Yannick Galipeau", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Martin Pelchat", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Stephanie Goguen", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Elinor Simons", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Theo J. Moraes", - "author_inst": "Division of Respiratory Medicine, Department of Pediatrics and Program in Translational Medicine, SickKids Research Institute, The Hospital for Sick Children, O" - }, - { - "author_name": "Piush J. Mandhane", - "author_inst": "Department of Pediatrics, University of Alberta, Edmonton, AB, Canada" - }, - { - "author_name": "Stuart E. Turvey", - "author_inst": "Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Shelly Bolotin", - "author_inst": "Centre for Vaccine Preventable Diseases, University of Toronto: Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "David M. Patrick", - "author_inst": "School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada" - }, - { - "author_name": "Jared Bullard", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Lisa M. Lix", - "author_inst": "Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Natasha Doucas", - "author_inst": "CHILD Cohort Study National Parent Engagement Committee" - }, - { - "author_name": "Natalie Rodriguez", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - }, - { - "author_name": "Fiona S.L. Brinkman", - "author_inst": "Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Padmaja Subbarao", - "author_inst": "Division of Respiratory Medicine, Department of Pediatrics and Program in Translational Medicine, SickKids Research Institute, The Hospital for Sick Children, O" - }, - { - "author_name": "Marc-Andr\u00e9 Langlois", - "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Meghan Azad", - "author_inst": "Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.08.23295177", "rel_title": "Systematical assessment of the impact of single spike mutations of SARS-CoV-2 Omicron sub-variants on the neutralization capacity of post-vaccination sera", @@ -46001,6 +46530,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.09.06.556620", + "rel_title": "Immunogenicity and tolerability of a SARS-CoV-2 TNX-1800, a live recombinant poxvirus vaccine candidate, in Syrian Hamsters and New Zealand White Rabbits.", + "rel_date": "2023-09-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.06.556620", + "rel_abs": "TNX-1800 is a preclinical stage synthetic derived live chimeric horsepox virus vaccine that comprises an engineered SARS-CoV-2 spike (S) gene expression cassette. The objectives of this study were to assess the immunogenicity and tolerability of TNX-1800 administration in Syrian golden hamsters and New Zealand white rabbits. Animals were vaccinated via percutaneous inoculation and evaluated for dose tolerance and immunogenicity at three different dose levels. The 28-day study data showed that the single percutaneous administration of three TNX-1800 vaccine dose levels was well tolerated in both hamsters and rabbits. For all dose levels, rabbits had more dermal observations than hamsters at the same dose levels. Vaccine-induced viral load four weeks post-dosing was below the detection level for both species.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mayanka Awasthi", + "author_inst": "Tonix Pharmaceutical, Frederick, MD, USA" + }, + { + "author_name": "Anthony Macaluso", + "author_inst": "Tonix Pharmaceutical, Frederick, MD, USA" + }, + { + "author_name": "Scott J Goebel", + "author_inst": "Tonix Pharmaceutical, Frederick, MD, USA" + }, + { + "author_name": "Erin Luea", + "author_inst": "Southern Research, Birmingham, AL, USA" + }, + { + "author_name": "Ryan S Noyce", + "author_inst": "University of Alberta, Edmonton, Alberta, Canada" + }, + { + "author_name": "Farooq Nasar", + "author_inst": "Tonix Pharmaceutical, Frederick, MD, USA" + }, + { + "author_name": "Bruce Daugherty", + "author_inst": "Tonix Pharmaceuticals, Chatham, NJ" + }, + { + "author_name": "Sina Bavari", + "author_inst": "Tonix Pharmaceutical, Frederick, MD, USA" + }, + { + "author_name": "Seth Lederman", + "author_inst": "Tonix Pharmaceuticals, Dartmouth, MA, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.09.06.556442", "rel_title": "Convergent Sequence Features of Antiviral B Cells", @@ -47277,105 +47857,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2023.09.01.555815", - "rel_title": "Antigenicity and infectivity characterization of SARS-CoV-2 BA.2.86", - "rel_date": "2023-09-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.01.555815", - "rel_abs": "The recently identified SARS-CoV-2 variant, BA.2.86, which carries a substantial number of Spike mutations, has raised a global alarm. An immediate assessment of its antigenic properties and infectivity is necessary. Here, we reveal the distinct antigenicity of BA.2.86 compared with previous variants including XBB.1.5. BA.2.86 significantly evades convalescent plasma from XBB breakthrough infection (BTI) and reinfections. Key mutations that mediate the enhanced resistance include N450D, K356T, L452W, A484K, V483del, and V445H on the RBD, while BA.2.86s NTD mutations and E554K on SD1 also largely contribute. However, we found that BA.2.86 pseudovirus exhibits compromised efficiency of infecting HEK293T-hACE2 cells compared to XBB.1.5 and EG.5, which may be caused by K356T, V483del, and E554K, and could potentially limit BA.2.86s transmissibility. In sum, it appears that BA.2.86 has traded its infectivity for higher immune evasion during long-term host-viral evolution. Close attention should be paid to monitoring additional mutations that could improve BA.2.86s infectivity.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Sijie Yang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yuanling Yu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Fanchong Jian", - "author_inst": "Peking University" - }, - { - "author_name": "Weiliang Song", - "author_inst": "Peking University" - }, - { - "author_name": "Ayijiang Yisimayi", - "author_inst": "Peking University" - }, - { - "author_name": "Xiaosu Chen", - "author_inst": "Nankai University" - }, - { - "author_name": "Yanli Xu", - "author_inst": "Beijing Ditan Hospital" - }, - { - "author_name": "Peng Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Lingling Yu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Jing Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Xiao Niu", - "author_inst": "Peking University" - }, - { - "author_name": "Jing Wang", - "author_inst": "Peking University" - }, - { - "author_name": "Tianhe Xiao", - "author_inst": "Peking University" - }, - { - "author_name": "Ran An", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Yao Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Qingqing Gu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Fei Shao", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Ronghua Jin", - "author_inst": "Beijing Ditan Hospital" - }, - { - "author_name": "Zhongyang Shen", - "author_inst": "Nankai University" - }, - { - "author_name": "Youchun Wang", - "author_inst": "Chinese Academy of Medical Science & Peking Union Medical College" - }, - { - "author_name": "Yunlong Richard Cao", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.09.02.556038", "rel_title": "Neutralization of SARS-CoV-2 EG.5/EG.5.1 by sera from ZF2001 RBD-dimer and its next-generation vaccines", @@ -47651,6 +48132,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.08.31.23294738", + "rel_title": "COVID-19-related school closures, United States, July 27, 2020 - June 30, 2022", + "rel_date": "2023-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.31.23294738", + "rel_abs": "As part of a multi-year project that monitored illness-related school closures, we conducted systematic daily online searches from July 27, 2020-June 30, 2022, to identify public announcements of COVID-19-related school closures (COVID-SCs) in the US lasting [≥]1 day. We explored the temporospatial patterns of COVID-SCs and analyzed associations between COVID-SCs and national COVID-19 surveillance data. COVID-SCs reflected national surveillance data: correlation was highest between COVID-SCs and both new PCR test positivity (correlation coefficient, r = 0{middle dot}73, CI: 0{middle dot}56, 0{middle dot}84) and new cases (r = 0{middle dot}72, CI: 0{middle dot}54, 0{middle dot}83) in school year (SY) 2020-21, and with hospitalization rates among all ages (rs = 0{middle dot}81, CI: [0{middle dot}67, 0{middle dot}89]) in SY 2021-22. The number of reactive COVID-SCs during SYs 2020-21 and 2021-22 greatly exceeded previously observed numbers of illness-related reactive school closures in the US, notably being nearly 5-fold greater than reactive closures observed during the 2009 H1N1 Pandemic (H1N1pdm09 virus).\n\nArticle summary lineCOVID-19-related school closures occurred annually in the US and their temporal patterns mirror the general patterns of COVID-19 activity at the national level as observed through routine COVID-19 epidemiological surveillance.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nicole Zviedrite", + "author_inst": "US Centers for Disease Control and Prevention" + }, + { + "author_name": "Ferdous A Jahan", + "author_inst": "US Centers for Disease Control and Prevention" + }, + { + "author_name": "Sarah Moreland", + "author_inst": "Henry M. Jackson Foundation" + }, + { + "author_name": "Faruque Ahmed", + "author_inst": "US Centers for Disease Control and Prevention" + }, + { + "author_name": "Amra Uzicanin", + "author_inst": "US Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.09.01.23294943", "rel_title": "A mathematical model for multiple COVID-19 waves applied to Kenya", @@ -49051,53 +49567,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.30.23294839", - "rel_title": "Vaccination status and re-infection among COVID patients admitted in COVID High Dependency Unit (HDU) of a tertiary hospital in Eastern Nepal: A cross-sectional study", - "rel_date": "2023-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.30.23294839", - "rel_abs": "IntroductionThe relationship between COVID-19 vaccination and Coronavirus disease severity and outcomes remain topics of significant interest. This cross-sectional study done among COVID-19 patients admitted to the High-dependency unit of a tertiary hospital in Eastern Nepal aimed to assess the association between vaccination status, prior infection, and disease outcomes, and the modification of these associations by the presence or absence of comorbidities.\n\nMethodologyDemographic and clinical data were collected from 102 COVID-19 patients admitted to the High-Dependency Unit of Mechi Zonal Hospital, including information on vaccination status, comorbidities, disease severity, and outcomes. Statistical analysis, including chi-square tests and Fishers exact tests, was performed to examine the associations.\n\nResultsAmong the study participants, 49% had received at least one dose of COVID-19 vaccine. Vaccinated individuals had a significantly lower rate of severe disease compared to non-vaccinated individuals ({chi}{superscript 2}=10.05, p=0.002). Recovery and mortality rates did not differ significantly between the two groups ({chi}{superscript 2}=1.008, p=0.315). However, when stratified by comorbidities, vaccinated individuals with comorbidities had higher recovery rates compared to non-vaccinated individuals (85.29% vaccinated vs. 25.00% non-vaccinated, Fishers exact test p=0.024). Vaccinated individuals, both with and without comorbidities, had lower rates of severe disease compared to non-vaccinated individuals. However, the association was found to be significant only in individuals with comorbidities (12.50% vaccinated without comorbidities vs. 47.92% non-vaccinated, p=0.017; 23.53% vaccinated with comorbidities vs. 75.00% non-vaccinated, p=0.065).\n\nConclusionOur findings suggest that COVID-19 vaccination is associated with a reduced risk of severe disease among individuals with or without comorbidities and decreased risk of mortality among those with comorbidities. However, larger studies are needed to validate these findings and further explore the impact of vaccination on disease outcomes. These findings support the ongoing efforts to promote COVID-19 vaccination as a crucial public health intervention.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sujan Kafle", - "author_inst": "Provincial Hospital Bhadrapur" - }, - { - "author_name": "Varsha Chhetri", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Joshan Lal Bajracharya", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Lenish Pokharel", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Suyash Dawadi", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Ujwal Basnet", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Shreya Dhungana", - "author_inst": "BP Koirala Institute of Health Sciences" - }, - { - "author_name": "Durga Neupane", - "author_inst": "BP Koirala Institute of Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.29.23293790", "rel_title": "Outpatient treatment with concomitant vaccine-boosted convalescent plasma for patients with immunosuppression and COVID-19", @@ -49569,6 +50038,45 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2023.08.29.555368", + "rel_title": "SARS-CoV-2 RNA Persists in the Central Nervous System of Non-Human Primates Despite Clinical Recovery", + "rel_date": "2023-08-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.29.555368", + "rel_abs": "Adverse neurological and psychiatric outcomes, collectively termed the post-acute sequelae of SARS-CoV-2 infection (PASC), persist in adults clinically recovered from COVID-19. Effective therapeutic interventions are fundamental to reducing the burden of PASC, necessitating an investigation of the pathophysiology underlying the debilitating neurological symptoms associated with the condition. Herein, eight non-human primates (Wild-Caught African Green Monkeys, n=4; Indian Rhesus Macaques, n=4) were inoculated with the SARS-CoV-2 isolate USA-WA1/2020 by either small particle aerosol or via multiple routes. At necropsy, tissue from the olfactory epithelium and pyriform cortex/amygdala of SARS-CoV-2 infected non-human primates were collected for ribonucleic acid in situ hybridization (i.e., RNAscope). First, angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) mRNA are downregulated in the pyriform cortex/amygdala of non-human primates clinically recovered from SARS-CoV-2 inoculation relative to wildtype controls. Second, abundant SARS-CoV-2 mRNA was detected in clinically recovered non-human primates; mRNA which is predominantly harbored in pericytes. Collectively, examination of post-mortem pyriform cortex/amygdala brain tissue of non-human primates clinically recovered from SARS-CoV-2 infection revealed two early pathophysiological mechanisms potentially underlying PASC. Indeed, therapeutic interventions targeting the downregulation of ACE2, decreased expression of TMPRSS2, and/or persistent infection of pericytes in the central nervous system may effectively mitigate the debilitating symptoms of PASC.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hailong Li", + "author_inst": "University of South Carolina" + }, + { + "author_name": "Kristen A McLaurin", + "author_inst": "University of South Carolina" + }, + { + "author_name": "Charles F Mactutus", + "author_inst": "University of South Carolina" + }, + { + "author_name": "Jay Rappaport", + "author_inst": "Tulane University National Primate Research Center" + }, + { + "author_name": "Prasun K Datta", + "author_inst": "Tulane University National Primate Research Center" + }, + { + "author_name": "Rosemarie Booze", + "author_inst": "University of South Carolina" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2023.08.30.555188", "rel_title": "Immune Evasion and Membrane Fusion of SARS-CoV-2 XBB Subvariants EG.5.1 and XBB.2.3", @@ -50239,7 +50747,7 @@ "rel_date": "2023-08-28", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.25.23294626", - "rel_abs": "Background: We sought to determine immune and behavioral pre-infection correlates of protection against SARS-CoV-2 post-vaccine infections in a joint analysis of epidemiological and immunological cohort data. Methods: Serum and saliva samples from 176 BNT162b2-vaccinated adults in the Prospective Assessment of SARS-CoV-2 Seroconversion study were collected between October and December 2021 and assessed for serum and saliva levels of Wuhan-1 wild-type (WT) SARS-CoV-2 Spike (S)-specific IgG and IgA binding antibodies (bAb) using a multiplex microsphere-based immunoassay (MMIA). Serum samples were also assessed for WT receptor binding domain (RBD)-specific bAb by two commercial assays, BA.1 S-specific IgG bAb by MMIA, and neutralization activity against D614G, Delta (B.1.617.2), and Omicron BA.1 and BA.1.1 variants using a lentiviral pseudovirus neutralization assay. After the Fall 2021 visit, participants reported all positive PCR and/or antigen tests for SARS-CoV-2. Duration, severity, and type of symptoms, as well as risk exposures and adherence to precautionary measures, were assessed by questionnaires during the Spring 2022 visit. Results: Thirty-two participants (18.2%) developed symptomatic post-vaccination SARS-CoV-2 infections (PVI) between December 7, 2021 and April 1, 2022. Pre-infection WT (geometric mean (GM) of 3,863 vs 2,736 binding antibody unit [BAU]/ml, uninfected vs PVI, p=0.0098) and BA.1 (GM of 276.9 vs 179.9 arbitrary bAb unit [AU]/ml, uninfected vs PVI, p=0.04) anti-S IgG bAb levels measured by MMIA and neutralizing titers (NT) against BA.1 (GM titer [GMT] of 493.6 vs 286.2, uninfected vs PVI, p=0.0313) and BA.1.1 (GMT of 552.0 vs 302.5, uninfected vs PVI, p=0.021) were significantly higher in individuals that did not develop PVIs. WT anti-S bAb levels greater than 5,000 BAU/ml were associated with > 90% protection against symptomatic PVI. In individuals that developed PVI, WT anti-S IgG bAb levels correlated with lower disease severity scores ({rho}= -0.3859, p=0.032) and shorter duration of clinical disease ({rho}= -0.5273, p=0.0023). WT anti-RBD bAb levels measured by commercial assays correlated strongly with bAb levels measured by MMIA ({rho}=0.8239, p<0.0001 and {rho}=0.6929, p<0.0001, Roche and Siemens assays, respectively), but did not reach statistical significance for correlation with protection against PVI. Home risk score, but neither work nor home precautionary measures, correlated strongly with risk of PVI (mean score of 20.77 vs 47.33, uninfected vs PVI respectively, p<0.0001). Conclusions: Anti-S IgG bAb levels (directed against either WT or Omicron BA.1 subvariant) and NTs served as correlates of protection against symptomatic SARS-CoV-2 infection. Anti-S (WT) IgG bAb levels remained a significant correlate of protection against PVIs when adjusting for demography and risk behavior. Results of this study also suggest that commercial assays for anti-S bAb may need to be reformatted to enable detection of higher maximum values for use as predictors of increased susceptibility to SARS-CoV-2 infection.", + "rel_abs": "We sought to determine pre-infection correlates of protection against SARS-CoV-2 post-vaccine infections (PVI) acquired during the first Omicron wave in the United States. Serum and saliva samples from 176 vaccinated adults were collected from October to December of 2021, immediately before the Omicron wave, and assessed for SARS-CoV-2 Spike-specific IgG and IgA binding antibodies (bAb). Sera were also assessed for bAb using commercial assays, and for neutralization activity against several SARS-CoV-2 variants. PVI duration and severity, as well as risk and precautionary behaviors, were assessed by questionnaires. Serum anti-Spike IgG levels assessed by research assay, neutralization titers against Omicron subvariants, and low home risk scores correlated with protection against PVIs after multivariable regression analysis. Commercial assays did not perform as well as research assay, likely due to their lower dynamic range. In the 32 participants that developed PVI, anti-Spike IgG bAbs correlated with lower disease severity and shorter duration of illness.", "rel_num_authors": 48, "rel_authors": [ { @@ -51101,61 +51609,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2023.08.21.553968", - "rel_title": "Antibody Neutralization of Emerging SARS-CoV-2: EG.5.1 and XBC.1.6", - "rel_date": "2023-08-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.21.553968", - "rel_abs": "SARS-CoV-2 variants EG.5.1 and XBC.1.6 have recently emerged, attracting increased attention due to their rapid expansion globally and in Australia, respectively. EG.5.1 evolved from Omicron subvariant XBB.1.9, harboring additional Q52H and F456L spike substitutions. The F456L mutation is located within the epitopes of many class-1 monoclonal antibodies (mAbs) directed to the receptor-binding domain (RBD), raising concerns about further antibody evasion. XBC.1.6, a descendant of a Delta-BA.2 recombinant, carries 15 additional spike mutations. The extent to which antibody evasion contributes to the growth advantage of XBC.1.6 in Australia remains to be determined. To assess the antibody evasion properties of the emergent variants, we conducted pseudovirus neutralization assays using sera from individuals who received three doses of COVID-19 mRNA monovalent vaccines plus one dose of a BA.5 bivalent vaccine, as well as from patients with BQ or XBB breakthrough infection. The assays were also performed using a panel of 14 mAbs that retained neutralizing activity against prior XBB subvariants. Our data suggested that EG.5.1 was slightly but significantly more resistant (< 2-fold) to neutralization by BQ and XBB breakthrough sera than XBB.1.16, which is known to be antigenically similar to XBB.1.5. Moreover, the F456L mutation in EG.5.1 conferred heightened resistance to certain RBD class-1 mAbs. In contrast, XBC.1.6 was more sensitive to neutralization by sera and mAbs than the XBB subvariants. Notably, XBB breakthrough sera retained only weak neutralization activity against XBB subvariants. In summary, EG.5.1 and XBC.1.6 exhibited distinct antibody evasion properties. The recent global expansion of EG.5.1 might be attributable, in part, to its enhanced neutralization resistance. That XBB breakthrough infections did not elicit a robust antibody neutralization response against XBB subvariants is indicative of immunological imprinting. The high prevalence of XBC.1.6 in Australia is not due to enhanced antibody evasion.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Qian Wang", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Yicheng Guo", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Richard Ma Zhang", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Jerren Ho", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Hiroshi Mohri", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Riccardo Valdez", - "author_inst": "University of Michigan" - }, - { - "author_name": "David M Manthei", - "author_inst": "University of Michigan" - }, - { - "author_name": "Aubree Gordon", - "author_inst": "University of Michigan School of Public Health" - }, - { - "author_name": "Lihong Liu", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "David D Ho", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.08.24.554732", "rel_title": "Mucosal antibody responses to SARS-CoV-2 booster vaccination and breakthrough infection", @@ -51383,6 +51836,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.08.24.23294557", + "rel_title": "An After-Action Review of COVID-19 Cases and Mitigation Measures at US Mission India, March 2020-July 2021", + "rel_date": "2023-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.24.23294557", + "rel_abs": "IntroductionBetween March 2020-June 2021, over 30 million COVID-19 cases were reported in India. We assessed the COVID-19 response across the US Mission India (US Embassy New Delhi, US Consulates - Mumbai, Hyderabad, Chennai and Kolkata) to plan future mitigation efforts and fill gaps in knowledge about COVID-19 transmission in a unique community like the US Mission.\n\nMethodWe described COVID-19 mitigation activities undertaken by the five US Mission India posts and conducted a secondary analysis of case investigation and contact tracing program data collected by the Health Unit from March 2020-July 2021.\n\nResultsUS Mission in India, in collaboration with multiple internal agencies, initiated COVID-19 mitigation activities in March 2020. Activities included educational sessions, training for infection prevention and control, health and safety assessments, and the development of standard operating procedures (SOPs). The Health Unit and US CDC India office initiated COVID-19 case investigations and conducted contact tracing. Between March 2020-July 2021, 636 COVID-19 cases (72% males), including 48 clusters (size range 2-10 cases), were reported. Overall case fatality rate was 1.5%. Of case patients, 82% (523) were Indians, and 18% (113) were Americans. On presentation, 22% (138/625) of cases were asymptomatic. The median time from symptom onset to notification to the Health Unit was three days (Interquartile range 1-5). The Health Unit identified 2,484 contacts (positivity rate 25%). Frequency of case presentation in the US Mission India closely resembled the pattern of COVID-19 waves in India. The attack rates ranged over the time period between 10-19%, the highest at 19% in Delhi.\n\nConclusionsCOVID-19 mitigation strategies were implemented in collaboration with multiple agencies and helped prevent the transmission of COVID-19 and large COVID-19 clusters in the US Mission India.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jaspreet Singh", + "author_inst": "US Department of State" + }, + { + "author_name": "Rajesh Yadav", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Samantha Robinson", + "author_inst": "US Department of State" + }, + { + "author_name": "Mark Vanelli", + "author_inst": "US Department of State" + }, + { + "author_name": "Melissa Nyendak", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Meghna Desai", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.08.24.23294588", "rel_title": "Modelling the Interplay between Responsive Individual Vaccination Decisions and the Spread of SARS-CoV-2", @@ -52683,65 +53175,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.08.23.554434", - "rel_title": "SARS-CoV-2 Nsp13 is a viral RHIM protein promoting cell death linked to Z-RNA sensing and ZBP1-RIPK3 signaling", - "rel_date": "2023-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.23.554434", - "rel_abs": "Interferons and regulated cell death pathways counteract virus spread and mount immune responses, but their deregulation often results in inflammatory pathologies. The RIP-homotypic interaction motif (RHIM) is a conserved protein domain critical for assembling higher-order amyloid-like signaling complexes inducing cell death. A few DNA viruses employ viral RHIMs mimicking host RHIMs to alleviate cell death-mediated antiviral defenses. Whether RNA viruses operate such viral RHIMs remains unknown. Host RHIM-protein signaling promotes lung damage and cytokine storm in respiratory RNA virus infections, arguing the presence of viral RHIMs in RNA viruses. Here, we report the identification of novel viral RHIMs in Nsp13 and Nsp14 of SARS-CoV-2 and other bat RNA viruses and provide a basis for bats as the hosts for the evolution of RHIMs in RNA viruses. Nsp13 expression promoted CoV-RHIM-1-dependent cell death after SARS-CoV-2 infection, and its RNA-binding channel conformation was critical for cell death function. Nsp13 interacted and promoted the formation of large insoluble complexes of ZBP1 and RIPK3. Unlike DNA virus RHIMs, SARS-CoV-2 Nsp13 did not restrict host RHIM-dependent cell death. Instead, it promoted ZBP1-RIPK3 signaling-mediated cell death dependent on intracellular RNA ligands. Intriguingly, SARS-CoV-2 genome fragments showed high Z-RNA forming propensity which bound to Z-RNA sensing Z domains and promoted Nsp13-dependent cell death. Our findings reveal the functional viral RHIMs in RNA viruses and the role of SARS-CoV-2 Nsp13 in cell death associated with Z-RNAs and ZBP1-RIPK3 signaling, allowing the understanding of mechanisms of cellular damage and cytokine storm in respiratory virus infections and COVID-19.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC=\"FIGDIR/small/554434v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (66K):\norg.highwire.dtl.DTLVardef@12bf222org.highwire.dtl.DTLVardef@25cc1forg.highwire.dtl.DTLVardef@17c2a2dorg.highwire.dtl.DTLVardef@b4f745_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sanchita Mishra", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Disha Jain", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Ayushi Amin Dey", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Sahana Nagaraja", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Mansi Srivastava", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Oyahida Khatun", - "author_inst": "Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bengaluru 560012, India. Centre for Infectious Diseas" - }, - { - "author_name": "Keerthana Balamurugan", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Micky Anand", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Shashank Tripathi", - "author_inst": "Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bengaluru 560012, India. Centre for Infectious Diseas" - }, - { - "author_name": "Mahipal Ganji", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - }, - { - "author_name": "Sannula Kesavardhana", - "author_inst": "Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bengaluru, Karnataka 560012, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.08.24.554561", "rel_title": "Rationally designed multimeric nanovaccines using icosahedral DNA origami for molecularly controlled display of SARS-CoV-2 receptor binding domain", @@ -53021,6 +53454,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.08.22.553458", + "rel_title": "Administration of vaccine-boosted COVID-19 convalescent plasma to SARS-CoV-2 infected hamsters decreases virus replication in lungs and hastens resolution of the infection despite transiently enhancing disease and lung pathology.", + "rel_date": "2023-08-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.22.553458", + "rel_abs": "The utility of COVID-19 convalescent plasma (CCP) for treatment of immunocompromised patients who are not able to mount a protective antibody response against SARS-CoV-2 and who have contraindications or adverse effects from currently available antivirals remains unclear. To better understand the mechanism of protection in CCP, we studied viral replication and disease progression in SARS-CoV-2 infected hamsters treated with CCP plasma obtained from recovered COVID patients that had also been vaccinated with an mRNA vaccine, hereafter referred to as Vaxplas. We found that Vaxplas dramatically reduced virus replication in the lungs and improved infection outcome in SARS-CoV-2 infected hamsters. However, we also found that Vaxplas transiently enhanced disease severity and lung pathology in treated animals likely due to the deposition of immune complexes, activation of complement and recruitment of increased numbers of macrophages with an M1 proinflammatory phenotype into the lung parenchyma.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Timothy Carroll", + "author_inst": "UC Davis: University of California Davis" + }, + { + "author_name": "Talia Wong", + "author_inst": "University of California Davis" + }, + { + "author_name": "Mary Kate Morris", + "author_inst": "Division of Viral and Rickettsial Diseases, California Department of Public Health, Richmond, California, USA" + }, + { + "author_name": "Clara Di Germanio", + "author_inst": "Vitalant Research Institute, San Francisco, CA, USA" + }, + { + "author_name": "Zhong-Min Ma", + "author_inst": "UC Davis" + }, + { + "author_name": "Mars Stone", + "author_inst": "Vitalant Research Institiute" + }, + { + "author_name": "Erin E Ball", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Linda Fritts", + "author_inst": "UC Davis: University of California Davis" + }, + { + "author_name": "Arjun Rustagi", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Graham Simmons", + "author_inst": "Vitalant Research Institute, San Francisco, CA, USA" + }, + { + "author_name": "Michael P Busch", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Christopher J Miller", + "author_inst": "UC Davis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.08.21.554138", "rel_title": "Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection", @@ -54449,29 +54945,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.16.23294160", - "rel_title": "Unraveling COVID-19: Descriptive Analytics in a Middle-Income Country, Paving the Path Forward", - "rel_date": "2023-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.16.23294160", - "rel_abs": "The outbreak of COVID-19 unleashed an unprecedented global pandemic, leaving a profound impact on lives and economies worldwide. Recognizing its severity, the World Health Organization swiftly declared it a public health emergency of international concern. Tragically, the Philippines reported the first death case outside China, leading to a surge in cases following the first instance of local transmission. In response to this crisis, collaborative efforts have been underway to control the disease and minimize its health and socio-economic impacts. The COVID-19 epidemic curve holds vital insights into the history of exposure, transmission, testing, tracing, social distancing measures, community lockdowns, quarantine, isolation, and treatment, offering a comprehensive perspective on the nations response. One approach to gaining crucial insights is through meticulous analysis of available datasets, empowering us to inform future strategies and responses effectively. This paper aims to provide descriptive data analytics of the COVID-19 pandemic in the Philippines, summarizing the countrys fight by visualizing epidemiological and mobility datasets, revisiting scientific papers and news articles, and creating a timeline of the key issues faced during the pandemic. By leveraging these multifaceted analyses, policymakers and health authorities can make informed decisions to enhance preparedness, expand inter-agency cooperation, and combat future public health crises effectively. This study seeks to serve as a valuable resource, guiding nations worldwide in comprehending and responding to the challenges posed by COVID-19 and beyond.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Norvin Patadon Bansilan", - "author_inst": "University of the Philippines Los Banos" - }, - { - "author_name": "Jomar Fajardo Rabajante", - "author_inst": "University of the Philippines Los Banos" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.08.17.553661", "rel_title": "Purification, crystallization, and preliminary structural analysis of multivalent immunogenic effector protein-anchored SARS-CoV-2 RBD", @@ -54635,6 +55108,177 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.08.16.553332", + "rel_title": "Virological characteristics of the SARS-CoV-2 XBB.1.5 variant", + "rel_date": "2023-08-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.16.553332", + "rel_abs": "Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the F486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determined the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. The intrinsic pathogenicity of XBB.1.5 in hamsters is lower than that of XBB.1. Importantly, we found that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC expression. In vivo experiments using recombinant viruses revealed that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, these data suggest that the mutations in ORF8 and S could enhance spreading of XBB.1.5 in humans.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Tomokazu Tamura", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Takashi Irie", + "author_inst": "Hiroshima University" + }, + { + "author_name": "Sayaka Deguchi", + "author_inst": "Kyoto University" + }, + { + "author_name": "Hisano Yajima", + "author_inst": "Kyoto University" + }, + { + "author_name": "Masumi Tsuda", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Hesham Nasser", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Keita Mizuma", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Arnon Plianchaisuk", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Saori Suzuki", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Keiya Uriu", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "MST Monira Begum", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Ryo Shimizu", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Michael Jonathan", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Rigel Suzuki", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Takeshi Kondo", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Hayato Ito", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Akifumi Kamiyama", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Kumiko Yoshimatsu", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Maya Shofa", + "author_inst": "University of Miyazaki" + }, + { + "author_name": "Rina Hashimoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Yuki Anraku", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Kanako Terakado Kimura", + "author_inst": "Kyoto University" + }, + { + "author_name": "Shunsuke Kita", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Jiei Sasaki", + "author_inst": "Kyoto University" + }, + { + "author_name": "Kaori Sasaki-Tabata", + "author_inst": "Kyushu University" + }, + { + "author_name": "Katsumi Maenaka", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Naganori Nao", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Lei Wang", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Yoshitaka Oda", + "author_inst": "Hokkaido University" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium", + "author_inst": "" + }, + { + "author_name": "Terumasa Ikeda", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Akatsuki Saito", + "author_inst": "University of Miyazaki" + }, + { + "author_name": "Keita Matsuno", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Jumpei Ito", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Shinya Tanaka", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Kei Sato", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Takao Hashiguchi", + "author_inst": "Kyoto University" + }, + { + "author_name": "Kazuo Takayama", + "author_inst": "Kyoto University" + }, + { + "author_name": "Takasuke Fukuhara", + "author_inst": "Hokkaido University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.08.15.553430", "rel_title": "Predicting host-based, synthetic lethal antiviral targets from omics data", @@ -55827,49 +56471,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.08.13.553144", - "rel_title": "Mutational basis of serum cross-neutralization profiles elicited by infection or vaccination with SARS-CoV-2 variants", - "rel_date": "2023-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.13.553144", - "rel_abs": "A series of SARS-CoV-2 variants emerged during the pandemic under selection for neutralization resistance. Convalescent and vaccinated sera show consistently different cross-neutralization profiles depending on infecting or vaccine variants. To understand the basis of this heterogeneity, we modeled serum cross-neutralization titers for 165 sera after infection or vaccination with historically prominent lineages tested against 18 variant pseudoviruses. Cross-neutralization profiles were well captured by models incorporating autologous neutralizing titers and combinations of specific shared and differing mutations between the infecting/vaccine variants and pseudoviruses. Infecting/vaccine variant-specific models identified mutations that significantly impacted cross-neutralization and quantified their relative contributions. Unified models that explained cross-neutralization profiles across all infecting and vaccine variants provided accurate predictions of holdout neutralization data comprising untested variants as infecting or vaccine variants, and as test pseudoviruses. Finally, comparative modeling of 2-dose versus 3-dose mRNA-1273 vaccine data revealed that the third dose overcame key resistance mutations to improve neutralization breadth.\n\nHIGHLIGHTSO_LIModeled SARS-CoV-2 cross-neutralization using mutations at key sites\nC_LIO_LIIdentified resistance mutations and quantified relative impact\nC_LIO_LIAccurately predicted holdout variant and convalescent/vaccine sera neutralization\nC_LIO_LIShowed that the third dose of mRNA-1273 vaccination overcomes resistance mutations\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kshitij Wagh", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Xiaoying Shen", - "author_inst": "Duke University" - }, - { - "author_name": "James Theiler", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Bethany Girard", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Jean-Claude Marshall", - "author_inst": "Moderna, Inc., Cambridge, MA 02319, USA" - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Bette Korber", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.08.14.553219", "rel_title": "Transmission bottleneck size estimation from de novo viral genetic variation", @@ -56069,6 +56670,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.08.09.23293776", + "rel_title": "Post-COVID conditions during Delta and early-Omicron SARS-CoV-2 variant periods among adults in the United States", + "rel_date": "2023-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.09.23293776", + "rel_abs": "BackgroundPost-COVID conditions after infection with new SARS-CoV-2 variants have been incompletely described. We compared the prevalence and risk factors for ongoing symptoms lasting 4 weeks or longer (often referred to as post-COVID Conditions) among adults who had tested positive vs. negative during the Delta and early-Omicron periods.\n\nMethodsSelf-reported survey data regarding symptoms and previous SARS-CoV 2 test results were collected from May 31 - July 6, 2022, from a probability sampling of United States adults. Respondents were classified according to their test result, predominant circulating variant when respondents first tested positive (Delta vs early-Omicron), and demographic risk factors.\n\nResultsAmong 2,421 respondents, 256 tested positive during Delta, 460 during early-Omicron, and 1,705 always tested negative. Nearly one-fourth (22.3%) of negative respondents reported [≥]1symptom that lasted [≥]4 weeks, compared to 60.6% (p<0.05) of respondents who tested positive during the Delta period and 47.8% (p<0.05) during the early-Omicron period. Fatigue, change in smell/taste, and cough were commonly reported by respondents who tested positive. Demographic risk factors associated with ongoing symptoms were being female and unemployed (aOR 1.28, 95% CI 1.06-1.55; aOR 1.48, 95% CI: 1.17-1.87).\n\nConclusionThe reported occurrence of ongoing symptoms associated with post-COVID conditions was reduced during the early-Omicron period, compared with Delta.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Deja L Edwards", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Pamela Logan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Leora Feldstein", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Emma Accorsi", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Tarayn Fairlie", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Sharon Saydah", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.08.08.23293808", "rel_title": "A community based cross-sectional study on impact assessment of COVID-19 on mental health in Central India", @@ -57209,69 +57849,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.07.23293304", - "rel_title": "High-throughput detection of neutralizing antibodies to SARS-CoV-2 variants using flow cytometry", - "rel_date": "2023-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.07.23293304", - "rel_abs": "Detecting neutralizing antibodies (NAbs) to SARS-CoV-2 variants is crucial for controlling the spread of COVID-19. In this work, we developed a high-throughput assay for the broad systematic examination of NAbs to eleven SARS-CoV variants of concern (VOCs), which include D614G, Alpha, Beta, Gamma, Delta, Kappa, and Omicron sub-lineages BA.1, BA.2, BA.3, BA.4, and BA.5. The assay is cost-effective, reliable, 35-fold more sensitive than Luminex technology, and can include the new variants during SARS-CoV-2 evolution. Importantly, our results highly correlated with a commercial IgG serological assay (R = 0.89) and cPass, a U.S. FDA-approved surrogate virus neutralization test (sVNT) assay (R = 0.93). With our high-throughput NAb platform, we constructed a comprehensive overview of the interactions between SARS-CoV-2 VOCs Spike trimer proteins and ACE2 receptors, leading to the identification of a monoclonal Ab with broad neutralizing activity. Furthermore, when compared to the D614G variant, we found that the serum NAbs elicited by the third dose vaccine (administered after 28 days) demonstrated decreased inhibition to multiple SARS-CoV-2 variants, including Gamma (0.94x), Alpha (0.91x), Delta (0.91x), Beta (0.81x), Kappa (0.81x), BA.2 (0.44x), BA.1 (0.43x), BA.3 (0.41x), BA.5 (0.35x) and BA.4 (0.33x), in cohort of 56 vaccinated individuals. Altogether, our proteomics platform proves to be an effective tool to detect broad NAbs in the population and aid in the development of future COVID-19 vaccines and vaccination strategies.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Xiaohan Zhang", - "author_inst": "College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine; State Key Laboratory of Proteomics, Beijing Proteome Research Center, Natio" - }, - { - "author_name": "Yajie Wang", - "author_inst": "Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University" - }, - { - "author_name": "Mansheng Li", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Haolong Li", - "author_inst": "Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College" - }, - { - "author_name": "Xiaomei Zhang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Xingming Xu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Di Hu", - "author_inst": "ProteomicsEra Medical Co., Ltd." - }, - { - "author_name": "Te Liang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Yunping Zhu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Yongzhe Li", - "author_inst": "Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College" - }, - { - "author_name": "Bingwei Wang", - "author_inst": "College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine" - }, - { - "author_name": "Xiaobo Yu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.08.552415", "rel_title": "Antiviral efficacy of the SARS-CoV-2 XBB breakthrough infection sera against Omicron subvariants including EG.5", @@ -57507,6 +58084,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.08.04.23293662", + "rel_title": "Socio-demographic determinants of COVID-19 vaccine uptake in Ontario: Exploring differences across the Health Region model", + "rel_date": "2023-08-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.04.23293662", + "rel_abs": "The COVID-19 pandemic continues to be a worldwide public health concern. Although vaccines against this disease were rapidly developed, vaccination uptake has not been equal across all the segments of the population. In particular, it has been shown that there have been differences in vaccine uptake across different segments of the population. However, there are also differences in vaccination across geographical areas, which might be important to consider in the development of future public health vaccination policies. In this study, we examined the relationship between vaccination status (having received the first dose of a COVID-19 vaccine), and different socio-economic and geographical factors. Our results show that between October of 2021 and January of 2022, individuals from underrepresented communities were three times less likely to be vaccinated than White/Caucasian individuals across the province of Ontario in Canada, and that in some cases, within these groups, individuals in low-income brackets had significantly higher odds of vaccination when compared to their peers in high income brackets. Finally, we identified significantly lower odds of vaccination in the Central, East and West Health Regions of Ontario within certain underrepresented groups. This study shows that there is an ongoing need to better understand and address differences in vaccination uptake across diverse segments of the population of Ontario that the pandemic has largely impacted.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ariel I Mundo Ortiz", + "author_inst": "Universite de Montreal" + }, + { + "author_name": "Bouchra Nasri", + "author_inst": "ESPUM: Universite de Montreal Ecole de Sante Publique" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.08.04.23293152", "rel_title": "Four Models of Wastewater-Based Surveillance for SARS-CoV-2 in Jail Settings: How Monitoring Wastewater Complements Individual Screening", @@ -58751,77 +59351,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.28.23293335", - "rel_title": "Healthcare resource utilization and costs associated with COVID-19 among pediatrics managed in the community or hospital setting in England: a population-based cohort study", - "rel_date": "2023-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.28.23293335", - "rel_abs": "BackgroundAlthough COVID-19 morbidity is significantly lower in pediatrics than in adults, the risk of severe COVID-19 may still pose substantial healthcare resource burden. This study aimed to describe healthcare resource utilization (HCRU) and costs associated with COVID-19 in pediatrics aged 1-17 years in England.\n\nMethodsA population-based retrospective cohort study of pediatrics with COVID-19 using Clinical Practice Research Datalink (CPRD Aurum) primary care data and, where available, linked Hospital Episode Statistics Admitted Patient Care (HES APC) secondary care data. HCRU and associated costs to the National Health Service (NHS) were stratified by age, risk of severe COVID-19, and immunocompromized status, separately for those with and without hospitalization records (hospitalized cohort: COVID-19 diagnosis August 2020-March 2021; primary care cohort: COVID-19 diagnosis August 2020-January 2022).\n\nResultsThis study included 564,644 patients in the primary care cohort and 60 in the hospitalized cohort. Primary care consultations were more common in those aged 1-4 years (face-to-face: 4.3%; telephone: 6.0%) compared to those aged 5-11 (2.0%; 2.1%) and 12-17 years (2.2%; 2.5%). In the hospitalized cohort, mean [SD] length of stay was longer (5.0 [5.8] days) among those aged 12-17 years (n=24) than those aged 1-4 (n=15; 1.8 [0.9] days) and 5-11 years (n=21; 2.8 [2.1] days).\n\nConclusionsMost pediatrics diagnosed with COVID-19 were managed in the community. However, hospitalizations were an important driver of HCRU and costs, particularly for those aged 12-17 years. Our results may help optimize the management and resource allocation of COVID-19 in this population.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jingyan Yang", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Kathleen M Andersen", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Kiran K Rai", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Theo Tritton", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Tendai Mugwagwa", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Carmen Tsang", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Maya Reimbaeva", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Leah McGrath", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Poppy Payne", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Bethany Emma Backhouse", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Diana Mendes", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Rebecca Butfield", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Robert Wood", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Jennifer L Nguyen", - "author_inst": "Pfizer Inc" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.28.23293338", "rel_title": "Systematic Review and Meta-Analysis Protocol of the Efficacy and Safety of COVID-19 Drug Candidates Targeting Host Enzymes Involved in Immune Response", @@ -59085,6 +59614,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.08.02.23293558", + "rel_title": "The Lancet peer reviewers and the COVID-19 pandemic", + "rel_date": "2023-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.02.23293558", + "rel_abs": "IntroductionPeer review is paramount to the scholarly article paradigm, helping to ensure the integrity and credibility of research. The Lancet played a crucial role in disseminating key information on the COVID-19 pandemic, publishing early clinical descriptions, risk factors for death, and effectiveness of measures like physical distancing and masks. Notably, The Lancet was the worlds most cited journal for COVID-19 research, emphasising its significant impact on disseminating critical findings during the pandemic.\n\nMethodsGeographic data for The Lancets peer reviewers in 2019 (pre-pandemic) and 2020 (pandemic) were analysed at the country level, ranking reviewer countries. A test of proportions compared reviewer numbers between the years.\n\nResultsIn 2020, China emerged as one of the top ten reviewer countries for the first time, with a significant increase from 1% (25 of 1843) in 2019 to 3% (54 of 1850), p=0.001. Italy also entered the top five reviewer countries, rising from 4% (67) to 5% (90), p=0.065. Reviewers from Africa 43 (2%) and South America 31 (2%) represented their continents in 2020. The top ten reviewer nations for The Lancet in 2020 largely mirrored the top ten countries in global COVID-19 research output.\n\nConclusionDuring the COVID-19 pandemics acute phase in 2020, The Lancet, the worlds most cited journal for COVID-19 research, featured peer reviewers who were largely representative of global COVID-19 research output. Notably, reviewers from China, the first country affected by COVID-19, increased significantly. However, underrepresentation of some continents persisted. To foster global idea exchange and enhance pandemic preparedness, research capacity worldwide must expand, broadening the reviewer pool--a vital step given uncertainties in future pandemic geographic origin.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Gwinyai Masukume", + "author_inst": "Tipperary, Munster, Ireland" + }, + { + "author_name": "Victor Grech", + "author_inst": "Academic Department of Paediatrics, Medical School, Mater Dei Hospital, Msida, Malta" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.07.31.23293471", "rel_title": "Exploring Disparities and Novel Insights into Metabo-Nutritional Comorbidities among COVID-19 Patients in Mexico", @@ -60481,129 +61033,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.07.28.550957", - "rel_title": "Epigenetic liquid biopsies reveal elevated vascular endothelial cell turnover and erythropoiesis in asymptomatic COVID-19 patients", - "rel_date": "2023-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.28.550957", - "rel_abs": "The full spectrum of tissues affected by SARS-CoV-2 infection is crucial for deciphering the heterogenous clinical course of COVID-19. Here, we analyzed DNA methylation and histone modification patterns in circulating chromatin to assess cell type-specific turnover in severe and asymptomatic COVID-19 patients, in relation to clinical outcome. Patients with severe COVID-19 had a massive elevation of circulating cell-free DNA (cfDNA) levels, which originated in lung epithelial cells, cardiomyocytes, vascular endothelial cells and erythroblasts, suggesting increased cell death or turnover in these tissues. The immune response to infection was reflected by elevated B cell and monocyte/macrophage cfDNA levels, and by evidence of an interferon response in cells prior to cfDNA release. Strikingly, monocyte/macrophage cfDNA levels (but not monocyte counts), as well as lung epithelium cfDNA and vascular endothelial cfDNA, predicted clinical deterioration and duration of hospitalization. Asymptomatic patients had elevated levels of immune-derived cfDNA but did not show evidence of pulmonary or cardiac damage. Surprisingly, these patients showed elevated levels of vascular endothelial cell and erythroblast cfDNA, suggesting that sub-clinical vascular and erythrocyte turnover are universal features of COVID-19, independent of disease severity. Epigenetic liquid biopsies provide non-invasive means of monitoring COVID-19 patients, and reveal sub-clinical vascular damage and red blood cell turnover.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Roni Ben Ami", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Netanel Loyfer", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Eden Cohn", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Gavriel Fialkoff", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Israa Sharkia", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Naama Bogot", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Danit Kochan", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "George Kalak", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Amir Jarjoui", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Chen Chen-Shuali", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Hava Azulai", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Hezi Barhoum", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Nissim Arish", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Moshe M Greenberger", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "David Velleman", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Ramzi Kurd", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Eli Ben Chetrit", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Davina Bohm", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Talya Wolak", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Ahmad Quteineh", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Gordon Cann", - "author_inst": "GRAIL LLC" - }, - { - "author_name": "Benjamin Glaser", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Nir Friedman", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Tommy Kaplan", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Ruth Shemer", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Ariel Rokach", - "author_inst": "Shaare Zedek Medical Center" - }, - { - "author_name": "Yuval Dor", - "author_inst": "Hebrew University of Jerusalem" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.08.01.551417", "rel_title": "Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning", @@ -60895,6 +61324,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.07.28.23293282", + "rel_title": "An updated research focus on the employment of computer-aided drug discovery and repurposing techniques for the identification and evaluation of SARS-CoV-2 Main protease inhibitors: A protocol for a systematic review and meta-analysis", + "rel_date": "2023-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.28.23293282", + "rel_abs": "BackgroundWith the onset of the COVID-19 pandemic caused by the novel coronavirus (SARS-CoV-2), there has been a surge in the pursuit of potential therapeutic interventions for this deadly disease. Given the urgency of the situation, computational drug repurposing methods have emerged as a promising strategy for identifying effective treatments from a pool of approved drugs. This systematic review and meta-analaysis will assess the existing research on the use of computational approaches for drug repurposing in the context of COVID-19. SARS-CoV-2 Main Protease is a critical enzyme that plays a vital role in the replication cycle of the SARS-CoV-2 virus, and its inhibition is a promising strategy for the development of antiviral therapies.\n\nMethods/DesignDifferent databases (PubMed, Cochrane Library, Cumulative Index to Nursing and Allied Health Literature (CINAHL), MEDLINE via EBSCOhost, Google Scholar, and WILEY online Library) will be utilized to identify and incorporate primary research articles in English and French that employed computational methodologies for drug repurposing in the context of COVID-19 and SARS-CoV-2 Main protease inhibition published between March 2020 to May 2023. According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-ScR), we will undertake a comprehensive search of relevant studies. Authors will also search peer-reviewed articles, grey literature sources, and reference lists to identify eligible studies. Title screening will be followed by independent abstract and full-text screening by two reviewers. Any study that focuses on the inhibition of the Mpro using computer aided methods will be included. The analysis of data will be carried out by utilizing two software tools - Review Manager software (version 5.3.5) and R software (version 3.6.1). To determine statistical heterogeneity, a standard chi-square test will be applied with a significance level of P < 0.10. Potential biases related to study size (such as publication bias) will be examined through the application of several techniques, including funnel plots, Eggers test, Beggs test, as well as Trim and Fill analysis.\n\nDiscussionThis study will provide evidence-based information and conduct a comprehensive analysis of the computer-aided drug discovery and repurposing of the SARS-CoV-2 Main protease inhibitors, thereby producing a high-quality synthesis of information. The study will also explore potential innovative therapeutic applications for preventing or treating the novel viral infection by the inhibition of the Main Protease. In addition, the review will highlight research gaps in the treatment of COVID-19 and provide suggestions for future research. The outcomes of this review will be shared through a peer-reviewed publication and presented at relevant conferences while ensuring proper dissemination to reach a wide audience.\n\nSystematic review registration: CRD42023409682(https://www.crd.york.ac.uk/prospero/display_record.asp?ID=CRD42023409682)", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "AGANZE GLOIRE-AIME MUSHEBENGE", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Samuel Chima Ugbaja", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Nonkululeko Avril Mbatha", + "author_inst": "University f KwaZulu Natal" + }, + { + "author_name": "Manimani Ghislain Riziki", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Tambwe Willy Muzumbukilwa", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Mukanda Gedeon Kadima", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Manimbulu Zephy Nlooto", + "author_inst": "University of Limpopo" + }, + { + "author_name": "Hezekiel M. Kumalo", + "author_inst": "University of KwaZulu-Natal" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.27.23293237", "rel_title": "SARS-CoV-2 in 30 Months, Indonesia Data Tells: Study from a Reference Laboratory in North Jakarta and Its Reflection for Regional to National COVID-19 Situation", @@ -62531,41 +63007,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.25.550568", - "rel_title": "Experimental infection of elk (Cervus canadensis) and mule deer (Odocoileus hemionus) with SARS-CoV-2", - "rel_date": "2023-07-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.25.550568", - "rel_abs": "Elk (Cervus canadensis) and mule deer (Odocoileus hemionus) were experimentally evaluated for susceptibility to SARS-CoV-2. Elk did not shed infectious virus but produced low-level serological responses. Mule deer shed and transmitted virus in addition to mounting pronounced serological responses; they could therefore play a role in the epidemiology of SARS-CoV-2.\n\nArticle Summary LineExperimental infection of elk (Cervus canadensis) and mule deer (Odocoileus hemionus) with SARS-CoV-2 revealed that while elk are minimally susceptible to infection, mule deer become infected, shed infectious virus, and can infect naive contacts.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Stephanie M Porter", - "author_inst": "United States Department of Agriculture" - }, - { - "author_name": "Airn E Hartwig", - "author_inst": "Colorado State University" - }, - { - "author_name": "Helle Bielefeldt-Ohmann", - "author_inst": "University of Queensland" - }, - { - "author_name": "Jeff Root", - "author_inst": "USDA" - }, - { - "author_name": "Angela Bosco-Lauth", - "author_inst": "Colorado State University" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.07.25.550460", "rel_title": "Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protect mice against severe disease using Fc-mediated effector functions", @@ -62925,6 +63366,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2023.07.24.550423", + "rel_title": "Predictive Systems Biology Modeling: Unraveling Host Metabolic Disruptions and Potential Drug Targets in SARS-CoV-2 and Its Variants", + "rel_date": "2023-07-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.24.550423", + "rel_abs": "BackgroundHost response is critical to the onset, progression, and outcome of viral infections. Since viruses hijack the host cellular metabolism for their replications, we hypothesized that restoring host cell metabolism can efficiently reduce viral production.\n\nResultsHere, we present a viral-host Metabolic Modeling (vhMM) method to systematically evaluate the disturbances in host metabolism in viral infection and computationally identify targets for modulation by integrating genome-wide precision metabolic modeling and cheminformatics. We applied vhMM to SARS-CoV-2 infections and identified consistent changes in host metabolism and gene and endogenous metabolite targets between the original SARS-COV-2 and different variants (Alpha, Delta, and Omicron). Among six compounds predicted for repurposing, methotrexate, cinnamaldehyde, and deferiprone were tested in vitro and effective in inhibiting viral production with IC50 less than 4uM. Further, an analysis of real-world patient data showed that cinnamon usage significantly reduced the SARS-CoV-2 infection rate with an odds ratio of 0.65 [95%CI: 0.55[~]0.75].\n\nConclusionsThese results demonstrated that vhMM is an efficient method for predicting targets and drugs for viral infections.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gong-Hua Li", + "author_inst": "Kunming Institute of Zoology, Chinese Academy of Sciences" + }, + { + "author_name": "Feifei Han", + "author_inst": "Massachusetts General Hospital, Harvard Medical School" + }, + { + "author_name": "Rong-Hua Luo", + "author_inst": "Kunming Institute of Zoology, Chinese Academy of Sciences" + }, + { + "author_name": "Peng Li", + "author_inst": "Massachusetts General Hospital, Harvard Medical Schoo" + }, + { + "author_name": "Chia-Jung Chang", + "author_inst": "Massachusetts General Hospital, Harvard Medical School" + }, + { + "author_name": "Weihong Xu", + "author_inst": "Massachusetts General Hospital, Harvard Medical School" + }, + { + "author_name": "Xin-Yan Long", + "author_inst": "Kunming Institute of Zoology, Chinese Academy of Sciences" + }, + { + "author_name": "Jing-Fei Huang", + "author_inst": "Kunming Institute of Zoology, Chinese Academy of Sciences" + }, + { + "author_name": "Yong-Tang Zheng", + "author_inst": "Kunming Institute of Zoology, Chinese Academy of Sciences" + }, + { + "author_name": "Qing-Peng Kong", + "author_inst": "Kunming Institute of Zoology, Chinese Academy of Sciences" + }, + { + "author_name": "Wenzhong Xiao", + "author_inst": "Massachusetts General Hospital, Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2023.07.24.550415", "rel_title": "Mammalian cells-based platforms for the generation of SARS-CoV-2 virus-like particles", @@ -63569,7 +64069,7 @@ "rel_date": "2023-07-24", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.23.549087", - "rel_abs": "SARS-CoV-2 employs its spike protein's receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our understanding of how RBD's biophysical properties contribute to SARS-CoV-2's epidemiological fitness remains largely incomplete. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the discovery of a fitness function based on binding thermodynamics, we unravel the relationship between the biophysical properties of RBD variants and their contribution to viral fitness. We developed a biophysical model that uses statistical mechanics to map the molecular phenotype space, characterized by binding constants of RBD to ACE2, LY-CoV016, LY-CoV555, REGN10987, and S309, onto a epistatic fitness landscape. We validate our findings through experimentally measured and machine learning (ML) estimated binding affinities, coupled with infectivity data derived from population-level sequencing. Our analysis reveals that this model effectively predicts the fitness of novel RBD variants and can account for the epistatic interactions among mutations, including explaining the later reversal of Q493R. Our study sheds light on the impact of specific mutations on viral fitness and delivers a tool for predicting the future epidemiological trajectory of previously unseen or emerging low frequency variants. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics.", + "rel_abs": "SARS-CoV-2 employs its spike proteins receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our understanding of how RBDs biophysical properties contribute to SARS-CoV-2s epidemiological fitness remains largely incomplete. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the discovery of a fitness function based on binding thermodynamics, we unravel the relationship between the biophysical properties of RBD variants and their contribution to viral fitness. We developed a biophysical model that uses statistical mechanics to map the molecular phenotype space, characterized by binding constants of RBD to ACE2, LY-CoV016, LY-CoV555, REGN10987, and S309, onto a epistatic fitness landscape. We validate our findings through experimentally measured and machine learning (ML) estimated binding affinities, coupled with infectivity data derived from population-level sequencing. Our analysis reveals that this model effectively predicts the fitness of novel RBD variants and can account for the epistatic interactions among mutations, including explaining the later reversal of Q493R. Our study sheds light on the impact of specific mutations on viral fitness and delivers a tool for predicting the future epidemiological trajectory of previously unseen or emerging low frequency variants. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics.\n\nSignificance StatementThis research presents a biophysical model that maps the molecular properties of SARS-CoV-2s receptor binding domain into an epistatic fitness landscape. By linking the binding affinities of the virus to its epidemic fitness, we offer a powerful tool for understanding and predicting the emergence and success of new viral variants. Our model, validated with real-world data and informed by theoretical insights, provides a foundation for interpreting the evolutionary trajectory of past pandemics and predicting those of the future. The adaptability of this biophysical model extends to the key proteins of other viruses as well, signifying its potential in guiding public health interventions, and advancing our understanding of viral evolution.", "rel_num_authors": 4, "rel_authors": [ { @@ -64105,33 +64605,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2023.07.19.23292810", - "rel_title": "Several Mathematical Aspects on Daily Number of COVID-19 Infection Cases in Eight Southeast Asian Places", - "rel_date": "2023-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.19.23292810", - "rel_abs": "The number of daily confirmed infected cases is a key parameter to determine emergency management actions to take. The mathematical characteristics of the daily infection number should be explored for working out appropriate control scheme. Several mathematical aspects on the daily number of infected cases will be discussed in 8 Southeastern Asian places using the confirmed daily infection numbers available in public websites. Phase space diagrams of plotting the daily infection rate estimated numerically against daily infection number on those tests are presented first. Modeling parameters including the Farrs Law are also discussed. A parameter is proposed to describe the extent of infection by estimating the transient daily infection number divided by the time.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "C.L. Chow", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "C.H. Cheng", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "W.K. Chow", - "author_inst": "The Hong Kong Polytechnic University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2023.07.21.23293001", "rel_title": "Unraveling COVID-19 Relationship with Anxiety Disorders and Symptoms", @@ -64387,6 +64860,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2023.07.18.23292858", + "rel_title": "Risk of SARS-CoV-2 infection and hospitalization in individuals with natural, vaccine-induced and hybrid immunity: a retrospective population-based cohort study from Estonia", + "rel_date": "2023-07-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.18.23292858", + "rel_abs": "A large proportion of the worlds population has some form of immunity against SARS-CoV- 2, through either infection ( natural), vaccination or both ( hybrid). This retrospective cohort study used data on SARS-CoV-2, vaccination, and hospitalization from national health system from February 2020 to June 2022 and Cox regression modelling to compare those with natural immunity to those with no (Cohort1, n=92917), hybrid (Cohort2, n=46813), and vaccine (Cohort3, n=252414) immunity. In Cohort 1, those with natural immunity were at lower risk for infection during the Delta (aHR 0.17, 95%CI 0.15-0.18) and higher risk (aHR 1.24, 95%CI 1.18-1.32) during the Omicron period than those with no immunity. Natural immunity conferred substantial protection against COVID-19-hospitalization. Cohort 2 - in comparison to natural immunity hybrid immunity offered strong protection during the Delta (aHR 0.61, 95%CI 0.46-0.80) but not the Omicron (aHR 1.05, 95%CI 0.93-1.1) period. COVID-19-hospitalization was extremely rare among individuals with hybrid immunity. In Cohort 3, individuals with vaccine-induced immunity were at higher risk than those with natural immunity for infection (Delta aHR 4.90, 95%CI 4.48-5.36; Omicron 1.13, 95%CI 1.06-1.21) and hospitalization (Delta aHR 7.19, 95%CI 4.02-12.84). These results show that risk of infection and severe COVID-19 are driven by personal immunity history and the variant of SARS-CoV-2 causing infection.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Anneli Uuskula", + "author_inst": "University of Tartu" + }, + { + "author_name": "Heti Pisarev", + "author_inst": "Department of Family Medicine and Public Health, University of Tartu, Tartu 50411, Estonia" + }, + { + "author_name": "Anna Tisler", + "author_inst": "Department of Family Medicine and Public Health, University of Tartu, Tartu 50411, Estonia" + }, + { + "author_name": "Tatjana Meister", + "author_inst": "Department of Family Medicine and Public Health, University of Tartu, Tartu 50411, Estonia" + }, + { + "author_name": "Kadri Suija", + "author_inst": "Department of Family Medicine and Public Health, University of Tartu, Tartu 50411, Estonia" + }, + { + "author_name": "Kristi Huik", + "author_inst": "Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia" + }, + { + "author_name": "Aare Abroi", + "author_inst": "Institute of Technology, University of Tartu, Tartu 50411, Estonia" + }, + { + "author_name": "Ruth Kalda", + "author_inst": "Department of Family Medicine and Public Health, University of Tartu, Tartu 50411, Estonia" + }, + { + "author_name": "Raivo Kolde", + "author_inst": "Institute of Computer Science, University of Tartu, Tartu 51009, Estonia" + }, + { + "author_name": "Krista Fischer", + "author_inst": "Institute of Mathematics and Statistics, University of Tartu, Tartu 51009, Estonia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.17.23292653", "rel_title": "Serum VEGF Levels on Admission in COVID-19 Patients Correlate with SP-D and Neutrophils, Reflecting Disease Severity: A Prospective Study", @@ -65667,25 +66195,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.17.23292426", - "rel_title": "Intranasal lavage with hypochlorous acid safely reduces the symptoms in the ambulatory patient with COVID-19.", - "rel_date": "2023-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.17.23292426", - "rel_abs": "OBJECTIVEThis study was designed to investigate intranasal lavage with a hypochlorous acid solution in the reduction of symptoms in the ambulatory COVID-19 patient.\n\nSTUDY DESIGNStudy approval granted by the Institutional Review Board of Reading Hospital (IRB 036-20), with informed consent obtained from all adult participants(age>18 years).\n\nSETTINGAll enrollees, taken from the same ambulatory testing facility, received nasopharyngeal swabs for COVID-19 testing by reverse transcription polymerase chain (RT-PCR) or the COVID-19 antigen specific test (Binax NOW, Abbott Lab)\n\nMETHODSConvenience sampling methodology was utilized. Each enrollee was provided with the study devices which included a Nasaflo Neti Pot (NeilMed Pharmaceutical, Inc.), and the hypochlorous acid solution (Vashe Wound Solution, Urgo Medical North America, LLC). Participants were instructed to irrigate each nostril with 120 cc (four ounces) of the solution for ten consecutive days, and record the presence or absence of symptoms in a scripted diary log.\n\nRESULTSThe study included 88 patients of which 74 (84.1%) completed the ten days of nasal lavage. All data analysis was conducted using SPSS version 25.0.\n\nChi square test of association found no significant difference related to gender, age group race, ethnicity, residence, or living arrangements (all p-values > 0.05). There were no statistical differences in any of the co-morbid conditions. Mild adverse reactions included burning, epistaxis, and oral metallic taste. No enrollees required mechanical ventilation. There were no deaths.\n\nCONCLUSIONThis study suggests the feasibility and safety of using intranasal lavage with a hypochlorous acid solution in relieving symptoms in the ambulatory Covid-19 patient.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Monique Lisa Abner", - "author_inst": "Tower Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.14.548971", "rel_title": "Deep spatial proteomic exploration of severe COVID-19-related pulmonary injury in post-mortem specimens", @@ -65973,6 +66482,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.07.14.23292660", + "rel_title": "Dynamics of T-cell responses following COVID-19 mRNA vaccination and breakthrough infection in older adults", + "rel_date": "2023-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.14.23292660", + "rel_abs": "IntroductionWhile older adults generally mount weaker antibody responses to a primary COVID-19 vaccine series, T-cell responses remain less well characterized in this population. We compared SARS-CoV-2 spike-specific T-cell responses after two- and three-dose COVID-19 mRNA vaccination and subsequent breakthrough infection in older and younger adults.\n\nMethodsWe quantified CD4+ and CD8+ T-cells reactive to overlapping peptides spanning the ancestral SARS-CoV-2 spike protein in 40 older adults (median age 79) and 50 younger health care workers (median age 39), all COVID-19 naive, using an activation induced marker assay. T-cell responses were further assessed in 24 participants, including 8 older adults, who subsequently experienced their first SARS-CoV-2 breakthrough infection.\n\nResultsA third COVID-19 mRNA vaccine dose significantly boosted spike-specific CD4+ and CD8+ T-cell frequencies to above two-dose levels in older and younger adults. T-cell frequencies did not significantly differ between older and younger adults after either dose. Multivariable analyses adjusting for sociodemographic, health and vaccine-related variables confirmed that older age was not associated with impaired cellular responses. Instead, the strongest predictors of CD4+ and CD8+ T-cell frequencies post-third-dose were their corresponding post-second-dose frequencies. Breakthrough infection significantly increased both CD4+ and CD8+ T cell frequencies, to comparable levels in older and younger adults. Exploratory analyses revealed an association between HLA-A*02:03 and higher post-vaccination CD8+ T-cell frequencies, which may be attributable to numerous strong-binding HLA-A*02:03-specific CD8+ T-cell epitopes in spike.\n\nConclusionOlder adults mount robust T-cell responses to two- and three-dose COVID-19 mRNA vaccination, which are further boosted following breakthrough infection.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Sneha Datwani", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Rebecca Kalikawe", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Francis Mwimanzi", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Sarah Speckmaier", + "author_inst": "BC Centre for Excellence in HIV/AIDS" + }, + { + "author_name": "Richard Liang", + "author_inst": "BC Centre for Excellence in HIV/AIDS" + }, + { + "author_name": "Yurou Sang", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Rachel Waterworth", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Fatima Yaseen", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Hope R Lapointe", + "author_inst": "BC Centre for Excellence in HIV/AIDS" + }, + { + "author_name": "Evan Barad", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Mari L DeMarco", + "author_inst": "St Pauls Hospital, Providence Healthcare" + }, + { + "author_name": "Daniel T Holmes", + "author_inst": "St Pauls Hospital, Providence Healthcare" + }, + { + "author_name": "Janet Simons", + "author_inst": "St Pauls Hospital, Providence Healthcare" + }, + { + "author_name": "Julio SG Montaner", + "author_inst": "BC Centre for Excellence in HIV/AIDS" + }, + { + "author_name": "Marc Gabriel Romney", + "author_inst": "St. Paul's Hospital, Providence Healthcare" + }, + { + "author_name": "Zabrina L Brumme", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Mark A Brockman", + "author_inst": "Simon Fraser University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.13.23292643", "rel_title": "Clinical manifestations and mortality among hospitalized COVID-19 patients in Tanzania, 2021-2022.", @@ -67269,33 +67861,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2023.07.12.548725", - "rel_title": "Endocytosis Inhibitors Block SARS-CoV-2 Pseudoparticle Infection of Mink Lung Epithelium", - "rel_date": "2023-07-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.12.548725", - "rel_abs": "Both spill over and spill back of SARS-CoV-2 virus have been reported on mink farms in Europe and the United States. Zoonosis is a public health concern as dangerous mutated forms of the virus could be introduced into the human population through spillback. The purpose of our study was to determine the SARS-CoV-2 entry mechanism using mink lung epithelial cell line (Mv1Lu) and to block entry with drug inhibitors. Mv1Lu cells were susceptible to SARS-CoV-2 viral pseudoparticle infection, validating them as a suitable disease model for COVID-19. Inhibitors of TMPRSS2 and of endocytosis, two pathways of viral entry, were tested to identify those that blocked infection. Dyngo4a, a small molecule endocytosis inhibitor, significantly reduced infection, while TMPRSS2 inhibitors had minimal impact, supporting the conclusion that the entry of the SARS-CoV-2 virus into Mv1Lu cells occurs primarily through endocytosis. The small molecule inhibitors that were effective in this study could potentially be used therapeutically to prevent SARS-CoV-2 infection in mink populations. This study will facilitate the development of therapeutics to prevent zoonotic transmission of SARS-CoV-2 variants to other animals, including humans.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ann Song", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Rattapol Phandthong", - "author_inst": "University of California Riverside" - }, - { - "author_name": "Prue Talbot", - "author_inst": "University of California, Riverside" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.07.12.23292570", "rel_title": "COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH", @@ -67499,6 +68064,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.07.06.23292300", + "rel_title": "The ratio between SARS-CoV-2 RNA viral load and culturable viral titer differs depending on stage of infection", + "rel_date": "2023-07-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.06.23292300", + "rel_abs": "Analysis of incident, longitudinal RNA viral loads in saliva and nasal swabs and culturable viral titers in nasal swabs collected twice-daily by a tricenarian male infected with SARS-CoV-2 revealed the ratio between viral load and viral titer can be five orders of magnitude higher during early infection than late infection.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Michael K Porter", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Alexander Viloria Winnett", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Linhui Hao", + "author_inst": "University of Washington" + }, + { + "author_name": "Natasha Shelby", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Jessica A Reyes", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Noah W Schlenker", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Anna E Romano", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Colton Tognazzini", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Matthew Feaster", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Ying-Ying Goh", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Michael Gale Jr.", + "author_inst": "University of Washington" + }, + { + "author_name": "Rustem F Ismagilov", + "author_inst": "California Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.11.23292499", "rel_title": "Understanding Health Service Utilisation Patterns for Care Home Residents During the COVID-19 Pandemic using Routinely Collected Healthcare Data", @@ -68983,45 +69611,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.07.06.23292296", - "rel_title": "Long-term symptom profiles after COVID-19 vs other acute respiratory infections: a population-based observational study (COVIDENCE UK)", - "rel_date": "2023-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.06.23292296", - "rel_abs": "BackgroundLong COVID is a well recognised, if heterogeneous, entity. Acute respiratory infections (ARIs) due to other pathogens may cause long-term symptoms, but few studies compare post-acute sequelae between SARS-CoV-2 and other ARIs. We aimed to compare symptom profiles between people with previous SARS-CoV-2 infection, people with previous non-COVID-19 ARIs, and contemporaneous controls, and to identify clusters of long-term symptoms.\n\nMethodsCOVIDENCE UK is a prospective, population-based UK study of ARIs in adults. We analysed data on 16 potential long COVID symptoms and health-related quality of life (HRQoL), reported in January, 2021, by participants unvaccinated against SARS-CoV-2. We classified participants as having previous SARS-CoV-2 infection or previous non-COVID-19 ARI ([≥]4 weeks prior) or no reported ARI. We compared symptoms by infection status using logistic and fractional regression, and identified symptom clusters using latent class analysis (LCA).\n\nFindingsWe included 10,203 participants (1343 [13.2%] with SARS-CoV-2 infection, 472 [4.6%] with non-COVID-19 ARI). Both types of infection were associated with increased prevalence/severity of most symptoms and decreased HRQoL compared with no infection. Participants with SARS-CoV-2 infection had increased odds of taste/smell problems and hair loss compared with participants with non-COVID-19 ARIs. Separate LCA models identified three symptom severity groups for each infection type. In the most severe groups (including 23% of participants with SARS-CoV-2, and 21% with non-COVID-19 ARI), SARS-CoV-2 infection presented with a higher probability of memory problems, difficulty concentrating, hair loss, and taste/smell problems than non-COVID-19 ARI.\n\nInterpretationBoth SARS-CoV-2 and non-COVID-19 ARIs are associated with a wide range of long-term symptoms. Research on post-acute sequelae of ARIs should extend from SARS-CoV-2 to include other pathogens.\n\nFundingBarts Charity.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and Google Scholar for studies on post-acute sequelae of COVID-19 and other acute respiratory infections (ARIs), published up to May 24, 2023. We used search terms relating to COVID-19 and other ARIs (\"COVID-19\", \"SARS\", \"severe acute respiratory syndrome\", \"Middle East respiratory\", \"MERS\", \"respiratory infection\", \"influenza\", \"flu\") and post-acute symptoms (\"long COVID\", \"post-acute\", \"PACS\", \"sequelae\", \"long-term\"). Previous studies have shown a wide range of post-acute sequelae for COVID-19, affecting people with all severities of the acute disease. The few studies that have compared long-term symptoms between people with COVID-19 and non-COVID-19 ARIs have generally found a higher symptom burden among people with COVID-19; however, these studies have been restricted to hospitalised patients or electronic health record data, and thus do not capture the full picture in the community. Research into long COVID phenotypes has been inconclusive, with some analyses classifying people with long COVID according to the types of symptoms experienced, and others classifying them according to the overall severity of their symptoms.\n\nAdded value of this studyIn this population-based study of ARIs in the community, we observed high symptom burden among people with previous SARS-CoV-2 infection when compared with controls, highlighting the extensive reach of long COVID. Our finding of a similar symptom burden among people with non-COVID-19 ARIs suggests that post-acute sequelae of other ARIs may be going unrecognised, particularly given that the vast majority did not experience a severe acute infection. Latent class analyses of symptoms identified groupings based on overall symptom severity, rather than symptom types, for both SARS-CoV-2 infections and non-COVID-19 ARIs, suggesting that overall symptom burden may best characterise the experience of people with post-acute sequelae. Notably, among participants with the most severe symptoms, only half of those with previous SARS-CoV-2 infection attributed their symptoms to long COVID, suggesting they either did not believe the infection was the cause, or they did not consider their symptoms severe enough to qualify as long COVID.\n\nImplications of all the available evidenceThe long-term symptoms experienced by some people with previous ARIs, including SARS-CoV-2, highlights the need for improved understanding, diagnosis, and treatment of post-acute infection syndromes. As much-needed research into long COVID continues, we must take the opportunity to investigate and consider the post-acute burden of ARIs due to other pathogens.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Giulia Vivaldi", - "author_inst": "Blizard Institute and Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Paul E Pfeffer", - "author_inst": "Barts Health NHS Trust, London, UK; Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Mohammad Talaei", - "author_inst": "Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Jayson Basera", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Seif O Shaheen", - "author_inst": "Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Adrian R Martineau", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry; and Asthma UK Centre for Applied Research; Queen Mary University of London, London, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2023.07.05.23292278", "rel_title": "Intracardiac Thrombus in COVID-19 Inpatients: A Nationwide Study of Incidence, Predictors and Outcomes", @@ -69337,6 +69926,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.07.05.547781", + "rel_title": "The receptor binding domain of SARS-CoV-2 spike protein fused with the type IIb E. coli heat-labile enterotoxin A subunit as an intranasal booster after mRNA vaccination", + "rel_date": "2023-07-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.05.547781", + "rel_abs": "The outbreak of SARS-CoV-2 infections had led to the COVID-19 pandemic which has a significant impact on global public health and the economy. The spike (S) protein of SARS-CoV-2 contains the receptor binding domain (RBD) which binds to human angiotensin-converting enzyme 2 receptor. Numerous RBD-based vaccines have been developed and recently focused on the induction of neutralizing antibodies against the immune evasive Omicron BQ.1.1 and XBB.1.5 subvariants. In this preclinical study, we reported the use of a direct fusion of the type IIb Escherichia coli heat-labile enterotoxin A subunit with SARS CoV-2 RBD protein (RBD-LTA) as an intranasal vaccine candidate. The results showed that intranasal immunization with the RBD-LTA fusion protein in BALB/c mice elicited potent neutralizing antibodies against the Wuhan-Hu-1 and several SARS-CoV-2 variants as well as the production of IgA antibodies in bronchoalveolar lavage fluids (BALFs). Furthermore, the RBD-LTA fusion protein was used as a second-dose booster after bivalent mRNA vaccination. The results showed that the neutralizing antibody titers elicited by the intranasal RBD-LTA booster were similar to the bivalent mRNA booster, but the RBD-specific IgA titers in sera and BALFs significantly increased. Overall, this preclinical study suggests that the RBD-LTA fusion protein could be a promising candidate as a mucosal booster COVID-19 vaccine.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "He-Chin Hsieh", + "author_inst": "National Tsing Hua University" + }, + { + "author_name": "Chung-Chu Chen", + "author_inst": "MacKay Memorial Hospital Hsinchu Branch" + }, + { + "author_name": "Pin-Han Chou", + "author_inst": "National Tsing Hua University" + }, + { + "author_name": "Wen-Chun Liu", + "author_inst": "Biomedical Translation Research Center, Academia Sinica, Taiwan" + }, + { + "author_name": "Suh-Chin Wu", + "author_inst": "National Tsing Hua University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/162941", "rel_title": "A Radically New Theory of how the Brain Represents and Computes with Probabilities", @@ -71137,193 +71761,6 @@ "type": "new results", "category": "developmental biology" }, - { - "rel_doi": "10.1101/2023.06.29.546792", - "rel_title": "Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures", - "rel_date": "2023-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.29.546792", - "rel_abs": "Variations in DNA methylation patterns in human tissues have been linked to various environmental exposures and infections. Here, we identified the DNA methylation signatures associated with multiple exposures in nine major immune cell types derived from peripheral blood mononuclear cells (PBMCs) at single-cell resolution. We performed methylome sequencing on 111,180 immune cells obtained from 112 individuals who were exposed to different viruses, bacteria, or chemicals. Our analysis revealed 790,662 differentially methylated regions (DMRs) associated with these exposures, which are mostly individual CpG sites. Additionally, we integrated methylation and ATAC-seq data from same samples and found strong correlations between the two modalities. However, the epigenomic remodeling in these two modalities are complementary. Finally, we identified the minimum set of DMRs that can predict exposures. Overall, our study provides the first comprehensive dataset of single immune cell methylation profiles, along with unique methylation biomarkers for various biological and chemical exposures.", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "Wenliang Wang", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Manoj Hariharan", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Anna Bartlett", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Cesar Barragan", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Rosa Castanon", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Vince Rothenberg", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Haili Song", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Joseph Nery", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Andrew Aldridge", - "author_inst": "Duke University School of Medicine, Bryan Research Building, 311 Research Drive, Durham, NC 27710, USA" - }, - { - "author_name": "Jordan Altshul", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Mia Kenworthy", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Wubin Ding", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Hanqing Liu", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Wei Tian", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Jingtian Zhou", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Huaming Chen", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Bei Wei", - "author_inst": "Department of Genetics, Stanford University, Stanford, CA 94305, USA" - }, - { - "author_name": "Irem B Gunduz", - "author_inst": "Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrucken, Germany" - }, - { - "author_name": "Todd Norell", - "author_inst": "Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA" - }, - { - "author_name": "Timothy J Broderick", - "author_inst": "Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA" - }, - { - "author_name": "Micah McClain", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA., Durham Veteran" - }, - { - "author_name": "Lisa Satterwhite", - "author_inst": "Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA" - }, - { - "author_name": "Thomas Burke", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA" - }, - { - "author_name": "Elizabeth Petzold", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA" - }, - { - "author_name": "Xiling Shen", - "author_inst": "Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA" - }, - { - "author_name": "Chris Woods", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA., Durham Veteran" - }, - { - "author_name": "Vance G Fowler", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA., Duke Clinical " - }, - { - "author_name": "Felicia Ruffin", - "author_inst": "Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA" - }, - { - "author_name": "Parinya Panuwet", - "author_inst": "Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA" - }, - { - "author_name": "Dana B Barr", - "author_inst": "Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA" - }, - { - "author_name": "Jennifer L Beare", - "author_inst": "Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA" - }, - { - "author_name": "Anthony K Smith", - "author_inst": "Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA" - }, - { - "author_name": "Rachel R Spurbeck", - "author_inst": "Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA" - }, - { - "author_name": "Sindhu Vangeti", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "Irene Ramos", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "German Nudelman", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "Stuart C Sealfon", - "author_inst": "Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA" - }, - { - "author_name": "Flora Castellino", - "author_inst": "U.S. Department of Health and Human Services, Administration for Strategic Preparedness and Response, Biomedical Advanced Research and Development Authority, Wa" - }, - { - "author_name": "Anna Maria Walley", - "author_inst": "Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom" - }, - { - "author_name": "Tom Evans", - "author_inst": "Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom" - }, - { - "author_name": "Fabian Muller", - "author_inst": "Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrucken, Germany" - }, - { - "author_name": "William J Greenleaf", - "author_inst": "Department of Genetics, Stanford University, Stanford, CA 94305, USA" - }, - { - "author_name": "Joseph R Ecker", - "author_inst": "Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA., Howard Hughes Medical Institute, The " - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2023.06.29.546885", "rel_title": "Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication", @@ -71699,6 +72136,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.06.22.23291740", + "rel_title": "Demography, hygiene and previous disease prevalence as plausible risk factors associated with Covid-19 deaths across Indian states", + "rel_date": "2023-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.22.23291740", + "rel_abs": "Severity of Covid-19 diseases has been disproportionate with higher case-fatality ratio affecting developed nations. In India, states with higher income have reported more number of deaths compared to lower income states. The global burden of diseases India 2019 and the National Health Profile 2019 data was used to draw correlations with Covid-19 mortality at two different dates of peak Covid-19 cases in India. We explored correlation of mortality in different states of India with prevalence of different diseases, demography, development, sanitation etc. The study found a positive correlation with known demographic parameters such as percentage of elderly population(spearman correlation coefficient(rho) =0.44 and 0.46 with 1st and 2nd peak respectively). Similarly, percentage urbanization was seen to correlate well with mortality(rho=0.71 and 0.57) suggesting Covid-19 to be a predominantly urban disease. Prevalence of Autoimmune diseases, and Cancer show higher correlation with deaths. A surprising positive correlation emerged between improved sanitation parameters, such as closed drainage and indoor toilets, with COVID-19 deaths. Overall the multivariate regression model achieved by combining demography, sanitation, autoimmune diseases and cancer gave us the best prediction for Covid-19 mortality(adjusted R square value of 0.71 with peak 1 and 0.85 with peak 2). Analysis of the Covid-19 related data seems to indicate that as the wealth of a state increases, the states urban landscape changes often leading to better sanitation facilities. The lifestyle and prevalence to autoimmune diseases as well as cancer also increases. However, this may affect the states ability to fight pandemics due to lower exposure to pathogens and immune training.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Bithika Chatterjee", + "author_inst": "National Centre For Cell Sciences" + }, + { + "author_name": "Shekhar C Mande", + "author_inst": "Bioinformatics Centre, Savitribai Phule Pune University, Pune" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.06.28.23292007", "rel_title": "Comparing reactions to COVID-19 and influenza vaccinations: data from patient self-reporting, smartwatches and electronic health records", @@ -73271,85 +73731,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.06.28.23291986", - "rel_title": "The Role of VSL#3 in the Treatment of Fatigue and Other Symptoms in Long Covid-19 Syndrome: a Randomized, Double-blind, Placebo-controlled Pilot Study (DELong#3)", - "rel_date": "2023-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.28.23291986", - "rel_abs": "Long COVID, also known as Post-acute COVID-19 Syndrome (PACS), is a chronic condition affecting individuals who have recovered from acute COVID-19. It is currently estimated that around 65 million people worldwide suffer from Long COVID. It is characterized by a range of symptoms, including fatigue, exertion intolerance, neurocognitive and sensory impairment, sleep disturbance, myalgia/arthralgia, and dysautonomia. Among them fatigue has emerged as a burdensome and pervasive issue, significantly impacting the quality of life and daily functioning of Long COVID patients. Alterations in the composition of the intestinal microbiota has been reported in COVID-19 patients. Dysbiosis persists even after several months of recovery from acute SARS-CoV-2 infection.\n\nBased on this evidence, we carried out a phase 3, randomized, double-blind, placebo-controlled trial aimed at evaluating the efficacy of VSL#3(R), a consortium of probiotic bacterial strains, in reducing fatigue and improving various aspects of patients well-being in patients with Long COVID syndrome.\n\nHighlightsO_LIPatients suffering from Long-COVID manifest a variety of persistent symptoms impacting daily functioning;\nC_LIO_LIFatigue emerged as a burdensome and pervasive issue, significantly impacting the quality of life;\nC_LIO_LIVSL#3(R) treatment significantly reduced the Chalder Fatigue Scale scores as compared to placebo\nC_LIO_LIChalder Fatigue Scale scores remained significantly reduced in the treatment group 4 weeks post intervention.\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Flavio Caprioli", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy; Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Gra" - }, - { - "author_name": "Beatrice Marinoni", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Alessandro Rimondi", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Federico Bottaro", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Clorinda Ciafardini", - "author_inst": "Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Chiara Amoroso", - "author_inst": "Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Martina Muia", - "author_inst": "Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Bruna Caridi", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Daniele Noviello", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Alessandra Bandera", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Infectious Disease Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Andrea Gori", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Infectious Disease Unit, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Marco Mantero", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca Granda Ospe" - }, - { - "author_name": "Francesco Blasi", - "author_inst": "Universita degli Studi di Milano, Milan, Italy; Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca Granda Ospe" - }, - { - "author_name": "Roberta Ferrucci", - "author_inst": "ASST Santi Paolo e Carlo, San Paolo University Hospital, 20142 Milan, Italy;6Aldo Ravelli Center for Neurotechnology and Experimental Brain Therapeutics, Depart" - }, - { - "author_name": "Federica Facciotti", - "author_inst": "Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy" - }, - { - "author_name": "Maurizio Vecchi", - "author_inst": "Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Milan, Italy; Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca Gran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.06.27.23291947", "rel_title": "Examining the inter-relationships between social isolation and loneliness and their correlates among older British adults before and during the COVID-19 lockdown: evidence from four British longitudinal studies", @@ -73601,6 +73982,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.06.22.23291669", + "rel_title": "Quantitative analysis of chest computed tomography of COVID-19 pneumonia using a software widely used in Japan", + "rel_date": "2023-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.22.23291669", + "rel_abs": "This study aimed to determine the optimal conditions to measure the percentage of area considered as pneumonia (pneumonia volume ratio, PVR) and the computed tomography (CT) score due to coronavirus disease 2019 (COVID-19) using the Ziostation2 image analysis software (Z2; Ziosoft, Tokyo, Japan), which is popular in Japan, and to evaluate its usefulness in assessing the clinical severity. We included 53 patients (41 men and 12 women, mean age: 61.3 years) diagnosed with COVID-19 using the polymerase chain reaction who had undergone chest CT and were hospitalized between January 2020 and January 2021. Based on the COVID-19 infection severity, the patients were classified as mild (n=38) or severe (n=15). For 10 randomly selected samples, the PVR and CT scores by Z2 under different conditions and the visual simple PVR and CT scores were compared, and the conditions with the highest statistical agreement were determined. The usefulness of the clinical severity assessment based on PVR and CT scores using Z2 under the determined conditions was statistically evaluated. The best agreement with the visual measurement was achieved by the Z2 measurement condition of [≥] -600 HU. The areas under the receiver operating characteristic curves, the Youden index, and the sensitivity, specificity, and p-values of PVR and CT scores by Z2 were as follows: PVR; 0.881, 18.69, 66.7, 94.7, and <0.001, CT score; 0.77, 7.5, 40, 74, and 0.002, respectively. We determined the optimal condition for assessing the PVR of COVID-19 pneumonia using Z2 and demonstrated that the AUC of PVR was higher than that of the CT score in the assessment of clinical severity. The introduction of new technologies is time-consuming and expensive; our method has high clinical utility and can be promptly used in any facility where Z2 has been introduced.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Minako Suzuki", + "author_inst": "Showa University Northern Yokohama Hospital" + }, + { + "author_name": "Yoshimi Fujii", + "author_inst": "Fujisawa City Hospital" + }, + { + "author_name": "Yurie Nishimura", + "author_inst": "Fujisawa City Hospital" + }, + { + "author_name": "Kazuma Yasui", + "author_inst": "Fujisawa City Hospital" + }, + { + "author_name": "Hidefumi Fujisawa", + "author_inst": "Showa University Northern Yokohama Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2023.06.20.23291653", "rel_title": "Managing the Infodemic: Leveraging Deep Learning to Evaluate the Maturity Level of AI-Based COVID-19 Publications for Knowledge Surveillance and Decision Support", @@ -74681,121 +75097,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.06.16.23291450", - "rel_title": "High rates of SARS-CoV-2 infection in pregnant Ugandan women and association with stunting in infancy", - "rel_date": "2023-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291450", - "rel_abs": "BackgroundSARS-CoV-2 has been well studied in resource-rich areas but many questions remain about effects of infection in African populations, particularly in vulnerable groups such as pregnant women.\n\nMethodsWe describe SARS-CoV-2 immunoglobulin (Ig) G and IgM antibody responses and clinical outcomes in mother-infant dyads enrolled in malaria chemoprevention trials in Uganda.\n\nResultsFrom December 2020 to February 2022, among 400 unvaccinated pregnant women, serologic assessments revealed that 128 (32%) were seronegative for anti-SARS-CoV-2 IgG and IgM at enrollment and delivery, 80 (20%) were infected either prior to or early in pregnancy, and 192 (48%) were infected or re-infected with SARS-CoV-2 during pregnancy. We observed preferential binding of plasma IgG to Wuhan-Hu-1-like antigens in individuals seroconverting up to early 2021, and to Delta variant antigens in a subset of individuals in mid-2021. Breadth of IgG binding to all variants improved over time. No participants experienced severe respiratory illness during the study. SARS-CoV-2 infection in early pregnancy was associated with lower median length-for-age Z-score at age 3 months compared with no infection or late pregnancy infection (- 1.54 versus -0.37 and -0.51, p=0.009).\n\nConclusionPregnant Ugandan women experienced high levels of SARS-CoV-2 infection without severe respiratory illness. Variant-specific serology testing demonstrated evidence of antibody affinity maturation at the population level. Early gestational SARS-CoV-2 infection was associated with shorter stature in early infancy.\n\nFundingThis work was supported by: Stanford MCHRI/Stephen Bechtel Endowed Fellowship in Pediatric Translational Medicine (KJ), Swiss National Science Foundation PRIMA grant PR00P3_208580 (KR), the Bill and Melinda Gates Foundation, and NIAID (T32-AI052073, U01- AI141308, U01-AI155325).", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Karen Blake Jacobson", - "author_inst": "Department of Medicine, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Katharina R\u00f6ltgen", - "author_inst": "Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland" - }, - { - "author_name": "Brandon Lam", - "author_inst": "Department of Pathology, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Patience Nayebare", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Abel Kakuru", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Jimmy Kizza", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Miriam Aguti", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Felistas Nankya", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Jessica Briggs", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Saki Takahashi", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Bryan Greenhouse", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Isabel Rodriguez-Barraquer", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Kattria van der Ploeg", - "author_inst": "Department of Medicine, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Jacob N. Wohlstadter", - "author_inst": "Meso Scale Diagnostics LLC, Rockville, MD, USA" - }, - { - "author_name": "George B. Sigal", - "author_inst": "Meso Scale Diagnostics LLC, Rockville, MD, USA" - }, - { - "author_name": "Michelle E. Roh", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Joaniter I. Nankabirwa", - "author_inst": "Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda" - }, - { - "author_name": "Gloria Cuu", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Stephanie L. Gaw", - "author_inst": "Department of Obstetrics, Gynecology & Reproductive Sciences, Division of Maternal-Fetal Medicine, UCSF, San Francisco, CA, USA" - }, - { - "author_name": "Philip J. Rosenthal", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Moses R. Kamya", - "author_inst": "Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda" - }, - { - "author_name": "Isaac Ssewanyana", - "author_inst": "Infectious Diseases Research Collaboration, Kampala, Uganda" - }, - { - "author_name": "Grant Dorsey", - "author_inst": "Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA" - }, - { - "author_name": "Scott D. Boyd", - "author_inst": "Department of Pathology, Stanford School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Prasanna Jagannathan", - "author_inst": "Department of Medicine, Stanford School of Medicine, Stanford, CA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.06.16.23291442", "rel_title": "Vaccines at Velocity: Evaluating Potential Lives Saved by Earlier Vaccination in the COVID-19 Pandemic", @@ -75094,7 +75395,7 @@ "rel_date": "2023-06-20", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291455", - "rel_abs": "Different vaccine platforms were developed in 2019 and 2020 to provide immunization for protection against the SARS-CoV-2-caused disease COVID-19. The majority of vaccinated individuals will develop antibodies against SARS-CoV-2. The isotype (subclass) and Fc-glycosylation of IgG antibodies determine their affinity for secondary effector functions. For protein subunit vaccines in COVID-19, the IgG profile of the subclass and glycosylation are unknown. Therefore, we measured the IgG subclass and N-297 Fc glycosylation by ELISA and LC-MS/MS of anti-spike IgG from individuals vaccinated with the Taiwanese protein subunit vaccine Medigen, the mRNA vaccines (BNT, Moderna), and the adenovector Astrazeneca. Samples were taken after the first and second doses. For all vaccine types, the main IgG response was dominated by IgG1 and IgG3 as subclasses. For glycosylation, mRNA vaccines presented with an afucosylation after the first dose and a constant significant higher galactosylation and sialylation than non-mRNA vaccines.", + "rel_abs": "Various vaccine platforms were developed and deployed against the COVID-19 disease. The Fc-mediated functions of IgG antibodies are essential in the adaptive immune response elicited by vaccines. However, the long-term changes of protein subunit vaccines and their combinations with mRNA vaccines are unknown. A total of 272 serum and plasma samples were collected from individuals who received first to third doses of the protein subunit Medigen, the mRNA (BNT), or the adenovector AstraZeneca vaccines. The IgG subclass level was measured using enzyme-linked immunosorbent assay, and Fc-N glycosylation was measured using LC-MS/MS. Antibody-dependent phagocytosis (ADCP) and complement deposition (ADCD) of anti-spike (S) IgG antibodies were measured. IgG1 and 3 reached the highest anti-S IgG subclass level. IgG1, 2, and 4 subclass levels significantly increased in mRNA- and Medigen-vaccinated individuals. Fc-glycosylation was stable, except in female BNT vaccinees, who showed increased bisection and decreased galactosylation. Female BNT vaccinees had a higher anti-S IgG titer than that of males. ADCP declined in all groups. ADCD increased in Medigen-vaccinated individuals after the third dose. Each vaccine produced specific long-term changes in Fc structure and function. This finding is critical when selecting a vaccine platform or combination to achieve the desired immune response.", "rel_num_authors": 6, "rel_authors": [ { @@ -75127,6 +75428,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2023.06.15.23291472", + "rel_title": "Covid19Vaxplorer: a free, online, user-friendly COVID-19 Vaccine Allocation Comparison Tool", + "rel_date": "2023-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.15.23291472", + "rel_abs": "BackgroundThere are many COVID-19 vaccines currently available, however, Low- and middle-income countries (LMIC) still have large proportions of their populations unvaccinated. Decision-makers must decide how to effectively allocate available vaccines (e.g. boosters or primary series vaccination, which age groups to target) but LMIC often lack the resources to undergo quantitative analyses of vaccine allocation, resulting in adhoc policies. We developed Covid19Vaxplorer (https://covid19vaxplorer.fredhutch.org/), a free, user-friendly online tool that simulates region-specific COVID-19 epidemics in conjunction with vaccination with the purpose of providing public health officials worldwide with a tool for vaccine allocation planning and comparison.\n\nMethodsWe developed an age-structured mathematical model of SARS-CoV-2 transmission and COVID-19 vaccination. The model considers vaccination with up to three different vaccine products, primary series and boosters. We simulated partial immunity derived from waning of natural infection and vaccination. The model is embedded in an online tool, Covid19Vaxplorer that was optimized for its ease of use. By prompting users to fill information through several windows to input local parameters (e.g. cumulative and current prevalence), epidemiological parameters (e.g basic reproduction number, current social distancing interventions), vaccine parameters (e.g. vaccine efficacy, duration of immunity) and vaccine allocation (both by age groups and by vaccination status). Covid19Vaxplorer connects the user to the mathematical model and simulates, in real time, region-specific epidemics. The tool then produces key outcomes including expected numbers of deaths, hospitalizations and cases, with the possibility of simulating several scenarios of vaccine allocation at once for a side-by-side comparison.\n\nResultsWe provide two usage examples of Covid19Vaxplorer for vaccine allocation in Haiti and Afghanistan, which had as of Spring 2023 2% and 33% of their populations vaccinated, and show that for these particular examples, using available vaccine as primary series vaccinations prevents more deaths than using them as boosters. Covid19Vaxplorer allows users in 183 regions in the world to compare several vaccination strategies simultaneously, adjusting parameters to their local epidemics, infrastructure and logistics. Covid19Vaxplorer is an online, free, user-friendly tool that facilitates evidence-based decision making for vaccine distribution.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Imelda Trejo", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Pei-Yao Hung", + "author_inst": "University of Michigan" + }, + { + "author_name": "Laura Matrajt", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.17.23291498", "rel_title": "High burden of viruses and bacterial pathobionts drives heightened nasal innate immunity in children with and without SARS-CoV-2", @@ -76683,57 +77011,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.06.14.544985", - "rel_title": "Inclusion of glycopeptides in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike ectodomain provides increased sequence coverage", - "rel_date": "2023-06-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.14.544985", - "rel_abs": "Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can provide precise analysis of a proteins conformational dynamics across varied states, such as heat-denatured vs. native protein structures, localizing regions that are specifically affected by such conditional changes. Maximizing protein sequence coverage provides high confidence that regions of interest were located by HDX-MS, but one challenge for complete sequence coverage is N-glycosylation sites. The deuteration of glycopeptides has not always been identified in previous reports of HDX-MS analyses, causing significant sequence coverage gaps in heavily glycosylated proteins and uncertainty in structural dynamics in many regions throughout a glycoprotein. We report HDX-MS analysis of the SARS-CoV-2 spike protein ectodomain in its trimeric pre-fusion form, which has 22 predicted N-glycosylation sites per monomer, with and without heat treatment. We identified glycopeptides and calculated their isotopic mass shifts from deuteration. Inclusion of the deu-terated glycopeptides increased sequence coverage of spike ectodomain from 76% to 84%, demonstrated that glycopeptides had been deuterated, and improved confidence in results localizing structural re-arrangements. Inclusion of deuterated glycopeptides improves the analysis of the conformational dynamics of glycoproteins such as viral surface antigens and cellular receptors.\n\nAbstract Figure\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC=\"FIGDIR/small/544985v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (34K):\norg.highwire.dtl.DTLVardef@1d8e1f6org.highwire.dtl.DTLVardef@1db0774org.highwire.dtl.DTLVardef@c68d1eorg.highwire.dtl.DTLVardef@15aed98_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Christopher A Haynes", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Theodore R Keppel", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Betlehem Mekonnen", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sarah H Osman", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Yu Zhou", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Adrian R Woolfitt", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jakub Baudys", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "John R Barr", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Dongxia Wang", - "author_inst": "Centers for Disease Control and Prevention (CDC)" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.06.14.544834", "rel_title": "Immunogenicity of COVID-19 vaccines and their effect on the HIV reservoir in older people with HIV", @@ -77265,6 +77542,41 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2023.06.13.544630", + "rel_title": "Biophysical evolution of the receptor binding domains of SARS-CoVs", + "rel_date": "2023-06-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.13.544630", + "rel_abs": "With hundreds of coronaviruses (CoVs) identified in bats that are capable of infecting humans, it is important to understand how CoVs that affected the human population have evolved. Seven known coronaviruses have infected humans, of which three CoVs caused severe disease with high mortality rates: SARS-CoV emerged in 2002, MERS-CoV in 2012, and SARS-CoV-2 in 2019. Both SARS-CoV and SARS-CoV-2 belong to the same family, follow the same receptor pathway, and use their receptor binding domain (RBD) of spike protein to bind to the ACE2 receptor on the human epithelial cell surface. The sequence of the two RBDs is divergent, especially in the receptor binding motif (RBM) that directly interacts with ACE2. We probed the biophysical differences between the two RBDs in terms of their structure, stability, aggregation, and function. Since RBD is being explored as an antigen in protein subunit vaccines against CoVs, determining these biophysical properties will also aid in developing stable protein subunit vaccines. Our results show that despite RBDs having a similar three-dimensional structure, they differ in their thermodynamic stability. RBD of SARS-CoV-2 is significantly less stable than that of SARS-CoV. Correspondingly, SARS-CoV-2 RBD shows a higher aggregation propensity. Regarding binding to ACE2, less stable SARS-CoV-2 RBD binds with a higher affinity than more stable SARS-CoV RBD. In addition, SARS-CoV-2 RBD is more homogenous in terms of its binding stoichiometry towards ACE2, compared to SARS-CoV RBD. These results indicate that SARS-CoV-2 RBD differs from SARS-CoV RBD in terms of its stability, aggregation, and function, possibly originating from the diverse RBMs. Higher aggregation propensity and decreased stability of SARS-CoV-2 RBD warrants further optimization of protein subunit vaccines that use RBD as an antigen either by inserting stabilizing mutations or formulation screening.\n\nStatement of SignificanceThis study holds significant relevance in the context of the COVID-19 pandemic and the broader understanding of coronaviruses. A comparison of the receptor binding domains (RBDs) of SARS-CoV and SARS-CoV-2 reveals significant differences in their structure, stability, aggregation, and function. Despite divergent sequences, the RBDs share a similar fold and ACE2 receptor binding capability, likely through convergent evolution. These findings are crucial for understanding coronavirus evolution, interactions with human receptors, and the spillover of coronaviruses from animals to humans. The study also has implications for vaccine design strategies for SARS-CoVs, where the RBD is used as an antigen in protein subunit vaccines. By anticipating future outbreaks and enhancing our understanding of zoonotic spillover, this research contributes to safeguarding human health.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Vaibhav Upadhyay", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Sudipta Panja", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Alexandra Lucas", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Casey Patrick", + "author_inst": "University of Colorado Anschutz Medical Campus" + }, + { + "author_name": "Krishna Mallela", + "author_inst": "University of Colorado Anschutz Medical Campus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.06.13.544519", "rel_title": "Partially hydrolyzed guar gum attenuates the symptoms of SARS-CoV-2 infection through gut microbiota modulation in an animal model.", @@ -78533,41 +78845,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2023.06.09.23291202", - "rel_title": "Trends in medication use after the onset of the COVID-19 pandemic in the Republic of Ireland: an interrupted time series study", - "rel_date": "2023-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.09.23291202", - "rel_abs": "The COVID-19 pandemic had a substantial impact on healthcare delivery, particularly in general practice. This study aimed to evaluate how dispensing of medications in primary care in Ireland changed following the COVID-19 pandemics onset compared to expected trends. This interrupted time series study used data on medications prescribed in general practice 2016-2022 to patient eligible for state health cover, approximately one third of the population. Dispensing volumes for all therapeutic subgroups (ATC2 codes) and commonly dispensed medications were summarised. Pre-pandemic data was used to forecast expected trends (with 99% prediction intervals) using the Holt-Winters method, and these were compared to observed dispensing from March 2020 onwards. Most (31/77) therapeutic subgroups had dispensing significantly different from forecast in March 2020. Drugs for obstructive airway disease had the largest difference, with dispensing 26.2% (99%CI 19.5%-33.6%) higher than forecasted. Only two subgroups were significantly lower than forecasted, other gynaecologicals (17.7% lower, 99%CI 6.3%-26.6%) and dressings (11.6%, 99%CI 9.4%-41.6%). Dispensing of amoxicillin products and oral prednisolone were lower than forecasted in the months following the pandemics onset, particularly during winter 2020/2021. There was a spike in dispensing for many long-term medications in March 2020, while pandemic restrictions likely contributed to reductions for other medications.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Molly Mattsson", - "author_inst": "RCSI University of Medicine and Health Sciences" - }, - { - "author_name": "Jung Ah Hong", - "author_inst": "RCSI University of Medicine and Health Sciences" - }, - { - "author_name": "John Scott Frazer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Glenn Ross Frazer", - "author_inst": "Unaffiliated" - }, - { - "author_name": "Frank Moriarty", - "author_inst": "RCSI University of Medicine and Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2023.06.07.23290927", "rel_title": "SARS-CoV-2 infections among 12 000 pregnant women, 2020, Finland - cross-testing of neutralization assays", @@ -78899,6 +79176,129 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.06.12.544667", + "rel_title": "Improving modelling for epidemic responses: reflections from members of the UK infectious disease modelling community on their experiences during the COVID-19 pandemic", + "rel_date": "2023-06-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.12.544667", + "rel_abs": "The COVID-19 pandemic both relied and placed significant burdens on the experts involved from research and public health sectors. The sustained high pressure of a pandemic on responders, such as healthcare workers, can lead to lasting psychological impacts including acute stress disorder, post-traumatic stress disorder, burnout, and moral injury, which can impact individual wellbeing and productivity. As members of the infectious disease modelling community, we convened a reflective workshop to understand the professional and personal impacts of response work on our community and to propose recommendations for future epidemic responses. The attendees represented a range of career stages, institutions, and disciplines. This piece was collectively produced by those present at the session based on our collective experiences. Key issues we identified at the workshop were lack of institutional support, insecure contracts, unequal credit and recognition, and mental health impacts. Our recommendations include rewarding impactful work, fostering academia-public health collaboration, decreasing dependence on key individuals by developing teams, increasing transparency in decision-making, and implementing sustainable work practices. Despite limitations in representation, this workshop provided valuable insights into the UK COVID-19 modelling experience and guidance for future public health crises. Recognising and addressing the issues highlighted is crucial, in our view, for ensuring the effectiveness of epidemic response work in the future.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Katharine Sherratt", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Anna C Carnegie", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Adam Kucharski", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Anne Cori", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Carl AB Pearson", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & South African DSI-NRF Centre of Excellence in Epide" + }, + { + "author_name": "Christopher I Jarvis", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Christopher Overton", + "author_inst": "All Hazards Intelligence, Data Analytics and Surveillance, UK Health Security Agency, UK & Department of Mathematical Sciences, University of Liverpool, UK & De" + }, + { + "author_name": "Dale Weston", + "author_inst": "Emergency Response Department Science & Technology Behavioural Science, UK Health Security Agency, UK" + }, + { + "author_name": "Edward M Hill", + "author_inst": "Warwick Mathematics Institute and The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, UK & Joint UNIvers" + }, + { + "author_name": "Edward Knock", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Elizabeth Fearon", + "author_inst": "Institute for Global Health, University College London, UK" + }, + { + "author_name": "Emily Nightingale", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Joel Hellewell", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK" + }, + { + "author_name": "W John Edmunds", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Julian Villabona Arenas", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Kiesha Prem", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & Saw Swee Hock School of Public Health, National Uni" + }, + { + "author_name": "Li Pi", + "author_inst": "Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & MRC Centre for Global Infectious Disease Analysis, " + }, + { + "author_name": "Michelle Kendall", + "author_inst": "Warwick Mathematics Institute and The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, UK" + }, + { + "author_name": "Neil Ferguson", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Nicholas Davies", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Sabine van Elsland", + "author_inst": "MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Timothy Russell", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK & European Molecular Biology Laboratory, European Bio" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Yang Liu", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + }, + { + "author_name": "Sam Abbott", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, UK" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2023.06.12.544552", "rel_title": "Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2", @@ -80115,41 +80515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.06.03.543542", - "rel_title": "Species and habitat specific changes in bird activity in an urban environment during Covid 19 lockdown", - "rel_date": "2023-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.03.543542", - "rel_abs": "Covid-19 lockdowns provided ecologists with a rare opportunity to examine how animals behave when humans are absent. Indeed many, sometimes contradicting, studies reported various effects of lockdowns on animal activity, especially in urban areas and other human-dominated habitats. We explored how Covid-19 lockdowns in Israel have influenced bird activity in an urban environment by using continuous acoustic recordings to monitor three common bird species that differ in their level of adaptation to the urban ecosystem: (1) the hooded crow, an urban exploiter, which depends heavily on anthropogenic resources; (2) the rose-ringed parakeet, an invasive alien species that has adapted to exploit human resources; and (3) the graceful prinia, an urban adapter, which is relatively shy of humans and can be found urban habitats with shrubs and prairies. Acoustic recordings provided continuous monitoring of bird activity without an effect of the observer on the animal. We performed dense sampling of a 1.3 square km area in northern Tel-Aviv by placing 17 recorders for more than a month in different micro-habitats within this region including roads, residential areas and urban parks. We monitored both lockdown and no-lockdown periods. We portray a complex dynamic system where the activity of specific bird species depended on many environmental parameters and decreases or increases in a habitat-dependent manner during lockdown. Specifically, urban exploiter species decreased their activity in most urban habitats during lockdown, while human adapter species increased their activity during lockdown especially in parks where humans were absent. Our results also demonstrate the value of different habitats within urban environments for animal activity, specifically highlighting the importance of urban parks. These species- and habitat-specific changes in activity might explain the contradicting results reported by others who have not performed a habitat specific analysis.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Congnan Sun", - "author_inst": "Hebei Normal university" - }, - { - "author_name": "Yoel Hassin", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Arjan Boonman", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Assaf Shwartz", - "author_inst": "Israel Institute of Technology" - }, - { - "author_name": "Yossi Yovel", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "animal behavior and cognition" - }, { "rel_doi": "10.1101/2023.06.03.543589", "rel_title": "A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism", @@ -80405,6 +80770,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2023.05.31.23290774", + "rel_title": "POST-COVID ORTHOPAEDIC ELECTIVE RESOURCE PLANNING USING SIMULATION MODELLING", + "rel_date": "2023-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.31.23290774", + "rel_abs": "ObjectivesTo develop a simulation model to support orthopaedic elective capacity planning.\n\nMethodsAn open-source, generalisable discrete-event simulation was developed, including a web-based application. The model used anonymised patient records between 2016-2019 of elective orthopaedic procedures from an NHS Trust in England. In this paper, it is used to investigate scenarios including resourcing (beds and theatres) and productivity (lengths-of-stay, delayed discharges, theatre activity) to support planning for meeting new NHS targets aimed at reducing elective orthopaedic surgical backlogs in a proposed ring fenced orthopaedic surgical facility. The simulation is interactive and intended for use by health service planners and clinicians.\n\nResultsA higher number of beds (65-70) than the proposed number (40 beds) will be required if lengths-of-stay and delayed discharge rates remain unchanged. Reducing lengths-of-stay in line with national benchmarks reduces bed utilisation to an estimated 60%, allowing for additional theatre activity such as weekend working. Further, reducing the proportion of patients with a delayed discharge by 75% reduces bed utilisation to below 40%, even with weekend working. A range of other scenarios can also be investigated directly by NHS planners using the interactive web app.\n\nConclusionsThe simulation model is intended to support capacity planning of orthopaedic elective services by identifying a balance of capacity across theatres and beds and predicting the impact of productivity measures on capacity requirements. It is applicable beyond the study site and can be adapted for other specialties.\n\nStrengths and Limitations of this studyO_LIThe simulation model provides rapid quantitative estimates to support post-COVID elective services recovery toward medium-term elective targets.\nC_LIO_LIParameter combinations include changes to both resourcing and productivity.\nC_LIO_LIThe interactive web app enables intuitive parameter changes by users while underlying source code can be adapted or re-used for similar applications.\nC_LIO_LIPatient attributes such as complexity are not included in the model but are reflected in variables such as length-of-stay and delayed discharge rates.\nC_LIO_LITheatre schedules are simplified, incorporating the five key orthopaedic elective surgical procedures.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Alison Harper", + "author_inst": "University of Exeter" + }, + { + "author_name": "Thomas Monks", + "author_inst": "University of Exeter" + }, + { + "author_name": "Rebecca Wilson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Maria Theresa Redaniel", + "author_inst": "University of Bristol" + }, + { + "author_name": "Emily Eyles", + "author_inst": "University of Bristol" + }, + { + "author_name": "Timothy Jones", + "author_inst": "University of Bristol" + }, + { + "author_name": "Chris Penfold", + "author_inst": "University of Bristol" + }, + { + "author_name": "Andrew Elliott", + "author_inst": "North Bristol NHS Foundation Trust" + }, + { + "author_name": "Tim Keen", + "author_inst": "North Bristol NHS Foundation Trust" + }, + { + "author_name": "Martin Pitt", + "author_inst": "University of Exeter" + }, + { + "author_name": "Ashley Blom", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Michael Whitehouse", + "author_inst": "University of Bristol" + }, + { + "author_name": "Andrew Judge", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "orthopedics" + }, { "rel_doi": "10.1101/2023.06.05.23290968", "rel_title": "Impact of patient gender on low back pain management before and after the COVID-19 pandemic in commercially insured and Medicare Advantage cohorts. A retrospective cohort study", @@ -82353,73 +82785,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2023.05.31.543022", - "rel_title": "Universal features of Nsp1-mediated translational shutdown by coronaviruses", - "rel_date": "2023-06-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.31.543022", - "rel_abs": "Nonstructural protein 1 (Nsp1) produced by coronaviruses shuts down host protein synthesis in infected cells. The C-terminal domain of SARS-CoV-2 Nsp1 was shown to bind to the small ribosomal subunit to inhibit translation, but it is not clear whether this mechanism is broadly used by coronaviruses, whether the N-terminal domain of Nsp1 binds the ribosome, or how Nsp1 specifically permits translation of viral mRNAs. Here, we investigated Nsp1 from three representative Betacoronaviruses - SARS-CoV-2, MERS-CoV, and Bat-Hp-CoV - using structural, biophysical, and biochemical assays. We revealed a conserved mechanism of host translational shutdown across the three coronaviruses. We further demonstrated that the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A binding. Structure-based biochemical experiments identified a conserved role of these inhibitory interactions in all three coronaviruses and showed that the same regions of Nsp1 are responsible for the preferential translation of viral mRNAs. Our results provide a mechanistic framework to understand how Betacoronaviruses overcome translational inhibition to produce viral proteins.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Katharina Schubert", - "author_inst": "Eidgenossische Technische Hochschule Zurich" - }, - { - "author_name": "Evangelos D. Karousis", - "author_inst": "University of Bern" - }, - { - "author_name": "Ivo Ban", - "author_inst": "Eidgenossische Technische Hochschule Zurich" - }, - { - "author_name": "Christopher Lapointe", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Marc Leibundgut", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Emilie Baeumlin", - "author_inst": "University of Bern" - }, - { - "author_name": "Eric Kummerant", - "author_inst": "ETH, Zurich" - }, - { - "author_name": "Alain Scaiola", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Tanja Schoenhut", - "author_inst": "ETH, Zurich" - }, - { - "author_name": "Jana Ziegelmueller", - "author_inst": "University of Bern" - }, - { - "author_name": "Joseph Puglisi", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Oliver Muehlemann", - "author_inst": "University of Bern" - }, - { - "author_name": "Nenad Ban", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.05.31.543129", "rel_title": "CD4+ T-cell immunity of SARS-CoV-2 patients determine pneumonia development", @@ -82767,6 +83132,89 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2023.05.26.23290622", + "rel_title": "ECHOCARDIOGRAPHIC MANIFESTATIONS OF COVID 19 ILLNESS AND DEVELOPMENT OF PERSISTENT RV DYSFUNCTION AND PULMANARY HYPERTENSION AS A LONG TERM SEQUELAE OF COVID 19 ILLNESS: A STUDY AMONG PATIENTS OF SOUTH EAST ASIAN REGION", + "rel_date": "2023-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.26.23290622", + "rel_abs": "ObjectivesTo study the Echocardiographic manifestations of covid 19 illness among patients admitted in our facility, Correlate MAPSE, TAPSE, PASP, CRP levels and CTSI among covid 19 patients with their 28 day outcome as survivors and non survivors and to look for evidence of residual RV dysfunction and Pulmonary hypertension using TTE after 1 year of follow-up.\n\nStudy designProspective observational study at various medical wards and ICUs in SMS medical college and associated hospitals.\n\nMethods258 patients with a Covid-19 RT-PCR positive report from a throat or a nasal swab within 72 hours of admission were included in the study. Each patient underwent a complete clinical assessment and routine blood investigations including CRP levels were done. A complete transthoracic echocardiogram was done within 48 hours of admission. Patients also underwent a HRCT chest and CTSI scores were estimated. All patients were followed for a period of 28 days. The MAPSE, TAPSE, PASP, CTSI and CRP levels were then correlated with the outcome of the patient. The survivors again underwent a TTE at 1 year after their recovery from covid-19 illness to look for residual RV dysfunction by TAPSE and the development of pulmonary hypertension as measured by PASP using Bernoullis equation.\n\nResultsAmongst patient of covid 19 illness the MAPSE, TAPSE, PASP, CTSI and CRP levels all correlated well with outcome of patients. While most covid-19 survivors recovered from their illness yet some patients showed evidence of persistent RV dysfunction and pulmonary hypertension even after 1 year of follow up.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "LALIT KUMAR", + "author_inst": "SMS medical college, Jaipur" + }, + { + "author_name": "HIMANSHU MAHLA", + "author_inst": "SMS MEDICAL COLLEGE JAIPUR" + }, + { + "author_name": "NEERAJ CHATURVEDI", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "NAVDEEP SINGH SIDHU", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "MANISHA KESHAV", + "author_inst": "UCMS AND ASSOCIATED HOSPTIAL" + }, + { + "author_name": "SHASHI MOHAN SHARMA", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "RAJEEV BAGARHATTA", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "V.V. AGRAWAL", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "VIJAY PATHAK", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "Chandra Bhan Meena", + "author_inst": "SMS Mdical College" + }, + { + "author_name": "DEEPAK MAHESHWARI", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "PRADEEP MEENA", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "BALBIR SINGH PACHAR", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "SOHAN KUMAR SHARMA", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "DINESH GAUTAM", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "SARITA CHOUDHARY", + "author_inst": "SMS MEDICAL COLLEGE" + }, + { + "author_name": "DHANANJAY SHEKHAWAT", + "author_inst": "SMS MEDICAL COLLEGE" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2023.05.30.23290747", "rel_title": "An explanation for SARS-CoV-2 rebound after Paxlovid treatment", @@ -84795,93 +85243,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.05.23.542024", - "rel_title": "A Multi-Epitope/CXCL11 Prime/Pull Coronavirus Mucosal Vaccine Boosts the Frequency and the Function of Lung-Resident CD4+ and CD8+ Memory T Cells and Protects Against COVID-19-like Symptoms and Death Caused by SARS-CoV-2 infection", - "rel_date": "2023-05-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.23.542024", - "rel_abs": "The pandemic of the coronavirus disease 2019 (COVID-19) has created the largest global health crisis in almost a century. Following exposure to SARS-CoV-2, the virus particles replicate in the lungs, induce a \"cytokine storm\" and potentially cause life-threatening inflammatory disease. Low frequencies of function SARS-CoV-2-specific CD4+ and CD8+ T cells in the lungs of COVID-19 patients were associated with severe cases of COVID-19. The apparent low level of T cell-attracting CXCL9, CXCL10, and CXCL11 chemokines in infected lungs may not be sufficient enough to assure the sequestration and/or homing of CD4+ and CD8+ T cells from the circulation into infected lungs. We hypothesize that a Coronavirus vaccine strategy that boosts the frequencies of functional SARS-CoV-2-specific CD4+ and CD8+ T cells in the lungs would lead to better protection against SARS-CoV-2 infection, COVID19-like symptoms, and death. In the present study, we designed and pre-clinically tested the safety, immunogenicity, and protective efficacy of a novel multi-epitope//CXCL11 prime/pull mucosal Coronavirus vaccine. This prime/pull vaccine strategy consists of intranasal delivery of a lung-tropic adeno-associated virus type 9 (AAV-9) vector that incorporates highly conserved human B, CD4+ CD8+ cell epitopes of SARS-CoV-2 (prime) and pulling the primed B and T cells into the lungs using the T cell attracting chemokine, CXCL-11 (pull). We demonstrated that immunization of HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice with this multi-epitope//CXCL11 prime/pull Coronavirus mucosal vaccine: (i) Increased the frequencies of CD4+ and CD8+ TEM, TCM, and TRM cells in the lungs; and (ii) reduced COVID19-like symptoms, lowered virus replication, and prevented deaths following challenge with SARS-CoV-2. These findings discuss the importance of bolstering the number and function of lung-resident memory CD4+ and CD8+ T cells for better protection against SARS-CoV-2 infection, COVID-19-like symptoms, and death.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Latifa Zayou", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Swayam Prakash", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Nisha R Dhanushkodi", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Afshana Quadiri", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Izabela Coimbra Ibraim", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Mahmoud Singer", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amirah Salem", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amin Mohammed Shaik", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Berfin Suzer", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amruth Chilukuri", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Jennifer Tran", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Pauline Chau Nguyen", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Miyo Sun", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Kathy K Hormi-Carver", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Ahmed Belmouden", - "author_inst": "Laboratory of Cell Biology and Molecular Genetics, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco" - }, - { - "author_name": "Hawa Vahed", - "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660; USA" - }, - { - "author_name": "Jeffrey B Ulmer", - "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660; USA" - }, - { - "author_name": "LBACHIR BENMOHAMED", - "author_inst": "GHEI/UCI School of Medecine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.05.25.542297", "rel_title": "Multi-omic Profiling Reveals Early Immunological Indicators for Identifying COVID-19 Progressors", @@ -85125,6 +85486,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2023.05.26.23290243", + "rel_title": "A Long COVID Risk Predictor Focused on Clinical Workflow Integration", + "rel_date": "2023-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.26.23290243", + "rel_abs": "For the NIH Long COVID Computational Challenge (L3C) in the Fall of 2022, we developed a machine learning model to predict who is at high risk for developing Long COVID, optimized for clinical deployment. Our submission won second prize in the competition. We present lessons learned, with details on the features, model selection and performance, fairness analysis, limitations, and deployment implications.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Biplab Bhattacharya", + "author_inst": "Geisinger" + }, + { + "author_name": "Grant DeLong", + "author_inst": "Geisinger" + }, + { + "author_name": "Elliot G Mitchell", + "author_inst": "Geisinger" + }, + { + "author_name": "Tamanna T. K. Munia", + "author_inst": "Geisinger" + }, + { + "author_name": "Gaurav Shetty", + "author_inst": "Geisinger" + }, + { + "author_name": "Abdul Tariq", + "author_inst": "Geisinger" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2023.05.24.541920", "rel_title": "Dichotomy of neutralizing antibody, B cell and T cell responses to SARS-CoV-2 vaccination and protection in healthy adults", @@ -86785,45 +87185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.16.23290033", - "rel_title": "Viral rebound among patients receiving COVID-19 convalescent plasma for treatment of Covid-19 in Uganda.", - "rel_date": "2023-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.16.23290033", - "rel_abs": "BackgroundViral rebound has been reported in people infected with COVID-19 treated with nirmatrelvir/ritonavir, and some cases been reported in patients who did not receive any antiviral treatment. Since the course of COVID-19 has not yet been well defined, we evaluated the incidence of viral rebound among COVID-19 patients treated with COVID-19 Convalescent Plasma (CCP) in Uganda.\n\nMethodsIn the CCP trail, 136 patients were enrolled between 21st September 2020 and 2nd December 2020 who presented to the Mulago National Referral COVID-19 treatment unit. Patients with a positive SARS-CoV-2 reverse transcriptase (RT)-PCR test irrespective of disease severity were hospitalised and randomised to receive either COVID-19 CCP plus standard of care (SOC) or SOC alone. SARS-CoV-2 RT-PCR was done at baseline and on days 3, 5, 7, 14 and 28 post randomisation or until two consecutive negative RT-PCR results were obtained, whichever occurred first. We analysed for occurrence of viral rebound. Viral rebound was defined as a positive SARS-CoV-2 RT-PCR test following a prior negative test.\n\nFindings20% of the participants had viral rebound. Viral rebounders were predominantly male. The median age was 45-64 years and they had at least one co-morbidity. There was no difference in the rebound rates in the study arms, and participants with hypertension had more rebound rates compared to those with other co-morbidities.\n\nInterpretationViral RNA rebound was common among patients receiving CCP. Viral rebound may be a result of the biphasic nature of COVID-19 infection, and not a consequence of the therapeutic interventions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Patricia Alupo", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Winters Muttamba", - "author_inst": "Makerere University Lung Institute ; 2.\tDivision of Infection and Global Health, School of Medicine, University of St Andrews; St. Andrews, United Kingdom" - }, - { - "author_name": "Levicatus Mugenyi", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Ivan Kimuli", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Winceslaus Katagira", - "author_inst": "Makerere University Lung Institute" - }, - { - "author_name": "Bruce Kirenga", - "author_inst": "Makerere University College of Health Sciences, Department of Medicine. 2. Makerere University Lung Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.19.23290234", "rel_title": "Defining the Subtypes of Long COVID and Risk Factors for Prolonged Disease", @@ -86991,6 +87352,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2023.05.18.541286", + "rel_title": "Contrasting the open access dissemination of COVID-19 and SDG research", + "rel_date": "2023-05-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.18.541286", + "rel_abs": "This paper examines the extent to which research has been published open access in response to two global threats: COVID-19 and the Sustainable Development Goals (SDGs), including climate change. We compare the accessibility of COVID-19 content versus SDG literature using the Dimensions database between 2000 and 2021, classifying each publication as gold open access, green, bronze, hybrid, or closed. We found that 79.9% of COVID-19 research papers published between January 2020 and December 2021 was open access, with 39.0% published with gold open access licenses. In contrast, just 55.7% of SDG papers were open access in the same time period, with only 36.0% published with gold open access licenses. Papers related to the climate emergency overall had the second-lowest level of open access at just 55.5%. Papers published by the largest for-profit publishers that committed to both the SDG Publishers Compact and climate actions were not predominantly published open access. The paper highlights the need for continued efforts to promote open access publishing to facilitate scientific research and technological development to address global challenges.\n\nOne-Sentence SummaryIn contrast to COVID-19 papers, research on UN Sustainable Development Goals including the climate emergency have not been made open access by leading global science publishers despite their corporate commitments to sustainability and climate action.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Vincent Lariviere", + "author_inst": "EBSI-UDEM" + }, + { + "author_name": "Isabel Basson", + "author_inst": "Universite de Montreal" + }, + { + "author_name": "Jocalyn Clark", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2023.05.17.541103", "rel_title": "Enhanced Airway Epithelial Response to SARS-CoV-2 Infection in Children is Critically Tuned by the Cross-Talk Between Immune and Epithelial Cells", @@ -88627,37 +89015,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.05.14.540726", - "rel_title": "Metformin an anti-diabetic drug, possess ACE-2 receptor-SARS- Cov-2 RBD binding antagonist activity, anti-inflammatory and cytokine inhibitory properties suitable for treatment of COVID-19", - "rel_date": "2023-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.14.540726", - "rel_abs": "Metformin is a widely used and is a safe anti-diabetic drug. It has also been shown to have anti-inflammatory and anti-viral activities in humans and animal models. Specifically we explored its activity in SARS-CoV-2 initiated COVID19 disease. Here we show that metformin 1. blocks the binding of SARS-CoV-2 spike protein receptor binding domain RBD to human ACE2 receptor 2. We also show that it has anti-inflammatory effects and reduces cytokine secretion as well as blocks the recruitment of monocytes to endothelial cells 3. Finally we show its activity in a hamster in vivo model of SARS-CoV-2 infection as a nasal formulation. Based on the safety and the therapeutic properties relevant to COVID-19 it is feasible to propose a nasal spray of metformin that can be used in treatment of this disease. A nasal spray would deliver the drug to the target organ lung and spare other organs which get exposed upon oral dosing.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Uday Saxena", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Kranti Meher", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Saranya K", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Subrahmanyam Vangala", - "author_inst": "Reagene Innovations Pvt Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2023.05.10.23289325", "rel_title": "Composite interventions on outcomes of severely and critically ill patients with COVID-19 in Shanghai, China", @@ -88845,6 +89202,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.05.13.540634", + "rel_title": "From Collection to Analysis: A Comparison of GISAID and the Covid-19 Data Portal", + "rel_date": "2023-05-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.13.540634", + "rel_abs": "Two distinct modes of data governance have emerged in accessing and reusing viral data pertaining to COVID-19: an unrestricted model, espoused by data repositories part of the International Nucleotide Sequence Database Collaboration and a regulated model promoted by the Global Initiative on Sharing All Influenza data. In this paper, we focus on publications mentioning either infrastructure in the period between January 2020 and January 2023, thus capturing a period of acute response to the COVID-19 pandemic. Through a variety of bibliometric and network science methods, we compare the extent to which either data governance strategy facilitated collaboration from different countries around the globe to understand how data reuse can enhance forms of diversity between institutions, cities, countries, and funding groups. Our findings reveal disparities in representation and usage between the two data infrastructures. We conclude that both approaches offers useful lessons, with the fully open model offering insights into complex data linkage and the partially open model demonstrating the importance of global representation.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Nathanael Peter Sheehan", + "author_inst": "Exeter University" + }, + { + "author_name": "Sabina Leonelli", + "author_inst": "University of Exeter" + }, + { + "author_name": "Federico Botta", + "author_inst": "Exeter University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2023.05.11.540343", "rel_title": "Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform", @@ -90265,57 +90649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.08.539897", - "rel_title": "Evolving spike-protein N-glycosylation in SARS-CoV-2 variants", - "rel_date": "2023-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.08.539897", - "rel_abs": "Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sabyasachi Baboo", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Jolene K Diedrich", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Jonathan L Torres", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Jeffrey Copps", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Bhavya Singh", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Patrick T Garrett", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "Andrew B Ward", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "James C Paulson", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - }, - { - "author_name": "John R Yates III", - "author_inst": "Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.05.08.539929", "rel_title": "Toll-like receptor 7 (TLR7)-mediated antiviral response protects mice from lethal SARS-CoV-2 infection", @@ -90603,6 +90936,85 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.05.05.539395", + "rel_title": "A multiadjuvant polysaccharide-amino acid-lipid (PAL) subunit nanovaccine generates robust systemic and lung-specific mucosal immune responses against SARS-CoV-2 in mice", + "rel_date": "2023-05-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.05.539395", + "rel_abs": "Existing parenteral SARS-CoV-2 vaccines produce only limited mucosal responses, which are essential for reducing transmission and achieving sterilizing immunity. Appropriately designed mucosal boosters could overcome the shortcomings of parenteral vaccines and enhance pre- existing systemic immunity. Here we present a new protein subunit nanovaccine using multiadjuvanted (e.g. RIG-I: PUUC, TLR9: CpG) polysaccharide-amino acid-lipid nanoparticles (PAL-NPs) that can be delivered both intramuscularly (IM) and intranasally (IN) to generate balanced mucosal-systemic SARS-CoV-2 immunity. Mice receiving IM-Prime PUUC+CpG PAL- NPs, followed by an IN-Boost, developed high levels of IgA, IgG, and cellular immunity in the lung, and showed robust systemic humoral immunity. Interestingly, as a purely intranasal vaccine (IN-Prime/IN-Boost), PUUC+CpG PAL-NPs induced stronger lung-specific T cell immunity than IM-Prime/IN-Boost, and a comparable IgA and neutralizing antibodies, although with a lower systemic antibody response, indicating that a fully mucosal delivery route for SARS-CoV-2 vaccination may also be feasible. Our data suggest that PUUC+CpG PAL-NP subunit vaccine is a promising candidate for generating SARS-CoV-2 specific mucosal immunity.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Bhawana Pandey", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Zhengying Wang", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Angela Jimenez", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Eshant Bhatia", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Ritika Jain", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Alexander Beach", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Drishti Maniar", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Justin Hosten", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Laura O'Farrell", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Casey Vantucci", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "David Hur", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Richard K Noel", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Rachel M Ringquist", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Clinton Smith", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Miguel Armenta Ochoa", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Krishnendu Roy", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2023.05.06.539326", "rel_title": "Robust identification of perturbed cell types in single-cell RNA-seq data", @@ -91771,89 +92183,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2023.05.03.23289435", - "rel_title": "Improved access to diabetic retinopathy screening through primary care-based teleophthalmology during the COVID-19 pandemic", - "rel_date": "2023-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.03.23289435", - "rel_abs": "BackgroundPrimary care practices play a critical role in ensuring that patients with diabetes undergo an annual eye examination, the importance of which is underscored by the Healthcare Effectiveness Data and Information Set (HEDIS) quality measures. Store-and-forward teleophthalmology, where ocular images are read remotely by an ophthalmologist, has the potential to facilitate this role.\n\nMethodsIn this report, we aim to measure if using a primary care-based teleophthalmology program improves access to eye examinations for diabetic patients as reflected in HEDIS measures. Over a 20-month period, non-mydriatic fundus photographs were obtained at five primary care sites in the San Francisco Bay Area from patients with a new or existing diagnosis of diabetes mellitus type 1 or 2 who needed an annual eye examination. Collected photographs were evaluated remotely by vitreoretinal specialists for diabetic retinopathy. Our primary measures were the proportion and number of annual eye exams of diabetic patients in primary care clinics that participated in the teleophthalmology program compared to clinics that did not participate. Additional measures included the number of patients with DR who were identified through the program, gradeability of fundus photographs, and characteristics of the study population.\n\nResultsThe program screened 760 unique patients, 84 of whom were found to have DR (11.1%). The rate of ungradable photos was 9.7%, which was greater for patients who self-reported as racially non-White. For the duration of the study, including during the COVID-19 pandemic, both the proportion and number of diabetic patients receiving annual eye examination increased (17.1% increase in proportion, 14.8% increase in number). In comparison, primary care sites that did not offer the teleophthalmology service declined in these measures (2.3% decrease in proportion, 17.0% decrease in number).\n\nConclusionsPrimary care-based teleophthalmology improves access to eye exam for diabetic patients and identifies patients with diabetic retinopathy across diverse communities.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Karen Chen", - "author_inst": "Columbia University Vagelos College of Physicians and Surgeons" - }, - { - "author_name": "Eliot Dow", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Marina Basina", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Jimmy Dang", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Nergis Khan", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Michael Kim", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Marcie Lynn Levine", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Kapil Mishra", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Chandrashan Perera", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Anuradha Phadke", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Marilyn Tan", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Kirsti Weng", - "author_inst": "Stanford Health Care" - }, - { - "author_name": "Diana Do", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Vinit B Mahajan", - "author_inst": "Stanford University" - }, - { - "author_name": "Prithvi Mruthyunjaya", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Ted Leng", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "David Myung", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "ophthalmology" - }, { "rel_doi": "10.1101/2023.05.02.23289345", "rel_title": "Persistent immune abnormalities discriminate post-COVID syndrome from convalescence", @@ -92233,6 +92562,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.05.04.539267", + "rel_title": "Broad-Spectrum Heavily Mutated Monoclonal Antibody Isolated from COVID-19 Convalescent Vaccinee with Capacity to Neutralize SARS-CoV2 Variants Ranging from B.1 to BQ.1.1", + "rel_date": "2023-05-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.04.539267", + "rel_abs": "O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC=\"FIGDIR/small/539267v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@f7dab8org.highwire.dtl.DTLVardef@388861org.highwire.dtl.DTLVardef@181a7c7org.highwire.dtl.DTLVardef@12e02cb_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG In briefChoudhary et al. have isolated and characterized Acovimab, a broadly neutralizing RBM-specific human monoclonal antibody with a relatively high level of somatic hypermutation, which potently neutralizes SARS-CoV2 variants ranging from WuhanB.1 to OmicronBQ.1.1, but not the XBB.1.5 variant. Acovimab also possesses strong synergistic neutralizing activity against some Omicron variants when combined with Sotrovimab. Polyclonal plasma antibodies from COVID-19 vaccinees who had recovered from SARS-CoV2 infection were shown to possess low neutralizing titers of antibodies against conserved RBD targets of CoV2 variants including XBB.1.5, which also synergistically neutralize with Sotrovimab against this variant.\n\nSummaryThe increasing prevalence of the highly antibody-evasive Omicron sublineages increases the risk of breakthrough infections and leaves high-risk and vulnerable immunocompromised individuals with no effective options for prophylactic or therapeutic antibody treatments. Here, we report a heavily mutated anti-RBD monoclonal antibody, Acovimab, directed against a site in the receptor-binding motif (RBM) region of the CoV2 receptor-binding domain (RBD), that possesses very broad and highly potent neutralizing activity against CoV2 variants, including many Omicron variants. This antibody is derived from the IGHV1-58*01 germline sequence and possesses a relatively high level of mutation (15.5% of the VH aa sequence), which is unusual for anti-RBD antibodies. Neutralizing activity was very potent (IC50s range of 1-9 ng/ml) for early Omicron subvariants that possess an unmutated F486 residue and is retained but less potent (IC50s of 200-650 ng/ml) for more resistant Omicron subvariants which contain the F486V mutation (BA4/5, BA4.6, and BQ1.1), but is lost for the later ultra-resistant variants that contain F486S (XBB) or F486P (XBB.1.5) mutations. Based on these specificities, it is predicted that Acovimab by itself should protect against CoV2 infections other than those caused by the XBB/XBB.1.5 family. Acovimab also shows strong synergy in neutralization when combined with Sotrovimab, which neutralizes all Omicron variants, including XBB.1.5. Plasma from subjects with hybrid immunity (induced by vaccination + infection) possessed low levels of XBB.1.5 RBM-targeting plasma-neutralizing antibodies, and these also neutralized synergistically when combined with Sotrovimab. These results suggest potentially novel immunotherapeutic options for treating most of the CoV2 variants responsible for current infections.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Alok K Choudhary", + "author_inst": "PHRI, NJMS, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "David Calianese", + "author_inst": "PHRI, NJMS, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "William Honnen", + "author_inst": "PHRI, NJMS, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "Afsal Kolloli", + "author_inst": "PHRI, NJMS, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "Ryan J Dikdan", + "author_inst": "PHRI, NJMS, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "Dabbu Jaijyan", + "author_inst": "MBMG, NJMS, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "Ge Song", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA" + }, + { + "author_name": "Tazio Capozzola", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA" + }, + { + "author_name": "Vikash Akkaraju", + "author_inst": "New Jersey Medical School, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "Arun Mattappallil", + "author_inst": "University Hospital, Newark, NJ 07103" + }, + { + "author_name": "Anthony Rosania", + "author_inst": "New Jersey Medical School, Newark, NJ, 07103" + }, + { + "author_name": "Salman Khan", + "author_inst": "Dallas Nephrology Associates, Dallas, TX 75235-2208" + }, + { + "author_name": "Mark Lerman", + "author_inst": "Dallas Nephrology Associates, Dallas, TX 75235-2208" + }, + { + "author_name": "Nikaein Afzal", + "author_inst": "Texas Medical Specialty, Dallas, TX 75235-2208" + }, + { + "author_name": "Selvakumar Subbian", + "author_inst": "PHRI, NJMS, Rutgers University, Newark, NJ 07103" + }, + { + "author_name": "Ting Chao Chou", + "author_inst": "PD Science, LLC" + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA" + }, + { + "author_name": "Dennis Burton", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA" + }, + { + "author_name": "Abraham Pinter", + "author_inst": "PHRI, NJMS, Rutgers University, Newark, NJ 07103" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.05.04.539332", "rel_title": "A bivalent ChAd nasal vaccine protects against SARS-CoV-2 BQ.1.1 and XBB.1.5 infection and disease in mice and hamsters", @@ -94349,29 +94769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2023.04.27.23289205", - "rel_title": "Characterization and Resistance to Mutation of a Single-Channel Multiplex PCR Assay for SARS-CoV-2", - "rel_date": "2023-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.27.23289205", - "rel_abs": "Throughout the COVID-19 pandemic, wastewater surveillance has been used worldwide to provide valuable public health data. RT-qPCR is frequently used as a quantitative methodology for wastewater surveillance but is susceptible to mutations in target regions. These mutations may lead to misinterpretation of surveillance data; a drop in signal could be concluded to be a result of lower viral load, when in fact it is caused by reduced detection efficiency. We describe a novel approach to mitigating the impacts of such mutations: monitoring the cumulative signal from two targets (N1 and N2) via independent amplification reactions using identically labeled probes; a \"single-channel multiplex\" approach. Using the IDEXX Water SARS-CoV-2 RT-qPCR test, we demonstrate equivalent intra-assay repeatability and quantitative results from the combined N1N2 test when compared to individual N1 and N2 assays. Furthermore, we show that while mutations in B.1.1.529, BA.5.2, and BA.5.2.1 significantly impact the performance of the N1 assay, the impact on the N1N2 assay was negligible, and nearly within acceptable margin of error for technical replicates. These findings demonstrate that a single-channel multiplex approach can be used to improve the robustness of wastewater surveillance and minimize the risk of future mutations leading to unreliable public health data.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Amy L. Pednault", - "author_inst": "IDEXX Laboratories, Inc." - }, - { - "author_name": "Brian M Swalla", - "author_inst": "IDEXX Laboratories, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.04.28.23289257", "rel_title": "The COV50 classifier predicts frailty and future death, independent from SARS-CoV-2 infection", @@ -94707,6 +95104,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.04.27.23289149", + "rel_title": "The epidemiological impact of digital and manual contact tracing on the SARS-CoV-2 epidemic in the Netherlands: empirical evidence.", + "rel_date": "2023-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.27.23289149", + "rel_abs": "BackgroundThe Dutch government introduced the CoronaMelder smartphone application for digital contact tracing (DCT) to complement manual contact tracing (MCT) by Public Health Services (PHS) during the 2020-2022 SARS-CoV-2 epidemic. Modelling studies showed great potential but empirical evidence of DCT and MCT impact is scarce.\n\nMethodsWe determined reasons for testing, and mean exposure-testing intervals by reason for testing, using routine data from PHS Amsterdam (1 December 2020 to 31 May 2021) and data from two SARS-CoV-2 rapid diagnostic test accuracy studies at other PHS sites in the Netherlands (14 December 2020 to 18 June 2021). Throughout the study periods, notification of DCT-identified contacts was via PHS contact-tracers, and self-testing was not yet widely available.\n\nResultsThe most commonly reported reason for testing was having symptoms. In asymptomatic individuals, it was having been warned by an index case. Only around 2% and 2-5% of all tests took place after DCT or MCT notification, respectively. About 20-36% of those who had received a DCT or MCT notification had symptoms at the time of test request. Test positivity after a DCT notification was significantly lower, and exposure-test intervals after a DCT or MCT notification were longer, than for the above-mentioned other reasons for testing.\n\nConclusionsOur data suggest that the impact of DCT and MCT on the SARS-CoV-2 epidemic in the Netherlands was limited. However, DCT impact might be enlarged if app use coverage is improved, contact-tracers are eliminated from the digital notification process to minimise delays, and DCT is combined with self-testing.\n\nAuthor summaryDuring the 2020-2022 SARS-CoV-2 epidemic, the Dutch government introduced digital contact tracing (DCT) using a smartphone application to complement manual contact tracing (MCT) by professional contact-tracers. Mathematical models had suggested that DCT could slow down virus spread by identifying more individuals with whom the smartphone user had been in close contact and by reducing notification and testing delays after exposure. We used data collected during the Dutch epidemic to evaluate whether this was indeed the case and found that DCT and MCT had limited impact. Only around 2% of all tests took place after a DCT notification, and 2-5% after a MCT notification depending on MCT capacity at the time. Test positivity was lower after a DCT notification, and exposure-test intervals were longer after a DCT or MCT notification, than for other reasons for testing. About 20-36% of those who had received a DCT or MCT notification had symptoms at the time of test request and might have tested anyway even without having received the notification. However, DCT impact might be enlarged in future epidemics if app use coverage is improved and all exposure-notification-testing delays are minimised (e.g. no involvement of professional contact tracers and enabling self-testing after DCT notification).", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Wianne Ter Haar", + "author_inst": "UMC Utrecht" + }, + { + "author_name": "Jizzo Bosdriesz", + "author_inst": "GGD Amsterdam" + }, + { + "author_name": "Roderick Venekamp", + "author_inst": "UMC Utrecht" + }, + { + "author_name": "Ewoud Schuit", + "author_inst": "UMC Utrecht" + }, + { + "author_name": "Susan van den Hof", + "author_inst": "RIVM" + }, + { + "author_name": "Wolfgang Ebbers", + "author_inst": "Erasmus Universiteit" + }, + { + "author_name": "Mirjam Kretzschmar", + "author_inst": "UMC Utrecht" + }, + { + "author_name": "Jan Kluytmans", + "author_inst": "UMC Utrecht" + }, + { + "author_name": "Carl Moons", + "author_inst": "UMC Utrecht" + }, + { + "author_name": "Maarten Schim van der Loef", + "author_inst": "GGD Amsterdam" + }, + { + "author_name": "Amy Matser", + "author_inst": "GGD Amsterdam" + }, + { + "author_name": "Janneke HHM van de Wijgert", + "author_inst": "University Medical Center Utrecht" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.04.28.23289254", "rel_title": "Population immunity of natural infection, primary-series vaccination, and booster vaccination in Qatar during the COVID-19 pandemic: An observational study", @@ -96331,57 +96791,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.04.20.23288904", - "rel_title": "Aerosol Jet Printing Enabled Dual-Function Electrochemical and Colorimetric Biosensor for SARS-CoV-2 Detection", - "rel_date": "2023-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.20.23288904", - "rel_abs": "An aerosol jet printing enabled dual-function biosensor for the sensitive detection of pathogens using SARS-CoV-2 RNA as an example has been developed. A CRISPR-Cas13: guide-RNA complex is activated in the presence of a target RNA, leading to the collateral trans-cleavage of ssRNA probes that contain a horseradish peroxidase (HRP) tag. This, in turn, catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by HRP, resulting in a color change and electrochemical signal change. The colorimetric and electrochemical sensing protocol does not require complicated target amplification and probe immobilization and exhibits a detection sensitivity in the femtomolar range. Additionally, our biosensor demonstrates a wide dynamic range of 5 orders of magnitude. This low-cost aerosol inkjet printing technique allows for an amplification-free and integrated dual-function biosensor platform, which operates at physiological temperature and is designed for simple, rapid, and accurate point-of-care (POC) diagnostics in either low-resource settings or hospitals.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Li Liu", - "author_inst": "University of California,Riverside" - }, - { - "author_name": "Zhiheng Xu", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Adrian Moises Molina Vargas", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Steve Dollery", - "author_inst": "Biological Mimetics, Inc." - }, - { - "author_name": "Michael Schrlau", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Denis Cormier", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Mitchell O'Connell", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Gregory Tobin", - "author_inst": "Biological Mimetics, Inc." - }, - { - "author_name": "Ke Du", - "author_inst": "University of California, Riverside" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.04.24.23288921", "rel_title": "Immune signature of patients with cardiovascular disease - in-depth immunophenotyping predicts increased risk for a severe course of COVID-19", @@ -96617,6 +97026,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2023.04.25.23289080", + "rel_title": "Risks of digestive diseases in long COVID: Evidence from a large-scale cohort study", + "rel_date": "2023-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.25.23289080", + "rel_abs": "ObjectivesThis study aims to evaluate the effect of coronavirus disease 2019 (COVID-19) on the long-term risk of digestive diseases in the general population.\n\nDesignLarge-scale population-based cohort study based on a prospective cohort.\n\nSettingUK Biobank cohort linked to multiple nationwide electronic health records databases.\n\nParticipantsThe cohort consisted of 112,311 individuals who survived the initial 30 days following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as well as two control groups: a contemporary group (n = 359,671) without any history of COVID-19, and a historical control group (n = 370,979) that predated the COVID-19 outbreak.\n\nMain outcome measuresMain outcomes were predefined digestive diseases. Hazard ratios and corresponding 95% confidence intervals (CI) were computed utilizing the Cox regression models after inverse probability weighting.\n\nResultsCompared with the contemporary control group, patients with previous COVID-19 infection had higher risks of digestive diseases, including functional gastrointestinal disorders (hazard ratios [HR] 1.95 (95% CI 1.62 to 2.35)); peptic ulcer disease (HR 1.27 (1.04 to 1.56)); gastroesophageal reflux disease (GERD) (HR 1.46 (1.34 to 1.58)); inflammatory bowel diseases (HR 1.40 (1.02 to 1.90)); gallbladder disease (HR 1.28 (1.13 to 1.46)); severe liver disease (HR 1.46 (1.12 to 1.90)); non-alcoholic liver disease (HR 1.33 (1.15 to 1.55)); and pancreatic disease (HR 1.43 (1.17 to 1.74)). The risks of GERD were stepwise increased with severity of the acute phase of COVID-19 infection. The results were consistent when using the historical cohort as the control group.\n\nConclusionsOur study provides important insights into the association between COVID-19 and the long-term risk of digestive system disorders. COVID-19 patients are at a higher risk of developing gastrointestinal disorders, with stepwise increased risk with the severity and persisting even after one year follow-up.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Yuying Ma", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Lijun Zhang", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Rui Wei", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Weiyu Dai", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Ruijie Zeng", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Dongling Luo", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Rui Jiang", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Huihuan Wu", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Zewei Zhuo", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Qi Yang", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Jingwei Li", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Felix W Leung", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Chongyang Duan", + "author_inst": "Southern Medical University" + }, + { + "author_name": "Weihong Sha", + "author_inst": "Guangdong Provincial People's Hospital" + }, + { + "author_name": "Hao Chen", + "author_inst": "Guangdong Provincial People's Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.04.19.23288796", "rel_title": "Time series analysis of daily data of COVID-19 reported cases in Japan from January 2020 to February 2023", @@ -98405,61 +98889,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.04.17.23288710", - "rel_title": "COVID-19 testing avoidance among patients with cardiovascular disease", - "rel_date": "2023-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.17.23288710", - "rel_abs": "BackgroundRapid coronavirus 2019 (COVID-19) testing in symptomatic cases is extremely important for preventing the spread of COVID-19 infection and early therapeutic intervention. In contrast, whether symptomatic patients are tested depends largely on their health literacy, interpretation, and knowledge of COVID-19. We aimed to investigate the rate of COVID-19 testing avoidance despite having common cold symptoms in patients with cardiovascular disease and examine factors related to testing avoidance.\n\nMethodsA large-scale epidemiological questionnaire survey, the Japan COVID-19 and Society Internet Survey 2022 (JACSIS), was conducted online from April to May 2022. The rate of COVID-19 testing avoidance was investigated in patients aged 20 to 80 years with cardiovascular risk factors (hypertension, dyslipidemia, or diabetes) or a history of cardiovascular disease (angina, myocardial infarction, or stroke), only those exhibiting common cold symptoms during the 2 months in the survey.\n\nResultsOf the 1,565 eligible patients, 58% (909 patients) did not undergo COVID-19 testing. Multivariate analysis revealed that older age, obesity, non-walking regularly, long sedentary time, eating alone, frequent snacking, and having received 4 COVID-19 vaccinations were independently associated with testing avoidance.\n\nConclusionsIn the chronic phase of the COVID-19 pandemic, prompt COVID-19 testing at the time of symptomatic disease is important, and strategies to reduce testing hesitancy should be considered.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Koichiro Matsumura", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Takahiro Tabuchi", - "author_inst": "Osaka International Cancer Institute" - }, - { - "author_name": "Eijiro Yagi", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Takeshi Ijichi", - "author_inst": "Tokai University School of Medicine" - }, - { - "author_name": "Misaki Hasegawa", - "author_inst": "Tokai University School of Medicine" - }, - { - "author_name": "Nobuhiro Yamada", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Yohei Funauchi", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Kazuyoshi Kakehi", - "author_inst": "Kindai University Faculty of Medicine" - }, - { - "author_name": "Takayuki Kawamura", - "author_inst": "Kinki University Faculty of Medicine" - }, - { - "author_name": "Gaku Nakazawa", - "author_inst": "Kindai University Faculty of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.04.18.23288715", "rel_title": "Preliminary clinical characteristics of Pediatric Covid-19 cases during the ongoing Omicron XBB.1.16 driven surge in a north Indian city", @@ -98623,6 +99052,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2023.04.17.23288664", + "rel_title": "Post COVID-19 Condition, Work Ability and Occupational Changes: Results from a Population-based Cohort", + "rel_date": "2023-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.17.23288664", + "rel_abs": "BackgroundEvidence from population-based studies on the impact of post COVID-19 condition (PCC) on ability to work is limited but critical due to its high prevalence among individuals of working-age.\n\nObjectiveTo evaluate the association between PCC, work ability, and occupational changes.\n\nDesignPopulation-based, longitudinal cohort.\n\nSettingGeneral population, Canton of Zurich, Switzerland.\n\nParticipants672 adults of working-age with SARS-CoV-2 infection.\n\nMeasurementsCurrent work ability, work ability related to physical and mental demands, and estimated future work ability in 2 years (assessed using Work Ability Index), as well as PCC-related occupational changes at one year after infection.\n\nResultsThere was very strong evidence that current work ability scores were 0.62 (95% confidence interval (CI) 0.30 to 0.95) points lower among those with PCC compared to those without. Similarly, there was very strong evidence for lower odds of reporting higher work ability with respect to physical (odds ratio (OR) 0.30, 95% CI 0.20 to 0.46) and mental (OR 0.40, 0.27 to 0.62) demands among those with PCC compared to those without. Higher age and history of psychiatric diagnosis were associated with a more substantial reduction in current work ability. 5.8% of those with PCC reported direct effects of PCC on their occupational situation, with 1.6% of those with PCC completely dropping out of the workforce and 43% of those with PCC-related occupational changes reporting financial difficulties as a result.\n\nLimitationsSelection, use of self-reported outcome measures, and limited generalizability to individuals with most severe COVID-19 or following vaccination.\n\nConclusionsThese findings highlight the need for providing support and interdisciplinary interventions to individuals affected by PCC to help them maintain or regain their work ability and productivity.\n\nPrimary Funding SourceFederal Office of Public Health, Department of Health of the Canton of Zurich, University of Zurich Foundation, Switzerland.\n\nStudy RegistrationISRCTN14990068.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Philipp Kerksieck", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Tala Ballouz", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Sarah R Haile", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Celine Schumacher", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Joanne Lacy", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Anja Domenghino", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Jan S Fehr", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Georg F Bauer", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Holger Dressel", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Milo A Puhan", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + }, + { + "author_name": "Dominik Menges", + "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.04.13.23288353", "rel_title": "Antibody Correlates of Protection for COVID-19 Convalescent Plasma Associated with Reduced Outpatient Hospitalizations", @@ -100431,37 +100919,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.04.11.23288130", - "rel_title": "Clinical Performance of BD Veritor\u2122 Assay Across SARS-CoV-2 Variants", - "rel_date": "2023-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.11.23288130", - "rel_abs": "BackgroundDifferent rates of morbidity, mortality, transmission, and immune escape are associated with various strains of the SARS-CoV-2 virus. With the emergence of new strains during seasonal outbreaks, ensuring that antigen-based immunoassays can detect SARS-CoV-2 infections across identified circulating viral variants is a crucial component of infection control efforts.\n\nObjectiveTo validate the performance of the BD Veritor System for Rapid Detection of SARS-CoV-2 Assay (BD Veritor assay) to detect SARS-CoV-2 across variants of concern (VOC) and variants of interest (VOI).\n\nMethodsUsing the Illumina NextSeq 2000 Sequencer, viral sequencing was performed on prospectively collected, then frozen, SARS-CoV-2 RT-PCR positive nasal swabs stored in universal transport media (UTM). Specimens from symptomatic and asymptomatic individuals were included in the study. Using the information obtained from the sequencing analysis, the performance of the BD Veritor System assay was evaluated against the highly sensitive molecular RT-PCR Quidel Lyra SARS-CoV-2 assay for each variant.\n\nResultsThe resulting PPA was 97.4% (95% CI: 86.8, 99.5) for detection of SARS-CoV-2 across all variants identified by Next Generation Sequencing (i.e., WHO-labeled variants Alpha, Delta, Gamma, Iota, Lambda, as well as two other non-labeled variants), with a 100% PPA for five of the six variant labels identified.\n\nConclusionThe results demonstrate the robust performance of the BD Veritor assay in detecting SARS-CoV-2 in clinical nasal specimens in selected variants. As new variants emerge, additional studies will be beneficial to ensure the sustained performance of SARS-CoV-2 assays.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Karen Eckert", - "author_inst": "Becton, Dickinson and Company, BD Life Sciences, Integrated Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA" - }, - { - "author_name": "Sebastian Gutierrez", - "author_inst": "Becton, Dickinson and Company, BD Life Sciences, Integrated Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA" - }, - { - "author_name": "Brittany Knight", - "author_inst": "MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd., Kansas City, MI" - }, - { - "author_name": "Lauren Cooper", - "author_inst": "Becton, Dickinson and Company, BD Life Sciences, Integrated Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.04.12.23288362", "rel_title": "Bivalent COVID-19 booster vaccines induce cross-reactive but not BA.5-specific antibodies in polyclonal serum", @@ -100741,6 +101198,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2023.04.11.23288200", + "rel_title": "Effect of face-covering use on adherence to other COVID-19 protective behaviours: a systematic review", + "rel_date": "2023-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.11.23288200", + "rel_abs": "During the COVID-19 pandemic, concerns were raised that face covering use may elicit risk compensation; a false sense of security resulting in reduced adherence to other protective behaviours such as physical distancing. This systematic review aimed to investigate the effect of face covering use on adherence to other COVID-19 related protective behaviours. Medline, Embase, PsychInfo, EmCare, medRxiv preprints, Research Square and WHO COVID-19 Research Database were searched. All primary research studies published from 1 January 2020 to 17th May 2022 which investigated the effect of face covering use on adherence to other protective behaviours in public settings during the COVID-19 pandemic were included. Papers were selected and screened in accordance with the PRISMA framework. Backwards and forwards citation searches of included papers were also conducted on 16th September 2022, with eligible papers published between 1st January 2020 and that date being included. A quality appraisal including risk of bias was assessed using the Academy of Nutrition and Dietetics Quality Criteria Checklist. This review is registered on PROSPERO, number CRD42022331961. 47 papers were included, with quality ranging from low to high. These papers investigated the effects of face covering use and face covering policies on adherence to six categories of behaviour: physical distancing; mobility; face-touching; hand hygiene; close contacts; and generalised protective behaviour. Results reveal no consistent evidence for or against risk compensation, with findings varying according to behaviour and across study types. There is a suggestion that face covering use might reduce face-touching and face covering mandates might increase mobility, though the lack of robust evidence means these are tentative claims. Evidence on the other protective behaviours is largely inconsistent, and therefore confident conclusions cannot be made in these areas. Any policy decisions related to face coverings must consider the inconsistencies and caveats in this evidence base.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Adam Millest", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Sidra Saeed", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Charles Symons", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Holly Carter", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.04.13.23288522", "rel_title": "Risk of new-onset Long Covid following reinfection with SARS-CoV-2: community-based cohort study", @@ -102428,29 +102916,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.04.07.23288262", - "rel_title": "COVID-19 Vaccine Uptake And Its Associated Factors among general population In Basmaia City in Baghdad 2022", - "rel_date": "2023-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.07.23288262", - "rel_abs": "ObjectiveVaccination is a vital cornerstone of public health, which has saved countless lives throughout history. Therefore, achieving high vaccination uptake rates is essential for successful vaccination programs. Unfortunately, vaccine uptake has been hindered by deferent factors and challenges. The objective of this study is to assess COVID-19 vaccine uptake and associated factors among the general population.\n\nMethodsThis study is a descriptive cross-sectional study conducted in Basmaia city, Baghdad from June to October 2022. Data were collected through a semi-structured questionnaire using multi-stage random sampling. Statistical analysis was performed using descriptive statistics, chi-square analysis, Mann-Whitney test, and binary and multivariable logistic regression.\n\nResultsThe prevalence of COVID-19 vaccine uptake was 70.4%. The most common reason for getting vaccinated was protection from the disease, while fear of side effects and not needing the vaccine were the main reasons for refusal.\n\nThe study found that gender, age, education level, job title, risk perception, knowledge, and attitude towards the vaccine were significantly associated with COVID-19 vaccine uptake. Males were 2.273 times more likely to get vaccinated than females, and older age groups had higher odds of vaccination than younger age groups. Those with higher education levels were also more likely to receive the vaccine. Participants with higher risk perception, knowledge, and positive attitude towards the vaccine were more likely to get vaccinated.\n\nAnd found that mandatory vaccination policies may negatively impact uptake of subsequent vaccine doses.\n\nConclusionThe study found a high prevalence of COVID-19 vaccine uptake, with gender, age, education level, and job title being significant factors associated with vaccine uptake. Additionally, mandatory vaccination policies may have a negative impact on the uptake of subsequent vaccine doses. Public health efforts should prioritize addressing these factors to increase vaccine uptake.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hussein Abdalrahim Alhlew", - "author_inst": "ministry of health" - }, - { - "author_name": "Mohammad Asaad Albayaty", - "author_inst": "al-Kindy college of medicine, Baghdad university" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.04.07.23288300", "rel_title": "Association between PM2.5 air pollution, temperature, and sunlight during different infectious stages with the case fatality of COVID-19 in the United Kingdom: a modeling study", @@ -102730,6 +103195,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.04.05.23288207", + "rel_title": "Integration of serial self-testing for COVID-19 as part of contact tracing in the Brazilian public health system: A pragmatic trial protocol", + "rel_date": "2023-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.05.23288207", + "rel_abs": "BackgroundThe coronavirus disease (COVID-19) pandemic has led to an unprecedented public health crisis. Insufficient testing continues to limit the effectiveness of the global response to the COVID-19 pandemic. Molecular testing methods such as reverse transcriptase polymerase chain reaction (RT-PCR) continue to be highly centralized and are a sub-optimal option for population surveillance. Rapid antigen tests (Ag-RDTs) offer multiple benefits including low costs, high flexibility to conduct tests in a wide variety of settings, and faster return of results. Recently, self-test Ag-RDTs (STs) have gained approval in several markets and offer the possibility to expand testing, reaching at-risk populations. While STs have the potential to assist the COVID-19 response, test result integrity, reporting, and appropriate linkage to care continue to hinder the widespread implementation of self-testing programs.\n\nMethodsThis protocol presents a mixed-methods pragmatic trial (ISRCTN91602092) to better understand the feasibility of self-testing as part of a contact tracing strategy within the Brazilian public health system. Approximately 604 close contacts of 150 index cases testing positive for COVID-19 will be enrolled. Close contacts will be randomized to either serial (daily) self-testing over a 10-day follow-up period or a more traditional approach to contact tracing with a professional Ag-RDT at one time point post-exposure. Usability workshops and focus group discussions will also be conducted.\n\nDiscussionThis study protocol presents a comprehensive plan to assess the effectiveness, operational feasibility, and stakeholder preferences of a serial self-testing strategy for contact tracing within the Brazilian public health system. Our results will contribute to better understanding of the feasibility of a self-testing strategy within the public sector. Potential risks and limitations are discussed. Our findings will have important implications as governments continue working to mitigate the impact of COVID-19, particularly in the context of where to direct limited resources for testing and healthcare infrastructure.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Rebecca Green", + "author_inst": "Program for Appropriate Technology in Health: PATH" + }, + { + "author_name": "Camilo Manchola", + "author_inst": "Global Health Strategies" + }, + { + "author_name": "Emily Gerth-Guyette", + "author_inst": "Program for Appropriate Technology in Health: PATH" + }, + { + "author_name": "Michelle Oliveira Silva", + "author_inst": "Centro de Pesquisa em Medicina Tropical de Rondnia" + }, + { + "author_name": "Raissa Stephanie", + "author_inst": "Centro de Pesquisa em Medicina Tropical de Rond\u00f4nia" + }, + { + "author_name": "Tain\u00e1 dos Santos Soares", + "author_inst": "Instituto Carlos Chagas - Fiocruz" + }, + { + "author_name": "Luiza Bastos Gottin", + "author_inst": "Global Health Strategies" + }, + { + "author_name": "Milena Coelho", + "author_inst": "Global Health Strategies" + }, + { + "author_name": "Kimberly E Green", + "author_inst": "Program for Appropriate Technology in Health: PATH" + }, + { + "author_name": "Alexandre Dias Tavares Costa", + "author_inst": "Instituto Carlos Chagas - Fiocruz" + }, + { + "author_name": "Dh\u00e9lio Batista Pereira", + "author_inst": "Centro de Pesquisa em Medicina Tropical de Rond\u00f4nia" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.04.06.535927", "rel_title": "SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in mice", @@ -104346,93 +104870,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2023.04.01.23287538", - "rel_title": "Trends in weight gain recorded in English primary care before and during the Coronavirus-19 pandemic: an observational cohort study using the OpenSAFELY platform", - "rel_date": "2023-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.01.23287538", - "rel_abs": "BackgroundWe investigated which clinical and sociodemographic characteristics were associated with unhealthy patterns of weight gain amongst adults living in England during the pandemic.\n\nMethodsWith the approval of NHS England we conducted an observational cohort study of Body Mass Index (BMI) changes between March 2015 and March 2022 using the OpenSAFELY-TPP platform. We estimated individual rates of weight gain before and during the pandemic, and identified individuals with rapid weight gain (>0{middle dot}5kg/m2/year) in each period. We also estimated the change in rate of weight gain between the prepandemic and pandemic period and defined extreme-accelerators as the ten percent of individuals with the greatest increase (>1{middle dot}84kg/m2/year). We estimated associations with these outcomes using multivariate logistic regression.\n\nFindingsWe extracted data on 17,742,365 adults (50{middle dot}1% female, 76{middle dot}1% White British). Median BMI increased from 27{middle dot}8kg/m2 [IQR:24{middle dot}3-32{middle dot}1] in 2019 (March 2019 to February 2020) to 28{middle dot}0kg/m2 [24{middle dot}4-32{middle dot}6] in 2021. Rapid pandemic weight gain (n=3,214,155) was associated with female sex (male vs female: aOR 0{middle dot}76 [95%CI:0{middle dot}76-0{middle dot}76]); younger age (50-59-years vs 18-29-years: aOR 0{middle dot}60 [0{middle dot}60-0{middle dot}61]); White British ethnicity (Black Caribbean vs White British: aOR 0{middle dot}91 [0{middle dot}89-0{middle dot}94]); deprivation (least-deprived-IMD-quintile vs most-deprived: aOR 0{middle dot}77 [0{middle dot}77-0{middle dot}78]); and long-term conditions, of which mental health conditions had the greatest effect (e.g. depression (aOR 1{middle dot}18[1{middle dot}17-1{middle dot}18])). Similar characteristics increased risk of extreme acceleration (n=2,768,695).\n\nInterpretationWe found female sex, younger age, deprivation and mental health conditions increased risk of unhealthy patterns of pandemic weight gain. This highlights the need to incorporate sociodemographic, physical, and mental health characteristics when formulating post-pandemic research, policies, and interventions targeting BMI.\n\nFundingNIHR", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Miriam Samuel", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Robin Y Park", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Sophie V Eastwood", - "author_inst": "University College London, London, United Kingdom" - }, - { - "author_name": "Fabiola Eto", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Daniel Stow", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Sebastian Bacon", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Jessica Morley", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "William J Hulme", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "Diabetes Research Centre, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "Jonathan Valabhji", - "author_inst": "Department of Diabetes and Endocrinology, Imperial College Healthcare NHS Trust, London, UK" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Sarah Finer", - "author_inst": "Wolfson Institute of Population Health, Queen Mary University of London, London, United Kingdom" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2023.03.30.23287969", "rel_title": "A Graph Embedding Approach for Deciphering the Longitudinal Associations of Global Mobility and COVID-19 Cases", @@ -104632,6 +105069,73 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.04.03.535401", + "rel_title": "nanoCLAMP potently neutralizes SARS-CoV-2 and protects K18-hACE2 mice from infection", + "rel_date": "2023-04-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.03.535401", + "rel_abs": "Intranasal treatments, combined with vaccination, has the potential to slow mutational evolution of virusues by reducing transmission and replication. Here we illustrate the development of a SARS-CoV-2 receptor binding domain (RBD) nanoCLAMP and demonstrate its potential as an intranasally administered therapeutic. A multi-epitope nanoCLAMP was made by fusing a pM affinity single-domain nanoCLAMP (P2710) to alternate epitope binding nanoCLAMP, P2609. The resulting multimerised nanoCLAMP P2712 had sub-pM affinity for the Wuhan and South African (B.1.351) RBD (KD < 1 pM), and decreasing affinity for the Delta (B.1.617.2) and Omicron (B.1.1.529) variants (86 pM and 19.7 nM, respectively). P2712 potently inhibited ACE2:RBD interaction, suggesting its utility as a therapeutic. With an IC50 = 0.4 {+/-} 0.1 nM obtained from neutralization experiments using pseudoviral particles as well as patient cultured SARS-CoV-2 samples, nanoCLAMP P2712 protected K18-hACE2 mice from SARS-CoV-2 infection, reduced viral loads in the lungs and brains, and reduced associated upregulation of inflammatory cytokines and chemokines. Together, our findings warrant further investigation into the development of nanoCLAMPs as effective intranasally delivered COVID19 therapeutics.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Quentin Pagneux", + "author_inst": "University of Lille" + }, + { + "author_name": "Nathalie Garnier", + "author_inst": "University of Lille" + }, + { + "author_name": "Manon Fabregue", + "author_inst": "INSERM" + }, + { + "author_name": "Sarah Sharkaoui", + "author_inst": "INSERM" + }, + { + "author_name": "Sophie Mazzoli", + "author_inst": "INSERM" + }, + { + "author_name": "Ilka Engelmann", + "author_inst": "CHU Montpellier" + }, + { + "author_name": "Rabah Boukherroub", + "author_inst": "University of Lille" + }, + { + "author_name": "Mary Strecker", + "author_inst": "Regis University" + }, + { + "author_name": "Eric Cruz", + "author_inst": "Celerion" + }, + { + "author_name": "Peter Ducos", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Ana Zarubica", + "author_inst": "CNRS" + }, + { + "author_name": "Richard Suderman", + "author_inst": "Nectagen" + }, + { + "author_name": "Sabine Szunerits", + "author_inst": "University of Lille" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2023.04.03.534161", "rel_title": "A broadly protective CHO cell expressed recombinant spike protein subunit based vaccine (IMT-CVAX) against SARS-CoV-2", @@ -106107,25 +106611,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2023.03.28.23287762", - "rel_title": "Early real world evidence on the relative SARS-COV-2 vaccine effectiveness of bivalent COVID-19 booster doses: a rapid review.", - "rel_date": "2023-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.28.23287762", - "rel_abs": "The objective of this review is to give an overall view of COVID-19 bivalent vaccines knowledge and to explore their early available real world effectiveness evidence in the Omicron era.\n\nPresently, bivalent vaccines are generally offered to all groups eligible for their next booster, as defined by the national vaccination campaign, with varying policies between countries.\n\nThe use of bivalent vaccines is supported by immunogenity studies, which, nevetheless, have led to contradictory conclusions, and are not generally designed to measure clinical impact.\n\nIn order to critically appraise the available research on real world effectiveness, a systematic literature search was performed: out of 876 references examined, 14 studies were finally included and extracted. The findings of this review demonstrate modest to moderate additional protection of vaccination with bivalent BA.4-5 or BA.1 mRNA-booster vaccines against COVID-19 associated illness and hospitalization, -if compared with having received a monovalent dose as booster-, during a period when BA.5 and other Omicron sublineage viruses predominated globally,\n\nConsidering the complexity of the current immunity situation at global level, and the high level of heterogeneity both at study and at review level, these findings must be taken with caution. Further research on SARS-CoV-2 vaccine effectiveness against emerging SARS-CoV-2 variants is encouraged.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Monica Sane Schepisi", - "author_inst": "UniCamillus, International Medical University, Rome, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.24.23287658", "rel_title": "Safety and Immunogenicity of the NVX-CoV2373 Vaccine as a Booster in Adults Previously Vaccinated with the BBIBP-CorV Vaccine: An Interim Analysis", @@ -106385,6 +106870,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.03.28.23287799", + "rel_title": "The effects of weather and mobility on respiratory viruses dynamics before and after the COVID-19 pandemic", + "rel_date": "2023-03-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.28.23287799", + "rel_abs": "The flu season is caused by a combination of different pathogens, including influenza viruses (IVS), that cause the flu, and non-influenza respiratory viruses (NIRVs), that cause common colds or influenza-like illness. These viruses have similar circulation patterns, and weather has been considered a main driver of their dynamics, with peaks in the winter and almost no circulation during the summer in temperate regions. However, after the emergence of SARS-CoV2, in 2019, the dynamics of these respiratory viruses were strongly perturbed worldwide: some infections almost disappeared, others were delayed or occurred \"off-season\". This disruption raised questions regarding the dominant role of weather while also providing an unique opportunity to investigate the relevance of different driving factors on the epidemiological dynamics of IVs and NIRVs, including viral interactions, non-pharmacological individual measures (such as masking), or mobility. Here, we use epidemiological surveillance data on several respiratory viruses from Canada and the USA from 2016 to 2023, and tested the effects of weather and mobility in their dynamics before and after the COVID-19 pandemic. Using statistical modelling, we found evidence that whereas in the pre-COVID-19 pandemic period, weather had a strong effect and mobility a limited effect on dynamics; in the post-COVID-19 pandemic period the effect of weather was strongly reduced and mobility played a more relevant role. These results, together with previous studies, indicate that at least some of the behavioral changes resulting from the non-pharmacological interventions implemented during COVID-19 pandemic had a strong effect on the dynamics of respiratory viruses. Furthermore, our results support the idea that these seasonal dynamics are driven by a complex system of interactions between the different factors involved, which probably led to an equilibrium that was disturbed, and perhaps permanently altered, by the COVID-19 pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "irma varela-lasheras", + "author_inst": "Nova School of Business and Economics, Rua da Holanda, 2775-405 Carcavelos, Portugal" + }, + { + "author_name": "Lilia Perfeito", + "author_inst": "Social Physics and Complexity Lab - SPAC, Laboratory of Instrumentation and Experimental Particles Physics" + }, + { + "author_name": "Sara Mesquita", + "author_inst": "Social Physics and Complexity Lab - SPAC, Laboratory of Instrumentation and Experimental Particles Physics / Nova Medical School, Campo dos Martires da Patria 1" + }, + { + "author_name": "Joana Goncalves-Sa", + "author_inst": "Social Physics and Complexity Lab - SPAC, Laboratory of Instrumentation and Experimental Particles Physics / Nova School of Business and Economics, Rua da Holan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.27.23287763", "rel_title": "Transient loss and recovery of oral chemesthesis, taste and smell with COVID-19", @@ -107617,65 +108133,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.24.23287700", - "rel_title": "The potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: Analysis of the ONS COVID-19 Infection Survey", - "rel_date": "2023-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287700", - "rel_abs": "ObjectivesTo assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection.\n\nDesignWe analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from December 1st 2020 to 11th May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups.\n\nSetting\n\nResultsEstimated rates of triple-vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%), and retail (85%). High rates were observed for individuals working in health (95% for office-based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios reduced from 1.38 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. Conversely, estimated relative risk for some occupational groups, such as people working in education, remained high despite high vaccine coverage.\n\nConclusionsVariation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jack D Wilkinson", - "author_inst": "University of Manchester" - }, - { - "author_name": "Evangelia Demou", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Mark Cherrie", - "author_inst": "Institute of Occupational Medicine" - }, - { - "author_name": "Rhiannon Edge", - "author_inst": "University of Lancaster" - }, - { - "author_name": "Matthew Gittins", - "author_inst": "University of Manchester" - }, - { - "author_name": "Srinivasa Vittal Katikireddi", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Theocharis Kromydas", - "author_inst": "University of Glasgow" - }, - { - "author_name": "WIll Mueller", - "author_inst": "Institute for Occupational Medicine" - }, - { - "author_name": "Neil Pearce", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Martie van Tongeren", - "author_inst": "University of Manchester" - }, - { - "author_name": "Sarah Rhodes", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2023.03.24.534062", "rel_title": "Intra-Host Mutation Rate of Acute SARS-CoV-2 Infection During the Initial Pandemic Wave", @@ -108103,6 +108560,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.24.23287674", + "rel_title": "Morbidity and mortality burden of COVID-19 in rural Madagascar: results from a longitudinal cohort and nested seroprevalence study", + "rel_date": "2023-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287674", + "rel_abs": "IntroductionThree years into the pandemic, there remains significant uncertainty about the true infection and mortality burden of COVID-19 in the WHO-Africa region. High quality, population-representative studies in Africa are rare and tend to be conducted in national capitals or large cities, leaving a substantial gap in our understanding of the impact of COVID-19 in rural, low-resource settings. Here, we estimated the spatio-temporal morbidity and mortality burden associated with COVID-19 in a rural health district of Madagascar until the first half of 2021.\n\nMethodsWe integrated a nested seroprevalence study within a pre-existing longitudinal cohort conducted in a representative sample of 1600 households in Ifanadiana District, Madagascar. Socio-demographic and health information was collected in combination with dried blood spots for about 6500 individuals of all ages, which were analysed to detect IgG and IgM antibodies against four specific proteins of SARS-CoV2 in bead-based multiplex immunoassay. We evaluated spatio-temporal patterns in COVID-19 infection history and its associations with several geographic, socio-economic and demographic factors via logistic regressions.\n\nResultsEighteen percent of people had been infected by April-June 2021, with seroprevalence increasing with individuals age. COVID-19 primarily spread along the only paved road and in major towns during the first epidemic wave, subsequently spreading along secondary roads during the second wave to more remote areas. Wealthier individuals and those with occupations such as commerce and formal employment were at higher risk of being infected in the first wave. Adult mortality increased in 2020, particularly for older men for whom it nearly doubled up to nearly 40 deaths per 1000. Less than 10% of mortality in this period could be directly attributed to COVID-19 deaths given known infection fatality ratios and observed seroprevalence in the district.\n\nConclusionOur study provides a very granular understanding on COVID-19 transmission and mortality in a rural population of sub-Saharan Africa and suggests that the disease burden in these areas may have been substantially underestimated.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Andres Garchitorena", + "author_inst": "MIVEGEC, Universite de Montpellier, CNRS, IRD, Montpellier, France" + }, + { + "author_name": "Lova T Rasoloharimanana", + "author_inst": "Institut Pasteur de Madagascar, Antananarivo, Madagascar" + }, + { + "author_name": "Rado JL Rakotonanahary", + "author_inst": "NGO Pivot, Ifanadiana, Madagascar" + }, + { + "author_name": "Michelle V Evans", + "author_inst": "MIVEGEC, Universite de Montpellier, CNRS, IRD, Montpellier, France" + }, + { + "author_name": "Ann C Miller", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Karen E Finnegan", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Laura F Cordier", + "author_inst": "NGO Pivot, Ifanadiana, Madagascar" + }, + { + "author_name": "Giovanna Cowley", + "author_inst": "NGO Pivot, Ifanadiana, Madagascar" + }, + { + "author_name": "Benedicte Razafinjato", + "author_inst": "NGO Pivot, Ifanadiana, Madagascar" + }, + { + "author_name": "Marius Randriamanambintsoa", + "author_inst": "Direction de la Demographie et des Statistiques Sociales, Institut National de la Statistique, Antananarivo, Madagascar" + }, + { + "author_name": "Samuel Andrianambinina", + "author_inst": "Direction de la Demographie et des Statistiques Sociales, Institut National de la Statistique, Antananarivo, Madagascar" + }, + { + "author_name": "Stephen Popper", + "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA" + }, + { + "author_name": "Raphael Hotahiene", + "author_inst": "Ministere de la Sante Publique, Antananarivo, Madagascar" + }, + { + "author_name": "Matthew H Bonds", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Matthieu Schoenhals", + "author_inst": "Institut Pasteur de Madagascar, Antananarivo, Madagascar" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.24.23287681", "rel_title": "Syndromic surveillance as a predictive tool for health-related school absences in COVID-19 Sentinel Schools in Catalonia, Spain.", @@ -109235,57 +109767,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.20.23287264", - "rel_title": "Nasopharyngeal Angiotensin Converting Enzyme 2 (ACE2) Expression as a Risk-Factor for SARS-CoV-2 Transmission in Concurrent Hospital Associated Outbreaks", - "rel_date": "2023-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.20.23287264", - "rel_abs": "BackgroundWidespread human-to-human transmission of the severe acute respiratory syndrome coronavirus two (SARS-CoV-2) stems from a strong affinity for the cellular receptor angiotensin converting enzyme two (ACE2). We investigate the relationship between a patients nasopharyngeal ACE2 transcription and secondary transmission within a series of concurrent hospital associated SARS-CoV-2 outbreaks in British Columbia, Canada.\n\nMethodsEpidemiological case data from the outbreak investigations was merged with public health laboratory records and viral lineage calls, from whole genome sequencing, to reconstruct the concurrent outbreaks using infection tracing transmission network analysis. ACE2 transcription and RNA viral load were measured by quantitative real-time polymerase chain reaction. The transmission network was resolved to calculate the number of potential secondary cases. Bivariate and multivariable analyses using Poisson and Negative Binomial regression models was performed to estimate the association between ACE2 transcription the number of SARS-CoV-2 secondary cases.\n\nResultsThe infection tracing transmission network provided n = 76 potential transmission events across n = 103 cases. Bivariate comparisons found that on average ACE2 transcription did not differ between patients and healthcare workers (P = 0.86). High ACE2 transcription was observed in 98.6% of transmission events, either the primary or secondary case had above average ACE2. Multivariable analysis found that the association between ACE2 transcription and the number of secondary transmission events differs between patients and healthcare workers. In health care workers Negative Binomial regression estimated that a one unit change in ACE2 transcription decreases the number of secondary cases (B = -0.132 (95%CI: -0.255 to -0.0181) adjusting for RNA viral load. Conversely, in patients a one unit change in ACE2 transcription increases the number of secondary cases (B = 0.187 (95% CI: 0.0101 to 0.370) adjusting for RNA viral load. Sensitivity analysis found no significant relationship between ACE2 and secondary transmission in health care workers and confirmed the positive association among patients.\n\nConclusionOur study suggests that ACE2 transcription has a positive association with SARS-CoV-2 secondary transmission in admitted inpatients, but not health care workers in concurrent hospital associated outbreaks, and it should be further investigated as a risk-factor for viral transmission.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Aidan M Nikiforuk", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Kevin S Kuchinski", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Katy Short", - "author_inst": "Fraser Health Authority" - }, - { - "author_name": "Susan Roman", - "author_inst": "Fraser Health Authority" - }, - { - "author_name": "Michael A Irvine", - "author_inst": "British Columbia Centre for Disease Control" - }, - { - "author_name": "Natalie Prystajecky", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Agatha N Jassem", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "David M Patrick", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Inna Sekirov", - "author_inst": "The University of British Columbia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.03.20.23287490", "rel_title": "The Change of Screen Time and Screen Addiction, and their Association with Psychological Well-being During the COVID-19 Pandemic: An Analysis of US Country-Wide School-Age Children and Adolescents Between 2018 and 2020", @@ -109569,6 +110050,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.13.23287183", + "rel_title": "Socio-demographic characteristics associated with COVID-19 vaccination uptake in Switzerland: longitudinal analysis of the CoMix study", + "rel_date": "2023-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.13.23287183", + "rel_abs": "BackgroundVaccination is an effective strategy to reduce morbidity and mortality from coronavirus disease 2019 (COVID-19). However, the uptake of COVID-19 vaccination has varied across and within countries. Switzerland has had lower levels of COVID-19 vaccination uptake in the general population than many other high-income countries. Understanding the socio-demographic factors associated with vaccination uptake can help to inform future vaccination strategies to increase uptake.\n\nMethodsWe conducted a longitudinal online survey in the Swiss population, consisting of six survey waves from June to September 2021. Participants provided information on socio-demographic characteristics, history of testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), social contacts, willingness to be vaccinated, and vaccination status. We used a multivariable Poisson regression model to estimate the adjusted rate ratio (aRR) and 95% confidence intervals (CI) of COVID-19 vaccine uptake.\n\nResultsWe recorded 6,758 observations from 1,884 adults. For the regression analysis, we included 3,513 observations from 1,883 participants. By September 2021, 600 (75%) of 806 study participants had received at least one vaccine dose. Participants who were older, male, and students, had a higher educational level, household income, and number of social contacts, and lived in a household with a medically vulnerable person were more likely to have received at least one vaccine dose. Female participants, those who lived in rural areas and smaller households, and people who perceived COVID-19 measures as being too strict were less likely to be vaccinated. We found no significant association between previous SARS-CoV-2 infections and vaccination uptake.\n\nConclusionsOur results suggest that socio-demographic factors as well as individual behaviours and attitudes played an important role in COVID-19 vaccination uptake in Switzerland. Therefore, appropriate communication with the public is needed to ensure that public health interventions are accepted and implemented by the population. Tailored COVID-19 vaccination strategies in Switzerland that aim to improve uptake should target specific subgroups such as women, people from rural areas or people with lower socio-demographic status.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Martina L Reichmuth", + "author_inst": "University Bern" + }, + { + "author_name": "Leonie Heron", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Julien Riou", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Andre Moser", + "author_inst": "CTU Bern, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Anthony Hauser", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Nicola Low", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Christian L Althaus", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.03.19.533338", "rel_title": "Enhanced protective efficacy of a novel, thermostable, RBD-S2 fusion immunogen against SARS-CoV-2 and its variants", @@ -111244,73 +111768,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.16.23287322", - "rel_title": "Serial SARS-CoV-2 antibody titers in vaccinated dialysis patients: prevalence of unrecognized infection and duration of seroresponse", - "rel_date": "2023-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.16.23287322", - "rel_abs": "Rationale & ObjectiveSARS-CoV-2 infections are likely underdiagnosed, but the degree of underdiagnosis among maintenance dialysis patients is unknown. Durability of the immune response after third vaccine doses in this population also remains uncertain. This study tracked antibody levels to 1) assess the rate of undiagnosed infections and 2) characterize seroresponse durability after third doses.\n\nStudy DesignRetrospective observational study\n\nSetting & ParticipantsSARS-CoV-2 vaccinated patients receiving maintenance dialysis through a national dialysis provider. Immunoglobulin G spike antibodies (anti-spike IgG) titers were assessed monthly following vaccination.\n\nExposure(s)Two and three doses of SARS-CoV-2 vaccine\n\nOutcome(s)Undiagnosed and diagnosed SARS-CoV-2 infections; anti-spike IgG titers over time\n\nAnalytical Approach\"Undiagnosed\" SARS-CoV-2 infections were identified as an increase in anti-spike IgG titer of [≥] 100 BAU/mL, not associated with receipt of vaccine or \"diagnosed\" SARS-CoV-2 infection (by PCR or antigen test). In descriptive analyses, anti-spike IgG titers were followed over time.\n\nResultsAmong 2660 patients without prior COVID-19 who received an initial two-dose vaccine series, 371 (76%) SARS-CoV-2 infections were diagnosed and 115 (24%) were undiagnosed. Among 1717 patients without prior COVID-19 who received a third vaccine dose, 155 (80%) SARS-CoV-2 infections were diagnosed and 39 (20%) were undiagnosed. In both cohorts, anti-spike IgG levels declined over time. Of the initial two-dose cohort, 66% had a titer [≥] 500 BAU/mL in the first month, with 23% maintaining a titer [≥] 500 BAU/mL at six months. Of the third dose cohort, 95% had a titer [≥] 500 BAU/mL in the first month after the third dose, with 76% maintaining a titer [≥] 500 BAU/mL at six months.\n\nLimitationsAssays used had upper limits.\n\nConclusionsAmong maintenance dialysis patients, 20-24% of SARS-CoV-2 infections were undiagnosed. Given this populations vulnerability to COVID-19, ongoing infection control measures are needed. A three-dose primary mRNA vaccine series optimizes seroresponse rate and durability.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Caroline M Hsu", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Daniel E Weiner", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Harold J Manley", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Dana Miskulin", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Vladimir Ladik", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Jill Frament", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Christos Argyropoulos", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Kenneth Abreo", - "author_inst": "Louisiana State University, Health Sciences Center" - }, - { - "author_name": "Andrew Chin", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Reginald Gladish", - "author_inst": "Nephrology of North Alabama" - }, - { - "author_name": "Loay Salman", - "author_inst": "Albany Medical College" - }, - { - "author_name": "Doug Johnson", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Eduardo K Lacson Jr.", - "author_inst": "Dialysis Clinic Inc" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2023.03.16.23287360", "rel_title": "Relative vaccine effectiveness (rVE) of mRNA COVID-19 boosters in the UK vaccination programme, during the Spring-Summer (monovalent vaccine) and Autumn-Winter 2022 (bivalent vaccine) booster campaigns: a prospective test negative case-control study", @@ -111754,6 +112211,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2023.03.17.533105", + "rel_title": "Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples", + "rel_date": "2023-03-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.17.533105", + "rel_abs": "Oxford Nanopore Technologies (ONT) allows direct sequencing of ribonucleic acids (RNA) and, in addition, detection of possible RNA modifications due to deviations from the expected ONT signal. The software available so far for this purpose can only detect a small number of modifications. Alternatively, two samples can be compared for different RNA modifications. We present Magnipore, a novel tool to search for significant signal shifts between samples of Oxford Nanopore data from similar or related species. Magnipore classifies them into mutations and potential modifications. We use Magnipore to compare SARS-CoV-2 samples. Included were representatives of the early 2020s Pango lineages (n=6), samples from Pango lineages B.1.1.7 (n=2, Alpha), B.1.617.2 (n=1, Delta), and B.1.529 (n=7, Omicron). Magnipore utilizes position-wise Gaussian distribution models and a comprehensible significance threshold to find differential signals. In the case of Alpha and Delta, Magnipore identifies 55 detected mutations and 15 sites that hint at differential modifications. We predicted potential virus-variant and variant-group-specific differential modifications. Magnipore contributes to advancing RNA modification analysis in the context of viruses and virus variants.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jannes Spangenberg", + "author_inst": "Friedrich Schiller University Jena" + }, + { + "author_name": "Christian Honer zu Siederdissen", + "author_inst": "Friedrich Schiller University Jena" + }, + { + "author_name": "Milena Zarkovic", + "author_inst": "Friedrich Schiller University Jena" + }, + { + "author_name": "Sandra Triebel", + "author_inst": "Friedrich Schiller University Jena" + }, + { + "author_name": "Ruben Rose", + "author_inst": "Christian-Albrechts-Universitat zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel" + }, + { + "author_name": "Christina Verena Martinez Christophersen", + "author_inst": "Labor Dr. Krause und Kollegen MVZ GmbH" + }, + { + "author_name": "Lea Paltzow", + "author_inst": "Labor Dr. Krause & Kollegen MVZ GmbH" + }, + { + "author_name": "Mohsen Mahmoud Hegab", + "author_inst": "Labor Dr. Krause und Kollegen MVZ GmbH" + }, + { + "author_name": "Anna Nora Wansorra", + "author_inst": "Labor Dr. Krause & Kollegen MVZ GmbH" + }, + { + "author_name": "Akash Srivastava", + "author_inst": "Friedrich Schiller University Jena" + }, + { + "author_name": "Andi Krumbholz", + "author_inst": "Christian-Albrechts-Universitat zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel" + }, + { + "author_name": "Manja Marz", + "author_inst": "Friedrich Schiller University Jena" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.03.14.23287246", "rel_title": "Longitudinal SARS-CoV-2 neutralization of Omicron BA.1, BA.5 and BQ.1.1 after four vaccinations and the impact of break-through infections in hemodialysis patients", @@ -113190,73 +113710,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2023.03.12.23287049", - "rel_title": "The cost of primary care consultations associated with long COVID in non-hospitalised patients: a retrospective cohort study using UK primary care data", - "rel_date": "2023-03-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.12.23287049", - "rel_abs": "ObjectivesTo assess incremental costs of primary care consultations associated with post-Covid-19 condition or long COVID, to estimate associated national costs for the United Kingdom population, and to assess risk factors associated with increased costs.\n\nDesignA retrospective cohort study using a propensity score matching approach with an incremental cost method to estimate primary care consultation costs associated with long COVID.\n\nSettingUK based primary care general practitioner (GP), nurse and physiotherapist consultation data from the Clinical Practice Research Datalink Aurum primary care database from 31st January 2020 to 15th April 2021.\n\nParticipants472,173 non-hospitalised adults with confirmed SARS-CoV-2 infection were 1:1 propensity score matched to a pool of eligible patients with the same index date, the same number of prior consultations, and similar background characteristics, but without a record of COVID-19. Patients diagnosed with Long COVID (3,871) and those with World Health Organisation (WHO) defined symptoms of long COVID (30,174) formed two subgroups within the cohort with confirmed SARS-CoV-2 infection.\n\nMain outcome measuresCosts were calculated using a bottom-up costing approach with consultation cost per working hour in pound sterling ({pound}) obtained from the Personal Social Services Research Units Unit Costs of Health and Social Care 2021. The average incremental cost in comparison to patients with no record of COVID-19 was produced for each patient group, considering only consultation costs at least 12 weeks from the SARS-CoV-2 infection date or matched date for the comparator group (from 15th April 2020 to 15th April 2021). A sensitivity analysis was undertaken which restricted the study population to only those who had at least 24 weeks of follow-up. National costs were estimated by extrapolating incremental costs to the cumulative incidence of COVID-19 in the UK Office for National Statistics COVID-19 Infection Survey. The impacts of risk factors on the cost of consultations beyond 12 weeks from SARS-CoV-2 infection were assessed using an econometric ordinary least squares (OLS) regression model, where coefficients were interpreted as the percentage change in cost due to a unit increase in the specific factor.\n\nResultsThe incremental cost of primary care consultations potentially associated with long COVID was {pound}2.44 per patient with COVID-19 per year. This increased to {pound}5.72 in the sensitivity analysis. Extrapolating this to the UK population produced a cost estimate of {pound}23,382,452 (90% credible interval: {pound}21,378,567 to {pound}25,526,052) or {pound}54,814,601 (90% credible interval: {pound}50,116,967 to {pound}59,839,762) in the sensitivity analysis. Among patients with COVID-19 infection, a long COVID diagnosis and longer-term reporting of symptoms were associated with a 43% and 44% increase in primary care consultation costs respectively, compared to patients without long COVID symptoms. Older age (49% relative increase in costs in those aged 80 years or older compared to those aged 18 to 29 years), female sex (4% relative increase in costs compared to males), obesity (4% relative increase in costs compared to those of normal weight), comorbidities and the number of prior consultations were all associated with an increase in the cost of primary care consultations. By contrast, those from black ethnic groups had a 6% reduced relative cost compared to those from white ethnic groups.\n\nConclusionsThe costs of primary care consultations associated with long COVID in non-hospitalised adults are substantial. Costs are significantly higher among those diagnosed with long COVID, those with long COVID symptoms, older adults, females, and those with obesity and comorbidities.\n\nWhat is already known on this topic?O_LILong COVID is a global public health challenge, with millions of people affected worldwide.\nC_LIO_LIPeople with a history of long COVID use health services, including primary care, at a higher rate than uninfected individuals even beyond the period of acute infection.\nC_LIO_LIThe cost of this increased healthcare use is unknown, impeding planning and forecasting of resource requirements needed to adequately support people with long COVID.\nC_LI\n\nWhat this study adds?O_LIBeyond 12 weeks from acute infection, non-hospitalised adults with a history of SARS-CoV-2 infection cost primary care services an additional {pound}2.44 per patient per year greater on average than patients with no prior evidence of infection.\nC_LIO_LIDue to the high incidence of COVID-19, this represents a substantial cost to primary care services, in the UK exceeding {pound}20 million for consultations associated with long COVID.\nC_LIO_LIThese incremental costs are greater in those with a formal diagnosis of long COVID, those reporting related symptoms, older adults, females, and those with obesity.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jake Tufts", - "author_inst": "University Hospitals of Morecambe Bay NHS Foundation Trust, Lancashire, UK" - }, - { - "author_name": "Dawit T Zemedikun", - "author_inst": "School of Population and Global Health (M431), The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia" - }, - { - "author_name": "Anuradhaa Subramanian", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Naijie Guan", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Krishna Gokhale", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Puja Myles", - "author_inst": "Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London" - }, - { - "author_name": "Tim Williams", - "author_inst": "Clinical Practice Research Datalink, Medicines and Healthcare products Regulatory Agency, London" - }, - { - "author_name": "Tom Marshall", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Melanie Calvert", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK; Birmingham Health Partners Centre for Regulatory Science and Innovati" - }, - { - "author_name": "Karen Matthews", - "author_inst": "Long Covid SOS, Charity registered in England & Wales, 11A Westland Road, Faringdon, Oxfordshire, UK" - }, - { - "author_name": "Krishnarajah Nirantharakumar", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Louise Jackson", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - }, - { - "author_name": "Shamil Haroon", - "author_inst": "Institute of Applied Health Research, University of Birmingham, Edgbaston, Birmingham, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2023.03.11.23287138", "rel_title": "How long is the long COVID? a retrospective analysis of football players in two major European Championships.", @@ -113528,6 +113981,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.03.14.532352", + "rel_title": "Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru", + "rel_date": "2023-03-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.14.532352", + "rel_abs": "Genomic surveillance in response to coronavirus disease (COVID-19) pandemic is crucial for tracking spread, identify variants of concern (VoCs) and understand the evolution of its etiological agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). India has experienced three waves of COVID-19 cases, which includes a deadly wave of COVID-19 that was driven by the Delta lineages (second/Delta wave) followed by another wave driven by the Omicron lineages (third/Omicron wave). These waves were particularly dramatic in the metropolitan cities due to high population density. We evaluated the prevalence, and mutational spectrum of SARS-CoV-2 variants/lineages in one such megapolis, Bengaluru city, across these three waves between October 2020 and June 2022. 15,134 SARS-CoV-2 samples were subjected to whole genome sequencing (WGS). Phylogenetic analysis revealed, SARS-CoV-2 variants in Bengaluru city belonged to 18 clades and 196 distinct lineages. As expected, the Delta lineages were the most dominant lineages during the second wave of COVID-19. The Omicron lineage BA.2 and its sublineages accounted for most of the COVID-19 cases in the third wave. Most number of amino acid changes were observed in spike protein. Among the 18 clades, majority of the mutations and least similarity at nucleotide sequence level with the reference genome were observed in Omicron clades.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Darshan S", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Vinay Kumar", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Kandasamy Kathirvel", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Rakesh Netha Vadnala", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Sachin Mishra", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Bhagyashree Shelar", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Srilatha Marate", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Lakshminarayanan CP", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Sai Disha K", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Manisha Bhardwaj", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Awadhesh Pandit", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Satyajit Mayor", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + }, + { + "author_name": "Uma Ramakrishnan", + "author_inst": "National Centre for Biological Sciences, TIFR" + }, + { + "author_name": "Dimple Notani", + "author_inst": "National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore-560065, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2023.03.10.23286644", "rel_title": "Pulmonary sequelae at six months in children with SARS-CoV-2 infection: A Single-Centre Study", @@ -114724,33 +115248,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.09.23287043", - "rel_title": "Integrated analyses of single-cell RNA-seq public data reveal the gene regulatory network landscape of respiratory epithelial and peripheral immune cells in COVID-19 patients", - "rel_date": "2023-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.09.23287043", - "rel_abs": "IntroductionInfection with SARS-CoV-2 leads to coronavirus disease 2019 (COVID-19), which can result in acute respiratory distress syndrome and multiple organ failure. However, its comprehensive influence on pathological immune responses in the respiratory epithelium and peripheral immune cells is not yet fully understood.\n\nMethodsIn this study, we integrated multiple public scRNA-seq datasets of nasopharyngeal swab and peripheral blood results to investigate the gene regulatory networks (GRNs) of healthy individuals and COVID-19 patients with mild/moderate and severe disease, respectively. Similar and dissimilar regulons were identified within or between epithelial and immune cells during COVID-19 severity progression. The relative transcription factors (TFs) and their targets were used to construct GRNs among different infection sites and conditions.\n\nResultsBetween respiratory epithelial and peripheral immune cells, different TFs tended to be used to regulate the activity of a cell between healthy individuals and COVID-19 patients, although they had some TFs in common. For example, XBP1, FOS, STAT1, and STAT2 were activated in both the epithelial and immune cells of virus-infected individuals. In contrast, severe COVID-19 cases exhibited activation of CEBPD in peripheral immune cells, while CEBPB was exclusively activated in respiratory epithelial cells. Moreover, in patients with severe COVID-19, CEBPD upregulated S100A8 and S100A9 in CD14 and CD16 monocytes, while S100A9 genes were co-upregulated by different regulators (SPEDEF and ELF3) in goblet and squamous cells. The cell-cell communication analysis suggested that epidermal growth factor receptor signaling among epithelial cells contributes to mild/moderate disease, and chemokine signaling among immune cells contributes to severe disease.\n\nConclusionsThis study identified cell type- and condition-specific regulons in a wide range of cell types from the initial infection site to the peripheral blood, and clarified the diverse mechanisms of maladaptive responses to SARS-CoV-2 infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lin Zhang", - "author_inst": "Tohoku University" - }, - { - "author_name": "Hafumi Nishi", - "author_inst": "Tohoku University; Ochanomizu University" - }, - { - "author_name": "Kengo Kinoshita", - "author_inst": "Tohoku University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.09.23287034", "rel_title": "Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 subvariant predominance: a systematic literature review", @@ -115030,6 +115527,413 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.03.09.23287038", + "rel_title": "Clinical Characteristics, Racial Inequities, and Outcomes in Patients with Breast Cancer and COVID-19: A COVID-19 and Cancer Consortium (CCC19) Cohort Study", + "rel_date": "2023-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.09.23287038", + "rel_abs": "BackgroundLimited information is available for patients with breast cancer (BC) and coronavirus disease 2019 (COVID-19), especially among underrepresented racial/ethnic populations.\n\nMethodsThis is a COVID-19 and Cancer Consortium (CCC19) registry-based retrospective cohort study of females with active or history of BC and laboratory-confirmed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection diagnosed between March 2020 and June 2021 in the US. Primary outcome was COVID-19 severity measured on a five-level ordinal scale, including none of the following complications, hospitalization, intensive care unit admission, mechanical ventilation, and all-cause mortality. Multivariable ordinal logistic regression model identified characteristics associated with COVID-19 severity.\n\nResults1,383 female patient records with BC and COVID-19 were included in the analysis, the median age was 61 years, and median follow-up was 90 days. Multivariable analysis revealed higher odds of COVID-19 severity for older age (aOR per decade, 1.48 [95% CI, 1.32 - 1.67]); Black patients (aOR 1.74; 95 CI 1.24-2.45), Asian Americans and Pacific Islander patients (aOR 3.40; 95 CI 1.70 - 6.79) and Other (aOR 2.97; 95 CI 1.71-5.17) racial/ethnic groups; worse ECOG performance status (ECOG PS [≥]2: aOR, 7.78 [95% CI, 4.83 - 12.5]); pre-existing cardiovascular (aOR, 2.26 [95% CI, 1.63 - 3.15])/pulmonary comorbidities (aOR, 1.65 [95% CI, 1.20 - 2.29]); diabetes mellitus (aOR, 2.25 [95% CI, 1.66 - 3.04]); and active and progressing cancer (aOR, 12.5 [95% CI, 6.89 - 22.6]). Hispanic ethnicity, timing and type of anti-cancer therapy modalities were not significantly associated with worse COVID-19 outcomes. The total all-cause mortality and hospitalization rate for the entire cohort was 9% and 37%, respectively however, it varied according to the BC disease status.\n\nConclusionsUsing one of the largest registries on cancer and COVID-19, we identified patient and BC related factors associated with worse COVID-19 outcomes. After adjusting for baseline characteristics, underrepresented racial/ethnic patients experienced worse outcomes compared to Non-Hispanic White patients.\n\nFundingThis study was partly supported by National Cancer Institute grant number P30 CA068485 to Tianyi Sun, Sanjay Mishra, Benjamin French, Jeremy L. Warner; P30-CA046592 to Christopher R. Friese; P30 CA023100 for Rana R McKay; P30-CA054174 for Pankil K. Shah and Dimpy P. Shah; and the American Cancer Society and Hope Foundation for Cancer Research (MRSG-16-152-01-CCE) and P30-CA054174 for Dimpy P. Shah. REDCap is developed and supported by Vanderbilt Institute for Clinical and Translational Research grant support (UL1 TR000445 from NCATS/NIH). The funding sources had no role in the writing of the manuscript or the decision to submit it for publication.\n\nClinical Trial NumberCCC19 registry is registered on ClinicalTrials.gov, NCT04354701.", + "rel_num_authors": 98, + "rel_authors": [ + { + "author_name": "Gayathri Nagaraj", + "author_inst": "Loma Linda University" + }, + { + "author_name": "- COVID-19 and Cancer Consortium", + "author_inst": "-" + }, + { + "author_name": "Shaveta Vinayak", + "author_inst": "Fred Hutchinson Cancer Center/University of Washington" + }, + { + "author_name": "Ali Raza Khaki", + "author_inst": "Stanford University" + }, + { + "author_name": "Tianyi Sun", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Nicole M. Kuderer", + "author_inst": "Advanced Cancer Research Group and University of Washington" + }, + { + "author_name": "David M. Aboulafia", + "author_inst": "Virginia Mason Cancer Institute" + }, + { + "author_name": "Jared D. Acoba", + "author_inst": "University of Hawaii Cancer Center" + }, + { + "author_name": "Joy Awosika", + "author_inst": "University of Cincinnati Cancer Center" + }, + { + "author_name": "Ziad Bakouny", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Nicole B. Balmaceda", + "author_inst": "The University of Kansas Cancer Center" + }, + { + "author_name": "Ting Bao", + "author_inst": "Memorial Sloan-Kettering Cancer Center" + }, + { + "author_name": "Babar Bashir", + "author_inst": "Sidney Kimmel Cancer Center at Thomas Jefferson University" + }, + { + "author_name": "Stephanie Berg", + "author_inst": "Loyola University Medical Center" + }, + { + "author_name": "Mehmet A. Bilen", + "author_inst": "Winship Cancer Institute of Emory University" + }, + { + "author_name": "Poorva Bindal", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Sibel Blau", + "author_inst": "Northwest Medical Specialties" + }, + { + "author_name": "Brianne E. Bodin", + "author_inst": "Herbert Irving Comprehensive Cancer Center at Columbia University" + }, + { + "author_name": "Hala T. Borno", + "author_inst": "UCSF Helen Diller Family Comprehensive Cancer Center at the University of California at San Francisco" + }, + { + "author_name": "Cecilia Castellano", + "author_inst": "Winship Cancer Institute of Emory University" + }, + { + "author_name": "Horyun Choi", + "author_inst": "University of Hawaii Cancer Center" + }, + { + "author_name": "John Deeken", + "author_inst": "Inova Schar Cancer Institute" + }, + { + "author_name": "Aakash Desai", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Natasha Edwin", + "author_inst": "ThedaCare Cancer Care" + }, + { + "author_name": "Lawrence E. Feldman", + "author_inst": "University of Illinois Hospital & Health Sciences System" + }, + { + "author_name": "Daniel B. Flora", + "author_inst": "St. Elizabeth Healthcare" + }, + { + "author_name": "Christopher R. Friese", + "author_inst": "University of Michigan Rogel Cancer Center" + }, + { + "author_name": "Matthew D. Galsky", + "author_inst": "Tisch Cancer Institute at the Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Cyndi Gonzalez Gomez", + "author_inst": "University of Michigan Rogel Cancer Center" + }, + { + "author_name": "Petros Grivas", + "author_inst": "Fred Hutchinson Cancer Center/University of Washington" + }, + { + "author_name": "Shilpa Gupta", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Marcy Haynam", + "author_inst": "The Ohio State University Comprehensive Cancer Center" + }, + { + "author_name": "Hannah Heilman", + "author_inst": "University of Cincinnati Cancer Center" + }, + { + "author_name": "Dawn L. Hershman", + "author_inst": "Herbert Irving Comprehensive Cancer Center at Columbia University" + }, + { + "author_name": "Clara Hwang", + "author_inst": "Henry Ford Cancer Institute, Henry Ford Hospital" + }, + { + "author_name": "Chinmay Jani", + "author_inst": "Mount Auburn Hospital" + }, + { + "author_name": "Sachin R. Jhawar", + "author_inst": "Ohio State University Comprehensive Cancer Center" + }, + { + "author_name": "Monika Joshi", + "author_inst": "Penn State Health St. Joseph Cancer Center" + }, + { + "author_name": "Virginia Kaklamani", + "author_inst": "Mays Cancer Center at UT Health San Antonio MD Anderson Cancer Center" + }, + { + "author_name": "Elizabeth J. Klein", + "author_inst": "Brown University and Lifespan Cancer Institute" + }, + { + "author_name": "Natalie Knox", + "author_inst": "Stritch School of Medicine at Loyola University" + }, + { + "author_name": "Vadim S. Koshkin", + "author_inst": "UCSF Helen Diller Family Comprehensive Cancer Center at the University of California at San Francisco" + }, + { + "author_name": "Amit A. Kulkarni", + "author_inst": "Masonic Cancer Center at the University of Minnesota" + }, + { + "author_name": "Daniel H. Kwon", + "author_inst": "UCSF Helen Diller Family Comprehensive Cancer Center at the University of California at San Francisco" + }, + { + "author_name": "Chris Labaki", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Philip E. Lammers", + "author_inst": "Baptist Cancer Center" + }, + { + "author_name": "Kate I. Lathrop", + "author_inst": "Mays Cancer Center at UT Health San Antonio MD Anderson Cancer Center" + }, + { + "author_name": "Mark A. Lewis", + "author_inst": "Intermountain Health Care" + }, + { + "author_name": "Xuanyi Li", + "author_inst": "Vanderbilt-Ingram Cancer Center at Vanderbilt University Medical Center" + }, + { + "author_name": "Gilbert de Lima Lopes", + "author_inst": "Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine" + }, + { + "author_name": "Gary H. Lyman", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Della F. Makower", + "author_inst": "Albert Einstein College of Medicine, Montefiore Medical Center" + }, + { + "author_name": "Abdul-Hai Mansoor", + "author_inst": "Kaiser Permanente Northwest" + }, + { + "author_name": "Merry-Jennifer Markham", + "author_inst": "University of Florida Division of Hematology and Oncology, UF Health Cancer Center" + }, + { + "author_name": "Sandeep H. Mashru", + "author_inst": "Kaiser Permanente Northwest" + }, + { + "author_name": "Rana R. McKay", + "author_inst": "Moores Cancer Center, University of California, San Diego" + }, + { + "author_name": "Ian Messing", + "author_inst": "Division of Radiation Oncology, George Washington University" + }, + { + "author_name": "Vasil Mico", + "author_inst": "Sidney Kimmel Cancer Center at Thomas Jefferson University" + }, + { + "author_name": "Rajani Nadkarni", + "author_inst": "Hartford HealthCare Cancer Institute" + }, + { + "author_name": "Swathi Namburi", + "author_inst": "Northwest Medical Specialties" + }, + { + "author_name": "Ryan H. Nguyen", + "author_inst": "University of Illinois Hospital & Health Sciences System" + }, + { + "author_name": "Taylor Kristian Nonato", + "author_inst": "Moores Cancer Center, University of California, San Diego" + }, + { + "author_name": "Tracey Lynn O'Connor", + "author_inst": "Roswell Park Comprehensive Cancer Center" + }, + { + "author_name": "Orestis Panagiotou", + "author_inst": "Brown University and Lifespan Cancer Institute" + }, + { + "author_name": "Kyu Park", + "author_inst": "Loma Linda University Cancer Center" + }, + { + "author_name": "Jaymin M. Patel", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Kanishka GopikaBimal Patel", + "author_inst": "UC Davis Comprehensive Cancer Center at the University of California at Davis" + }, + { + "author_name": "Jeffrey Peppercorn", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Hyma Polimera", + "author_inst": "Penn State Health St. Joseph Cancer Center" + }, + { + "author_name": "Matthew Puc", + "author_inst": "Virtua Health" + }, + { + "author_name": "Yuan James Rao", + "author_inst": "Division of Radiation Oncology, George Washington University" + }, + { + "author_name": "Pedram Razavi", + "author_inst": "Moores Cancer Center, University of California, San Diego" + }, + { + "author_name": "Sonya A. Reid", + "author_inst": "Vanderbilt-Ingram Cancer Center at Vanderbilt University Medical Center" + }, + { + "author_name": "Jonathan W. Riess", + "author_inst": "UC Davis Comprehensive Cancer Center at the University of California at Davis" + }, + { + "author_name": "Donna R. Rivera", + "author_inst": "Division of Cancer Control and Population Sciences, National Cancer Institute" + }, + { + "author_name": "Mark Robson", + "author_inst": "Memorial Sloan-Kettering Cancer Center" + }, + { + "author_name": "Suzanne J. Rose", + "author_inst": "Carl & Dorothy Bennett Cancer Center at Stamford Hospital" + }, + { + "author_name": "Atlantis D. Russ", + "author_inst": "University of Florida Division of Hematology and Oncology, UF Health Cancer Center" + }, + { + "author_name": "Lidia Schapira", + "author_inst": "Stanford Cancer Institute at Stanford University" + }, + { + "author_name": "Pankil K. Shah", + "author_inst": "Mays Cancer Center at UT Health San Antonio MD Anderson Cancer Center" + }, + { + "author_name": "M. Kelly Shanahan", + "author_inst": "METAvivor" + }, + { + "author_name": "Lauren C. Shapiro", + "author_inst": "Albert Einstein College of Medicine, Montefiore Medical Center" + }, + { + "author_name": "Melissa Smits", + "author_inst": "ThedaCare Cancer Care" + }, + { + "author_name": "Daniel G. Stover", + "author_inst": "Ohio State University Comprehensive Cancer Center, Division of Medical Oncology" + }, + { + "author_name": "Mitrianna Streckfuss", + "author_inst": "Aurora Cancer Care, Advocate Aurora Health" + }, + { + "author_name": "Lisa Tachiki", + "author_inst": "Fred Hutchinson/University of Washington Cancer Consortium" + }, + { + "author_name": "Michael A. Thompson", + "author_inst": "Aurora Cancer Care, Advocate Aurora Health" + }, + { + "author_name": "Sara M. Tolaney", + "author_inst": "Dana Farber Cancer Institute" + }, + { + "author_name": "Lisa B. Weissmann", + "author_inst": "Mount Auburn Hospital" + }, + { + "author_name": "Grace Wilson", + "author_inst": "Masonic Cancer Center at the University of Minnesota" + }, + { + "author_name": "Michael T. Wotman", + "author_inst": "Tisch Cancer Institute at the Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Elizabeth M. Wulff-Burchfield", + "author_inst": "The University of Kansas Cancer Center" + }, + { + "author_name": "Sanjay Mishra", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Benjamin French", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Jeremy L. Warner", + "author_inst": "Vanderbilt-Ingram Cancer Center" + }, + { + "author_name": "Maryam B. Lustberg", + "author_inst": "Yale Cancer Center at Yale University School of Medicine" + }, + { + "author_name": "Melissa K. Accordino", + "author_inst": "Herbert Irving Comprehensive Cancer Center at Columbia University" + }, + { + "author_name": "Dimpy Shah", + "author_inst": "University of Texas Health Science Center at San Antonio" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2023.03.01.23286637", "rel_title": "Assessment of the Performance of Expired and Unexpired BinaxNOW COVID Rapid Antigen Test Kits Using Positive and Negative Controls", @@ -116038,165 +116942,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.06.23286834", - "rel_title": "SARS-CoV-2 viral replication persists in the human lung for several weeks after onset of symptomatic severe COVID-19 and is associated with attenuated pulmonary immunity and variant-specific clinical sequalae", - "rel_date": "2023-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.06.23286834", - "rel_abs": "RationaleIn the upper respiratory tract replicating (culturable) SARS-CoV-2 is recoverable for [~] 4 to 8 days after symptom onset, however, there is paucity of data about the frequency or duration of replicating virus in the lower respiratory tract (i.e. the human lung).\n\nObjectivesWe undertook lung tissue sampling (needle biopsy), shortly after death, in 42 mechanically ventilated decedents during the Beta and Delta waves. An independent group of 18 ambulatory patents served as a control group.\n\nMethodsLung biopsy cores from decedents underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling and immunohistochemistry.\n\nResults38% (16/42) of mechanically ventilated decedents had culturable virus in the lung for a median of 15 days (persisting for up to 4 weeks) after symptom onset. Lung viral culture positivity was not associated with comorbidities or steroid use. Delta but not Beta variant lung culture positivity was associated with accelerated death and secondary bacterial infection (p<0.05). Nasopharyngeal culture was negative in 23.1% (6/26) of decedents despite lung culture positivity. This, hitherto, undescribed bio-phenotype of lung-specific persisting viral replication was associated with an enhanced transcriptomic pulmonary pro-inflammatory response but with concurrent viral culture positivity.\n\nConclusionsConcurrent, rather than sequential active viral replication continues to drive a heightened pro-inflammatory response in the human lung beyond the second week of illness and was associated with variant-specific increased mortality and morbidity. These findings have potential implications for the design of interventional strategies and clinical management of patients with severe COVID-19 disease.\n\nAt a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSInvestigations to understand SARS-CoV-2 viral shedding (determined by PCR or antigen testing) have extensively focused on samples from the upper respiratory tract. The widely accepted view is that acute severe SARS-CoV-2 infection is characterised by a viral replicative phase in the first week of symptomatic illness followed by a pro-inflammatory immunopathologic phase peaking in the second and third weeks of illness. However, it remains unclear whether detection of SARS-CoV-2 beyond 2 weeks after symptom onset in published studies represent active replication competent virus because it may represent residual genomic or antigenic material in the tissue.\n\nWhat This Study Adds to the FieldWe have identified a, hitherto, undescribed bio-phenotype of acute severe COVID-19 characterised by persisting viral replication in the lung for up to 4 weeks after symptom onset. [~]40% of acute severe COVID-19 intensive care unit (ICU) decedents (n=42) had nasopharyngeal swab culture positivity at [~]2 weeks post-symptom onset versus only [~]5% in a group of ambulatory control patients (n=18). There was compartment-specific (nasopharynx versus lung) discordance. The phenotype of lung-specific persisting viral replication was associated with variant-specific accelerated death, an exaggerated inflammatory response, and attenuated T-cell immunity in the lung (based on histopathological and transcriptomic studies). This challenges the traditional view that viral replication occurs during the first 5 to 10 days of illness, which is followed by an effector or hyperinflammatory phase. This is the first study, to our knowledge, to systematically culture virus from the human lung and map out its related clinical determinants, and which describes the human lung transcriptomic profile of culture-positive versus culture-negative patients with severe COVID-19 disease.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Michele Tomasicchio", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Shameem Jaumdally", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Lindsay Wilson", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Andrea Kotze", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Lynn Semple", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Stuart Meier", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Anil Pooran", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Aliasgar Esmail", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Komala Pillay", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Riyaadh Roberts", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Raymond Kriel", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Richard Meldau", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Suzette Oelofse", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Carley Mandviwala", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Jessica Burns", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Rolanda Londt", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Malika Davids", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Charnay van der Merwe", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Aqeedah Roomaney", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Louie Kuhn", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Tahlia Perumal", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Alex Scott", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Martin Hale", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Vicky Baillie", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Sana Mahtab", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Rageema Joseph", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Ivan Joubert", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Jenna Piercy", - "author_inst": "University of Cape Town" - }, - { - "author_name": "David Thomson", - "author_inst": "University of Cape Town" - }, - { - "author_name": "David Fredericks", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Malcolm Miller", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Marta Nunes", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Shabir Madhi", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Keertan Dheda", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.06.531252", "rel_title": "Unraveling the Interactions between Human DPP4 Receptor, SARS-CoV-2 Variants, and MERS-CoV, converged for Pulmonary Disorders Integrating through Immunoinformatics and Molecular Dynamics", @@ -116424,6 +117169,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.03.07.23286910", + "rel_title": "Giving a voice to adults with COVID-19: An analysis of open-ended comments from smell longhaulers and non-longhaulers", + "rel_date": "2023-03-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.07.23286910", + "rel_abs": "Smell disorders are commonly reported with COVID-19 infection. Some patients show prolonged smell-related issues, even after the respiratory symptoms are resolved. To explore the concerns of patients, and to provide an overview for each specific smell disorder, we explored the longitudinal survey that was conducted by 1, and contained self-reports on the changes of smell that participants experienced at two time points. People who still suffered from smell disorders at the second time point, hence named longhaulers, were compared to those who were not, hence named non-longhaulers. Specifically, three aims were pursued in this study. First, to classify smell disorders based on the participants self-reports. Second, to classify the sentiment of each self-report using a machine learning approach, and third, to find specific keywords that best describe the smell dysfunction in those self-reports. We found that the prevalence of parosmia and hyposmia was higher in longhaulers than in non-longhaulers. Furthermore, the results suggest that longhaulers stated self-reports with more negative sentiment than non-longhaulers. Finally, we found specific keywords that were more typical for either longhaulers compared to non-longhaulers. Taken together, our work shows consistent findings with previous studies, while at the same time, provides new insights for future studies investigating smell disorders.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Nick S. Menger", + "author_inst": "Eberhard Karls University of Tubingen" + }, + { + "author_name": "Arnaud Tognetti", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Michael C. Farruggia", + "author_inst": "Yale University, Interdepartmental Neuroscience Program" + }, + { + "author_name": "Carla Mucignat", + "author_inst": "University of Padova" + }, + { + "author_name": "Surabhi Bhutani", + "author_inst": "School of Exercise and Nutritonal Sciences, San Diego State University" + }, + { + "author_name": "Keiland W. Cooper", + "author_inst": "Department of Neurobiology and Behavior, University of California, Irvine" + }, + { + "author_name": "Paloma Rohlfs Dominguez", + "author_inst": "University of Basque Country. Dept. of Developmental and Educational Psychology" + }, + { + "author_name": "Thomas Heinbockel", + "author_inst": "Howard University College of Medicine, Department of Anatomy" + }, + { + "author_name": "Vonnie Shields", + "author_inst": "Biological Sciences Department, Fisher College of Science and Mathematics, Towson University" + }, + { + "author_name": "Anna D'Errico", + "author_inst": "Freelance science Writer- former at Goethe University Frankfurt" + }, + { + "author_name": "Veronica Pereda-Loth", + "author_inst": "Laboratoire EVOLSAN, Universite Toulouse III, France" + }, + { + "author_name": "Denis Pierron", + "author_inst": "Laboratoire EVOLSAN, Universite Toulouse III, France" + }, + { + "author_name": "Sachiko Koyama", + "author_inst": "Indiana University, School of Medicine, Department of Medicine" + }, + { + "author_name": "Ilja Croijmans", + "author_inst": "Radboud University, Language and Communication Department" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2023.02.26.23286474", "rel_title": "Improving the representativeness of UKs national COVID-19 Infection Survey through spatio-temporal regression and post-stratification", @@ -117944,41 +118760,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.02.23286561", - "rel_title": "Bivalent booster effectiveness against severe COVID-19 outcomes in Finland, September 2022 - January 2023", - "rel_date": "2023-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.02.23286561", - "rel_abs": "Bivalent COVID-19 vaccines were introduced in 2022 but knowledge of their effectiveness against severe COVID-19 outcomes is currently limited. In Finnish register-based cohort analyses, we compared the risk of severe COVID-19 outcomes among those who received bivalent vaccination (exposed) between September 2022 and March 2023 to those who did not (unexposed). Among elderly aged 65-110 years, bivalent vaccination reduced the risk of hospitalisation and death due to COVID-19 in September-December 2022; the hazard ratios comparing exposed and unexposed ranged from 0.37 to 0.45 during the first 31-60 days since bivalent vaccination. However, in January-March 2023 the effect disappeared possibly indicating immune evasion of new SARS-CoV-2 variants, waning of vaccine effectiveness and increased presence of hybrid immunity. Among the chronically ill aged 18-64 years bivalent vaccination did not reduce the risk of severe COVID-19 outcomes. These results are important for developing COVID-19 vaccines and programmes worldwide.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Eero Poukka", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Hanna Nohynek", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Sirkka Goebeler", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Tuija Leino", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Ulrike Baum", - "author_inst": "Finnish Institute for Health and Welfare" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.02.23286686", "rel_title": "Impact of COVID-19 pandemic on the etiology and characteristics of community-acquired pneumonia among children requiring bronchoalveolar lavage in northern China", @@ -118274,6 +119055,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.01.23286616", + "rel_title": "Virological evidence of the impact of non-pharmaceutical interventions against COVID-19 in a resource-limited setting", + "rel_date": "2023-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.01.23286616", + "rel_abs": "Ecuador was an early COVID-19 hotspot with substantial COVID-19-mortality. In developed countries, low socioeconomic status is associated with COVID-19 infection and low compliance with non-pharmaceutical interventions (NPIs). However, if NPI were successful in resource-limited settings with high human mobility and informal labour is still unclear. We performed a retrospective observational molecular and serological study of Ecuadors reference laboratory. We tested 1,950 respiratory samples from COVID-19 surveillance for SARS-CoV-2 and 12 respiratory viruses using RT-PCR, characterized 642 SARS-CoV-2 genomes, and examined SARS-CoV-2 seroprevalence in 1,967 samples from patients with fever in Ecuadors reference laboratory during 2020-2021. Molecular and serological data were compared to NPI stringency in Bayesian, maximum-likelihood and modelling frameworks.\n\nSARS-CoV-2 (Pearson correlation test; r=-0.74; p=0.01) and other respiratory viruses (r=-0.68; p=0.02) detection correlated negatively with NPI stringency. SARS-CoV-2 seroprevalence increased from <1% during February-March 2020 to 50% within 6 weeks and plateaued after NPI implementation. Decrease of effective reproduction number <1 and antibody reactivity over time suggested intense SARS-CoV-2 transmission during pandemic onset, subsequently limited by NPIs. Phylogeographic analyses revealed that travel restrictions were implemented late not preventing 100 near-parallel SARS-CoV-2 introductions, and implementation of NPIs modified SARS-CoV-2 geographic spread by restricting recreational activity. NPIs stringency correlated negatively with the number of circulating SARS-CoV-2 lineages (r=-0.69; p=0.02). Virological evidence supports NPIs restricting human movement as an effective public health tool to control the spread of respiratory pathogens in resource-limited settings, providing a template for emerging SARS-CoV-2 variants and future epidemics.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Andres Moreira-Soto", + "author_inst": "Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Virology, Berlin, Germany." + }, + { + "author_name": "Alfredo Bruno", + "author_inst": "Instituto Nacional de Investigacion en Salud Publica, Guayaquil, Ecuador" + }, + { + "author_name": "Domenica de Mora", + "author_inst": "Instituto Nacional de Investigacion en Salud Publica, Guayaquil, Ecuador" + }, + { + "author_name": "Michelle Paez", + "author_inst": "Instituto Nacional de Investigacion en Salud Publica, Guayaquil, Ecuador" + }, + { + "author_name": "Jimmy Garcez", + "author_inst": "Instituto Nacional de Investigacion en Salud Publica, Guayaquil, Ecuador" + }, + { + "author_name": "Ben Wulf", + "author_inst": "Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Virology, Berlin, Germany." + }, + { + "author_name": "Anna-Lena Sander", + "author_inst": "Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Virology, Berlin, Germany." + }, + { + "author_name": "Maritza Olmedo", + "author_inst": "Instituto Nacional de Investigacion en Salud Publica, Guayaquil, Ecuador" + }, + { + "author_name": "Maria Jose Basantes Mantilla", + "author_inst": "Instituto Nacional de Investigacion en Salud Publica, Guayaquil, Ecuador" + }, + { + "author_name": "Manuel Gonzalez", + "author_inst": "Instituto Nacional de Investigacion en Salud Publica, Guayaquil, Ecuador" + }, + { + "author_name": "Alberto Orlando Narvaez", + "author_inst": "Instituto Nacional de Investigacion en Salud Publica, Guayaquil, Ecuador" + }, + { + "author_name": "Silvia Paola Salgado Cisneros", + "author_inst": "Instituto Nacional de Investigacion en Salud Publica, Guayaquil, Ecuador" + }, + { + "author_name": "Juan Carlos Zevallos", + "author_inst": "Health Science Faculty, Universidad Espiritu Santo, Guayaquil, Ecuador (UEES)" + }, + { + "author_name": "Jan Drexler", + "author_inst": "Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Virology, Berlin, Germany." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.03.530798", "rel_title": "The infectivity of SARS-CoV-2 progeny virions requires the activity of host cell N-myristoyltransferases and it is severely compromised by their inhibition", @@ -119682,33 +120534,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2023.02.28.530489", - "rel_title": "Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers : Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants", - "rel_date": "2023-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.28.530489", - "rel_abs": "The evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity, conformational plasticity, protein stability and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined conformational dynamics of the spike trimers that agrees with the recent functional studies, suggesting that BA.2.75 trimers are the most stable among these variants. A systematic mutational scanning of the inter-protomer interfaces in the spike trimers revealed a group of conserved structural stability hotspots that play a key role in modulation of functional dynamics and are also involved in the inter-protomer couplings through local contacts and interaction networks with the Omicron mutational sites. The results of mutational scanning provided evidence that BA.2.75 trimers are more stable than BA.2 and comparable in stability to BA.1 variant. Using dynamic network modeling of the S Omicron BA.1, BA.2 and BA.2.75 trimers we showed that the key network positions driving long-range signaling are associated with the major stability hotspots that are inter-connected along potential communication pathways, while sites of Omicron mutations may often correspond to weak spots of stability and allostery but are coupled to the major stability hotspots through interaction networks. The presented analysis of the BA.1, BA.2 and BA.2.75 trimers suggested that thermodynamic stability of BA.1 and BA.2.75 variants may be intimately linked with the residue interaction network organization that allows for a broad ensemble of allosteric communications in which signaling between structural stability hotspots may be modulated by the Omicron mutational sites. The findings provided plausible rationale for mechanisms in which Omicron mutations can evolve to balance thermodynamic stability and conformational adaptability in order to ensure proper tradeoff between stability, binding and immune escape.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Gennady Verkhivker", - "author_inst": "Chapman University School of Pharmacy" - }, - { - "author_name": "Mohammed Alshahrani", - "author_inst": "Chapman University" - }, - { - "author_name": "Grace Gupta", - "author_inst": "Chapman Unversity" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2023.02.26.23286261", "rel_title": "SARS-CoV-2 post-vaccine surveillance studies in Australian children and adults with cancer: SerOzNET Statistical Analysis Plan", @@ -120092,6 +120917,49 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.02.28.530444", + "rel_title": "SARS-CoV-2 surveillance between 2020 and 2021 of all mammalian species in two Flemish zoos (Antwerp Zoo and Planckendael Zoo)", + "rel_date": "2023-02-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.28.530444", + "rel_abs": "The COVID-19 pandemic has led to millions of human infections and deaths worldwide. Several other mammal species are also susceptible to SARS-CoV-2, and multiple instances of transmission from humans to pets, farmed mink, wildlife and zoo animals have been recorded. We conducted a systematic surveillance of SARS-CoV-2 in all mammal species in two zoos in Belgium between September and December 2020 and July 2021 in four sessions, and a targeted surveillance of selected mammal enclosures following SARS-CoV-2 infection in hippos in December 2021. A total of 1523 faecal samples were tested for SARS-CoV-2 via real-time PCR. None of the samples tested positive for SARS-CoV-2. Additional surrogate virus neutralization tests conducted on 50 routinely collected serum samples during the same period were all negative. This study is a first to our knowledge to conduct active SARS-CoV-2 surveillance for several months in all mammal species of a zoo. We conclude that at the time of our investigation, none of the screened animals were excreting SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Lea Joffrin", + "author_inst": "Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Tine Cooreman", + "author_inst": "Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Erik Verheyen", + "author_inst": "OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium ; Evolutionary Ecology Group, Department of Biology, University of Ant" + }, + { + "author_name": "Francis Vercammen", + "author_inst": "Centre for Research and Conservation, Antwerp Zoo Society, Antwerp, Belgium" + }, + { + "author_name": "Joachim Marien", + "author_inst": "Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Herwig Leirs", + "author_inst": "Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Sophie Gryseels", + "author_inst": "Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Scienc" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2023.02.26.530067", "rel_title": "Genomic perspectives of SARS CoV-2 in liver disease patients with its clinical correlation: A single centre retrospective study", @@ -121468,25 +122336,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.02.15.23285880", - "rel_title": "Has the COVID-19 pandemic ended or not? opinions from the public in the U.S.", - "rel_date": "2023-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.15.23285880", - "rel_abs": "Recently President Joe Biden announced the end to the COVID-19 pandemic in the US but some scientists expressed different opinions. This study aimed to examine the view of the end of the COVID-19 pandemic among the public. Data were collected in September 2022 from an online crowdsourcing platform, and respondents answered if they believed that the pandemic has ended in the United States or not. Logistic regressions were used to estimate the likelihood of agreeing on the end of the pandemic, adjusted by demographics and several related variables. Among 2983 respondents, 78.1% believed that the COVID-19 pandemic had ended, and the percentage decreased to 66.5% after adding weights. Males, younger adults, Hispanics, those with higher levels of educational attainment, those with middle levels of household income, those living in suburban or rural areas, and those living in states that voted for the Republican party in the 2020 Presidential Election were more likely to believe that the pandemic had ended, compared with their counterparts. With about one-third of Americans did not agree that the pandemic had ended and marked demographical and geographical differences, the timing and the way of the pandemic end announcement should be deliberately cautious.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Yong Yang", - "author_inst": "University of Memphis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.16.23286009", "rel_title": "Vaccine-induced correlate of protection against fatal COVID-19 in the old and frail during waves of neutralization resistant variants of concern.", @@ -121994,6 +122843,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2023.02.16.23285979", + "rel_title": "Characteristics and Outcomes of Multisystem Inflammatory Syndrome in Children: A Multicenter, Retrospective, Observational Cohort Study in Mexico", + "rel_date": "2023-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.16.23285979", + "rel_abs": "Multisystem inflammatory syndrome in children temporally associated with coronavirus disease 2019 (MIS-C), a novel hyperinflammatory condition secondary to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, is associated with severe outcomes such as coronary artery aneurysm and death. This multicenter, retrospective, observational cohort study including eight centers in Mexico, aimed to describe the clinical characteristics and outcomes of patients with MIS-C. Patient data were evaluated using latent class analysis to categorize patients into three phenotypes: toxic shock syndrome-like (TSSL)-MIS-C, Kawasaki disease-like (KDL)-MIS-C, and nonspecific MIS-C (NS-MIS-C). Risk factors for adverse outcomes were estimated using multilevel mixed-effects logistic regression. The study included 239 patients with MIS-C, including 61 (26%), 70 (29%), and 108 (45%) patients in the TSSL-MIS-C, KDL-MIS-C, and NS-MIS-C groups, respectively. Fifty-four percent of the patients were admitted to the intensive care unit, and 42%, 78%, and 41% received intravenous immunoglobulin, systemic glucocorticoids, and anticoagulants, respectively. Coronary artery dilatation and aneurysm were found in 5.7% and 13.2% of the patients, respectively. The rate of mortality due to SARS-CoV-2-related factors was 4.6%. Delay of [≥]10 days in hospital admission was associated with coronary artery aneurysm or dilatation (odds ratio [OR] 1.6, 95% confidence interval [CI] 1.2-2.0). Age [≥] 10 years (OR 5.6, 95% CI 1.4-2.04), severe underlying condition (OR 9.3, 95% CI 2.8-31.0), platelet count < 150,000/mm3 (OR 4.2, 95% CI 1.2-14.7), international normalized ratio > 1.2 at admission (OR 3.8, 95% CI 1.05-13.9), and serum ferritin concentration > 1500 mg/dL (OR 52, 95% CI 5.9-463) were risk factors for death.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Nadia Gonzalez-Garcia", + "author_inst": "Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico" + }, + { + "author_name": "Marco Antonio Yamazaki-Nakashimada", + "author_inst": "National Institute of Pediatrics (Mexico), Mexico City, Mexico" + }, + { + "author_name": "Horacio Marquez-Gonzalez", + "author_inst": "Hospital Infantil de Mexico Federico Gomez" + }, + { + "author_name": "Guadalupe Miranda-Novales", + "author_inst": "Analysis and Synthesis of Evidence Research Unit, XXI Century National Medical Center, Mexican Social Security Institute, Mexico City, Mexico" + }, + { + "author_name": "Gonzalo Antonio Neme Diaz", + "author_inst": "Hospital del Nino Dr. Rodolfo Nieto Padron, Villahermosa, Mexico" + }, + { + "author_name": "Sandhi Anel Prado Duran", + "author_inst": "HGZ No 15, Mexican Social Security Institutte, Tamaulipas, Mexico" + }, + { + "author_name": "Antonio Luevanos Velazquez", + "author_inst": "Antiguo Hospital Civil de Guadalajara Fray Antonio Alcalde, Guadalajara, Mexico" + }, + { + "author_name": "MARIA FERNANDA CASTILLA PEON", + "author_inst": "HOSPITAL INFANTIL DE MEXICO FEDERICO GOMEZ" + }, + { + "author_name": "Miguel Alejandro Sanchez Duran", + "author_inst": "National Institute of Pediatrics (Mexico), Mexico City, Mexico" + }, + { + "author_name": "Martha Patricia Marquez Aguirre", + "author_inst": "National Institute of Pediatrics (Mexico), Mexico City, Mexico" + }, + { + "author_name": "Miguel Angel Villasis-Keever", + "author_inst": "Analysis and Synthesis of Evidence Research Unit, XXI Century National Medical Center" + }, + { + "author_name": "Ranferi Aragon Nogales", + "author_inst": "XXI Century National Medical Center, Mexican Social Security Institute, Mexico City, Mexico" + }, + { + "author_name": "Carlos Nunez Enriquez", + "author_inst": "XXI Century National Medical Center, Mexican Social Security Institute, Mexico City, Mexico" + }, + { + "author_name": "Maria Elena Martinez Bustamante", + "author_inst": "Department of Pediatric Infectious Diseases, Centro Medico Nacional 20 de Noviembre (CMN), Mexico City, Mexico" + }, + { + "author_name": "Lourdes Anais Palacios Cantu", + "author_inst": "HGR No 270, Mexican Social Security Institute, Tamaulipas, Mexico" + }, + { + "author_name": "Jesus Membrila Mondragon", + "author_inst": "HGR No 270, Mexican Social Security Institute, Tamaulipas, Mexico" + }, + { + "author_name": "Paloma Vizcarra Alvarado", + "author_inst": "Antiguo Hospital Civil de Guadalajara Fray Antonio Alcalde, Guadalajara, Mexico" + }, + { + "author_name": "Rodolfo Norberto Jimenez Juarez", + "author_inst": "Federico Gomez Children's Hospital Mexico City, Mexico" + }, + { + "author_name": "Victor Olivar Lopez", + "author_inst": "Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico" + }, + { + "author_name": "Adrian Lopez Chavez", + "author_inst": "Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico" + }, + { + "author_name": "Alejandra Perez Barrera", + "author_inst": "Hospital del Nino Dr. Rodolfo Nieto Padron, Villahermosa, Mexico" + }, + { + "author_name": "Carlos Aguilar Arguello", + "author_inst": "Hospital del Nino Dr. Rodolfo Nieto Padron, Villahermosa, Mexico" + }, + { + "author_name": "Jesus Ramirez de los Santos", + "author_inst": "Department of Infectious Diseases, Hospital del Nino Dr. Rodolfo Nieto Padron, Villahermosa, Mexico" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2023.02.23.529497", "rel_title": "Analysis of the SARS-CoV-2 spike protein revealed that blocked receptor-binding domain antigenicity decreases the production of neutralizing antibodies in vivo", @@ -123234,65 +124190,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.02.21.23286181", - "rel_title": "Associations between SARS-CoV-2 infection and incidence of new chronic condition diagnoses: a systematic review", - "rel_date": "2023-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.21.23286181", - "rel_abs": "Because of the large number of infected individuals, an estimate of the future burdens of the long-term consequences of SARS-CoV-2 infection is needed. This systematic review examined associations between SARS-CoV-2 infection and incidence of categories of and selected chronic conditions, by age and severity of infection (inpatient vs. outpatient/mixed care). MEDLINE and EMBASE were searched (Jan 1, 2020 to Oct 4, 2022) and reference lists scanned. We included observational studies from high-income OECD countries with a control group adjusting for sex and comorbidities. Identified records underwent a two-stage screening process. Two reviewers screened 50% of titles/abstracts, after which DistillerAI acted as second reviewer. Two reviewers then screened the full texts of stage one selections. One reviewer extracted data and assessed risk of bias; results were verified by another. Random-effects meta-analysis estimated pooled hazard ratios (HR). GRADE assessed certainty of the evidence. Twenty-five studies were included. Among the outpatient/mixed SARS-CoV-2 care group, there is high certainty of a small-to-moderate increase (i.e., HR 1.26 to 1.99) among adults [≥]65 years of any cardiovascular condition, and of little-to-no difference (i.e., HR 0.75 to 1.25) in anxiety disorders for individuals <18, 18-64, and [≥]65 years old. Among 18-64 and [≥]65 year-olds receiving outpatient/mixed care there are probably (moderate certainty) large increases (i.e., HR [≥]2.0) in encephalopathy, interstitial lung disease, and respiratory failure. After SARS-CoV-2 infection, there is probably an increased risk of diagnoses for some chronic conditions; whether the magnitude of risk will remain stable into the future is uncertain.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Lindsay A. Gaudet", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jennifer Pillay", - "author_inst": "University of Alberta" - }, - { - "author_name": "Sabrina Saba", - "author_inst": "University of Alberta" - }, - { - "author_name": "Dianne Zakaria", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Nicholas Cheta", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "H\u00e9l\u00e8ne Gardiner", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Larry Shaver", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Jacqueline Middleton", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Maria Tan", - "author_inst": "University of Alberta" - }, - { - "author_name": "Ben Vandermeer", - "author_inst": "University of Alberta" - }, - { - "author_name": "Lisa Hartling", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.14.23285860", "rel_title": "REAL-WORLD EFFECTIVENESS OF NIRMATRELVIR/RITONAVIR ON COVID-19-ASSOCIATED HOSPITALIZATION PREVENTION: A POPULATION-BASED COHORT STUDY IN THE PROVINCE OF QUEBEC, CANADA", @@ -123460,6 +124357,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, + { + "rel_doi": "10.1101/2023.02.13.23285848", + "rel_title": "Intrinsic and effective severity of COVID-19 cases infected with the ancestral strain and Omicron BA.2 variant in Hong Kong", + "rel_date": "2023-02-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.13.23285848", + "rel_abs": "BackgroundUnderstanding severity of infections with SARS-CoV-2 and its variants is crucial to inform public health measures. Here we used COVID-19 patient data from Hong Kong to characterise the severity profile of COVID-19 and to examine factors associated with fatality of infection.\n\nMethodsTime-varying and age-specific effective severity measured by case-hospitalization risk and hospitalization risk was estimated with all individual COVID-19 case data collected in Hong Kong from 23 January 2020 through to 26 October 2022 over six epidemic waves, in comparison with estimates of influenza A(H1N1)pdm09 during the 2009 pandemic. The intrinsic severity of Omicron BA.2 was compared with the estimate for the ancestral strain with the data from unvaccinated patients without previous infections. Factors potentially associated with the fatality risk of hospitalized Omicron patients were also examined.\n\nResultsWith 32,222 COVID-19 hospitalizations and 9,669 deaths confirmed over 6 epidemic waves in Hong Kong, the time-varying hospitalization fatality risk dramatically increased from below 10% before the largest fifth wave of Omicron BA.2, to 41% during the peak of the fifth wave when hospital resources were severely constrained. The age-specific fatality risk in unvaccinated hospitalized Omicron cases was comparable to the estimates for unvaccinated cases with the ancestral strain. During epidemics predominated by Omicron BA.2, the highest fatality risk was amongst unvaccinated patients aged [≥]80 years and the risk was inversely associated with the number of vaccination doses received.\n\nConclusionsOmicron has comparable intrinsic severity to the ancestral Wuhan strain although the effective severity is substantially lower in Omicron cases due to vaccination. With a moderate-to-high coverage of vaccination, hospitalized COVID-19 patients caused by Omicron subvariants appeared to have similar age-specific risks of fatality to patients hospitalized with influenza A(H1N1)pdm09.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jessica Y. Wong", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Justin K. Cheung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Yun Lin", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Helen S. Bond", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Eric H. Y. Lau", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Dennis K. M. Ip", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Benjamin J. Cowling", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Peng Wu", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.13.23285859", "rel_title": "Poor sleep quality, insomnia, and short sleep duration before infection predict long-term symptoms after COVID-19", @@ -124800,69 +125744,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.02.17.23286083", - "rel_title": "Prevalence of anti-SARS-CoV-2 antibodies in people attending the two main Goma markets in the eastern Democratic Republic of Congo", - "rel_date": "2023-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286083", - "rel_abs": "According to official data, the Democratic Republic of the Congo (DRC) has a low prevalence of the coronavirus disease 19 (COVID-19) pandemic. The goal of this cross-sectional study was to determine the COVID-19 seroprevalence in people attending Gomas two largest markets, Kituku and Virunga. This study was conducted between September and November 2021, overlapping by one month with another similar study carried out in a slum of Bukavu, and using the same methodology.\n\nCOVID-19 unvaccinated participants (n = 796 including 454 vendors and 342 customers, 60% of whom were women) were surveyed. The median age of vendors and customers was 34.2 and 30.1 years, respectively.\n\nThe crude and adjusted anti-SARS-CoV-2 antibody seroprevalence rates were 70.2% (95 % CI 66.9-73.4%) and 98.8% (95% CI 94.1-100%), respectively, with no difference between vendors and customers. COVID-19 symptoms were mild or absent in 58.9% and 41.1% of participants with anti-SARS-CoV-2 antibodies respectively. COVID-19 did not require hospitalisation for any of the seropositive participants.\n\nThese findings are consistent with those reported in Bukavu. They confirm that SARS-CoV-2 spread without causing severe symptoms in densely populated settlements and markets, and suggest that many COVID-19 cases went unreported. Based on these results, relevance of an untargeted hypothetical vaccination programme in these communities should be questioned.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Prudence Ndeba Mitangala", - "author_inst": "Universite Catholique de Bukavu, Bukavu, Sud Kivu, Democratic Republic of Congo and Universite Officielle de Ruwenzori, Butembo, Nord Kivu, Democratic Republic" - }, - { - "author_name": "Leonid Mwana Wa Bene Irenge", - "author_inst": "Center for Applied Molecular Technologies (CTMA) Universite catholique de Louvain (UCLouvain) Avenue Hippocrate 54-B1.54.01, 1200 Woluwe-Saint-Lambert, Belgium " - }, - { - "author_name": "Edgar Tsongo Musubao", - "author_inst": "Institut de Techniques Medicales, Goma, Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Jean Bosco Mbeva Kahindo", - "author_inst": "Universite Officielle de Ruwenzori, Butembo, Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Patrick Ndeba Ayonga", - "author_inst": "Departement des maladies infectieuses et tropicales, Universite de Bordeaux, France" - }, - { - "author_name": "Israel Kyembwa Safari", - "author_inst": "Inspection provinciale de la sante du Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Janvier Bonane Kubuya", - "author_inst": "Division provinciale de la sante du Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Edmon Namegabe Ntabe", - "author_inst": "Universite libre des pays des grands lacs, Goma Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Raphael Kakongo Senga Kabangwa", - "author_inst": "Laboratoire Provincial Ami Labo Nord Kivu , Democratic Republic of Congo" - }, - { - "author_name": "Guy Ndongala Mutombo", - "author_inst": "Division provinciale de la sante du Nord Kivu, Democratic Republic of Congo" - }, - { - "author_name": "Jerome Ambroise", - "author_inst": "Center for Applied Molecular Technologies, Universite catholique de Louvain (UCLouvain) Avenue Hippocrate 54/B1.54.01, 1200 Woluwe-Saint-Lambert, Belgium" - }, - { - "author_name": "JEAN-LUC GALA", - "author_inst": "Center for Applied Molecular Technologies, Universite catholique de Louvain (UCLouvain) Avenue Hippocrate 54/B1.54.01, 1200 Woluwe-Saint-Lambert, Belgium" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.16.23286061", "rel_title": "How well do we do social distancing?", @@ -125050,6 +125931,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.02.16.528881", + "rel_title": "Evaluation of SARS-CoV-2 isolation in cell culture from nasal/nasopharyngeal swabs or saliva specimens of patients with COVID-19", + "rel_date": "2023-02-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.16.528881", + "rel_abs": "It has been revealed that SARS-CoV-2 can be efficiently isolated from clinical specimens such as nasal/nasopharyngeal swabs or saliva in cultured cells. In this study, we examined the efficiency of viral isolation including SARS-CoV-2 mutant strains between nasal/nasopharyngeal swab or saliva specimens. Furthermore, we also examined the comparison of viral isolation rates by sample species using simulated specimens for COVID- 19. As a result, it was found that the isolation efficiency of SARS-CoV-2 in the saliva specimens was significantly lower than that in the nasal/nasopharyngeal swab specimens. In order to determine which component of saliva is responsible for the lower isolation rate of saliva specimens, we tested the abilities of lactoferrin, amylase, cathelicidin, and mucin, which are considered to be abundant in saliva, to inhibit the infection of SARS-CoV-2 pseudotyped viruses (SARS-CoV-2pv). Lactoferrin and amylase were found to inhibit SARS-CoV-2pv infection. In conclusion, even if the same number of viral genome copies was detected by the real-time RT-PCR test, infection of SARS-CoV-2 present in saliva is thought to be inhibited by inhibitory factors such as lactoferrin and amylase, compared to nasal/nasopharyngeal swab specimens.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Shunsuke Yazawa", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Emiko Yamazaki", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Yumiko Saga", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Masae Itamochi", + "author_inst": "Toyama Insitute of Health" + }, + { + "author_name": "Noriko Inasaki", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Takahisa Shimada", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Kazunori Oishi", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Hideki Tani", + "author_inst": "Toyama Institute of Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.02.14.23285831", "rel_title": "Vaccine waning and immune escape drive the second surge of Omicron spread in Hong Kong: A modeling study", @@ -126850,65 +127778,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.02.13.528349", - "rel_title": "Propylene glycol inactivates respiratory viruses and prevents airborne transmission", - "rel_date": "2023-02-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.13.528349", - "rel_abs": "Viruses are vulnerable as they transmit between hosts and we aimed to exploit this critical window. We found that the ubiquitous, safe, inexpensive and biodegradable small molecule propylene glycol (PG) has robust virucidal activity. Propylene glycol rapidly inactivates influenza, SARS-CoV-2 and a broad range of other enveloped viruses, and reduces disease burden in mice when administered intranasally at concentrations commonly found in nasal sprays. Most critically, aerosolized PG efficiently abolishes influenza and SARS-CoV-2 infectivity within airborne droplets, potently preventing infection at levels significantly below those well-tolerated by mammals. We present PG vapor as a first-in-class non-toxic airborne virucide, to prevent transmission of existing and emergent viral pathogens, with clear and immediate implications for public health.\n\nOne-sentence summaryPropylene glycol is a potent and safe virucidal compound that could be used to limit and control infections.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christine T Styles", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Imperial College London" - }, - { - "author_name": "Katie E Flight", - "author_inst": "University College London" - }, - { - "author_name": "Jonathan C Brown", - "author_inst": "Imperial College London" - }, - { - "author_name": "Michael Vanden Oever", - "author_inst": "Imperial College London" - }, - { - "author_name": "Thomas P Peacock", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ziyin Wang", - "author_inst": "Imperial College London" - }, - { - "author_name": "Rosie Millns", - "author_inst": "Imperial College London" - }, - { - "author_name": "Wendy S Barclay", - "author_inst": "Imperial College London" - }, - { - "author_name": "John S Tregoning", - "author_inst": "Imperial College London" - }, - { - "author_name": "Rachel S Edgar", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.02.13.528235", "rel_title": "P-Selectin promotes SARS-CoV-2 interactions with platelets and the endothelium", @@ -127172,6 +128041,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.10.23285776", + "rel_title": "Quantifying the rate and magnitude of the Omicron outbreak in China after sudden exit from 'zero-COVID' restrictions", + "rel_date": "2023-02-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.10.23285776", + "rel_abs": "In late 2022, China transitioned from a strict zero-COVID policy to rapidly abandoning nearly all interventions and data reporting. This raised great concern about the presumably-rapid but undisclosed spread of the SARS-CoV-2 Omicron variant in a very large population of very low pre-existing immunity. A quantitative understanding of the epidemic dynamics of COVID-19 during this period is urgently needed. Here, by modeling a combination of case count and survey data, we show that Omicron spread extremely fast, at a rate of 0.42/day (95% CrI: [0.35, 0.51]/day) after the full exit from zero-COVID policies on Dec. 7, 2022. Consequently, we estimate that the vast majority of the population (97%, 95% CrI [95%, 99%]) was infected during December, with the nation-wide epidemic peaking on Dec. 23. Overall, our results highlight the extremely high transmissibility of the variant and the importance of proper design of intervention exit strategies to avoid large infection waves.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Emma E. Goldberg", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Qianying Lin", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ethan Obie Romero-Severson", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ruian Ke", + "author_inst": "Los Alamos National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.09.23285740", "rel_title": "Impact of the COVID-19 pandemic on tuberculosis control in Indonesia: a nationwide analysis of programme data and health system vulnerabilities", @@ -128428,61 +129328,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.02.08.23285645", - "rel_title": "Mental health, gender, and care-seeking behavior during the COVID-19 pandemic in Sweden: An exploratory study", - "rel_date": "2023-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285645", - "rel_abs": "ObjectiveTo explore the prevalence of care-seeking avoidance behavior in relation to gender and to describe the effect of (and potential interaction between) gender and care-seeking on mental health during the COVID-19 pandemic in Sweden.\n\nMethodsWe performed a cross-sectional study among 27,562 participants of the Omtanke2020 Study, using data collected at three time points concerning sociodemographic factors, mental health symptoms, and care-seeking behavior. Network analysis and prevalence ratios calculated from modified Poisson regressions were used to explore the relationship between gender, care-seeking behavior, and mental health symptoms (depression, anxiety, and COVID-19-related distress).\n\nResultsIn our study, women reported a higher prevalence of mental health symptoms and avoidance of care-seeking due to COVID-19, compared to men. At baseline and six months thereafter, female gender was positively associated with COVID-19-related distress and previous mental health diagnosis. At 12 months after baseline, female gender was positively associated with anxiety and avoidance of care-seeking for mental health. However, previous mental health diagnosis and care avoidance were more strongly associated with a higher prevalence of mental health symptoms among men, compared to women.\n\nConclusionThis study highlights gender differences in mental health outcomes and care-seeking behavior during the COVID-19 pandemic in Sweden.\n\nFundingThis work was supported with grants from Nordforsk (COVIDMENT, 105668 and 138929).", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Katalin Vincze", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Gillian Murphy", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Mary Barker", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Juan Gonz\u00e1lez-Hij\u00f3n", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Anna K K\u00e4hler", - "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Emma M Frans", - "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden" - }, - { - "author_name": "Patrick F Sullivan", - "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden; Department of Psychiatry, University of North Carolina, Chapel Hill," - }, - { - "author_name": "Unnur A Valdimarsd\u00f3ttir", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Center of Public Health Sciences, University of" - }, - { - "author_name": "Fang Fang", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Anik\u00f3 Lovik", - "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Unit of Methodology and Statistics, Department " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.02.08.23285589", "rel_title": "Clinical severity prediction of COVID-19 admitted patients in Spain: SEMI and REDISSEC cohorts", @@ -128830,6 +129675,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.08.23285658", + "rel_title": "Benefits of near-universal vaccination and treatment access to manage COVID-19 burden in the United States", + "rel_date": "2023-02-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285658", + "rel_abs": "BackgroundAs we enter the fourth year of the COVID-19 pandemic, SARS-CoV-2 infections still cause high morbidity and mortality in the United States. During 2020-2022, COVID-19 was one of the leading causes of death in the United States and by far the leading cause among infectious diseases. Vaccination uptake remains low despite this being an effective burden reducing intervention. The development of COVID-19 therapeutics provides hope for mitigating severe clinical outcomes. This modeling study examines combined strategies of vaccination and treatment to reduce the burden of COVID-19 epidemics over the next decade.\n\nMethodsWe use a validated mathematical model to evaluate the reduction of incident cases, hospitalized cases, and deaths in the United States through 2033 under various levels of vaccination and treatment coverage. We assume that future seasonal transmission patterns for COVID-19 will be similar to those of influenza virus. We account for the waning of infection-induced immunity and vaccine-induced immunity in a future with stable COVID-19 dynamics. Due to uncertainty in the duration of immunity following vaccination or infection, we consider two exponentially-distributed waning rates, with means of 365 days (one year) and 548 days (1.5 years). We also consider treatment failure, including rebound frequency, as a possible treatment outcome.\n\nResultsAs expected, universal vaccination is projected to eliminate transmission and mortality. Under current treatment coverage (13.7%) and vaccination coverage (49%), averages of 89,000 annual deaths (548-day waning) and 120,000 annual deaths (365-day waning) are expected by the end of this decade. Annual mortality in the United States can be reduced below 50,000 per year with >81% annual vaccination coverage, and below 10,000 annual deaths with >84% annual vaccination coverage. Universal treatment reduces hospitalizations by 88% and deaths by 93% under current vaccination coverage. A reduction in vaccination coverage requires a comparatively larger increase in treatment coverage in order for hospitalization and mortality levels to remain unchanged.\n\nConclusionsAdopting universal vaccination and universal treatment goals in the United States will likely lead to a COVID-19 mortality burden below 50,000 deaths per year, a burden comparable to that of influenza virus.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fuhan Yang", + "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University" + }, + { + "author_name": "Thu Nguyen-Anh Tran", + "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University" + }, + { + "author_name": "Emilly Howerton", + "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University" + }, + { + "author_name": "Maciej F Boni", + "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University" + }, + { + "author_name": "Joseph L Servadio", + "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.09.23285515", "rel_title": "Epidemiological analysis of the gender-age structure of hospitalized patients with COVID-19 and their mortality in 2020-2021.", @@ -130210,33 +131090,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.02.08.23285651", - "rel_title": "Individual costs and societal benefits of interventions during the COVID-19 pandemic", - "rel_date": "2023-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285651", - "rel_abs": "Individual and societal reactions to an ongoing pandemic can lead to social dilemmas: In some cases, each individual is tempted to not follow an intervention, but for the whole society it would be best if they did. Now that in most countries the extent of regulations to reduce SARS-CoV-2 transmission is very small, interventions are driven by individual decision-making. Assuming that individuals act in their best own interest, we propose a framework in which this situation can be quantified, depending on the protection the intervention provides to a user and to others, the risk of getting infected, and the costs of the intervention. We discuss when a tension between individual and societal benefits arises and which parameter comparisons are important to distinguish between different regimes of intervention use.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Arne Traulsen", - "author_inst": "MPI Evolutionary Biology" - }, - { - "author_name": "Simon A Levin", - "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University" - }, - { - "author_name": "Chadi M Saad-Roy", - "author_inst": "University of California Berkeley, Berkeley" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.02.23285352", "rel_title": "Safety, Virology, Pharmacokinetics, and Clinical Experience of High-dose Intravenous Sotrovimab for the Treatment of Mild to Moderate COVID-19: An Open-label Clinical Trial", @@ -130640,6 +131493,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.02.06.527330", + "rel_title": "Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers", + "rel_date": "2023-02-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.06.527330", + "rel_abs": "Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. We characterized antibody binding and functionality in convalescent plasma from postpartum women and their infants infected with SARS-CoV-2 from a vaccine-naive prospective cohort in Nairobi, Kenya. Antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels were significantly higher in infants than in mothers. Plasma antibodies from mothers and infants bound to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants displayed higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants had significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, neutralization titers between infants and mothers were similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody repertoires and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Caitlin I Stoddard", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Kevin Sung", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Zak A Yaffe", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Haidyn Weight", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Guillaume Beaudoin-Bussieres", + "author_inst": "CRCHUM" + }, + { + "author_name": "Jared G Galloway", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Soren Gantt", + "author_inst": "University of Montreal" + }, + { + "author_name": "Judith Adhiambo", + "author_inst": "University of Nairobi" + }, + { + "author_name": "Emily R Begnel", + "author_inst": "University of Washington" + }, + { + "author_name": "Ednah Ojee", + "author_inst": "University of Nairobi" + }, + { + "author_name": "Jennifer Slyker", + "author_inst": "University of Washington" + }, + { + "author_name": "Dalton Wamalwa", + "author_inst": "University of Nairobi" + }, + { + "author_name": "John Kinuthia", + "author_inst": "University of Washington" + }, + { + "author_name": "Andres Finzi", + "author_inst": "Universite de Montreal" + }, + { + "author_name": "Frederick A Matsen IV", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Dara A Lehman", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Julie Overbaugh", + "author_inst": "Fred Hutchinson Cancer Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.02.06.527382", "rel_title": "A COVID-19 DNA Vaccine Candidate Elicits Broadly Neutralizing Antibodies Against Multiple SARS-CoV-2 Variants Including the Currently Circulating Omicron BF.5, BF.7, BQ.1 and XBB", @@ -131904,29 +132840,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.02.03.526970", - "rel_title": "Epidemic patterns of emerging variants with dynamical social distancing", - "rel_date": "2023-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.03.526970", - "rel_abs": "Motivated by the emergence of new variants during the COVID-19 pandemic, we consider an epidemiological model of disease transmission dynamics, where novel strains appear by mutations of the virus. In the considered scenarios, disease prevalence in the population is modulated by social distancing. We study the various patterns that are generated under different assumptions of cross-immunity. If recovery from a given strain provides immunity against all previous strains, but not against more novel strains, then we observe a very regular sequential pattern of strain replacement where newer strains predominate over older strains. However, if protection upon recovery holds only against that particular strain and none of the others, we find much more complicated dynamics with potential recurrence of earlier strains, and co-circulation of various strains. We compare the observed patterns with genomic analysis we have seen during the COVID-19 pandemic.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Golsa Sayyar", - "author_inst": "University of Szeged" - }, - { - "author_name": "Gergely Rost", - "author_inst": "University of Szeged" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2023.02.02.526749", "rel_title": "Investigations on SARS-CoV-2 and other coronaviruses in mink farms in France at the end of the first year of COVID-19 pandemic", @@ -132186,6 +133099,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2023.01.30.23285220", + "rel_title": "Development of a mobile laboratory system in hydrogen fuel cell buses and evaluation of the performance for COVID-19", + "rel_date": "2023-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.30.23285220", + "rel_abs": "IntroductionWe newly designed and developed two types of hydrogen fuel cell (HFC) buses (motorcoach type and minibus type) with a mobile laboratory system. Feasibility studies have been performed for mobile laboratory testing, especially for the laboratory performance of COVID-19 RT-PCR (PCR).\n\nMethodsWe evaluated the driving range capability, PCR sample size capacity, turn-around time (TAT), and analytical performance for the detection of SARS-CoV-2. Saliva samples were used for the current research and the analytical performance was compared with reference PCR.\n\nResultsThe estimated driving range and sample size capacity were 432 km and 3,258 samples, respectively for the HFC motorcoach and 313 km and 2,146 samples for the HFC minibus, respectively. For the TAT, the median time between the sample submission and the completion of PCR were 86 min for the motorcoach and 76 min for the minibus, and the median time between sample submission and the electronic reporting of the result to each visitor were 182 min for the motorcoach and 194 min for the minibus. A secondary analysis of 1,574 HFC mobile laboratory testing samples was conducted and all negative samples were negative by reference PCR. Furthermore, all positive samples were confirmed as positive by reference PCR or other molecular examinations.\n\nConclusionWe confirmed the feasibility of HFC mobile laboratory systems for achieving the rapid reporting of highly accurate PCR results.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Miho Okude", + "author_inst": "LSI Medience Corporation" + }, + { + "author_name": "Kenji Suzuki", + "author_inst": "University of Tsukuba" + }, + { + "author_name": "Asami Naito", + "author_inst": "LSI Medience Corporation" + }, + { + "author_name": "Akio Ebashi", + "author_inst": "University of Tsukuba Hospital" + }, + { + "author_name": "Tomoka Kusama", + "author_inst": "University of Tsukuba Hospital" + }, + { + "author_name": "Junichi Kiyotaki", + "author_inst": "Miroku Medical Laboratory Inc" + }, + { + "author_name": "Yusaku Akashi", + "author_inst": "Faculty of Medicine, University of Tsukuba" + }, + { + "author_name": "Yoshihiko Kiyasu", + "author_inst": "Faculty of Medicine, University of Tsukuba" + }, + { + "author_name": "Yoko Kurihara", + "author_inst": "University of Tsukuba Hospital" + }, + { + "author_name": "Shigeyuki Notake", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Masaki Takansahi", + "author_inst": "LSI Medience Corporation" + }, + { + "author_name": "Tomokazu Setoyama", + "author_inst": "LSI Medience Corporation" + }, + { + "author_name": "Yasushi Kawakami", + "author_inst": "Faculty of Medicine, University of Tsukuba" + }, + { + "author_name": "Hiromichi Suzuki", + "author_inst": "Faculty of Medicine, University of Tsukuba" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.01.23285224", "rel_title": "Clinical Characteristics and Long-term Symptomology of Post-COVID-19 Olfactory and Gustatory Dysfunction", @@ -133894,61 +134878,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.29.23285159", - "rel_title": "Probable transmission of SARS-CoV-2 from an African lion to zoo employees", - "rel_date": "2023-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.29.23285159", - "rel_abs": "Animal to human transmission of SARS-CoV-2 has not previously been reported in a zoo setting. A vaccinated African lion with physical limitations requiring hand feeding tested positive for SARS-CoV-2 after development of respiratory signs. Zoo employees were screened, monitored prospectively for development of symptoms, then re-screened as indicated, with confirmation by RT-PCR and whole-genome virus sequencing when possible. Trace-back investigation narrowed the source of infection to one of five people. Three exposed employees subsequently developed symptoms, two with viral genomes identical to the lions. Forward contact tracing investigation confirmed probable lion-to-human transmission.\n\nClose contact with large cats is a risk factor for bidirectional zoonotic SARS-CoV-2 transmission that should be considered when occupational health and biosecurity practices at zoos are designed and implemented. SARS-CoV-2 rapid testing and detection methods in big cats and other susceptible animals should be developed and validated to facilitate timely implementation of One Health investigations.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Audrey A Siegrist", - "author_inst": "Potawatomi Zoo" - }, - { - "author_name": "Kira L Richardson", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Ria R Ghai", - "author_inst": "Centers for Disease Control" - }, - { - "author_name": "Brian Pope", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Jamie Yeadon", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Betsy Culp", - "author_inst": "Potawatomi Zoo" - }, - { - "author_name": "Casey Barton Behravesh", - "author_inst": "Centers for Disease Control" - }, - { - "author_name": "Lixia Liu", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Jennifer A Brown", - "author_inst": "Indiana Department of Health" - }, - { - "author_name": "Leslie Boyer", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.30.526314", "rel_title": "Fitness effects of mutations to SARS-CoV-2 proteins", @@ -134180,6 +135109,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.31.526458", + "rel_title": "Scalable neighbour search and alignment with uvaia", + "rel_date": "2023-01-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.31.526458", + "rel_abs": "Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences, which uvaia alleviates by using measures of sequence similarity that consider partially ambiguous sites. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but also for improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Leonardo de Oliveira Martins", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Alison E Mather", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Andrew J Page", + "author_inst": "Quadram Institute Bioscience" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.01.28.23285135", "rel_title": "Migrant healthcare workers during COVID-19: bringing an intersectional health system-related approach into pandemic protection. A German case study", @@ -135728,81 +136684,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2023.01.25.23284428", - "rel_title": "Primary care coding activity related to the use of online consultation systems or remote consulting: an analysis of 53 million peoples' health records using OpenSAFELY", - "rel_date": "2023-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.25.23284428", - "rel_abs": "BackgroundThe pandemic accelerated work by the NHS in England to enable and stimulate use of online consultation systems across all practices, for improved access to primary care.\n\nObjectiveWe aimed to explore general practice coding activity associated with the use of online consultation systems in terms of trends, COVID-19 effect, variation and quality.\n\nMethodsWith the approval of NHS England, OpenSAFELY-TPP and OpenSAFELY-EMIS were used to query and analyse in situ records of electronic health record systems of over 53 million patients in over 6,400 practices, mainly in 2019-2020. SNOMED CT codes relevant to online consultation systems and written online consultations were identified. Coded events were described by volumes, practice coverage, trends pre- and post-COVID-19 and inter-practice and sociodemographic variation.\n\nResults3,550,762 relevant coding events were found in TPP practices, with code eConsultation detected in 84% of practices. Coding activity related to digital forms of interaction increased rapidly from March 2020 at the onset of the COVID-19 pandemic, though we found large variation in coding instance rates among practices in England. Code instances were more commonly found among females, those aged 18-40, those least deprived or white. eConsultation coded activity was more commonly found recorded among patients with a history of asthma or depression.\n\nConclusionsWe successfully queried general practice coding activity relevant to the use of online consultation systems, showing increased adoption as well as key areas of variation during the COVID-19 pandemic. The work can be expanded to support monitoring of coding quality and underlying activity. In future, large-scale impact evaluation studies can be implemented within the platform, namely looking at resource utilisation and patient outcomes.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Martina Fonseca", - "author_inst": "NHS England" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "-" - }, - { - "author_name": "Caroline E Walters", - "author_inst": "University of Oxford" - }, - { - "author_name": "George Hickman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jonathan Pearson", - "author_inst": "NHS England" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "William Hulme", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ofra Koffman", - "author_inst": "NHS England" - }, - { - "author_name": "Minal Bakhai", - "author_inst": "NHS England" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2023.01.24.23284885", "rel_title": "Impact of vaccination and risk factors on COVID-19 mortality amid delta surge in Libya: a single centre cohort study", @@ -136018,6 +136899,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.24.23284890", + "rel_title": "SARS-CoV-2 Spike Protein Receptor Binding-ACE2 Interaction Increases Carbohydrate Sulfotransferases and Reduces N-Acetylgalactosamine-4-Sulfatase through Phospho-p38-MAPK and RB-E2F1", + "rel_date": "2023-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.24.23284890", + "rel_abs": "Immunohistochemistry of post-mortem lung tissue from patients with SARS-CoV2 infection showed marked decline in intensity and distribution of N-acetylgalactosamine-4-sulfatase (Arylsulfatase B; ARSB), increase of total chondroitin sulfate by immunohistochemistry, and increase of vascular-associated carbohydrate sulfotransferase (CHST)15 [1]. The mechanisms leading to these observations were not explained by signaling pathways known to be activated by exposure to coronaviruses. This report addresses the underlying reactions leading to these observations in a cell-based model, using normal, human, primary small airway epithelial cells, treated with the SARS-CoV-2 spike protein receptor binding domain protein.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Joanne K Tobacman", + "author_inst": "University of Illinois at Chicago and Jesse Brown VAMC" + }, + { + "author_name": "Sumit Bhattacharyya", + "author_inst": "Jesse Brown VAMC and University of Illinois at Chicago" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.25.23284831", "rel_title": "Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco - Brazil", @@ -137710,33 +138614,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.23.525275", - "rel_title": "Genome-wide CRISPR screens identify noncanonical translation factor eIF2A as an enhancer of SARS-CoV-2 programmed -1 ribosomal frameshifting", - "rel_date": "2023-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.23.525275", - "rel_abs": "Many positive-strand RNA viruses, including all known coronaviruses, employ programmed -1 ribosomal frameshifting (-1 PRF) to regulate the translation of polycistronic viral RNAs. However, only a few host factors have been shown to regulate -1 PRF. Through a reporter-based genome-wide CRISPR/Cas9 knockout screen, we identified several host factors that either suppressed or enhanced -1 PRF of SARS-CoV-2. One of these factors is eukaryotic translation initiation factor 2A (eIF2A), which specifically and directly enhanced -1 PRF in vitro and in cells. Consistent with the crucial role of efficient -1 PRF in transcriptase/replicase expression, loss of eIF2A reduced SARS-CoV-2 replication in cells. Transcriptome-wide analysis of eIF2A-interacting RNAs showed that eIF2A primarily interacted with 18S ribosomal RNA near the contacts between the SARS-CoV-2 frameshift-stimulatory element (FSE) and the ribosome. Thus, our results revealed an unexpected role for eIF2A in modulating the translation of specific RNAs independent of its previously described role during initiation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lian-Huan Wei", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA" - }, - { - "author_name": "Yu Sun", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA" - }, - { - "author_name": "Junjie U. Guo", - "author_inst": "Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2023.01.24.525203", "rel_title": "Multimodal characterization of antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection.", @@ -138132,6 +139009,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.01.23.524390", + "rel_title": "Lack of Fzd6 in Ciliated Cells Suppresses Ferroptotic Pulmonary Alveolar Cell Death Induced by LPS and Coronavirus", + "rel_date": "2023-01-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.23.524390", + "rel_abs": "Pulmonary inflammation compromises lung barrier function and underlies many lung diseases including acute lung injury and acute respiratory distress syndrome (ARDS). However, mechanisms by which lung cells respond to the damage caused by the inflammatory insults are not completely understood. Here we show that Fzd6-deficiency in Foxj1+ ciliated cells reduces pulmonary permeability, lipid peroxidation, and alveolar cell death accompanied with an increase in alveolar number in lungs insulted by LPS or a mouse coronavirus. Single-cell RNA sequencing of lung cells indicates that the lack of Fzd6, which is expressed in Foxj1+ cells, increases expression of the aldo-keto reductase Akr1b8 in Foxj1+ cells. Intratracheal administration of the Akr1b8 protein phenocopies Fzd6-deficient lung phenotypes. In addition, ferroptosis inhibitors also phenocopy Fzd6-deficient lung phenotypes and exert no further effects in Fzd6-deficient lungs. These results reveal an important mechanism for protection of alveolar cells from ferroptotic death during pulmonary inflammation by Foxj1+ ciliated cells via paracrine action of Akr1b8.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Qianying Yuan", + "author_inst": "Yale University" + }, + { + "author_name": "Yi Luan", + "author_inst": "Yale University" + }, + { + "author_name": "Barani Kumar Rajendran", + "author_inst": "Yale University" + }, + { + "author_name": "Susan Compton", + "author_inst": "Yale University" + }, + { + "author_name": "Wenwen Tang", + "author_inst": "Yale University" + }, + { + "author_name": "Dianqing Wu", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2023.01.22.525079", "rel_title": "Waning Immunity Against XBB.1.5 Following Bivalent mRNA Boosters", @@ -139460,77 +140376,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2023.01.16.23284626", - "rel_title": "High proportion of Ugandans with pre-pandemic SARS-CoV-2 cross-reactive CD4+ and CD8+ T-cell responses", - "rel_date": "2023-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.16.23284626", - "rel_abs": "The estimated mortality rate of the SARS-CoV-2 pandemic varied greatly around the world with multiple countries in East, Central, and West Africa having significantly lower rates of COVID-19 related fatalities than many resource-rich nations with significantly earlier wide-spread access to life-saving vaccines. One possible reason for this lower mortality could be the presence of pre-existing cross-reactive immunological responses in these areas of the world. To explore this hypothesis, stored peripheral blood mononuclear cells (PBMC) from Ugandans collected from 2015-2017 prior to the COVID-19 pandemic (n=29) and from hospitalized Ugandan COVID-19 patients (n=3) were examined using flow-cytometry for the presence of pre-existing SARS-CoV-2 cross-reactive CD4+ and CD8+ T-cell populations using four T-cell epitope mega pools. Of pre-pandemic participants, 89.7% (26/29) had either CD4+ or CD8+, or both, SARS-CoV-2 specific T-cell responses. Specifically, CD4+ T-cell reactivity (72.4%) and CD8+ T-cell reactivity (65.5%) were relatively similar, and 13 participants (44.8%) had both types of cross-reactive types of T-cells present. There were no significant differences in response by sex in the population. The rates of cross-reactive T-cell populations in these Ugandans is higher than previous estimates from resource-rich countries like the United States (20-50% reactivity). It is unclear what role, if any, this cross-reactivity played in decreasing COVID-19 related mortality in Uganda and other African countries, but does suggest that a better understanding of global pre-existing immunological cross-reactivity could be an informative data of epidemiological intelligence moving forward.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Annemarie Namuniina", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Enoch S Muyanja", - "author_inst": "Emory University" - }, - { - "author_name": "Victoria M Biribawa", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Brenda A Okech", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Aloysious Ssemaganda", - "author_inst": "University of Manitoba Max Rady College of Medicine" - }, - { - "author_name": "Matt A Price", - "author_inst": "IAVI: International Aids Vaccine Initiative" - }, - { - "author_name": "Nancy Hills", - "author_inst": "UCSF: University of California San Francisco" - }, - { - "author_name": "Ann Nanteza", - "author_inst": "Makerere University" - }, - { - "author_name": "Bernard Ssentalo Bagaya", - "author_inst": "Makerere University" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Catherine Riou", - "author_inst": "UCT Faculty of Health Sciences: University of Cape Town Faculty of Health Sciences" - }, - { - "author_name": "Steven J Reynolds", - "author_inst": "NIAID: National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Ronald M Galwango", - "author_inst": "RHSP: Rakai Health Sciences Program" - }, - { - "author_name": "Andrew Davidson Redd", - "author_inst": "NIAID: National Institute of Allergy and Infectious Diseases" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.20.23284812", "rel_title": "Immunogenicity, Safety and Effectiveness of COVID-19 Pfizer-BioNTech (BNT162b2) mRNA Vaccination in Immunocompromised Adolescents and Young Adults: A systematic Review and Meta-Analyses", @@ -139806,6 +140651,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.01.19.23284738", + "rel_title": "A computable phenotype for patients with SARS-CoV2 testing that occurred outside the hospital", + "rel_date": "2023-01-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.19.23284738", + "rel_abs": "ObjectiveTo identify a cohort of COVID-19 cases, including when evidence of virus positivity was only mentioned in the clinical text, not in structured laboratory data in the electronic health record (EHR).\n\nMaterials and MethodsStatistical classifiers were trained on feature representations derived from unstructured text in patient electronic health records (EHRs). We used a proxy dataset of patients with COVID-19 polymerase chain reaction (PCR) tests for training. We selected a model based on performance on our proxy dataset and applied it to instances without COVID-19 PCR tests. A physician reviewed a sample of these instances to validate the classifier.\n\nResultsOn the test split of the proxy dataset, our best classifier obtained 0.56 F1, 0.6 precision, and 0.52 recall scores for SARS-CoV2 positive cases. In an expert validation, the classifier correctly identified 90.8% (79/87) as COVID-19 positive and 97.8% (91/93) as not SARS-CoV2 positive. The classifier identified an additional 960 positive cases that did not have SARS-CoV2 lab tests in hospital, and only 177 of those cases had the ICD-10 code for COVID-19.\n\nDiscussionProxy dataset performance may be worse because these instances sometimes include discussion of pending lab tests. The most predictive features are meaningful and interpretable. The type of external test that was performed is rarely mentioned.\n\nConclusionCOVID-19 cases that had testing done outside of the hospital can be reliably detected from the text in EHRs. Training on a proxy dataset was a suitable method for developing a highly performant classifier without labor intensive labeling efforts.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lijing Wang", + "author_inst": "New Jersey Institute of Technology" + }, + { + "author_name": "Amy Zipursky", + "author_inst": "Boston Children's Hospital/Harvard Medical School" + }, + { + "author_name": "Alon Geva", + "author_inst": "Boston Children's Hospital/Harvard Medical School" + }, + { + "author_name": "Andrew McMurry", + "author_inst": "Boston Children's Hospital/Harvard Medical School" + }, + { + "author_name": "Kenneth D Mandl", + "author_inst": "Boston Children's Hospital/Harvard Medical School" + }, + { + "author_name": "Timothy A Miller", + "author_inst": "Boston Children's Hospital/Harvard Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2023.01.18.23284742", "rel_title": "Long COVID brain fog and muscle pain are associated with longer time to clearance of SARS-CoV-2 RNA from the upper respiratory tract during acute infection", @@ -141310,61 +142194,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2023.01.18.524384", - "rel_title": "Cell division tracing combined with single-cell transcriptomics reveals new cell types and differentiation paths in the regenerating mouse lung", - "rel_date": "2023-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.18.524384", - "rel_abs": "Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of new therapeutic approaches for lung diseases. We combined new mouse models that allow diphtheria toxin (DTA)-mediated depletion of specific epithelial cell types and GFP-labeling of dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncovered new cell types, some of which likely represent epithelial precursors, propose goblet cells as progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also found that DTA-expressing cells can persist in the lung, express specific inflammatory factors, and resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to defined epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Leila R Martins", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Lina Sieverling", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Michelle Michelhans", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Chiara Schiller", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Cihan Erkut", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Sergio Triana", - "author_inst": "European Molecular Biology Laboratory (EMBL), Heidelberg, Germany" - }, - { - "author_name": "Stefan Froehling", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Lars Velten", - "author_inst": "Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain." - }, - { - "author_name": "Hanno Glimm", - "author_inst": "National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germ" - }, - { - "author_name": "Claudia Scholl", - "author_inst": "German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.01.17.524469", "rel_title": "A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease", @@ -141636,6 +142465,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.18.23284681", + "rel_title": "Suicide deaths during the COVID-19 pandemic in the United States, by region, March 1, 2020-June 30, 2022", + "rel_date": "2023-01-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.18.23284681", + "rel_abs": "IntroductionThere were concerns that suicide deaths might increase due to Covid-19 pandemic-related stressors. Previous research demonstrated that suicide deaths actually decreased in 2020 in the US. An update covering 2021-2022 with regional data is warranted.\n\nMethodsObservational cohort, US and regional data. Expected monthly deaths were modeled using pre-pandemic US and regional data (2015-2020). Mortality data was accessed from CDC public reporting.\n\nResultsWe find that suicide deaths in the United States were below expected levels throughout the pandemic period (March 1, 2020-June 30,2022) with >4,100 fewer suicide deaths than would have been expected to occur during the study period. Stratifying suicide mortality by US Census Bureau region yielded statistically significant decreases from expected suicide deaths in all regions except the Midwest, (which recorded no significant change in suicide deaths during the overall pandemic period).\n\nConclusionSuicide mortality is down in the US since the pandemic began, through June 30, 2022. Possible explanations include an early \"coming together\" effect; Later, increased access to mental health resources and a greater focus on mental health in the media may have reduced stigma and barriers in seeking necessary psychiatric care.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jeremy Samuel Faust", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts" + }, + { + "author_name": "Benjamin Renton", + "author_inst": "Ariadne Labs, Boston Massachusetts" + }, + { + "author_name": "Chengan Du", + "author_inst": "Center for Outcomes Research and Evaluation, Yale University School of Medicine, New Haven, Connecticut" + }, + { + "author_name": "Sejal B. Shah", + "author_inst": "Harvard Medical School, Brigham and Women's Hospital Department of Psychiatry, Boston, Massachusetts" + }, + { + "author_name": "Alexander Junxiang Chen", + "author_inst": "Harvard University, Cambridge, Massachusetts" + }, + { + "author_name": "Shu-Xia Li", + "author_inst": "Center for Outcomes Research and Evaluation, Yale University School of Medicine, New Haven, Connecticut" + }, + { + "author_name": "Harlan M. Krumholz", + "author_inst": "Center for Outcomes Research and Evaluation, Yale University School of Medicine, New Haven, Connecticut" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2023.01.17.23284673", "rel_title": "Mixed Attention with Deep Supervision for Delineation of COVID Infection in Lung CT", @@ -143220,65 +144092,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.10.523518", - "rel_title": "Anthracyclines inhibit SARS-CoV-2 infection", - "rel_date": "2023-01-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.10.523518", - "rel_abs": "Vaccines and drugs are two effective medical interventions to mitigate SARS-CoV-2 infection. Three SARS-CoV-2 inhibitors, remdesivir, paxlovid, and molnupiravir, have been approved for treating COVID-19 patients, but more are needed, because each drug has its limitation of usage and SARS-CoV-2 constantly develops drug resistance mutations. In addition, SARS-CoV-2 drugs have the potential to be repurposed to inhibit new human coronaviruses, thus help to prepare for future coronavirus outbreaks. We have screened a library of microbial metabolites to discover new SARS-CoV-2 inhibitors. To facilitate this screening effort, we generated a recombinant SARS-CoV-2 Delta variant carrying the nano luciferase as a reporter for measuring viral infection. Six compounds were found to inhibit SARS-CoV-2 at the half maximal inhibitory concentration (IC50) below 1 M, including the anthracycline drug aclarubicin that markedly reduced viral RNA-dependent RNA polymerase (RdRp)-mediated gene expression, whereas other anthracyclines inhibited SARS-CoV-2 by activating the expression of interferon and antiviral genes. As the most commonly prescribed anti-cancer drugs, anthracyclines hold the promise of becoming new SARS-CoV-2 inhibitors.\n\nIMPORTANCEMicrobial metabolites are a rich source of bioactive molecules. The best examples are antibiotics and immunosuppressants that have transformed the practice of modern medicine and saved millions of lives. Recently, some microbial metabolites were reported to have antiviral activity, including the inhibition of Zika virus and Ebola virus. In this study, we discovered several microbial metabolites that effectively inhibit SARS-CoV-2 infection, including anthracyclines that have also been shown to inhibit other viruses including Ebola virus through enhancing interferon responses, which indicates potentially broad antiviral properties of these microbial metabolites and can lead to the discovery of pan-antiviral molecules.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Zhen Wang", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Qinghua Pan", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Ling Ma", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Jianyuan Zhao", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Fiona McIntosh", - "author_inst": "Research Institute of the McGill University Health Centre" - }, - { - "author_name": "Zhenlong Liu", - "author_inst": "McGill University" - }, - { - "author_name": "Shilei Ding", - "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Rongtuan Lin", - "author_inst": "Lady Davis Institute for Medical Research, McGill University" - }, - { - "author_name": "Cen Shan", - "author_inst": "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College" - }, - { - "author_name": "Andr\u00e9s Finzi", - "author_inst": "CRCHUM, Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Chen Liang", - "author_inst": "Lady Davis Institute for Medical Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.01.12.23284481", "rel_title": "Data-driven Targeting of COVID-19 Vaccination Programs: An Analysis of the Evidence on Impact, Implementation, Ethics and Equity", @@ -143430,6 +144243,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.11.23284098", + "rel_title": "Safety and Efficacy of Oral administrated Cepharathine in Non-hospitalized, asymptomatic or mild COVID-19 patients: A Double-blind, Randomized, Placebo-controlled Trial", + "rel_date": "2023-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.11.23284098", + "rel_abs": "Cepharanthine (CEP) is a natural remedy that potently inhibits SARS-CoV-2 activity both in vitro and in vivo. We conducted a proof-of-concept, double-blind, randomized, placebo-controlled trial among adults with asymptomatic or mild coronavirus disease 2019 (COVID-19). Patients were stratified randomly to de novo infection or viral rebound, and assigned in a 1:1:1 ratio to receive 60 mg/day or 120 mg/day of CEP or placebo. Primary outcome the time from randomization to negative nasopharyngeal swab, and safety were evaluated. A total of 262 de novo infected and 124 viral rebound patients underwent randomization. In the 188 de novo patients included in modified intention-to-treat (mITT) population, when compared with placebo, 60 mg/day CEP slightly shortened the time to negative (difference=-0.77 days, hazard ratio (HR)=1.40, 95% CI 0.97 to 2.01, p=0.072), and 120 mg/day CEP did not show the trend. Among de novo patients in the per-protocol set (PPS), 60 mg/day CEP significantly shortened the time to negative (difference=-0.87 days, HR=1.56, 95% CI 1.03 to 2.37, p=0.035). Among viral rebound patients in the mITT population, neither 120 mg/day nor 60 mg/day CEP significantly shortened the time to negative compared to placebo. Adverse events were not different among the three groups, and no serious adverse events occurred. Treatment of asymptomatic or mild Covid-19 with 120 mg/day or 60 mg/day CEP did not shorten the time to negative compared with placebo, without evident safety concerns. Among de novo infected patients with good compliance, 60 mg/day CEP significantly shortened the time to negative compared with placebo (NCT05398705).", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Jianyi Wei", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NH" + }, + { + "author_name": "Shuming Pan", + "author_inst": "Department of Emergency, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, China." + }, + { + "author_name": "Shupeng Liu", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shan" + }, + { + "author_name": "Biyun Qian", + "author_inst": "Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/School of Public Health, Shanghai Jiao Tong University School of Medicine" + }, + { + "author_name": "Zixuan Shen", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shan" + }, + { + "author_name": "Yan Zhang", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shan" + }, + { + "author_name": "Yuexiang Bian", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shan" + }, + { + "author_name": "ADila ABuduaini", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shan" + }, + { + "author_name": "Fuchen Dong", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shan" + }, + { + "author_name": "Xin Zhang", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shan" + }, + { + "author_name": "Jinhui Li", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shan" + }, + { + "author_name": "Yongpei Yu", + "author_inst": "Peking University Clinical Research Institute, Peking University First Hospital, Beijing, China." + }, + { + "author_name": "Weituo Zhang", + "author_inst": "Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China" + }, + { + "author_name": "Jun Wang", + "author_inst": "Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Rd, Pudong, Shanghai 200127, China." + }, + { + "author_name": "Wei Zhai", + "author_inst": "Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China" + }, + { + "author_name": "Qixiang Song", + "author_inst": "Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China" + }, + { + "author_name": "Yu Zheng", + "author_inst": "Department of Respiratory Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China." + }, + { + "author_name": "Lei Li", + "author_inst": "Department of Otorhinolaryngology-Head & Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China." + }, + { + "author_name": "Weihua Pan", + "author_inst": "Department of Pediatric Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China." + }, + { + "author_name": "Lanlan Yu", + "author_inst": "Peking University Clinical Research Institute, Peking University First Hospital, Beijing, China." + }, + { + "author_name": "Qimin Zhang", + "author_inst": "Peking University - Yunnan Baiyao International Medical Research Center" + }, + { + "author_name": "Ning Zhang", + "author_inst": "Peking University - Yunnan Baiyao International Medical Research Center" + }, + { + "author_name": "Junhua Zheng", + "author_inst": "Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China." + }, + { + "author_name": "Chen Yao", + "author_inst": "Peking University Clinical Research Institute, Peking University First Hospital, Beijing, China." + }, + { + "author_name": "Hai Li", + "author_inst": "Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.11.23284137", "rel_title": "Effectiveness of second booster compared to first booster and protection conferred by previous SARS CoV-2 infection against symptomatic Omicron BA.2 and BA.4/5 in France", @@ -144858,65 +145786,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.09.23284380", - "rel_title": "Effectiveness of an eHealth Intervention for Reducing Psychological Distress and Increasing COVID-19 Knowledge and Protective Behaviors among Ethnoracially Diverse Sexual and Gender Minority Adults: A Quasi-experimental Study (#SafeHandsSafeHearts)", - "rel_date": "2023-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.09.23284380", - "rel_abs": "PurposeLesbian, gay, bisexual, transgender, queer, and other persons outside of heteronormative and cisgender identities (LGBTQ+) and ethnic/racial minority populations are at heightened vulnerability amid the Covid-19 pandemic. Systemic marginalization and resulting adverse social determinants of health contribute to health disparities among these populations that result in more severe consequences due to Covid-19 and the public health measures to control it. We developed and tested a tailored online intervention (#SafeHandsSafeHearts) to support ethnoracially diverse LGBTQ+ individuals in Toronto, Canada amid the pandemic.\n\nMethodsWe used a quasi-experimental pre-test post-test design to evaluate the effectiveness of a 3-session, peer-delivered eHealth intervention in reducing psychological distress and increasing Covid-19 knowledge and protective behaviors. Individuals [≥]18-years-old, resident in Toronto, and self-identified as sexual or gender minority were recruited online. Depressive and anxiety symptoms, Covid-19 knowledge and protective behaviors were assessed at baseline, 2-weeks postintervention, and 2-months follow-up. We used generalized estimating equations and zero-truncated Poisson models to evaluate the effectiveness of the intervention on the four primary outcomes.\n\nResultsFrom March to November 2021, 202 participants (median age, 27 years [Interquartile rage: 23-32]) were enrolled in #SafeHandsSafeHearts. Over half (54%, n=110) identified as cisgender lesbian or bisexual women or women who have sex with women, 26.2% (n=53) cisgender gay or bisexual men or men who have sex with men, and 19.3% (n=39) transgender or nonbinary individuals. The majority (75.7%, n=143) were Black and other people of color. The intervention led to statistically significant reductions in the prevalence of clinically significant depressive and anxiety symptoms, and increases in Covid-19 protective behaviors from baseline to postintervention.\n\nConclusionWe demonstrated the effectiveness of a brief, peer-delivered eHealth intervention for ethnoracially diverse LGBTQ+ communities in reducing psychological distress and increasing protective behaviors amid the Covid-19 pandemic. Implementation through community-based health services with trained peer educators supports feasibility, acceptability, and the importance of engaging ethnoracially diverse LGBTQ+ communities in pandemic response preparedness. This trial is registered with ClinicalTrials.gov, number NCT04870723.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Peter A. Newman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Venkatesan Chakrapani", - "author_inst": "Centre for Sexuality and Health Research and Policy" - }, - { - "author_name": "Notisha Massaquoi", - "author_inst": "University of Toronto Scarborough" - }, - { - "author_name": "Charmaine C. Williams", - "author_inst": "University of Toronto" - }, - { - "author_name": "Wangari Tharao", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - }, - { - "author_name": "Suchon Tepjan", - "author_inst": "VOICES-Thailand Foundation" - }, - { - "author_name": "Surachet Roungprakhon", - "author_inst": "Rajamangala University of Technology Phra Nakhon" - }, - { - "author_name": "Joelleann Forbes", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - }, - { - "author_name": "Sarah Sebastian", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - }, - { - "author_name": "Pakorn Akkakanjanasupar", - "author_inst": "VOICES-Thailand Foundation" - }, - { - "author_name": "Muna Aden", - "author_inst": "Women's Health in Women's Hands Community Health Centre" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.11.23284427", "rel_title": "Genetic determinants of severe COVID-19 in young Asian and Middle Eastern patients", @@ -145200,6 +146069,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.01.09.23284360", + "rel_title": "Analysis of recurrent research pathways for assessing and improving effectiveness in life sciences laboratories", + "rel_date": "2023-01-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.09.23284360", + "rel_abs": "BackgroundLife sciences research often turns out to be ineffective. Our aim was to develop a method for mapping repetitive research processes, detecting practice variations, and exploring inefficiencies.\n\nMethodsThree samples of R&I projects were used: companion diagnostics of cancer treatments, identification of COVID-19 variants, and COVID-19 vaccine development. Major steps involved: defined starting points, desired end points; measurement of transition times and success rates; exploration of variations, and recommendations for improved efficiency.\n\nResultsOver 50% of CDX developments failed to reach market simultaneously with new drugs. There were significant variations among phases of co-development (Bartlett test P<0.001). Length of time in vaccine development also shows variations (P<0.0001). Similarly, subject participation indicates unexplained variations in trials (Phase I: 489.7 ({+/-}461.8); Phase II: 857.3 ({+/-}450.1); Phase III: 35402 ({+/-}18079).\n\nConclusionAnalysis of repetitive research processes can highlight inefficiencies and show ways to improve quality and productivity in life sciences.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "E Andrew Balas", + "author_inst": "Augusta University" + }, + { + "author_name": "Charmi Patel", + "author_inst": "Augusta University" + }, + { + "author_name": "Ben Ewing", + "author_inst": "Augusta University" + }, + { + "author_name": "Nauka Patel", + "author_inst": "Augusta University" + }, + { + "author_name": "Tiana Curry McCoy", + "author_inst": "Augusta University" + }, + { + "author_name": "Scott Wise", + "author_inst": "Augusta University" + }, + { + "author_name": "Yara H Abdelgawad", + "author_inst": "Augusta University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2023.01.09.523288", "rel_title": "HOGVAX: Exploiting Peptide Overlaps to Maximize Population Coverage in Vaccine Design with Application to SARS-CoV-2", @@ -146540,153 +147452,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.05.23284214", - "rel_title": "The impact of the COVID-19 pandemic on Antipsychotic Prescribing in individuals with autism, dementia, learning disability, serious mental illness or living in a care home: A federated analysis of 59 million patients primary care records in situ using OpenSAFELY", - "rel_date": "2023-01-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.05.23284214", - "rel_abs": "BackgroundThe COVID-19 pandemic significantly affected health and social care services. We aimed to explore whether this impacted the prescribing rates of antipsychotics within at-risk populations.\n\nMethodsWith the approval of NHS England, we completed a retrospective cohort study, using the OpenSAFELY platform to explore primary care data of 59 million patients. We identified patients in five at-risk groups: autism, dementia, learning disability, serious mental illness and care home residents. We then calculated the monthly prevalence of antipsychotic prescribing in the population, as well as the incidence of new prescriptions in each month over the study period (Jan 2019-Dec 2021).\n\nResultsThe average monthly rate of antipsychotic prescribing increased in dementia from 82.75 patients prescribed an antipsychotic per 1000 patients (95% CI 82.30-83.19) in Q1 2019 to 90.1 (95% CI 89.68-90.60) in Q4 2021 and from 154.61 (95% CI 153.79-155.43) in Q1 2019 to 166.95 (95% CI 166.23-167.67) in Q4 2021 in care homes. There were notable spikes in the rate of new prescriptions issued to patients with dementia and in care homes. In learning disability and autism groups, the average monthly rate of prescribing per 1000 decreased from 122.97 (95% CI 122.29-123.66) in Q1 2019 to 119.29 (95% CI 118.68-119.91) in Q4 2021, and from 54.91 (95% CI 54.52-55.29) in Q1 2019 to 51.04 (95% CI 50.74-51.35) in Q4 2021 respectively.\n\nConclusionsDuring each of the lockdowns in 2020, we observed a significant spike in antipsychotic prescribing in the dementia and care home groups. We have shown that these peaks are likely due to prescribing of antipsychotics for palliative care purposes and may have been linked to pre-emptive prescribing, when on-site medical visits would have been restricted. Over the study period, we observed gradual increases in antipsychotic use in patients with dementia and in care homes and a decrease in their use in patients with learning disability or autism.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Orla Macdonald", - "author_inst": "Oxford Health NHS FT" - }, - { - "author_name": "Amelia Green", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Alex J Walker", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Richard Croker", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Andrew Brown", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Ben Butler-Cole", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Colm Andrews", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "David Evans", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Jon Massey", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Tom Ward", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "William Hulme", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Jessica Morley", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP" - }, - { - "author_name": "John Parry", - "author_inst": "TPP" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP" - }, - { - "author_name": "Shaun O'Hanlon", - "author_inst": "EMIS" - }, - { - "author_name": "Alex Eavis", - "author_inst": "EMIS" - }, - { - "author_name": "Richard Jarvis", - "author_inst": "EMIS" - }, - { - "author_name": "Dima Avramov", - "author_inst": "EMIS" - }, - { - "author_name": "Ian Wood", - "author_inst": "EMIS" - }, - { - "author_name": "Nasreen Parkes", - "author_inst": "EMIS" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.01.05.23284247", "rel_title": "Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals", @@ -146886,6 +147651,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.01.06.23284282", + "rel_title": "OmiCrisp: A CRISPR SARS-CoV-2 test with Omicron detection", + "rel_date": "2023-01-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.06.23284282", + "rel_abs": "We have developed a CRISPR based assay that can detect the presence of SARS-CoV-2 in RNA extracted from human samples and also predict if it is an Omicron or non-Omicron variant of the virus. This is a nucleic acid amplification-based test (NAAT). The amplification and detection are carried out in two independent steps in this assay. Amplification is done using a standard one-step RT-PCR method. The detection is done using a method that utilizes the trans-cleavage activity of the Cas12a enzyme. We have evaluated the performance of OmiCrisp in more than 80 clinical samples and observed an agreement of 100% with the sequencing results, in labeling SARS-CoV-2 positive samples as Omicron or non-Omicron. OmiCrisp -like platform can be developed quickly and can potentially complement sequencing for quick and rapid tracking of the transmission of new pathogen variants.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Suruchi Sharma", + "author_inst": "CrisprBits Private Limited" + }, + { + "author_name": "Manasa Bagur Prakash", + "author_inst": "CrisprBits Private Limited" + }, + { + "author_name": "Nimisha Gupta", + "author_inst": "CrisprBits Private Limited" + }, + { + "author_name": "Vaijayanti Gupta", + "author_inst": "CrisprBits Private Limited" + }, + { + "author_name": "Vijay Chandru", + "author_inst": "CrisprBits Private Limited" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.06.23284229", "rel_title": "Down-regulation of MALAT1 is a hallmark of tissue and peripheral proliferative T cells in COVID-19", @@ -148906,45 +149706,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.02.23284119", - "rel_title": "Participant Demographics and Testing Trends: A Community Pandemic Response Program", - "rel_date": "2023-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.02.23284119", - "rel_abs": "ObjectiveThis study aimed to identify demographic characteristics of test participants and changes in testing participation over time in a community pandemic-response program launched in a college town in California, USA.\n\nMethodsWe described overall testing participation, identified demographic characteristics of frequent testers, and evaluated changes in testing participation over four different periods of the COVID-19 pandemic.\n\nResultsA total of 770,165 tests were performed between November 18, 2020, and June 30, 2022, among 89,924 residents of Yolo County (41.1% of population), with significant participation from racially/ethnically diverse participants and across age groups. Most positive cases (49.9%) were captured during Omicron, which also corresponds to the period with the highest daily participation (895 per 100K population). The proportion of participants which we considered \"frequent testers\" (28.9% vs. 39.7%, p < 0.0001) and individuals that tested once (39.5% vs. 47.9%, p < 0.0001) increased significantly from Delta to Omicron. Women (58.8%), participants of age 19-34 years (38.8%), and White (53.2%) tested more frequently throughout the program. The proportion of tests conducted among Latinos remained steady around 18% over time, with the exception of the post-Omicron period (13%).\n\nConclusionThe unique features of a pandemic response program that supported communitywide access to free asymptomatic testing provides a unique opportunity to evaluate adherence to testing recommendations, and testing trends over time. Identification of individual and group-level factors associated with testing behaviors is essential to improve access and protect communities at-large.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Yury E Garcia", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Leslie Solis", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Maria L Daza-Torres", - "author_inst": "University of California, Davis" - }, - { - "author_name": "J Cricelio Montesinos-Lopez", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Brad H Pollock", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Miriam Nuno", - "author_inst": "University of California, Davis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.02.23284120", "rel_title": "The time between vaccination and infection impacts immunity against SARS-CoV-2 variants", @@ -149260,6 +150021,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.02.23284123", + "rel_title": "Early risk-assessment of pathogen genomic variants emergence", + "rel_date": "2023-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.02.23284123", + "rel_abs": "Accurate, reliable, and timely estimates of pathogen variant risk are essential for informing public health responses. Unprecedented rates of genomic sequencing have generated new insights into variant dynamics. However, estimating the fitness advantage of a novel variant shortly after emergence, or its dynamics more generally in data-sparse settings, remains difficult. This challenge is exacerbated in countries where surveillance is limited or intermittent. To stabilize inference in these data-sparse settings, we develop a hierarchical modeling approach to estimate variant fitness advantage and prevalence by pooling data across geographic regions. We demonstrate our method by reconstructing SARS-CoV-2 BA.5 variant emergence, and assess performance using retrospective, out-of-sample validation. We show that stable and robust estimates can be obtained even when sequencing data are sparse. Finally, we discuss how this method can inform risk assessment of novel variants and provide situational awareness on circulating variants for a range of pathogens and use-cases.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zachary Susswein", + "author_inst": "The Rockefeller Foundation" + }, + { + "author_name": "Kaitlyn E Johnson", + "author_inst": "The Rockefeller Foundation" + }, + { + "author_name": "Robel Kassa", + "author_inst": "The Rockefeller Foundation" + }, + { + "author_name": "Mina Parastaran", + "author_inst": "The Rockefeller Foundation" + }, + { + "author_name": "Vivian Peng", + "author_inst": "The Rockefeller Foundation" + }, + { + "author_name": "Leo Wolansky", + "author_inst": "The Rockefeller Foundation" + }, + { + "author_name": "Samuel V Scarpino", + "author_inst": "Northeastern University" + }, + { + "author_name": "Ana I Bento", + "author_inst": "The Rockefeller Foundation, Indiana University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.03.23284145", "rel_title": "The impact of the COVID-19 pandemic on health related quality of life in head and neck cancer survivors: an observational cohort study", @@ -150792,53 +151600,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.24.22283920", - "rel_title": "COVID-19 in Cambodia: Epidemiology, Response, and Lessons Learned, 27 January 2020 to 30 June 2022", - "rel_date": "2022-12-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.24.22283920", - "rel_abs": "As a member state of the International Health Regulation 2005, Cambodia has been continuously strengthening its capacity to respond to health emergencies and prevent the international spread of diseases. Despite this, Cambodias capacity to prevent, detect, and rapidly respond to public health threats remained limited at the onset of the pandemic. This paper describes epidemiological phases, response phases, strategy, and lessons learned in Cambodia between 27 January 2020 and 30 June 2022. We classified epidemiological phases in Cambodia into three phases, in which Cambodia responded using eight measures: (1) detect, isolate/quarantine; (2) face coverings, hand hygiene, and physical distancing measures; (3) risk communication and community engagement; (4) school closures; (5) border closures; (6) public event and gathering cancellation; (7) vaccination; and (8) lockdown. The measures corresponded to six strategies: (1) setting up and managing a new response system, (2) containing the spread with early response, (3) strengthening the identification of cases and contacts, (4) strengthening care for COVID-19 patients, (5) boosting vaccination coverage, and (6) supporting disadvantaged groups. Finally, ten lessons were learned for future health emergency responses. Findings suggest that Cambodia successfully contained the spread of SARS-CoV-2 in the first year and quickly attained high vaccine coverage by the second year of the response. The core of this success was the strong political will and high level of cooperation from the public. However, Cambodia needs to further improve its infrastructure for quarantining and isolating cases and close contacts and laboratory capacity for future health emergencies.\n\nSUMMARY BOXO_LICOVID-19 spread globally, but how the pandemic played out in each country depended on various factors, including government responses and the general publics adherence to COVID-19 measures.\nC_LIO_LIEarly response--Early detection, Early isolation, Early tracing, Early treatment, and Early education--is the core of successful SARS-CoV-2 containment.\nC_LIO_LIAchieving high vaccination coverage quickly leads to a decline in the number of deaths and to eventual full re-opening of the country.\nC_LIO_LIResponding to the pandemic requires decisive leadership and good governance, that refers to decisions being made quickly, in a timely manner, and without delay.\nC_LIO_LIHigh level of cooperation from the public is a fundamental factor for success in containing the spread in the early phase, and the massively successful vaccination campaign in the later stage.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Srean Chhim", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Grace Marie Ku", - "author_inst": "Institute of Tropical Medicine, Antwerp" - }, - { - "author_name": "Sothiro Mao", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Willem van de Put", - "author_inst": "Institute of Tropical Medicine, Antwerp" - }, - { - "author_name": "Wim Van Damme", - "author_inst": "Institute of Tropical Medicine, Antwerp" - }, - { - "author_name": "Por Ir", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Chhorvann Chhea", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Vandine Or", - "author_inst": "Ministry of Health, Phnom Penh, Cambodia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.12.27.22283698", "rel_title": "Safety and Effectiveness of SA58 Nasal Spray against COVID-19 Infection in Medical Personnel\uff1aAn Open-label, Blank-controlled Study", @@ -151142,6 +151903,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2022.12.29.22284048", + "rel_title": "Estimated of expected COVID-19 deaths in Mainland China after abandoning zero COVID policy", + "rel_date": "2022-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.29.22284048", + "rel_abs": "BackgroundChina witnessed a surge of Omicron infections after abandoning zero COVID strategies on December 7, 2022. The authorities report very sparse deaths based on very restricted criteria, but massive deaths are speculated.\n\nMethodsWe aimed to estimate the COVID-19 fatalities in Mainland China until summer 2023 using the experiences of Hong Kong and of South Korea in 2022 as prototypes. Both these locations experienced massive Omicron waves after having had very few SARS-CoV-2 infections during 2020-2021. We estimated age-stratified infection fatality rates (IFRs) in Hong Kong and South Korea during 2022 and extrapolated to the population age structure of Mainland China. We also accounted separately for deaths of residents in long-term care facilities in both Hong Kong and South Korea.\n\nResultsIFR estimates in non-elderly strata were modestly higher in Hong Kong than South Korea and projected 987,455 and 619,549 maximal COVID-19 deaths, respectively, if the entire China population was infected. Expected COVID-19 deaths in Mainland China until summer 2023 ranged from 49,962 to 691,219 assuming 25-70% of the non-elderly population being infected and variable protection of elderly (from none to three-quarter reduction in fatalities). The main analysis (45% of non-elderly population infected and fatality impact among elderly reduced by half) estimated 152,886-249,094 COVID-19 deaths until summer 2023. Large uncertainties exist regarding potential changes in dominant variant, health system strain, and impact on non-COVID-19 deaths.\n\nConclusionsThe most critical factor that can affect total COVID-19 fatalities in China is the extent to which the elderly can be protected.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "John P.A. Ioannidis", + "author_inst": "Stanford University" + }, + { + "author_name": "Francesco Zonta", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Michael Levitt", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.30.22284061", "rel_title": "Bridging the gap_Estimation of 2022/2023 SARS-CoV-2 healthcare burden in Germany based on multidimensional data from a rapid epidemic panel", @@ -152546,57 +153334,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.12.25.22283942", - "rel_title": "Study COVID-19 Severity of Patients Admitted to Emergency Room (ER) with Chest X-ray Images", - "rel_date": "2022-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.25.22283942", - "rel_abs": "We have conducted a study of the COVID-19 severity with the chest x-ray images, a private dataset collected from our collaborator St Bernards Medical Center. The dataset is comprised of chest x-ray images from 1,550 patients who were admitted to emergency room (ER) and were all tested positive for COVID-19. Our study is focused on the following two questions: (1) To predict patients hospital staying duration, based on the chest x-ray image which was taken when the patient was admitted to the ER. The length of stay ranged from zero hours to 95 days in the hospital and followed a power law distribution. Based on our testing results, it is hard for the prediction models to detect strong signal from the chest x-ray images. No model was able to perform better than a trivial most-frequent classifier. However, each model was able to outperform the most-frequent classifier when the data was split evenly into four categories. This would suggest that there is signal in the images, and the performance may be further improved by the addition of clinical features as well as increasing the training set. (2) To predict if a patient is COVID-19 positive or not with the chest x-ray image. We also tested the generalizability of training a prediction model on chest x-ray images from one hospital and then testing the model on images captures from other sites. With our private dataset and the COVIDx dataset, the prediction model can achieve a high accuracy of 95.9%. However, for our hold-one-out study of the generalizability of the models trained on chest x-rays, we found that the model performance suffers due to a significant reduction in training samples of any class.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jonathan Stubblefield", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Christopher Saldivar", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Anna De Feria", - "author_inst": "St. Bernards Medical Center" - }, - { - "author_name": "James Riddle", - "author_inst": "St. Bernards Medical Center" - }, - { - "author_name": "Abhijit Shivkumar", - "author_inst": "St. Bernards Medical Center" - }, - { - "author_name": "Jason Causey", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Jake Qualls", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Jennifer Fowler", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Xiuzhen Huang", - "author_inst": "Arkansas State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.12.24.22283835", "rel_title": "Literature analysis of the efficacy of COVID-19 vaccinations", @@ -152948,6 +153685,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.22.22283851", + "rel_title": "TaME-seq2: Tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling", + "rel_date": "2022-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.22.22283851", + "rel_abs": "BackgroundPreviously developed TaME-seq method for deep sequencing of HPV, allowed simultaneous identification of the HPV DNA consensus sequence, low-frequency variable sites, and chromosomal integration events. The method has been successfully validated and applied to the study of five carcinogenic high-risk (HR) HPV types (HPV16, 18, 31, 33, and 45). Here, we present TaME-seq2 with an updated laboratory workflow and bioinformatics pipeline. The HR-HPV type repertoire was expanded with HPV51, 52, and 59. As a proof-of-concept, TaME-seq2 was applied on SARS-CoV-2 positive samples showing the methods flexibility to a broader range of viruses, both DNA and RNA.\n\nResultsCompared to TaME-seq version 1, the bioinformatics pipeline of TaME-seq2 is approximately 40x faster. In total, 23 HPV-positive samples and seven SARS-CoV-2 clinical samples passed the threshold of 300x mean depth and were submitted to further analysis. The mean number of variable sites per 1000 bp was [~] 1.5x higher in SARS-CoV-2 than in HPV-positive samples. Reproducibility and repeatability of the method were tested on a subset of samples. A viral integration breakpoint followed by a partial genomic deletion was found in within-run replicates of HPV59-positive sample. Identified viral consensus sequence in two separate runs was >99.9 % identical between replicates, differing by a couple of nucleotides identified in only one of the replicates. Conversely, the number of identical minor nucleotide variants (MNVs) differed greatly between replicates, probably caused by PCR-introduced bias. The total number of detected MNVs, calculated gene variability and mutational signature analysis, were unaffected by the sequencing run.\n\nConclusionTaME-seq2 proved well suited for consensus sequence identification, and the detection of low-frequency viral genome variation and viral-chromosomal integrations. The repertoire of TaME-seq2 now encompasses seven HR-HPV types. Our goal is to further include all HR-HPV types in the TaME-seq2 repertoire. Moreover, with a minor modification of previously developed primers, the same method was successfully applied for the analysis of SARS-CoV-2 positive samples, implying the ease of adapting TaME-seq2 to other viruses.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alexander Hesselberg L\u00f8vestad", + "author_inst": "Oslo Metropolitan University" + }, + { + "author_name": "Milan Stosic", + "author_inst": "Oslo Metropolitan University" + }, + { + "author_name": "Jean-Marc Costanzi", + "author_inst": "Akershus University Hospital" + }, + { + "author_name": "Irene Kraus Christiansen", + "author_inst": "Akershus University Hospital" + }, + { + "author_name": "Hege Vangstein Aamot", + "author_inst": "Akershus University Hospital" + }, + { + "author_name": "Ole Herman Ambur", + "author_inst": "Oslo Metropolitan University" + }, + { + "author_name": "Trine Ballestad Rounge", + "author_inst": "University of Oslo" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.23.22283887", "rel_title": "Unequal Recovery in Colorectal Cancer Screening Following the COVID-19 Pandemic: A Comparative Microsimulation Analysis", @@ -154728,65 +155508,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.12.22.521201", - "rel_title": "Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 Omicron sub-lineages", - "rel_date": "2022-12-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.22.521201", - "rel_abs": "The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple sub-variants originating from BA.2, BA.4 and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1 and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1 and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1 and XBB variants.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Franck Touret", - "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France." - }, - { - "author_name": "Emilie Giraud", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Jerome Bourret", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France" - }, - { - "author_name": "Flora Donati", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France" - }, - { - "author_name": "Jaouen Tran-Rajau", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Jeanne Chiaravalli", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Frederic Lemoine", - "author_inst": "Institut Pasteur, Universite Paris Cite, G5 Evolutionary Genomics of RNA Viruses, Paris, France" - }, - { - "author_name": "Fabrice Agou", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur, Universite Paris Cite, G5 Evolutionary Genomics of RNA Viruses, Paris, France" - }, - { - "author_name": "Sylvie Van Der Werf", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France" - }, - { - "author_name": "Xavier de Lamballerie", - "author_inst": "Unite des Virus Emergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.12.22.22283830", "rel_title": "To test or not to test? A new behavioral epidemiology framework for COVID-19", @@ -154926,6 +155647,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.22.22283842", + "rel_title": "Adiposity and Mortality among Patients Severely Ill with COVID-19 and non-COVID-19 Respiratory Conditions: A Cross-Context Comparison Study in the UK", + "rel_date": "2022-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.22.22283842", + "rel_abs": "ObjectiveTo assess the causality of adiposity for mortality among patients severely ill with COVID-19 and non-COVID-19 respiratory conditions by examining the consistency of associations across temporal and geographical contexts where biases vary\n\nDesignProspective cohort study\n\nSetting297 intensive care units (ICUs) in England, Wales, and Northern Ireland monitored by the Intensive Care National Audit and Research Centre Case Mix Programme\n\nParticipantsPatients aged [≥]16 years admitted to ICU with COVID-19 (N=33,352; Feb 2020-Aug 2021) and non-COVID-19 respiratory conditions (N=24,739; Feb 2018-Aug 2019)\n\nMain outcome measure30-day mortality post ICU admission\n\nResultsCompared with non-COVID-19 respiratory patients, COVID-19 patients were younger, less often of a white ethnic group, and more often with extreme obesity (body mass index (BMI) [≥] 40kg/m2). COVID-19 patients had fewer comorbidities but higher mortality (35% vs. 23% mortality in non-COVID-19). Socio-demographic and comorbidity factors and their associations with BMI and mortality varied more by date than geographical region of ICU admission, particularly among COVID-19 patients. Among COVID-19 patients, higher BMI was associated with a small excess mortality (hazard ratio (HR) per standard deviation (SD)=1.05; 95% CI=1.03, 1.08), driven by extreme obesity (HR per SD=1.21; 95% CI=1.13, 1.31 vs. normal-weight). Extreme obesity was strongly associated with higher mortality only during Feb-April 2020 (HR=1.49, 95% CI=1.27, 1.73 vs. normal-weight); this association weakened thereafter (BMI-date interaction P=0.03). Among non-COVID-19 respiratory patients, higher BMI was associated with lower mortality (HR per SD=0.84; 95% CI=0.82, 0.87), seen across all overweight/obesity groups. These negative obesity-mortality associations were similar across most admission dates and regions.\n\nConclusionsObesity is associated with higher mortality among COVID-19 patients, but lower mortality among non-COVID respiratory patients. These associations appear vulnerable to confounding/selection bias in both patient groups, questioning the existence or stability of causal effects. Among COVID-19 patients, unfavourable obesity-mortality associations differ by admission date. Among non-COVID-19 respiratory patients, favourable obesity-mortality associations may reflect comorbidity-induced weight loss.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Joshua A Bell", + "author_inst": "University of Bristol" + }, + { + "author_name": "David Carslake", + "author_inst": "University of Bristol" + }, + { + "author_name": "Amanda Hughes", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Tilling", + "author_inst": "University of Bristol" + }, + { + "author_name": "James W Dodd", + "author_inst": "University of Bristol" + }, + { + "author_name": "James C Doidge", + "author_inst": "Intensive Care National Audit & Research Centre (ICNARC)" + }, + { + "author_name": "David A Harrison", + "author_inst": "Intensive Care National Audit & Research Centre (ICNARC)" + }, + { + "author_name": "Kathryn M Rowan", + "author_inst": "Intensive Care National Audit & Research Centre (ICNARC)" + }, + { + "author_name": "George Davey Smith", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.22.22283672", "rel_title": "Dynamics of Covid-19 Vaccine-Hesitancy among Primary Health Care Workers in an Urban City in India", @@ -156194,25 +156966,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.19.22283681", - "rel_title": "Tracking the COVID-19 vaccine equity, distribution, and cases in the global south", - "rel_date": "2022-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.19.22283681", - "rel_abs": "The rapid development of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proved to make an important contribution in reducing both viral transmission and disease burden. In this study, we tracked the COVID-19 vaccine equity, distribution, and cases in global south countries using country-level data from Our World in Data using an event study analysis. We used data from 149 global south and 59 non-global south countries from January 2020 to May 2022. All non-global south and 90.32% of global south countries had universal availability of vaccines. The median time since the introduction of the first COVID-19 vaccine in the global south was almost eight weeks later than in non-global south countries. The median number of people fully vaccinated per hundred (68.8 vs 50.31), and the total number of boosters administered per hundred (45.7 vs. 13.02) were higher in non-global south countries compared to global south countries. Using the event study analysis, we found a significant reduction of COVID-19 new cases and deaths after the first COVID-19 vaccination rollout compared to the baseline in global south countries, average coefficient p-value <0.001. Programs aiming at improving vaccine access and distribution to global south countries are essential to effectively control COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Tigist Mekonnen Melesse", - "author_inst": "World Bank Group" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.12.20.22282909", "rel_title": "The onset of late severe lung impairment in COVID-19 is associated with high inflammation markers at admission and metabolic syndrome markers", @@ -156612,6 +157365,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.20.22283719", + "rel_title": "Impact of Age, Race, and Family History on COVID-19 Related Changes in Breast Cancer Screening among the Boston Mammography Cohort Study", + "rel_date": "2022-12-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.20.22283719", + "rel_abs": "BackgroundWe studied women enrolled in the Boston Mammography Cohort Study to investigate whether subgroups defined by age, race, or family history of breast cancer experienced differences in trends of screening or diagnostic imaging rates during the COVID-19 lockdown and had slower rebound in trends of these rates during reopening.\n\nMethodsWe compared trends of monthly breast cancer screening and diagnostic imaging rates over time between the pre-COVID-19, lockdown, and reopening periods and tested for differences in the monthly trend within the same period by age (<50 vs [≥]50), race (White vs non-White), and first-degree family history of breast cancer (yes vs no).\n\nResultsOverall, we observed a decline in breast cancer screening and diagnostic imaging rates. The monthly trend of breast cancer screening rates for women age [≥]50 was 5% higher (p=0.005) in the pre-COVID-19 period but was 19% lower in the reopening phase than that of women aged<50 (p<0.001). White participants had 36% higher monthly trend of breast cancer diagnostic imaging rates than non-White participants (p=0.018).\n\nDiscussionThe rebound in screening was lower in women age [≥]50 and lower in non-White women for diagnostic imaging. Careful attention must be paid as the COVID-19 recovery continues to ensure equitable resumption of care.\n\nFundingThe project was supported by the Breast Cancer Research Foundation (RT). Researchers were supported by the University of Louisville CIEHS P30 ES030283 (NCD), K01CA188075 (ETW), T32CA09001 (NCD, MOS, MEB) P30 ES000002 (JH, FL), and NIH/NCI K00 CA212222 (MEB). This manuscript is the responsibility of the authors and does not represent the official views of the National Institutes of Health.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Naiyu Chen", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "David Cheng", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Michelle O. Sodipo", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Mollie E. Barnard", + "author_inst": "Huntsman Cancer Institute" + }, + { + "author_name": "Natalie C. DuPre", + "author_inst": "University of Louisville" + }, + { + "author_name": "Rulla Tamimi", + "author_inst": "Weill Cornell Medical College" + }, + { + "author_name": "Erica T. Warner", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.20.22283720", "rel_title": "Systematic review: Longitudinal effects of the COVID-19 pandemic on child and adolescent mental health", @@ -158336,97 +159132,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.18.22283646", - "rel_title": "Association between SARS-CoV-2 Infection and Select Symptoms and Conditions 31 to 150 Days After Testing among Children and Adults", - "rel_date": "2022-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.18.22283646", - "rel_abs": "BackgroundAn increasing number of studies have described new and persistent symptoms and conditions as potential post-acute sequelae of SARS-CoV-2 infection (PASC). However, it remains unclear whether certain symptoms or conditions occur more frequently among persons with SARS-CoV-2 infection compared with those never infected with SARS-CoV-2. We compared the occurrence of specific COVID-associated symptoms and conditions as potential PASC 31 to 150 days following a SARS-CoV-2 test among adults ([≥]20 years) and children (<20 years) with positive and negative test results documented in the electronic health records (EHRs) of institutions participating in PCORnet, the National Patient-Centered Clinical Research Network.\n\nMethods and FindingsThis study included 3,091,580 adults (316,249 SARS-CoV-2 positive; 2,775,331 negative) and 675,643 children (62,131 positive; 613,512 negative) who had a SARS-CoV-2 laboratory test (nucleic acid amplification or rapid antigen) during March 1, 2020-May 31, 2021 documented in their EHR. We identified hospitalization status in the day prior through the 16 days following the SARS-CoV-2 test as a proxy for the severity of COVID-19. We used logistic regression to calculate the odds of receiving a diagnostic code for each symptom outcome and Cox proportional hazard models to calculate the risk of being newly diagnosed with each condition outcome, comparing those with a SARS-CoV-2 positive test to those with a negative test. After adjustment for baseline covariates, hospitalized adults and children with a positive test had increased odds of being diagnosed with [≥]1 symptom (adults: adjusted odds ratio[aOR], 1.17[95% CI, 1.11-1.23]; children: aOR, 1.18[95% CI, 1.08-1.28]) and shortness of breath (adults: aOR, 1.50[95% CI, 1.38-1.63]; children: aOR, 1.40[95% CI, 1.15-1.70]) 31-150 days following a SARS-CoV-2 test compared with hospitalized individuals with a negative test. Hospitalized adults with a positive test also had increased odds of being diagnosed with [≥]3 symptoms (aOR, 1.16[95% CI, 1.08 - 1.26]) and fatigue (aOR, 1.12[95% CI, 1.05 - 1.18]) compared with those testing negative. The risks of being newly diagnosed with type 1 or type 2 diabetes (aHR, 1.25[95% CI, 1.17-1.33]), hematologic disorders (aHR, 1.19[95% CI, 1.11-1.28]), and respiratory disease (aHR, 1.44[95% CI, 1.30-1.60]) were higher among hospitalized adults with a positive test compared with those with a negative test. Non-hospitalized adults with a positive SARS-CoV-2 test had higher odds of being diagnosed with fatigue (aOR, 1.11[95% CI, 1.05-1.16]) and shortness of breath (aOR, 1.22[95% CI, 1.15-1.29]), and had an increased risk (aHR, 1.12[95% CI, 1.02-1.23]) of being newly diagnosed with hematologic disorders (i.e., venous thromboembolism and pulmonary embolism) 31-150 days following SARS-CoV-2 test compared with those testing negative. The risk of being newly diagnosed with certain conditions, such as mental health conditions and neurological disorders, was lower among patients with a positive viral test relative to those with a negative viral test.\n\nConclusionsPatients with SARS-CoV-2 infection were at higher risk of being diagnosed with certain symptoms and conditions, particularly fatigue, respiratory symptoms, and hematological abnormalities, after acute infection. The risk was highest among adults hospitalized after SARS-CoV-2 infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Yongkang Zhang", - "author_inst": "Cornell University Joan and Sanford I Weill Medical College" - }, - { - "author_name": "Alfonso Romieu-Hernandez", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Tegan K Boehmer", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Eduardo Azziz-Baumgartner", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Thomas Carton", - "author_inst": "Louisiana Public Health Institute" - }, - { - "author_name": "Adi V. Gundlapalli", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Julia Fearrington", - "author_inst": "Harvard Pilgrim Health Care Inc" - }, - { - "author_name": "Kshema Nagavedu", - "author_inst": "Harvard Pilgrim Health Care Inc" - }, - { - "author_name": "Katherine Dea", - "author_inst": "Statlog" - }, - { - "author_name": "Erick Moyneur", - "author_inst": "Statlog" - }, - { - "author_name": "Lindsey G. Cowell", - "author_inst": "UT Southwestern: The University of Texas Southwestern Medical Center" - }, - { - "author_name": "Rainu Kaushal", - "author_inst": "Weill Cornell Medical College: Weill Cornell Medicine" - }, - { - "author_name": "Kenneth H Mayer", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Jon Puro", - "author_inst": "OCHIN: Oregon Community Health Information Network" - }, - { - "author_name": "Sonja A Rasmussen", - "author_inst": "University of Florida" - }, - { - "author_name": "Deepika Thacker", - "author_inst": "Nemours Children's Clinic" - }, - { - "author_name": "Mark G Weiner", - "author_inst": "Weill Cornell Medical College: Weill Cornell Medicine" - }, - { - "author_name": "Sharon Saydeh", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jason P Block", - "author_inst": "Harvard Pilgrim Health Care Inc" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.19.22283668", "rel_title": "A retrospective analysis of COVID-19 non-pharmaceutical interventions for Mexico and Peru: a modeling study", @@ -158714,6 +159419,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.12.16.22283603", + "rel_title": "Booster Vaccination with SARS-CoV-2 mRNA Vaccines and Myocarditis Risk in Adolescents and Young Adults: A Nordic Cohort Study of 8.9 Million Residents", + "rel_date": "2022-12-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.16.22283603", + "rel_abs": "ImportanceThe SARS-CoV-2 mRNA vaccines are associated with an increased risk of myocarditis. This association appears to be strongest in male adolescents and younger males and after the second dose. Few studies have evaluated the association after booster doses.\n\nObjectiveTo evaluate the risk of myocarditis following SARS-CoV-2 mRNA booster vaccination in 12-to-39-year-olds.\n\nDesignA multinational cohort study using nationwide register data.\n\nSettingDenmark, Finland, Norway, and Sweden.\n\nParticipantsCohorts comprising all 8.9 million individuals residing in each of the four countries, born 1982-2009, and alive at start of study on December 27, 2020, without a previous diagnosis of myocarditis or pericarditis or laboratory-confirmed SARS-CoV-2 infection.\n\nExposuresThe 28-day acute risk periods following the second and third dose of BNT162b2 and mRNA-1273, respectively, in a homologous schedule defines the exposures of interest.\n\nMain Outcomes and MeasuresCohort participants were followed until an inpatient diagnosis of myocarditis, loss to follow-up, or end of study (latest data availability in each country), whichever occurred first. In each of the four countries, Poisson regression was used to estimate adjusted incidence rate ratios (IRRs) of myocarditis, with associated 95% confidence intervals (CIs), according to vaccination status. Country-specific results were combined in meta-analyses.\n\nResultsA total of 8.9 million residents were followed for 12,271,861 person-years. We identified 1533 cases of myocarditis. In 12-to-39-year-old males, the 28-day acute risk period following the third dose of BNT162b2 or mRNA-1273 was associated with an increased incidence rate of myocarditis compared to the post-acute risk period 28 days or more after a second homologous dose (IRR, 2.08 [95% CI, 1.31 to 3.33] and 8.89 [95% CI, 2.26 to 35.03], respectively). The corresponding incidence rates following the third dose of BNT162b2 and mRNA-1273 were 0.86 and 1.95, respectively, within 28 days of follow-up among 100,000 individuals.\n\nConclusions and RelevanceOur results suggest that a booster dose is associated with increased myocarditis risk in male adolescents and young male adults.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSIs a first booster dose of SARS-CoV-2 messenger RNA (mRNA) vaccine associated with increased risk of myocarditis in male adolescents and young male adults?\n\nFindingsIn a cohort study of 8.9 million residents in Denmark, Finland, Norway, and Sweden, a booster dose of BNT162b2 or mRNA-1273 vaccine was associated with increased risk of myocarditis in 12-to-39-year-old males, with incidence rates 0.86 and 1.95, respectively, within 28 days of follow-up per 100,000 vaccinated individuals.\n\nMeaningA booster dose with a SARS-CoV-2 mRNA vaccine is associated with increased myocarditis risk in male adolescents and young male adults. Compared to after a primary course, the risk appears attenuated.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Anders Hviid", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Tuomo Nieminen", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Nicklas Pihlstrom", + "author_inst": "Swedish Medical Products Agency" + }, + { + "author_name": "Ninna Gunnes", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Jesper Dahl", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Oystein Karlstad", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Hanne Lovdal Gulseth", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Anders Sunstrom", + "author_inst": "Swedish Medical Products Agency" + }, + { + "author_name": "Anders Husby", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Jorgen Vinslov Hansen", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Rickard Ljung", + "author_inst": "Swedish Medical Products Agency" + }, + { + "author_name": "Petteri Hovi", + "author_inst": "Finnish Institute for Health and Welfare (former National Institute for Health and welfare)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.16.22283557", "rel_title": "The effect of COVID-19 lockdowns on fertility in the Democratic Republic of the Congo", @@ -160018,45 +160786,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.12.16.520599", - "rel_title": "Cholesterol and ceramide facilitate SARS-CoV-2 Spike protein-mediated membrane fusion", - "rel_date": "2022-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.16.520599", - "rel_abs": "SARS-CoV-2 entry into host cells is mediated by the Spike (S) protein of the viral envelope. The S protein is composed of two subunits: S1 that induces binding to the host cell via its interaction with the ACE2 receptor of the cell surface and S2 that triggers fusion between viral and cellular membranes. Fusion by S2 depends on its heptad repeat domains that bring membranes close together, and its fusion peptide (FP) that interacts with and perturb the membrane structure to trigger fusion. Recent studies suggest that cholesterol and ceramide lipids from the cell surface may facilitate SARS-CoV-2 entry into host cells, but their exact mode of action remains unknown. We have used a combination of in vitro liposome-liposome and in situ cell-cell fusion assays to study the lipid determinants of S-mediated membrane fusion. We found that cholesterol and ceramide both facilitated fusion, suggesting that targeting lipids could be effective against SARS-CoV-2. As proof of concept, we examined the effect of chlorpromazine (CPZ), an antipsychotic drug known to perturb membrane structure. We found that CPZ inhibited S-mediated membrane fusion and thus potentially SARS-CoV-2 entry.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kristina Niort", - "author_inst": "Inserm" - }, - { - "author_name": "Julia Dancourt", - "author_inst": "Inserm" - }, - { - "author_name": "Erwan Boedec", - "author_inst": "Inserm" - }, - { - "author_name": "Zahra Al Amir Dache", - "author_inst": "Inserm" - }, - { - "author_name": "Gregory Lavieu", - "author_inst": "Inserm" - }, - { - "author_name": "David Tareste", - "author_inst": "Inserm" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.12.14.520265", "rel_title": "COVID-19 Associated Pulmonary Aspergillosis isolates are genomically diverse but similar to each other in their responses to infection-relevant stresses", @@ -160388,6 +161117,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.12.15.520561", + "rel_title": "SARS-CoV-2 causes periodontal fibrosis by deregulating mitochondrial beta-oxidation", + "rel_date": "2022-12-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.15.520561", + "rel_abs": "The global high prevalence of COVID-19 is a major challenge for health professionals and patients. SARS-CoV-2 virus mutate predominantly in the spike proteins, whilst the other key viral components remain stable. Previous studies have shown that the human oral cavity can potentially act as reservoir of the SARS-CoV-2 virus. COVID-19 can cause severe oral mucosa lesions and is likely to be connected with poor periodontal conditions. However, the consequence of SARS-CoV-2 viral infection on human oral health has not been systematically examined. In this research, we aimed to study the pathogenicity of SARS-CoV-2 viral components on human periodontal tissues and cells. We found that by exposing to SARS-CoV-2, especially to the viral envelope and membrane proteins, the human periodontal fibroblasts could develop fibrotic pathogenic phenotypes, including hyperproliferation that was concomitant induced together with increased apoptosis and senescence. The fibrotic degeneration was mediated by a down-regulation of mitochondrial {beta}-oxidation in the fibroblasts. Fatty acid {beta}-oxidation inhibitor, etomoxir treatment could mirror the same pathological consequence on the cells, similar to SARS- CoV-2 infection. Our results therefore provide novel mechanistic insights into how SARS- CoV-2 infection can affect human periodontal health at the cell and molecular level with potential new therapeutic targets for COVID-19 induced fibrosis.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Yan Gao", + "author_inst": "Peninsula Dental School, Faculty of Health, University of Plymouth" + }, + { + "author_name": "Wai Ling Kok", + "author_inst": "Peninsula Dental School, Faculty of Health, University of Plymouth" + }, + { + "author_name": "Vikram Sharma", + "author_inst": "School of Biomedical Sciences, Faculty of Health, University of Plymouth" + }, + { + "author_name": "Charlotte Sara Illsley", + "author_inst": "Peninsula Dental School, Faculty of Health, University of Plymouth" + }, + { + "author_name": "Sally Hanks", + "author_inst": "Peninsula Dental School, Faculty of Health, University of Plymouth" + }, + { + "author_name": "Christopher Tredwin", + "author_inst": "Peninsula Dental School, Faculty of Health, University of Plymouth" + }, + { + "author_name": "Bing Hu", + "author_inst": "Peninsula Dental School, Faculty of Health, University of Plymouth" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.12.14.22283492", "rel_title": "The estimated disease burden of COVID-19 in Japan from 2020 to 2021", @@ -162031,73 +162803,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.10.22283287", - "rel_title": "Reduced mortality among COVID-19 ICU patients after treatment with HemoClear convalescent plasma in Suriname", - "rel_date": "2022-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.10.22283287", - "rel_abs": "Convalescent plasma is a promising therapy for coronavirus disease 2019 (COVID-19), but its efficacy in intensive care unit (ICU) patients in a low and middle income country setting such as Suriname is unknown. Bedside plasma separation using the HemoClear device made convalescent plasma therapy accessible as treatment option in Suriname. Two hundred patients with severe SARS-CoV-2 infection requiring intensive care were recruited. Fifty eight patients (29%) received COVID-19 convalescent plasma (CCP) treatment in addition to standard of care (SOC). The CCP treatment and SOC groups were matched by age, sex, and disease severity scores. Mortality in the CCP treatment group was significantly lower than in the SOC group (21% versus 39%; Fishers exact P = 0.0133). Multivariate analysis using ICU days showed that CCP treatment reduced mortality (hazard ratio [HR], 0.35; 95% CI, 0.18-0.66; P = 0.001), while complication of acute renal failure (creatinine levels >110 mol/L; HR, 4.45; 95%CI, 2.54-7.80; P < 0.0001) was independently associated with death. Decrease in chest X-ray score in the CCP treatment group (median -3 points, IQR -4 to -1) was significantly greater than in the SOC group (median -1 point, IQR -3 to 1, Mann Whitney P = 0.0004). Improvement in PaO2/FiOs ratio was also significantly greater in the CCP treatment group (median 83, IQR 8 to 140) than in the SOC group (median 35, IQR -3 to 92, Mann Whitney P = 0.0234). Further research is needed for HemoClear-produced CCP as therapy in SARS-CoV-2 infections together with adequately powered, randomized controlled trials.\n\nImportanceThis study compares mortality and other endpoints between intensive care unit (ICU) COVID-19 patients treated with convalescent plasma plus standard of care (CCP), and a control group of patients hospitalized in the same medical ICU facility treated with standard of care alone (SOC) in a low and middle income country (LMIC) setting using bedside donor whole blood separation by gravity (HemoClear) to produce the CCP. It demonstrates a significant 65% survival improvement in HemoClear-produced CCP recipients (HR 0.35; 95% CI, 0.19-0.66; P = 0.001). Although this is an exploratory study, it clearly shows the benefit of using the HemoClear-produced CCP in ICU patients in the Suriname LMIC setting. Additional studies can further substantiate our findings and their applicability to both LMICs and high income countries and the use of CCP as a prepared readiness method to combat new viral pandemics.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Rosita Bihariesingh-Sanchit", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Rakesh Bansie", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Navin Ramdhani", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Rishi Mangroo", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Debra Bustamente", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Ernesto Diaz", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Cesar Fung A Foek", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Iswardath Thakoer", - "author_inst": "Academisch Ziekenhuis Paramaribo" - }, - { - "author_name": "Stephen C. Vreden", - "author_inst": "Foundation for Scientific Research Suriname (SWOS)" - }, - { - "author_name": "Zaheeb Choudry", - "author_inst": "Horacio Oduber Hospital" - }, - { - "author_name": "Angelique Bastienne van 't Wout", - "author_inst": "Van 't Wout Pharma Consulting" - }, - { - "author_name": "Dimitri A. Diavatopoulos", - "author_inst": "Radboud University Medical Center, Radboud Institute for Molecular Life Sciences" - }, - { - "author_name": "Arno P. Nierich", - "author_inst": "HemoClear BV" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.10.22283298", "rel_title": "The Use and Safety Risk of Repurposed Drugs for COVID-19 patients: Lessons Learned Utilizing the Food and Drug Administrations Adverse Event Reporting System", @@ -162389,6 +163094,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.12.12.520172", + "rel_title": "Fortuitous Somatic Mutations during Antibody Evolution Endow Broad Neutralization against SARS-CoV-2 Omicron Variants", + "rel_date": "2022-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.12.520172", + "rel_abs": "Striking antibody evasion by emerging circulating SARS-CoV-2 variants drives the identification of broadly neutralizing antibodies (bNAbs). However, how a bNAb acquires increased neutralization breadth during antibody evolution is still elusive. Here, we identified a clonally-related antibody family from a convalescent individual. One of the members, XG005, exhibited potent and broad neutralizing activities against SARS-CoV-2 variants, while the other members showed significant reductions in neutralization breadth and potency, especially against the Omicron sublineages. Structural analysis visualizing the XG005-Omicron spike binding interface revealed how crucial somatic mutations endowed XG005 with greater neutralization potency and breadth. A single administration of XG005 with extended half-life, reduced antibody-dependent enhancement (ADE) effect, and increased antibody product quality, exhibited a high therapeutic efficacy in BA.2- and BA.5-challenged mice. Our results provided a natural example to show the importance of somatic hypermutation during antibody evolution for SARS-CoV-2 neutralization breadth and potency.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Jianbo Wu", + "author_inst": "Fudan University" + }, + { + "author_name": "Zhenguo Chen", + "author_inst": "Fudan University" + }, + { + "author_name": "Yidan Gao", + "author_inst": "Fudan University" + }, + { + "author_name": "Zegen Wang", + "author_inst": "Advaccine Biopharmaceuticals Suzhou Co., Ltd" + }, + { + "author_name": "Jiarong Wang", + "author_inst": "Advaccine Biopharmaceuticals Suzhou Co., Ltd" + }, + { + "author_name": "Bing-Yu Chiang", + "author_inst": "Advaccine Biopharmaceuticals Suzhou Co., Ltd" + }, + { + "author_name": "Yunjiao Zhou", + "author_inst": "Fudan University" + }, + { + "author_name": "Yuru Han", + "author_inst": "Fudan University" + }, + { + "author_name": "Wuqiang Zhan", + "author_inst": "Fudan University" + }, + { + "author_name": "Minxiang Xie", + "author_inst": "Fudan University" + }, + { + "author_name": "Weiyu Jiang", + "author_inst": "Fudan University" + }, + { + "author_name": "Xiang Zhang", + "author_inst": "Fudan University" + }, + { + "author_name": "Aihua Hao", + "author_inst": "Fudan University" + }, + { + "author_name": "Anqi Xia", + "author_inst": "Fudan University" + }, + { + "author_name": "Jiaying He", + "author_inst": "Fudan University" + }, + { + "author_name": "Song Xue", + "author_inst": "Fudan University" + }, + { + "author_name": "Christian T. Mayer", + "author_inst": "National Cancer Institute" + }, + { + "author_name": "Fan Wu", + "author_inst": "Fudan University" + }, + { + "author_name": "Bin Wang", + "author_inst": "Fudan University" + }, + { + "author_name": "Lunan Zhang", + "author_inst": "Fudan University" + }, + { + "author_name": "Lei Sun", + "author_inst": "Fudan University" + }, + { + "author_name": "Qiao Wang", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.12.12.520032", "rel_title": "Live-attenuated pediatric parainfluenza vaccine expressing 6P-stabilized SARS-CoV-2 spike protein is protective against SARS-CoV-2 variants in hamsters", @@ -163701,33 +164509,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2022.12.08.22283265", - "rel_title": "Mental health self-care during the COVID-19 pandemic: a prospective cohort study in Australia", - "rel_date": "2022-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.08.22283265", - "rel_abs": "Pandemic public health measures have affected mental health for many people, resulting in varied approaches to mental health self-care. During 27 April - 26 July 2020, we surveyed a cohort of 1646 Australians, who were in paid employment prior to the pandemic, on changes in work, health, and managing their mental health concerns. Lifestyle changes were most the most frequently reported action to manage mental health concerns (78%), and were more common for women (OR=2.33, 95%CI=[1.82, 3.03]), and people experiencing recent work loss (OR=1.54, 95%CI=[1.04, 2.28]). Mental health self-care was more common for people experiencing psychological distress, or with pre-exisiting mental health conditions. Talking to friends about mental health, exercise and dietary changes, were more common for women and younger adults. Findings highlight potential benefits of reducing barriers to formal mental health services and supports during crises, particularly for people who less commonly seek help, and those experiencing psychological distress.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Daniel Griffiths", - "author_inst": "Monash University" - }, - { - "author_name": "Vinsensia Maharani Kanya Dhira Pradipta", - "author_inst": "Monash University" - }, - { - "author_name": "Alex Collie", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.12.08.22283272", "rel_title": "Duration of viral shedding of the Omicron variant in asymptomatic and mild COVID-19 cases from Shanghai, China", @@ -164031,6 +164812,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.12.08.519651", + "rel_title": "Biochemistry-informed design selects potent siRNAs against SARS-CoV-2", + "rel_date": "2022-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.08.519651", + "rel_abs": "RNA interference (RNAi) offers an efficient way to repress genes of interest, and it is widely used in research settings. Clinical applications emerged more recently, with 5 approved siRNAs (the RNA guides of the RNAi effector complex) against human diseases. The development of siRNAs against the SARS-CoV-2 virus could therefore provide the basis of novel COVID-19 treatments, while being easily adaptable to future variants or to other, unrelated viruses. Because the biochemistry of RNAi is very precisely described, it is now possible to design siRNAs with high predicted activity and specificity using only computational tools. While previous siRNA design algorithms tended to rely on simplistic strategies (raising fully complementary siRNAs against targets of interest), our approach uses the most up-to-date mechanistic description of RNAi to allow mismatches at tolerable positions and to force them at beneficial positions, while optimizing siRNA duplex asymmetry. Our pipeline proposes 8 siRNAs against SARS-CoV-2, and ex vivo assessment confirms the high antiviral activity of 6 out of 8 siRNAs, also achieving excellent variant coverage (with several 3-siRNA combinations recognizing each correctly-sequenced variant as of September 2022). Our approach is easily generalizable to other viruses as long as a variant genome database is available. With siRNA delivery procedures being currently improved, RNAi could therefore become an efficient and versatile antiviral therapeutic strategy.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "\u00c9lisabeth Houbron", + "author_inst": "CNRS" + }, + { + "author_name": "Sophie Mockly", + "author_inst": "CNRS" + }, + { + "author_name": "Sophia Rafasse", + "author_inst": "CNRS" + }, + { + "author_name": "Nathalie Gros", + "author_inst": "CNRS" + }, + { + "author_name": "Delphine Muriaux", + "author_inst": "CNRS" + }, + { + "author_name": "Herv\u00e9 Seitz", + "author_inst": "CNRS" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.12.08.518776", "rel_title": "Transboundary hotspots associated with SARS-like coronavirus spillover risk: implications for mitigation", @@ -165515,53 +166335,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.02.22281853", - "rel_title": "Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies", - "rel_date": "2022-12-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22281853", - "rel_abs": "The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. \"Superspreading,\" or \"over-dispersion,\" is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological heterogeneity. In contrast, the average number of secondary infections per contact is routinely estimated from household surveys, and these studies can minimize biases by testing all members of a household. However, the models used to analyze household transmission data typically assume that infectiousness and susceptibility are the same for all individuals or vary only with predetermined traits such as age. Here we develop and apply a combined forward simulation and inference method to quantify the degree of inter-individual variation in both infectiousness and susceptibility from observations of the distribution of infections in household surveys. First, analyzing simulated data, we show our method can reliably ascertain the presence, type, and amount of these heterogeneities with data from a sufficiently large sample of households. We then analyze a collection of household studies of COVID-19 from diverse settings around the world, and find strong evidence for large heterogeneity in both the infectiousness and susceptibility of individuals. Our results also provide a framework to improve the design of studies to evaluate household interventions in the presence of realistic heterogeneity between individuals.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Thayer L Anderson", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Anjalika Nande", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Carter Merenstein", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Brinkley Raynor", - "author_inst": "Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Anisha Oommen", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, " - }, - { - "author_name": "Brendan J Kelly", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Michael Z Levy", - "author_inst": "Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104" - }, - { - "author_name": "Alison L Hill", - "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, " - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.12.04.22282996", "rel_title": "COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting", @@ -165861,6 +166634,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.12.06.22283103", + "rel_title": "Heterologous boosting of neutralizing activity against Delta and Omicron SARS-CoV-2 variants in CoronaVac-primed adults; a randomized study with SCB-2019 vaccine", + "rel_date": "2022-12-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.06.22283103", + "rel_abs": "BackgroundThe global COVID-19 pandemic has peaked but some countries such as China are reporting serious infectious outbreaks due to SARS-CoV-2 variants. Waning vaccine-derived immunogenicity and mutations in variants allowing vaccine evasion require new booster immunization approaches. We compared homologous and heterologous boosting in adults previously fully primed with a whole-virus inactivated COVID-19 vaccine.\n\nMethodsAt multiple sites in the Philippines we enrolled 430 adults (18-72 years) immunized with two doses of CoronaVac at least 3 months previously and randomly assigned them to receive homologous (CoronaVac, n = 216) or heterologous (recombinant protein vaccine, SCB-2019, n = 214) booster doses. Non-inferiority/superiority of the neutralizing antibody (NAb) response 15 days after boosting was measured by microneutralization against prototype SARS-CoV-2, and Delta and Omicron variants in subsets (50 per arm). Participants recorded solicited local and systemic adverse events for 7 days, unsolicited AEs until Day 29, and serious adverse events until Day 60.\n\nResultsNAb geometric mean titers (GMT) against prototype on Day 15 were 744 (95% CI: 669-828) and 164 (143-189) in heterologous and homologous groups, respectively, with a heterologous/homologous GMT ratio of 4.63 (3.95-5.41), meeting both pre-defined non-inferiority and superiority criteria. Similarly, geometric mean-fold rises for NAb against Delta and Omicron BA.1, BA.2, BA.4 and BA.5 variants were superior after heterologous SCB-2019 (range 3.01-4.66) than homologous CoronaVac (range 0.85-1.6) in an exploratory analysis. Reactogenicity and safety measures were evenly balanced between groups; the most frequent local reaction was mild or moderate injection site pain; mild or moderate headache and fatigue were the most frequent systemic adverse events. No vaccine-related serious adverse events were reported.\n\nConclusionHeterologous boosting of CoronaVac-immunized adults with SCB-2019 was well tolerated with superior immunogenicity than homologous boosting, particularly for newly emerged variants, supporting use of SCB-2019 for booster vaccination.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Camilo C. Rao Jr.", + "author_inst": "Department of Physiology, Philippine General Hospital, University of the Philippines, Manila 1000, Philippines" + }, + { + "author_name": "Maria Rose A. de Los Reyes", + "author_inst": "Las Pinas Doctors Hospital, Las Pinas City, Philippines" + }, + { + "author_name": "Eric Plennevaux", + "author_inst": "Clover Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Igor Smolenov", + "author_inst": "Clover Biopharmaceuticals, Boston, MA, USA" + }, + { + "author_name": "Branda Hu", + "author_inst": "Clover Biopharmaceuticals, Boston, MA, USA" + }, + { + "author_name": "Faith Gao", + "author_inst": "Clover Biopharmaceuticals, Boston, MA, USA" + }, + { + "author_name": "Hannalyn Ilagan", + "author_inst": "Clover Biopharmaceuticals, Boston, MA, USA" + }, + { + "author_name": "Donna Ambrosino", + "author_inst": "Independent Advisor, Stuart, FL, USA" + }, + { + "author_name": "George Siber", + "author_inst": "Independent Advisor, New York, NY, USA" + }, + { + "author_name": "Ralf Clemens", + "author_inst": "Global Research in Infectious Diseases, Rio de Janeiro, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.06.22283185", "rel_title": "Preferences of health care workers using tongue swabs for tuberculosis diagnosis during COVID-19", @@ -167377,77 +168205,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.12.02.22283026", - "rel_title": "Healthcare in England was affected by the COVID-19 pandemic across the pancreatic cancer pathway: a cohort study using OpenSAFELY-TPP", - "rel_date": "2022-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22283026", - "rel_abs": "BackgroundHealthcare across all sectors, in the UK and globally, was negatively affected by the COVID-19 pandemic. We analysed healthcare services delivered to people with pancreatic cancer from January 2015 to March 2023 to investigate the effect of the COVID-19 pandemic.\n\nMethodsWith the approval of NHS England, and drawing from a nationally representative OpenSAFELY-TPP dataset of 24 million patients (over 40% of the English population), we undertook a cohort study of people diagnosed with pancreatic cancer. We queried electronic healthcare records for information on the provision of healthcare services across the pancreatic cancer pathway. To estimate the effect of the COVID-19 pandemic, we predicted the rates of healthcare services if the pandemic had not happened. We used generalised linear models (GLM) and the pre-pandemic data from January 2015 to February 2020 to predict rates in March 2020 to March 2023. The 95% confidence intervals of the predicted values were used to estimate the significance of the difference between the predicted and observed rates.\n\nResultsThe rate of pancreatic cancer and diabetes diagnoses in the cohort was not affected by the pandemic. There were 26,840 people diagnosed with pancreatic cancer from January 2015 to March 2023. The mean age at diagnosis was 72 ({+/-}11 SD), 48% of people were female, 95% were of White ethnicity and 40% were diagnosed with diabetes. We found a reduction in surgical resections by 25% to 28% during the pandemic. In addition, 20%, 10% and 4% fewer people received BMI, HbA1c and liver function tests respectively before they were diagnosed with pancreatic cancer. There was no impact of the pandemic on the number of people making contact with primary care, but the number of contacts increased on average by 1 to 2 per person amongst those who made contact. Reporting of jaundice decreased by 28%, but recovered within twelve months into the pandemic. Emergency department visits, hospital admissions and deaths were not affected.\n\nConclusionsThe pandemic affected healthcare in England across the pancreatic cancer pathway. Positive lessons could be learnt from the services that were resilient and those that recovered quickly. The reductions in healthcare experienced by people with cancer have the potential to lead to worse outcomes. Current efforts should focus on addressing the unmet needs of people with cancer.\n\nFundingThis work was jointly funded by the Wellcome Trust (222097/Z/20/Z); MRC (MR/V015757/1, MC_PC-20059, MR/W016729/1); NIHR (NIHR135559, COV-LT2-0073), and Health Data Research UK (HDRUK2021.000, 2021.0157). This work was funded by Medical Research Council (MRC) grant reference MR/W021390/1 as part of the postdoctoral fellowship awarded to AL and undertaken at the Bennett Institute, University of Oxford. The views expressed are those of the authors and not necessarily those of the NIHR, NHS England, UK Health Security Agency (UKHSA) or the Department of Health and Social Care. Funders had no role in the study design, collection, analysis, and interpretation of data; in the writing of the report; and in the decision to submit the article for publication.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Agnieszka Lemanska", - "author_inst": "University of Surrey" - }, - { - "author_name": "Colm D Andrews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Adam Frampton", - "author_inst": "Oncology Section, Surrey Cancer Research Institute, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK and HPB Surgical Unit," - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Keith J Roberts", - "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK" - }, - { - "author_name": "Praveetha Patalay", - "author_inst": "University College London" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "" - }, - { - "author_name": "Alex J Walker", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.30.22282946", "rel_title": "Discovering Social Determinants of Health from Case Reports using Natural Language Processing: Algorithmic Development and Validation", @@ -167651,6 +168408,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.12.02.22283040", + "rel_title": "Evaluating primary and booster vaccination prioritization strategies for COVID-19 by age and high-contact employment status using data from contact surveys", + "rel_date": "2022-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22283040", + "rel_abs": "The debate around vaccine prioritization for COVID-19 has revolved around balancing the benefits from: (1) the direct protection conferred by the vaccine amongst those at highest risk of severe disease outcomes, and (2) the indirect protection through vaccinating those that are at highest risk of being infected and of transmitting the virus. While adults aged 65+ are at highest risk for severe disease and death from COVID-19, essential service and other in-person workers with greater rates of contact may be at higher risk of acquiring and transmitting SARS-CoV-2. Unfortunately, there have been relatively little data available to understand heterogeneity in contact rates and risk across these demographic groups. Here, we retrospectively analyze and evaluate vaccination prioritization strategies by age and worker status. We use a mathematical model of SARS-CoV-2 transmission and uniquely detailed contact data collected as part of the Berkeley Interpersonal Contact Survey to evaluate five vaccination prioritization strategies: (1) prioritizing only adults over age 65, (2) prioritizing only high-contact workers, (3) splitting prioritization between adults 65+ and high-contact workers, (4) tiered prioritization of adults over age 65 followed by high-contact workers, and (5) tiered prioritization of high-contact workers followed by adults. We find that for the primary two-dose vaccination schedule, assuming 70% uptake, a tiered roll-out that first prioritizes adults 65+ averts the most deaths (31% fewer deaths compared to a no-vaccination scenario) while a tiered roll-out that prioritizes high contact workers averts the most number of clinical infections (14% fewer clinical infections compared to a no-vaccination scenario). We also consider prioritization strategies for booster doses during a subsequent outbreak of a hypothetical new SARS-CoV-2 variant. We find that a tiered roll-out that prioritizes adults 65+ for booster doses consistently averts the most deaths, and it may also avert the most number of clinical cases depending on the epidemiology of the SARS-CoV-2 variant and the vaccine efficacy.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ethan Michael Roubenoff", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Dennis Feehan", + "author_inst": "UC Berkeley" + }, + { + "author_name": "Ayesha Michael Mahmud", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.02.22282921", "rel_title": "Durability of immune responses to the booster mRNA vaccination against COVID-19", @@ -169347,61 +170131,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.11.29.22282857", - "rel_title": "Vaccine hesitancy, reactogenicity and immunogenicity of BNT162b2 and CoronaVac in pediatric patients with neuromuscular diseases", - "rel_date": "2022-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282857", - "rel_abs": "IntroductionCOVID-19 causes global health and psychosocial devastation, particularly to high-risk patients such as those with neuromuscular diseases (NMDs). The mRNA-based BNT162b2 and inactivated whole-virus CoronaVac are two novel COVID-19 vaccines widely used across the world that confer immune protection to healthy individuals. However, hesitancy towards COVID-19 vaccination was common for patients with NMDs early in the pandemic due to the paucity of data on the safety and efficacy in this specific patient population. Therefore, we examined the underlying factors associated with vaccine hesitancy across time for these patients and included the assessment of the reactogenicity and immunogenicity of these two vaccines.\n\nMethodsPediatric patients were screened from our NMD registry. For the vaccine hesitancy arm, those aged 8-18 years with no cognitive delay were invited to complete surveys in January and April 2022. For the reactogenicity and immunogenicity arm, patients aged 2-21 years were enrolled for COVID-19 vaccination between June 2021 to April 2022. Participants recorded adverse reactions (ARs) for 7 days after vaccination. Peripheral blood was obtained before BNT162b2 or CoronaVac and within 49 days after vaccination to measure their serological antibody responses as compared to healthy children and adolescents.\n\nResultsForty-one patients completed vaccine hesitancy surveys for both timepoints, and 22 joined our reactogenicity and immunogenicity arm of the study. Two or more family members vaccinated against COVID-19 was positively associated with intention of vaccination (odds ratio 11.7, 95% CI 1.81-75.1, p=0.010). Pain at the injection site, fatigue and myalgia were the commonest ARs. Most ARs were mild (75.5%, n=71/94). All 19 patients seroconverted against the wildtype SARS-CoV-2 after two doses of BNT162b2 or CoronaVac, although there was lower neutralization against the Omicron BA.1 variant.\n\nDiscussionThis study demonstrated vaccine hesitancy amongst patients with NMDs was influenced by family members and changed across time. BNT162b2 and CoronaVac were safe and immunogenic even for patients on low-dose corticosteroids. Future research is required to assess the durability of the COVID-19 vaccines, the effectiveness of booster doses and other routes of administration against emerging SARS-CoV-2 variants for these patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael Kwan Leung Yu", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Hoi Shan Sophelia Chan", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Samuel Cheng", - "author_inst": "School of Public Health, The University of Hong Kong" - }, - { - "author_name": "Daniel Leung", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Sau Man Chan", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Amy Ka Yan Suen", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Wilfred Hing Sang Wong", - "author_inst": "1Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Malik Peiris", - "author_inst": "School of Public Health, The University of Hong Kong" - }, - { - "author_name": "Yu Lung Lau", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - }, - { - "author_name": "Jaime S Rosa Duque", - "author_inst": "Department of Paediatrics and Adolescent Medicine, The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.11.30.22282922", "rel_title": "Epidemiological impact of a large number of incorrect negative SARS-CoV-2 test results in South West England during September and October 2021", @@ -169725,6 +170454,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.29.518438", + "rel_title": "Targeted photodynamic neutralization of SARS-CoV-2 mediated by singlet oxygen", + "rel_date": "2022-11-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.29.518438", + "rel_abs": "The SARS-CoV-2 virus has been on a rampage for more than two years. Vaccines in combination with neutralizing antibodies (NAbs) against SARS-CoV-2 carry great hope in the treatment and final elimination of COVID-19. However, the relentless emergence of variants of concern (VOC), including the most recent Omicron variants, presses for novel measures to counter these variants that often show immune evasion. Hereby we developed a targeted photodynamic approach to neutralize SARS-CoV-2 by engineering a genetically encoded photosensitizer (SOPP3) to a diverse list of antibodies targeting the WT spike protein, including human antibodies isolated from a 2003 SARS patient, potent monomeric and multimeric nanobodies targeting RBD, and non-neutralizing antibodies (non-NAbs) targeting the more conserved NTD region. As confirmed by pseudovirus neutralization assay, this targeted photodynamic approach significantly increased the efficacy of these antibodies, especially that of non-NAbs, against not only the WT but also the Delta strain and the heavily immune escape Omicron strain (BA.1). Subsequent measurement of infrared phosphorescence at 1270 nm confirmed the generation of singlet oxygen (1O2) in the photodynamic process. Mass spectroscopy assay uncovered amino acids in the spike protein targeted by 1O2. Impressively, Y145 and H146 form an oxidization \"hotspot\", which overlaps with the antigenic \"supersite\" in NTD. Taken together, our study established a targeted photodynamic approach against the SARS-CoV-2 virus and provided mechanistic insights into the photodynamic modification of protein molecules mediated by 1O2.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Ruhui Yao", + "author_inst": "Shenzhen Bay Laboratory" + }, + { + "author_name": "Jian Hou", + "author_inst": "Shenzhen Bay Laboratory" + }, + { + "author_name": "Xin Zhang", + "author_inst": "Shenzhen Bay Laboratory" + }, + { + "author_name": "Yi Li", + "author_inst": "Shenzhen Bay Laboratory" + }, + { + "author_name": "Junhui Lai", + "author_inst": "Shenzhen Bay Laboratory" + }, + { + "author_name": "Qinqin Wu", + "author_inst": "Shenzhen Bay Laboratory" + }, + { + "author_name": "Qinglian Liu", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Lei Zhou", + "author_inst": "Shenzhen Bay Laboratory" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2022.11.29.22282907", "rel_title": "Mental Health, Substance Use, and the Importance of Religion during the COVID-19 Pandemic", @@ -170953,45 +171729,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.29.22282887", - "rel_title": "Disruption in seasonality, patient characteristics and disparities of respiratory syncytial virus infection among young children in the US during and before the COVID-19 pandemic: 2010-2022", - "rel_date": "2022-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.29.22282887", - "rel_abs": "Respiratory syncytial virus (RSV) infections and hospitalization have surged sharply among young children. Here we test how the seasonal patterns of RSV infections in 2022 compared with those from other COVID-19 pandemic and pre-pandemic years. For this purpose, we analyzed a nation-wide and real-time database of electronic health records of 56 million patients across 50 states in the US. The monthly incidence rate of first-time RSV infection in young children (<5 years of age) and very young children (<1 year of age) followed a seasonal pattern from 2010 to 2019 with increases during the autumn, peaking in winter, subsiding in spring and summer. This seasonal pattern was significantly disrupted during the COVID-19 pandemic. In 2020, the incidence rate of RSV infections was remarkably low throughout the year. In 2021, the RSV season expanded to 9 months starting in the early summer and peaking in October. In 2022, RSV infections started to rise in May and were significantly higher than in previous years reaching a historically highest incidence rate in November 2022. There were significant racial and ethnic disparities in the peak RSV infection rate during 2010-2021 and the disparities further exacerbated in 2022 with peak incidence rate in black and Hispanic children 2-3 times that in white children. Among RSV-infected children in 2022, 19.2% had prior documented COVID-19 infection, significantly higher than the 9.7% among uninfected children, suggesting that prior COVID-19 could be a risk factor for RSV infection or that there are common risk factors for both viral infections. Our study calls for continuous monitoring of RSV infection in young children alongside its clinical outcomes and for future work to assess potential COVID-19 related risk factors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Lindsey Wang", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "pamela B Davis", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Nathan A Berger", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "David C Kaelber", - "author_inst": "Metrohealth" - }, - { - "author_name": "Nora Volkow", - "author_inst": "National Institute on Drug Abuse" - }, - { - "author_name": "Rong Xu", - "author_inst": "Case Western Reserve University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.29.518406", "rel_title": "Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins", @@ -171287,6 +172024,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.11.22.22282627", + "rel_title": "Strengthening response coordination through public health emergency operations centers in Africa: Lessons learned from 56-week webinar sessions, 2020-2021", + "rel_date": "2022-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.22.22282627", + "rel_abs": "BackgroundFollowing the declaration of coronavirus disease 2019 (COVID-19) as a pandemic on 11 March 2020, in-person events including trainings were canceled to limit the spread of the pandemic. A virtual learning program was established in May 2020 by Africa Centers for Disease Control and Prevention, the World Health Organization, and other partners to strengthen COVID-19 response coordination through the public health emergency operations centers (PHEOCs). We present a review of the webinar series, the experience, and the lessons learned.\n\nMethodA data extraction tool was developed to retrieve data from the Africa CDCs webinar data repository. Major findings were synthesized and described per thematic area.\n\nResultsA total of 12,715 (13% of the 95,230 registrants) attended the 56 PHEOC webinar sessions between June 2020 and December 2021 and 47% of the attendees came from 17 countries. Of those who attended, 8,528 (70%) were from Africa. The webinars provided 97 learning hours with an average length of 1.18 hours per session. On average, there were 235 attendees per session. In addition, there was an average of 26 interactions between participants and facilitators per session. A total of 4,084 (44%) of the participants (9,283) responded to the post-session surveys, with over 95% rating the webinar topics as being relevant to their work, contributed to improving their understanding of PHEOC operationalization, and with extensive ease of comprehension.\n\nConclusionThe virtual training served the intended audience given the high number of participants from African member states, with satisfactory feedback on training relevance. We highlighted a just-in-time, progressively adaptive experience in delivering a PHEOC/PHEM virtual learning in Africa with a consequential global audience at the peak of the COVID-19 pandemic.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Womi Eteng", + "author_inst": "AU: African Union" + }, + { + "author_name": "Abrham Lilay Gebrewahid", + "author_inst": "World Health Organization Regional Office for Africa: Organisation mondiale de la Sante pour Afrique" + }, + { + "author_name": "Senait Tekeste", + "author_inst": "World Health Organization Regional Office for Africa: Organisation mondiale de la Sante pour Afrique" + }, + { + "author_name": "Wessam Mankoula", + "author_inst": "African Union" + }, + { + "author_name": "Emily Collard", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Chimwemwe Waya", + "author_inst": "AU: African Union" + }, + { + "author_name": "Emily Rosenfeld", + "author_inst": "CDC: Centers for Disease Control and Prevention" + }, + { + "author_name": "Chuck Menchion Wilton", + "author_inst": "CDC: Centers for Disease Control and Prevention" + }, + { + "author_name": "Martin Muita", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Liz McGinley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Yan Kawe", + "author_inst": "World Health Organization Regional Office for Africa: Organisation mondiale de la Sante pour Afrique" + }, + { + "author_name": "Ali Abdullah", + "author_inst": "Eastern Mediterranean Regional Office: World Health Organisation Regional Office for the Eastern Mediterranean" + }, + { + "author_name": "Ariane Halm", + "author_inst": "Robert Koch Institut" + }, + { + "author_name": "Jian Li", + "author_inst": "World Health Organization" + }, + { + "author_name": "Virgil L Lokossou", + "author_inst": "ECOWAS: Economic Community of West African States" + }, + { + "author_name": "Youssouf Kanoute", + "author_inst": "World Health Organization" + }, + { + "author_name": "Ibrahima Sonko", + "author_inst": "AU: African Union" + }, + { + "author_name": "Merawi Aragaw", + "author_inst": "AU: African Union" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.11.24.515932", "rel_title": "Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2", @@ -172979,49 +173803,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.23.22282686", - "rel_title": "Assessment of Attitude and Hesitancy Towards Covid-19 Vaccine among Hepatitis B and C Patients in Pakistan", - "rel_date": "2022-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.23.22282686", - "rel_abs": "OBJECTIVEThe research aimed to evaluate the attitude and perceptions towards the covid-19 vaccine among Hepatitis B and C patients in Peshawar, Khyber Pakhtunkhwa, Muzaffarabad, Azad Kashmir, Pakistan.\n\nMETHODSA survey-based study was adopted to evaluate the attitude of Hepatitis B and C patients towards immunization against covid-19 in Peshawar (KPK) and Muzaffarabad (AJK) cities of Pakistan. The study continued from January 2020 to February 2021. Participants were also assessed for their perception towards covid-19 vaccination.\n\nRESULTSA total of 839 (33.6%) individuals participated in the study. About 52 % of Hepatitis B patients were immunized against Covid-19, whereas the number of Hepatitis C patients was recorded at around 48%. About 53.7 % of participants refused to get the vaccine without any reason. About 63.2% of patients showed concern about the insufficient data available on the vaccine safety and efficacy published by the Public Health Department. Individuals with higher education were observed to be more open towards vaccination then those without a formal education. More than half of the participants (61.5 %) were concerned about the interference of the vaccine with their hepatitis treatment whereas 54.7 % patients refused vaccine because of a poor liver condition.\n\nCONCLUSIONSThe data indicated that limited data availability regarding the vaccine efficacy in viral hepatitis patients and negative attitudes of people toward covid-19 vaccination is the main cause of Covid-19 vaccination refusal among hepatitis B and C patients.\n\nDESCRIPTORSHepatitis B, Hepatitis C, covid-19, immunization, vaccine refusal, Pakistan.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Farheen Shafique", - "author_inst": "University of Azad Jammu and Kashmir Muzaffarabad, Pakistan" - }, - { - "author_name": "Mahreen Ul Hassan", - "author_inst": "Shaheed Benazir Bhutto Women University Peshawar, Pakistan" - }, - { - "author_name": "Sadia Butt", - "author_inst": "Shaheed Benazir Bhutto Women University Peshawar, Pakistan" - }, - { - "author_name": "Sadia Siddique", - "author_inst": "Shaheed Benazir Bhutto Women University Peshawar, Pakistan" - }, - { - "author_name": "Nazia Akbar", - "author_inst": "Hazara University" - }, - { - "author_name": "Azra Abrar", - "author_inst": "Abasyn University Peshawar, Pakistan" - }, - { - "author_name": "Irshad Rehman", - "author_inst": "University of Peshawar, Pakistan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.23.22282648", "rel_title": "An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint-Petersburg, Russia", @@ -173397,6 +174178,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.11.20.22282552", + "rel_title": "Use of whole genome sequencing to identify low-frequency mutations in COVID-19 patients treated with remdesivir", + "rel_date": "2022-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.20.22282552", + "rel_abs": "BackgroundWe investigate the effects of remdesivir (RDV) treatment on intra-host SARS-CoV-2 diversity and low-frequency mutations in moderately ill hospitalized COVID-19 patients and compare them to patients without RDV treatment.\n\nMethodsSequential collections of nasopharyngeal and mid-turbinate swabs were obtained from 16 patients with and 31 patients without RDV treatment. A total of 113 samples were sequenced and mutation analyses were performed.\n\nResultsWe did not identify any drug resistant mutations during RDV therapy. In genes encoding and associated with the replication complex, low-frequency minority variants that do not reach fixation within the sampling period were detected in 6/16 (37.5%) and 14/31 (45%) patients with and without RDV treatment respectively. We did not detect significant differences in within-host diversity and positive selection between the RDV-treated and untreated groups.\n\nConclusionsMinimal intra-host variability and stochastic low-frequency variants detected in moderately ill patients suggests little selective pressure in patients receiving short courses of RDV. Patients undergoing short regimens of RDV therapy should continue to be monitored.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Kuganya Nirmalarajah", + "author_inst": "Sunnybrook Research Institute" + }, + { + "author_name": "Finlay Maguire", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Winfield Yim", + "author_inst": "Sunnybrook Research Institute" + }, + { + "author_name": "Patryk Aftanas", + "author_inst": "Shared Hospital Labs" + }, + { + "author_name": "Angel X Li", + "author_inst": "Sinai Health System" + }, + { + "author_name": "Altynay Shigayeva", + "author_inst": "Sinai Health System" + }, + { + "author_name": "Lily Yip", + "author_inst": "Sunnybrook Research Institute" + }, + { + "author_name": "Xi Zoe Zhong", + "author_inst": "Sinai Health System" + }, + { + "author_name": "Allison J McGeer", + "author_inst": "Sinai Health System" + }, + { + "author_name": "Samira Mubareka", + "author_inst": "Sunnybrook Research Institute" + }, + { + "author_name": "Robert Kozak", + "author_inst": "Sunnybrook Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.22.517465", "rel_title": "Nirmatrelvir treatment blunts the development of antiviral adaptive immune responses in SARS-CoV-2 infected mice", @@ -174773,49 +175613,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.11.20.517193", - "rel_title": "Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines", - "rel_date": "2022-11-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.20.517193", - "rel_abs": "Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression allelic imbalance can be measured by allele-specific expression analysis (ASE) across heterozygous informative expressed single nucleotide variants (eSNVs). ASE reflects many regulatory biological phenomena that can be assessed by combining genome and transcriptome information. ASE contributes to the interindividual variability associated with disease. We aim to estimate the transcriptome-wide impact of SARS-CoV-2 infection by analyzing eSNVs. We compared ASE profiles in the human lung cell lines Calu-3, A459, and H522 before and after infection with SARS-CoV-2 using RNA-Seq experiments. We identified 34 differential ASE (DASE) sites in 13 genes (HLA-A, HLA-B, HLA-C, BRD2, EHD2, GFM2, GSPT1, HAVCR1, MAT2A, NQO2, SUPT6H, TNFRSF11A, UMPS), all of which are enriched in protein binding functions and play a role in COVID-19. Most DASE sites were assigned to the MHC class I locus and were predominantly upregulated upon infection. DASE sites in the MHC class I locus also occur in iPSC-derived airway epithelium basal cells infected with SARS-CoV-2. Using an RNA-Seq haplotype reconstruction approach, we found DASE sites and adjacent eSNVs in phase (i.e., predicted on the same DNA strand), demonstrating differential haplotype expression upon infection. We found a bias towards the expression of the HLA alleles with a higher binding affinity to SARS-CoV-2 epitopes. Independent of gene expression compensation, SARS-CoV-2 infection of human lung cell lines induces transcriptional allelic switching at the MHC loci. This suggests a response mechanism to SARS-CoV-2 infection that swaps HLA alleles with poor epitope binding affinity, an expectation supported by publicly available proteome data.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ronaldo da Silva Francisco Junior", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Jairo R Temerozo", - "author_inst": "Oswaldo Cruz Institute" - }, - { - "author_name": "Cristina dos Santos Ferreira", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Yasmmin Martins", - "author_inst": "Instituto de Calculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina" - }, - { - "author_name": "Thiago Moreno L Souza", - "author_inst": "Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro" - }, - { - "author_name": "Enrique Medina-Acosta", - "author_inst": "Molecular Identification and Diagnostics Unit (NUDIM), Laboratory of Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Flu" - }, - { - "author_name": "Ana Tereza Ribeiro de Vasconcelos", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.11.21.517338", "rel_title": "Ultrasound treatment inhibits SARS-CoV-2 in vitro infectivity", @@ -175095,6 +175892,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.19.22282546", + "rel_title": "Oligosymptomatic long-term carriers of SARS-CoV-2 display impaired innate resistance and high Spike-specific neutralizing antibodies", + "rel_date": "2022-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.19.22282546", + "rel_abs": "The vast spectrum of clinical features of COVID-19 keeps challenging scientists and clinicians. Control of pathogen load (host resistance) and prevention of tissue damage (disease tolerance) are essential for the outcome of infectious diseases. Both low resistance and high disease tolerance might result in long-term viral persistence, but the underlying mechanisms remain unclear. Here, we studied the immune response of immunocompetent COVID-19 patients with prolonged SARS-CoV-2 infection by immunophenotyping, cytokine and serological analysis. Despite viral loads and symptoms comparable to regular mildly-symptomatic patients, long-term carriers displayed weaker systemic IFN-I responses and fewer circulating pDCs and NK cells at disease onset. Type 1 cytokines remained low, while type-3 cytokines were in turn enhanced. Interestingly, the plasma of these patients showed a higher spike-specific neutralization capacity. The identification of very early distinct immune responses in long-term carriers adds up to our understanding on essential host protective mechanisms to ensure tissue damage control despite prolonged viral infection.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Elena Montes-Cobos", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Victoria C Bastos", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Clarice Monteiro", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Joao CR Freitas", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Heiny DP Fernandes", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Clarice S Constancio", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Danielle AS Rodrigues", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Andreza MDS Gama", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Vinicius M Vidal", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Leticia S Alves", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Laura Zalcberg-Renault", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Guilherme S Lira", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Victor A Ota", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Carolina Caloba", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Luciana Conde", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Isabela C Leitao", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Amilcar Tanuri", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Orlando DC Ferreira", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Renata M Pereira", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Andre M Vale", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Terezinha M Castineiras", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Dominique Kaiserlian", + "author_inst": "INSERM" + }, + { + "author_name": "Juliana Echevarria-Lima", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Marcelo T Bozza", + "author_inst": "Universidade Federal do Rio de Janeiro" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.19.22282543", "rel_title": "Elevated circulating monocytes and monocyte activation in pulmonary post-acute sequelae of SARS-CoV-2 infection", @@ -176507,45 +177415,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.11.18.22282510", - "rel_title": "Mindfulness supports emotional resilience in children during the COVID-19 Pandemic", - "rel_date": "2022-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.18.22282510", - "rel_abs": "An important aspect of mental health in children is emotional resilience, the capacity to adapt to, and recover from, stressors and emotional challenges. Variation in trait mindfulness, ones disposition to attend to experiences with an open and nonjudgmental attitude, may be an important individual difference in children that supports emotional resilience. In this study, we investigated whether trait mindfulness was related to emotional resilience in response to stressful changes in education and home-life during the COVID-19 pandemic in the United States. We conducted a correlational study examining self-report data from July 2020 to February 2021, from 163 eight-to-ten-year-old children living in the US. Higher trait mindfulness scores correlated with less stress, anxiety, depression, and negative affect in children, and lower ratings of COVID-19 impact on their lives. Mindfulness moderated the relationship between COVID-19 child impact and negative affect. Children scoring high on mindfulness showed no correlation between rated COVID-19 impact and negative affect, whereas those who scored low on mindfulness showed a positive correlation between child COVID-19 impact and negative affect. Higher levels of trait mindfulness may have helped children to better cope with a wide range of COVID-19 stressors. Future studies should investigate the mechanisms by which trait mindfulness supports emotional resilience in children.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Isaac N Treves", - "author_inst": "MIT: Massachusetts Institute of Technology" - }, - { - "author_name": "Cindy Li", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Kimberly Wang", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ola Ozernov-Palchik", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Halie Olson", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "John Gabrieli", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.11.16.22282406", "rel_title": "Special Olympics global report on COVID-19 vaccination and reasons not to vaccinate among adults with intellectual disabilities", @@ -176857,6 +177726,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2022.11.16.22282100", + "rel_title": "Particulate matter air pollution and COVID-19 infection, severity, and mortality: A systematic review", + "rel_date": "2022-11-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.16.22282100", + "rel_abs": "Background and objectiveEcological studies indicate ambient particulate matter [≤]2.5mm (PM2.5) air pollution is associated with poorer COVID-19 outcomes. However, these studies cannot account for individual heterogeneity and often have imprecise estimates of PM2.5 exposure. We review evidence from studies using individual-level data to determine whether PM2.5 increases risk of COVID-19 infection, severe disease, and death.\n\nMethodsSystematic review of case-control and cohort studies, searching Medline, Embase, and WHO COVID-19 up to 30 June 2022. Study quality was evaluated using the Newcastle-Ottawa Scale. Results were pooled with a random effects meta-analysis, with Eggers regression, funnel plots, and leave-one-out and trim-and-fill analyses to adjust for publication bias.\n\nResultsN=18 studies met inclusion criteria. A 10g/m3 increase in PM2.5 exposure was associated with 66% (95% CI: 1.31-2.11) greater odds of COVID-19 infection (N=7) and 127% (95% CI: 1.41-3.66) increase in severe illness (hospitalisation or worse) (N=6). Pooled mortality results (N=5) were positive but non-significant (OR 1.40; 0.94 to 2.10). Most studies were rated \"good\" quality (14/18 studies), though there were numerous methodological issues; few used individual-level data to adjust for confounders like socioeconomic status (4/18 studies), instead using area-based indicators (12/18 studies) or not adjusting for it (3/18 studies). Most severity (9/10 studies) and mortality studies (5/6 studies) were based on people already diagnosed COVID-19, potentially introducing collider bias.\n\nConclusionThere is strong evidence that ambient PM2.5 increases the risk of COVID-19 infection, and weaker evidence of increases in severe disease and mortality.\n\nFundingThis review was completed as a Scholarly Intensive Placement project by NS, which received no funding.\n\nCompeting interestsThe authors declare no competing interests.\n\nRegistrationThis study was registered on PROSPERO on 8 July 2022 (CRD42022345129): https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022345129", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Nicola Sheppard", + "author_inst": "Monash School of Medicine, Monash University" + }, + { + "author_name": "Matthew Carroll", + "author_inst": "Monash Rural Health Churchill, Monash University" + }, + { + "author_name": "Caroline X Gao", + "author_inst": "School of Public Health and Preventive Medicine, Monash University" + }, + { + "author_name": "Tyler J Lane", + "author_inst": "School of Public Health and Preventive Medicine, Monash University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.11.16.22282426", "rel_title": "The prevalence of probable mental health disorders among hospital healthcare workers during COVID-19: A systematic review and meta-analysis", @@ -178269,109 +179169,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.11.12.22282116", - "rel_title": "Conceptualising the Episodic Nature of Disability among Adults Living with Long COVID: A Qualitative Study", - "rel_date": "2022-11-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.12.22282116", - "rel_abs": "ObjectivesTo describe episodic nature of disability among adults living with Long COVID.\n\nMethodsWe conducted a community-engaged qualitative descriptive study involving online semi-structured interviews and participant visual illustrations. We recruited participants via collaborator community organizations in Canada, Ireland, United Kingdom, and United States.\n\nParticipantsAdults who self-identified as living with Long COVID. We purposively recruited for diversity in age, gender, race/ethnicity, sexual orientation, and duration since initial COVID-19 infection.\n\nMain Outcome Measure(s)We used a semi-structured interview guide to explore experiences of disability living with Long COVID, specifically health-related challenges and how they were experienced over time. We asked participants to draw their health trajectory and conducted a group-based content analysis.\n\nResultsAmong the 40 participants, the median age was 39 years (interquartile range: 32, 49); majority were women (63%), white (73%), heterosexual (75%), and living with Long COVID for [≥]1 year (83%). Participants described their disability experiences as episodic in nature, characterized by fluctuations in presence and severity of health-related challenges (disability) that may occur both within a day and over the long-term living with Long COVID. They described living with ups and downs, flare-ups, and peaks followed by crashes, troughs, and valleys, likened to a yo-yo rolling hills, and rollercoaster ride with relapsing/remitting, waxing/waning, fluctuations in health. Drawn illustrations demonstrated variety of trajectories across health dimensions, some more episodic than others. Uncertainty intersected with the episodic nature of disability, characterized as unpredictability of episodes, their length, severity and triggers, and process of long-term trajectory, which had implications on broader health.\n\nConclusionsAmong this sample of adults living with Long COVID, experiences of disability were described as episodic, characterized by fluctuating health challenges, which may be unpredictable in nature. Results help to better understand experiences of disability among adults living with Long COVID to inform healthcare and rehabilitation.\n\nKEY MESSAGESO_LIWhat is already known on this topic: Globally, a growing number of individuals are living with persistent and prolonged signs and symptoms following infection consistent with COVID-19, referred to as Long COVID, Post COVID-19 Condition (PCC) or Post-acute sequelae of SARS-CoV2 (PASC). Individuals living with Long COVID are experiencing a range of symptoms and impairments that impact their ability to carry out day to day activities or engage in social and community life roles.\nC_LIO_LIWhat this study adds: Disability living with Long COVID was described as episodic, characterized by fluctuations in presence and severity of health related challenges, which may be unpredictable in nature, occurring both within the day, and over the long-term of months and years living with Long COVID.\nC_LIO_LIHow this study might affect research, practice or policy: Results will help researchers, healthcare providers, policymakers, employers, and community members to better understand experiences of disability among adults living with Long COVID, to inform future disability measurement, health and rehabilitation care and service delivery, programs and policies for insurance, return to work, and workplace accommodations.\nC_LI", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Kelly O'Brien", - "author_inst": "Univesrity of Toronto" - }, - { - "author_name": "Darren A Brown", - "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust" - }, - { - "author_name": "Kiera McDuff", - "author_inst": "University of Toronto" - }, - { - "author_name": "Natalie St. Clair-Sullivan", - "author_inst": "Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom" - }, - { - "author_name": "Patricia Solomon", - "author_inst": "McMaster University" - }, - { - "author_name": "Soo Chan Carusone", - "author_inst": "McMaster University" - }, - { - "author_name": "Lisa McCorkell", - "author_inst": "Patient-Led Research Collaborative" - }, - { - "author_name": "Hannah Wei", - "author_inst": "Patient-Led Research Collaborative" - }, - { - "author_name": "Susie Goulding", - "author_inst": "COVID Long-Haulers Support Group Canada, Canada" - }, - { - "author_name": "Margaret O'Hara", - "author_inst": "Long Covid Support, United Kingdom" - }, - { - "author_name": "Catherine Thomson", - "author_inst": "Long COVID Physio, United Kingdom" - }, - { - "author_name": "Niamh Roche", - "author_inst": "Long COVID Ireland" - }, - { - "author_name": "Ruth Stokes", - "author_inst": "Long COVID Ireland" - }, - { - "author_name": "Jaime H. Vera", - "author_inst": "Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom" - }, - { - "author_name": "Kristine Erlandson", - "author_inst": "University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado, United States" - }, - { - "author_name": "Colm Bergin", - "author_inst": "St James's Hospital, Dublin, Ireland" - }, - { - "author_name": "Larry Robinson", - "author_inst": "Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada" - }, - { - "author_name": "Angela M. Cheung", - "author_inst": "University Health Network, Toronto, Ontario, Canada; University of Toronto, Ontario, Canada" - }, - { - "author_name": "Brittany Torres", - "author_inst": "University of Toronto, Ontario, Canada" - }, - { - "author_name": "Lisa Avery", - "author_inst": "University Health Network, Toronto, Ontario, Canada; University of Toronto, Ontario, Canada" - }, - { - "author_name": "Ciaran Bannan", - "author_inst": "St James's Hospital" - }, - { - "author_name": "Richard Harding", - "author_inst": "King's College London, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2022.11.11.22282032", "rel_title": "COVID Seq as Laboratory Developed Test (LDT) for diagnosis of SARS-CoV-2 Variants of Concern (VOC)", @@ -178675,6 +179472,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.11.11.516052", + "rel_title": "Genetic and structural data on the SARS-CoV-2 Omicron BQ.1 variant reveal its low potential for epidemiological expansion", + "rel_date": "2022-11-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.11.516052", + "rel_abs": "The BQ.1 SARS-CoV-2 variant, also known as Cerberus, is one of the most recent Omicron descendant lineages. Compared to its direct progenitor BA.5, BQ.1 carries out some additional spike mutations in some key antigenic site which confer it further immune escape ability over other circulating lineage. In such a context, here we performed a genome-based survey aimed to obtain an as complete as possible nuance of this rapidly evolving Omicron subvariant. Genetic data suggests that BQ.1 represents an evolutionary blind background, lacking of the rapid diversification which is typical of a dangerous lineage. Indeed, the evolutionary rate of BQ.1 is very similar to that of BA.5 (7.6 x 10-4 and 7 x 10-4 subs/site/year, respectively), which is circulating by several months. Bayesian Skyline Plot reconstruction, indicates low level of genetic variability, suggesting that the peak has been reached around September 3, 2022. Structure analyses performed by comparing the properties of BQ.1 and BA.5 RBD indicated that the impact of the BQ.1 mutations on the affinity for ACE2 may be modest. Likewise, immunoinformatic analyses showed modest differences between the BQ.1 and the BA5 potential B-cells epitope. In conclusion, genetic and structural analysis on SARS-CoV-2 BQ.1 suggest that, it does not show evidence about its particular dangerous or high expansion capability. The monitoring genome-based must continue uninterrupted for a better understanding of its descendant and all other lineages.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Fabio Scarpa", + "author_inst": "University of Sassari" + }, + { + "author_name": "Daria Sanna", + "author_inst": "Department of Biomedical Sciences, University of Sassari, Sassari, Italy" + }, + { + "author_name": "Domenico Benvenuto", + "author_inst": "Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy;" + }, + { + "author_name": "Alessandra Borsetti", + "author_inst": "National HIV/AIDS Research Center, Istituto Superiore di Sanita, Rome, Italy" + }, + { + "author_name": "Ilenia Azzena", + "author_inst": "Department of Veterinary Medicine, University of Sassari, Sassari, Italy" + }, + { + "author_name": "Marco Casu", + "author_inst": "Department of Veterinary Medicine, University of Sassari, Sassari, Italy" + }, + { + "author_name": "Pier Luigi Fiori", + "author_inst": "Department of Biomedical Sciences, University of Sassari, Sassari, Italy" + }, + { + "author_name": "Marta Giovanetti", + "author_inst": "Flavivirus Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil;" + }, + { + "author_name": "Antonello Maruotti", + "author_inst": "Department GEPLI, Libera Universita Ss Maria Assunta, 00193 Rome, Italy" + }, + { + "author_name": "Giancarlo Ceccarelli", + "author_inst": "Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of 19 Rome, 00161 Rome, Italy;" + }, + { + "author_name": "Arnaldo Caruso", + "author_inst": "Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy;" + }, + { + "author_name": "Francesca Caccuri", + "author_inst": "Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy;" + }, + { + "author_name": "Roberto Cauda", + "author_inst": "UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Francesco Vito 1, 00168, Rome, Italy" + }, + { + "author_name": "Antonio Cassone", + "author_inst": "Universita degli Studi di Siena-Sede di Arezzo, 52100 Arezzo, Italy;" + }, + { + "author_name": "Stefano Pascarella", + "author_inst": "Department of Biochemical Sciences A Rossi Fanelli, Sapienza Universita di Roma, Rome, Italy" + }, + { + "author_name": "Massimo Ciccozzi", + "author_inst": "Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy;" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.11.14.516398", "rel_title": "Multi-omic spatial profiling reveals the unique virus-driven immune landscape of COVID-19 placentitis", @@ -180167,89 +181043,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.11.07.22282028", - "rel_title": "Comparison of the reactogenicity and immunogenicity between two-dose mRNA COVID-19 vaccine and inactivated followed by an mRNA vaccine in children aged 5 - 11 years", - "rel_date": "2022-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.07.22282028", - "rel_abs": "ObjectiveTo compare the reactogenicity and immunogenicity between the two-dose mRNA COVID-19 vaccine regimen and one or two doses of inactivated vaccine followed by an mRNA vaccine regimen in healthy children between 5-11 years of age.\n\nMethodsA prospective cohort study was performed at King Chulalongkorn Memorial Hospital in Thailand between March to June 2022. Healthy children between 5-11 years of age were enrolled and received the two-dose mRNA COVID-19 vaccine (BNT162b2) regimen or the inactivated (CoronaVac) vaccine followed by the BNT162b2 vaccine regimen. In addition, healthy children who received two doses of BBIBP-CorV between 1-3 months prior were enrolled to receive a heterologous BNT162b2 as a third dose (booster).\n\nReactogenicity was assessed by a self-reported online questionnaire. Immunogenicity analysis was performed to determine binding and surrogate neutralizing antibodies to SARS-CoV-2 wild-type and Omicron variants.\n\nResultsOverall, 166 eligible children were enrolled. Local and systemic AE which occurred within 7 days after vaccination were mild to moderate and well-tolerated. At one-month, post-two or post-three doses, children vaccinated with two-dose BNT162b2, CoronaVac/BNT162b2, and two-dose BBIBP-CorV followed by BNT162b2 elicited similar levels of anti-receptor-binding domain (RBD) IgG. However, the two-dose BNT162b2 and two-dose BBIBP-CorV followed by BNT162b2 groups elicited higher neutralizing activities against Omicron BA.2 variant than the CoronaVac/BNT162b2 group.\n\nConclusionThe heterologous, CoronaVac vaccine followed by the BNT162b2 vaccine, regimen elicited lower neutralizing activities against the emerging Omicron BA.2 variant than the two-dose mRNA regimen. A third dose (booster) mRNA vaccine should be prioritized for this group.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Nasamon Wanlapakorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Sitthichai Kanokudom", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Harit Phowatthanasathian", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Jira Chansaenroj", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Nungruthai Suntronwong", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Suvichada Assawakosri", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Ritthideach Yorsaeng", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Pornjarim Nilyanimit", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Preeyaporn Vichaiwattana", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Sirapa Klinfueng", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Thanunrat Thongmee", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Ratchadawan Aeemjinda", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Nongkanok Khanarat", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Donchida Srimuan", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Thaksaporn Thatsanatorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Natthinee Sudhinaraset", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Yong Poovorawan", - "author_inst": "Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.11.07.22282030", "rel_title": "Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses.", @@ -180525,6 +181318,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.11.05.22281903", + "rel_title": "Virtual Home Visits Reduce Asthma Burden in Underserved Communities amidst the COVID-19 Pandemic", + "rel_date": "2022-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.05.22281903", + "rel_abs": "ObjectivesPilot an asthma virtual home visits program, and evaluate its reach and ability to promote asthma self-management strategies in underserved communities.\n\nMethodsParticipants were continuously recruited into the 3-month-long program starting March 2021 and provided with materials related to asthma education. Participants reporting poorly-controlled asthma and home-based triggers were also offered three virtual home visits with a respiratory therapist. All participants were asked to complete a pre- and post-intervention knowledge test and Asthma Control Test (ACT), and a final survey assessing perceptions regarding asthma management and environmental trigger reduction.\n\nResultsAs of October 2022, 147 participants were enrolled, and 52 had consented and received at least one virtual home visit. Approximately 77% of virtual visit recipients were children, 76% were non-Hispanic Black persons, and 90% were from extremely low or low income families. Asthma symptoms improved across the whole group, with a median increase of 2.39 points on the ACT score. Knowledge tests revealed that 86% of participants learned about at least one new asthma trigger, with a larger fraction of virtual visit recipients (68% vs. 36% non-recipients) showing an improved score post-intervention. About 75% of participants reported feeling more empowered to self-manage their asthma after participating in the program, and reported a significant improvement in their quality of life due to asthma.\n\nConclusionsThe program successfully provided virtual asthma education to underserved, at-risk communities, and improved asthma outcomes for participants. Similar virtual models can be used to promote health equity, especially in areas with limited access to healthcare.\n\nSummary BoxO_ST_ABSWhat is the current understanding on this subject?C_ST_ABSHome-based interventions are known to be beneficial for improving asthma outcomes, especially among children; however, in-person visits have been a challenge during the COVID-19 pandemic.\n\nWhat does this report add to the literature?This report suggests that virtual, home-based models for asthma education are a viable alternative to in-person visits. As such, they can be an important tool for promoting health equity, especially in areas with limited access to healthcare.\n\nWhat are the implications for public health practice?Public health practitioners should be educated regarding the benefits of home-based asthma interventions, including virtual programs, as an adjuvant to standard clinical practices.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Arundhati Bakshi", + "author_inst": "Louisiana Department of Health" + }, + { + "author_name": "Elora Apantaku", + "author_inst": "Louisiana Department of Health" + }, + { + "author_name": "Tracy Marquette", + "author_inst": "Our Lady of the Lake Children's Hospital" + }, + { + "author_name": "Colette Jacob", + "author_inst": "Louisiana Department of Health" + }, + { + "author_name": "S. Amanda Dumas", + "author_inst": "Louisiana Department of Health" + }, + { + "author_name": "Kate Friedman", + "author_inst": "Louisiana Department of Health" + }, + { + "author_name": "Kathleen Aubin", + "author_inst": "Louisiana Department of Health" + }, + { + "author_name": "Shannon Soileau", + "author_inst": "Louisiana Department of Health" + }, + { + "author_name": "Shaun Kemmerly", + "author_inst": "Our Lady of the Lake Children's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.11.07.22281809", "rel_title": "Clinical accuracy of SARS-CoV-2 rapid antigen testing in screening children and adolescents in comparison to RT-qPCR, November 2020 to September 2022", @@ -181853,69 +182697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2022.11.04.22281855", - "rel_title": "Disproportionate impacts of COVID-19 in a large US city", - "rel_date": "2022-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.04.22281855", - "rel_abs": "COVID-19 has disproportionately impacted individuals depending on where they live and work, and based on their race, ethnicity, and socioeconomic status. Studies have documented catastrophic disparities at critical points throughout the pandemic, but have not yet systematically tracked their severity through time. Using anonymized hospitalization data from March 11, 2020 to June 1, 2021, we estimate the time-varying burden of COVID-19 by age group and ZIP code in Austin, Texas. During this 15-month period, we estimate an overall 16.9% (95% CrI: 16.1-17.8%) infection rate and 34.1% (95% CrI: 32.4-35.8%) case reporting rate. Individuals over 65 were less likely to be infected than younger age groups (8.0% [95% CrI: 7.5-8.6%] vs 18.1% [95% CrI: 17.2-19.2%]), but more likely to be hospitalized (1,381 per 100,000 vs 319 per 100,000) and have their infections reported (51% [95% CrI: 48-55%] vs 33% [95% CrI: 31-35%]). Children under 18, who make up 20.3% of the local population, accounted for only 5.5% (95% CrI: 3.8-7.7%) of all infections between March 1 and May 1, 2020 compared with 20.4% (95% CrI: 17.3-23.9%) between December 1, 2020 and February 1, 2021. We compared ZIP codes ranking in the 75th percentile of vulnerability to those in the 25th percentile, and found that the more vulnerable communities had 2.5 (95% CrI: 2.0-3.0) times the infection rate and only 70% (95% CrI: 61%-82%) the reporting rate compared to the less vulnerable communities. Inequality persisted but declined significantly over the 15-month study period. For example, the ratio in infection rates between the more and less vulnerable communities declined from 12.3 (95% CrI: 8.8-17.1) to 4.0 (95% CrI: 3.0-5.3) to 2.7 (95% CrI: 2.0-3.6), from April to August to December of 2020, respectively. Our results suggest that public health efforts to mitigate COVID-19 disparities were only partially effective and that the CDCs social vulnerability index may serve as a reliable predictor of risk on a local scale when surveillance data are limited.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Spencer J Fox", - "author_inst": "The University of Georgia" - }, - { - "author_name": "Emily Javan", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Remy Pasco", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Graham C Gibson", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Briana Betke", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jos\u00e9 L Herrera Diestra", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Spencer Woody", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Kelly Pierce", - "author_inst": "The Texas Advanced Computing Center" - }, - { - "author_name": "Kaitlyn E Johnson", - "author_inst": "The Rockefeller Foundation" - }, - { - "author_name": "Maureen Johnson-Le\u00f3n", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Michael Lachmann", - "author_inst": "The Santa Fe Institute" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.04.22281943", "rel_title": "Fine scale human mobility changes in 26 US cities in 2020 in response to the COVID-19 pandemic were associated with distance and income", @@ -182159,6 +182940,81 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2022.11.06.515327", + "rel_title": "Temporal Vascular Endothelial Growth Factor Sub-type gene Switching in SARS-CoV Pathogenesis. Interpretation through in vivo Murine C57BL Models", + "rel_date": "2022-11-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.06.515327", + "rel_abs": "This study examines temporal gene expression (GE) patterns in a murine model of SARS-CoV infection. We focused on a Temporal Gene Set (TGS) comprising pro-inflammatory genes (TNF, NFKB1, VEGF-A) and VEGF-B. A systematic search of the NCBI Geo database for MA15 (SARS-CoV) pulmonary studies using C57BL Wild (WT) mice and filtering according to TGS GE patterns eluded seven datasets for further analysis. Encompassing the GE profiles from these datasets alluded to a rising and falling pattern in TNF and NFKB1 GE. Also, our findings reveal a temporal decrease in VEGF-A GE coinciding with an increase in VEGF-B GE post-immunogenic stimulation. Notably, differential responses were observed with the MA15 dosage and in comparison, to other antigens (dORF6 and NSP16). Further, the human SARS-CoV-2 gene enrichment in this murine study confirms the MA15 murine models relevance for SARS research. Our study also suggests potential interactions between SARS-CoV-2 Spike protein and VEGF-related receptors, hinting at other pathophysiological mechanisms. Our results indicate severe inflammation may lead to a flattened VEGF-B GE response, influencing VEGF-Bs cell survival role. We underline the significance of considering VEGF-A/B interactions, particularly temporal differences, in manipulating angiogenic processes. Future research needs to consider temporal changes in VEGF-A and VEGF-B GE, in terms of time-associated gene-switching, in line with changing host inflammation.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Asrar Rashid", + "author_inst": "Napier Edinburgh University" + }, + { + "author_name": "Govind Benakatti", + "author_inst": "Yas Clinic Abu Dhabi" + }, + { + "author_name": "Feras Al-Obeidat", + "author_inst": "University of New Brunswick" + }, + { + "author_name": "Zainab A Malik", + "author_inst": "College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences. Dubai, U.A.E" + }, + { + "author_name": "Joe Brierley", + "author_inst": "Great Ormond Street Childrens Hospitak" + }, + { + "author_name": "Varun Sharma", + "author_inst": "NMC Genetics" + }, + { + "author_name": "Anuka Sharma", + "author_inst": "NMC Genetics" + }, + { + "author_name": "Love Gupta", + "author_inst": "NMC Genetics" + }, + { + "author_name": "Hoda Alkhazaimi", + "author_inst": "New York University Abu Dhabi" + }, + { + "author_name": "Guftar Shaikh", + "author_inst": "Royal Hospital for Children Galsgow" + }, + { + "author_name": "Ahmed Al-Dubai", + "author_inst": "Edinburgh Napier University" + }, + { + "author_name": "Nasir Quraishi", + "author_inst": "Nottingham University" + }, + { + "author_name": "Syed Ahmed Zaki", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Wael Wael Hafez", + "author_inst": "NMC Royal Hospital, Abu Dhabi, UAE" + }, + { + "author_name": "Amir Hussain", + "author_inst": "Edinburgh Napier University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.11.06.515367", "rel_title": "Mathematical Modeling of Impacts of Patient Differences on COVID-19 Lung Fibrosis Outcomes", @@ -183443,57 +184299,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.11.03.22281925", - "rel_title": "Prior infections and effectiveness of SARS-CoV-2 vaccine in test-negative study: A systematic review and meta-analysis", - "rel_date": "2022-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.03.22281925", - "rel_abs": "BackgroundPrior infection with SARS-CoV-2 can provide protection against infection and severe COVID-19. In settings with high pre-existing immunity, vaccine effectiveness (VE) should decrease with higher levels of immunity among unvaccinated individuals. Here, we conducted a systematic review and meta-analysis to understand the influence of prior infection on VE.\n\nMethodsWe included test-negative design (TND) studies that examined VE against infection or severe disease (hospitalization, ICU admission, or death) for primary vaccination series. To determine the impact of prior infections on VE estimates, we compared studies that excluded or included people with prior COVID-19 infection. We also compared VE estimates by the cumulative incidence of cases before the start of and incidence rates during each study in the study locations, as further measures of prior infections in the community.\n\nFindingsWe identified 67 studies that met inclusion criteria. Pooled VE among studies that included people with prior COVID-19 infection was lower against infection (pooled VE: 77%; 95% confidence interval (CI): 72%, 81%) and severe disease (pooled VE: 86%; 95% CI: 83%, 89%), compared with studies that excluded people with prior COVID-19 infection (pooled VE against infection: 87%; 95% CI: 85%, 89%; pooled VE against severe disease: 93%; 95% CI: 91%, 95%). There was a negative correlation between the cumulative incidence of cases before the start of the study and VE estimates against infection (spearman correlation ({rho}) = -0.32; 95% CI: -0.45, -0.18) and severe disease ({rho} = -0.49; 95% CI: -0.64, -0.30). There was also a negative correlation between the incidence rates of cases during the study period and VE estimates against infection ({rho} = - 0.48; 95% CI: -0.59, -0.34) and severe disease ({rho} = -0.42; 95% CI: -0.58, -0.23).\n\nInterpretationBased on a review of published VE estimates we found clear empirical evidence that higher levels of pre-existing immunity in a population were associated with lower VE estimates. Excluding previously infected individuals from VE studies may result in higher VE estimates with limited generalisability to the wider population. Prior infections should be treated as confounder and effect modificatory when the policies were targeted to whole population or stratified by infection history, respectively.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Tim Tsang", - "author_inst": "The university of Hong Kong" - }, - { - "author_name": "SheenaG Sullivan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Xiaotong Huang", - "author_inst": "The university of Hong Kong" - }, - { - "author_name": "Can Wang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yifan Wang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Joshua Nealon", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Bingyi Yang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kylie E.C Ainslie", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ben J Cowling", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.02.22281821", "rel_title": "Screening COVID-19 by Swaasa AI Platform using cough sounds: A cross-sectional study", @@ -183765,6 +184570,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.11.01.22281787", + "rel_title": "Use of Interviewer-Administered Telephone Surveys during Infectious Disease Outbreaks, Epidemics, and Pandemics: A Scoping Review", + "rel_date": "2022-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.01.22281787", + "rel_abs": "IntroductionDuring the COVID-19 crisis, researchers had to collect data remotely. Telephone surveys and interviews can quickly gather data from a distance without heavy expense. Although interviewer-administered telephone surveys (IATS) can accommodate the needs in international public health research, the literature on its use during infectious disease outbreaks is scarce. This scoping review aimed to map characteristics of IATS during infectious disease outbreaks.\n\nMethodsIATS conducted principally during infectious disease outbreaks and answered by informants at least 18 years old were searched from PubMed and EBSCO. There was a manual addition of relevant documents identified during an initial search. Global trends were reported using different groupings, and study details were compared between before and during the COVID-19 pandemic.\n\nResults70 IATS published between 2003 and 2022 were identified. 57.1 % were conducted during the COVID-19 pandemic. During the COVID-19 pandemic, some changes in the use of this data collection modality were observed. The proportion of IATS in LMICs rose from 3.3 % before the COVID-19 pandemic to 32.5 %. The share of qualitative studies grew from 6.7 % to 32.5 %. IATS performed during the COVID-19 pandemic focused on more diverse, specific population groups, such as patients and healthcare professionals. The usage of mobile phones to do IATS studies increased from 3.3 % to 25.0 %.\n\nConclusionIATS are used globally with high frequency in the Western Pacific Region and high income countries. During the COVID-19 pandemic, IATS was performed in more countries to investigate more diverse target populations. Nonetheless, researchers should consider how to address technical and financial challenges for ITAS to be more inclusive and representative. For better use and more efficient deployment of IATS, methodological details need to be exchanged.\n\nWhat is already known on this topicO_LITelephones have been playing an important role in data collection especially when data needs to be gathered quickly and remotely during infectious disease outbreaks, humanitarian crises, and natural disasters.\nC_LIO_LIThe use of online surveys is increasing globally alongside digitalization and technological development.\nC_LIO_LIHowever, the transformation regarding the use of telephone surveys is not well documented.\nC_LI\n\nWhat this study addsO_LIWe performed a scoping review to grasp characteristics and trends of telephone surveys.\nC_LIO_LIWe found that more telephone surveys have been conducted in low and middle income countries during the COVID-19 pandemic (32.5 %) compared to before COVID-19 (3.3 %).\nC_LIO_LIWe learned that telephone surveys during the pandemic have investigated more specific and diverse population groups than the pre-pandemic period.\nC_LI\n\nHow this study might affect research, practice or policyO_LIThe increased usage of cell phones to operate IATS align with the growing mobile phone ownership, thanks to which the global mobilization of this survey mode might be accelerated in the future.\nC_LIO_LIHowever, we observed inadequate information on study details, including the number of languages spoken by interviewers as well as technical enhancement or optimization.\nC_LIO_LIWe encourage sharing techniques and knowledge among researchers whereby ITAS could be further improved and contribute to more inclusive public health research.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sayaka Arita", + "author_inst": "EHESP" + }, + { + "author_name": "Mouhamadou Faly Ba", + "author_inst": "Institut de Sant\u00e9 et D\u00e9veloppement, Universit\u00e9 Cheikh Anta Diop de Dakar" + }, + { + "author_name": "Zoumana Traor\u00e9", + "author_inst": "CloudlyYours" + }, + { + "author_name": "Emmanuel Bonnet", + "author_inst": "Institut de recherche pour le d\u00e9veloppement" + }, + { + "author_name": "Adama Faye", + "author_inst": "Institut de Sant\u00e9 et D\u00e9veloppement, Universit\u00e9 Cheikh Anta Diop de Dakar" + }, + { + "author_name": "Val\u00e9ry Ridde", + "author_inst": "Universit\u00e9 de Paris, IRD, INSERM, Ceped, F-75006" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.11.01.22281793", "rel_title": "Prevalence and pattern of adverse events following COVID 19 vaccination among adult population in Sokoto metropolis, northwest, Nigeria", @@ -184761,20 +185605,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.10.31.22281764", - "rel_title": "SARS-CoV-2 antibody prevalence among industrial livestock operation workers and nearby community residents, North Carolina, USA, 2021-2022", - "rel_date": "2022-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.31.22281764", - "rel_abs": "Industrial livestock operations (ILOs), particularly processing facilities, emerged as centers of coronavirus disease 2019 (COVID-19) outbreaks in spring 2020. Confirmed cases of COVID-19 underestimate true prevalence. To investigate prevalence of antibodies against SARS-CoV-2, we enrolled 279 participants in North Carolina from February 2021 to July 2022: 90 from households with at least one ILO worker (ILO), 97 from high-ILO intensity areas (ILO neighbors - ILON), and 92 from metropolitan areas (Metro). Participants provided a saliva swab we analyzed for SARS-CoV-2 IgG using a multiplex immunoassay. Prevalence of infection-induced IgG (positive for nucleocapsid and receptor binding domain) was higher among ILO (63%) compared to ILON (42.9%) and Metro (48.7%) participants (prevalence ratio [PR] =1.38; 95% confidence interval [CI]: 1.06, 1.80; ref. ILON and Metro combined). Prevalence of infection-induced IgG was also higher among ILO participants compared to an Atlanta healthcare worker cohort (PR=2.45, 95% CI: 1.8, 3.3) and a general population cohort in North Carolina (PRs 6.37-10.67). Infection-induced IgG prevalence increased over the study period. Participants reporting not masking in public in the past two weeks had higher infection-induced IgG prevalence (78.6%) compared to participants reporting masking (49.3%) (PR=1.59; 95% CI: 1.19, 2.13). Lower education, more people per bedroom, Hispanic/Latino ethnicity, and more contact with people outside the home were also associated with higher infection-induced IgG prevalence. Similar proportions of ILO (51.6%), ILON (48.4%), and Metro (55.4%) participants completed the COVID-19 primary vaccination series; median completion was more than four months later for ILO compared to ILON and Metro participants.\n\nImportanceFew studies have measured COVID-19 seroprevalence in North Carolina, especially among rural, Black, and Hispanic/Latino communities that have been heavily affected. Antibody results show high rates of COVID-19 among industrial livestock operation workers and their household members. Antibody results add to evidence of health disparities in COVID-19 by socioeconomic status and ethnicity. Associations between masking and physical distancing with antibody results also add to evidence of the effectiveness of these prevention strategies. Delays in the timing of receipt of COVID-19 vaccination reinforce the importance of dismantling vaccination barriers, especially for industrial livestock operation workers and their household members.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.28.22281588", "rel_title": "A novel hospital-at-home model for patients with COVID-19 built by a team of local primary care clinics and clinical outcomes: A multi-center retrospective cohort study", @@ -184994,6 +185824,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.30.22281627", + "rel_title": "Evaluation of real and perceived risk to health care workers caring for patients with the Omicron variant of the SARS-CoV-2 virus in surgery and obstetrics", + "rel_date": "2022-10-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.30.22281627", + "rel_abs": "IntroductionThe Omicron variant of the SARS-CoV-2 virus is described as more contagious than previous variants. We sought to assess risk to healthcare workers (HCWs) caring for patients with COVID-19 in surgical/obstetrical settings, and the perception of risk amongst this group.\n\nMethodsFrom January to April, 2022, reverse transcription polymerase chain reaction was used to detect the presence of SARS-CoV-2 viral RNA in patient, environmental (floor, equipment, passive air) samples, and HCWs masks (inside surface) during urgent surgery or obstetrical delivery for patients with SARS-CoV-2 infection. The primary outcome was the proportion of HCWs masks testing positive. Results were compared with our previous cross-sectional study involving obstetrical/surgical patients with earlier variants (2020/21). HCWs completed a risk perception electronic questionnaire.\n\nResults11 patients were included: 3 vaginal births and 8 surgeries. 5/108 samples (5%) tested positive (SARS-CoV-2 Omicron) viral RNA: 2/5 endotracheal tubes, 1/22 floor samples, 1/4 patient masks and 1 nasal probe. No samples from the HCWs masks (0/35), surgical equipment (0/10) and air samples (0/11) tested positive. No significant differences were found between the Omicron and 2020/21 patient groups positivity rates (Mann-Whitney U test, p = 0.838) or the level of viral load from the nasopharyngeal swabs (p = 0.405). Nurses had a higher risk perception than physicians (p = 0.038).\n\nConclusionNo significant difference in contamination rates were found between SARS-CoV-2 Omicron BA.1 and previous variants in surgical/obstetrical settings. This is reassuring as no HCW mask was positive and no HCW tested positive for COVID-19 post-exposure.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Chaithanya Nair", + "author_inst": "Sunnybrook Health Sciences Centre, University of Toronto, Temerty Faculty of Medicine" + }, + { + "author_name": "Robert Kozak", + "author_inst": "Sunnybrook Health Sciences Centre, Dept of Medicine, Division of Microbiology" + }, + { + "author_name": "Nasrin Alavi", + "author_inst": "Sunnybrook Health Sciences Centre, Sunnybrook Research Institute Toronto, ON, CAN" + }, + { + "author_name": "Hamza Mbareche", + "author_inst": "Sunnybrook Health Sciences Centre, Sunnybrook Research Institute Toronto, ON, CAN" + }, + { + "author_name": "Rose C Kung", + "author_inst": "Sunnybrook Health Sciences Centre, Dept of Obstetrics and Gynecology, Division of Urogynecology, University of Toronto" + }, + { + "author_name": "Kellie Murphy", + "author_inst": "Sinai Health System, Dept of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, University of Toronto" + }, + { + "author_name": "Darian L Perruzza", + "author_inst": "Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON, CAN" + }, + { + "author_name": "Stephanie Jarvi", + "author_inst": "Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON, CA" + }, + { + "author_name": "Elsa Salvant", + "author_inst": "Sunnybrook Health Sciences Centre, Sunnybrook Research Institute Toronto, ON, CAN" + }, + { + "author_name": "Noor Niyar N Ladnani", + "author_inst": "Sunnybrook Health Sciences Centre, Dept of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, University of Toronto" + }, + { + "author_name": "Albert Yee", + "author_inst": "Sunnybrook Health Sciences Centre, Dept of Surgery, Division of Orthopaedic Surgery, University of Toronto" + }, + { + "author_name": "Louise Gagnon", + "author_inst": "Sunnybrook Health Sciences Centre, Dept of Obstetrics and Gynecology, Division of Urogynecology, University of Toronto" + }, + { + "author_name": "Richard Jenkinson", + "author_inst": "Sunnybrook Health Sciences Centre, Dept of Surgery, Division of Orthopaedic Surgery, University of Toronto" + }, + { + "author_name": "Grace Y Liu", + "author_inst": "Sunnybrook Health Sciences Centre, Obstetrics and Gynecology, Division of Minimally Invasive Gynecologic Surgery, University of Toronto" + }, + { + "author_name": "Patricia Lee", + "author_inst": "Sunnybrook Health Sciences Centre, Dept of Obstetrics and Gynecology, Division of Urogynecology, University of Toronto, Toronto, Ontario, Canada" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.26.22281511", "rel_title": "Older Adults' Attitudes Regarding COVID-19 and Associated Infection Control Measures in Shanghai, and Impact on Well-Being", @@ -186766,53 +187671,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.26.22281575", - "rel_title": "Impact of COVID-19 related maternal stress on fetal brain development: A Multimodal MRI study", - "rel_date": "2022-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.26.22281575", - "rel_abs": "BackgroundDisruptions in perinatal care and support due to the COVID-19 pandemic was an unprecedented but significant stressor among pregnant women. Various neurostructural differences have been re-ported among fetuses and infants born during the pandemic compared to pre-pandemic counterparts. The relationship between maternal stress due to pandemic related disruptions and fetal brain is yet unexamined.\n\nMethodsPregnant participants with healthy pregnancies were prospectively recruited in 2020-2022 in the greater Los Angeles Area. Participants completed multiple self-report assessments for experiences of pandemic related disruptions, perceived stress, and coping behaviors and underwent fetal MRI. Maternal perceived stress exposures were correlated with quantitative multimodal MRI measures of fetal brain development using ltivariate models.\n\nResultsFetal brain stem volume increased with increased maternal perception of pandemic related stress positively correlated with normalized fetal brainstem volume (suggesting accelerated brainstem maturation). In contrast, increased maternal perception of pandemic related stress correlated with reduced global fetal brain temporal functional variance (suggesting reduced functional connectivity).\n\nConclusionsWe report alterations in fetal brainstem structure and global functional fetal brain activity associated with increased maternal stress due to pandemic related disruptions, suggesting altered fetal programming. Long term follow-up studies are required to better understand the sequalae of these early multi-modal brain disruptions among infants born during the COVID-19 pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vidya Rajagopalan", - "author_inst": "Childrens Hospital Los Angeles" - }, - { - "author_name": "William T. Reynolds", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Jeremy Zepeda", - "author_inst": "Childrens Hospital Los Angeles" - }, - { - "author_name": "Jeraldine Lopez", - "author_inst": "The Saban Research Institute" - }, - { - "author_name": "Skorn Ponrartana", - "author_inst": "Keck School of Medicine University of Southern California" - }, - { - "author_name": "John Wood", - "author_inst": "Childrens Hospital Los Angeles" - }, - { - "author_name": "Rafael Ceschin", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Ashok Panigrahy", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2022.10.26.22278866", "rel_title": "Experiences in the use of multiple doses of convalescent plasma in critically ill patients with COVID-19", @@ -187148,6 +188006,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.10.24.513632", + "rel_title": "Characterization of Three Variants of SARS-CoV-2 in vivo Shows Host-Dependent Pathogenicity in Hamsters", + "rel_date": "2022-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.24.513632", + "rel_abs": "Animal models are used in preclinical trials to test vaccines, antivirals, monoclonal antibodies, and immunomodulatory drug therapies against SARS-CoV-2. However, these drugs often do not produce equivalent results in human clinical trials. Here, we show how different animal models infected with some of the most clinically relevant SARS-CoV-2 variants, WA1/2020, B.1.617.2/Delta, B.1.1.529/Omicron and BA5.2/Omicron, have independent outcomes. We show that in mice, B.1.617.2 is more pathogenic, followed by WA1, while B.1.1.529 showed an absence of clinical signs. Only B.1.1.529 was able to infect C57BL/6J mice, which lack the human ACE2 receptor. B.1.1.529-infected ACE2 mice had different T cell profiles compared to infected K18-hACE2 mice, while viral shedding profiles and viral titers in lungs were similar between the ACE2 and the C57BL/6J mice. These data suggest B.1.1.529 virus adaptation to a new host and shows that asymptomatic carriers can accumulate and shed virus. Next, we show how B.1.617.2, WA1 and BA5.2/Omicron have similar viral replication kinetics, pathogenicity, and viral shedding profiles in hamsters, demonstrating that the increased pathogenicity of B.1.617.2 observed in mice is host-dependent. Overall, these findings suggest that small animal models are useful to parallel human clinical data, but the experimental design places an important role in interpreting the data.\n\nIMPORTANCEThere is a need to investigate SARS-CoV-2 variants phenotypes in different animal models due to the lack of reproducible outcomes when translating experiments to the human population. Our findings highlight the correlation of clinically relevant SARS-CoV-2 variants in animal models with human infections. Experimental design and understanding of correct animal models are essential to interpreting data to develop antivirals, vaccines, and other therapeutic compounds against COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Gabriela Toomer", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Whitney Burns", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Monica Melendez", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Liliana Garcia", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Gerelyn Henry", + "author_inst": "Charles River Laboratories, Inc." + }, + { + "author_name": "Anthony Biancofiori", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Albert Geroge", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Ciera Duffy", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Justin Chu", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Morgan Sides", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Melissa Mu\u00f1oz", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Kelly Garcia", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Anya Nikolai-Yogerst", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + }, + { + "author_name": "Xinjian Peng", + "author_inst": "IIT Research Institute" + }, + { + "author_name": "Landon Westfall", + "author_inst": "Southern Research Institute" + }, + { + "author_name": "Robert O. Baker", + "author_inst": "Illinois Institute of Technology Research Institute (IITRI)" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "confirmatory results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.25.513701", "rel_title": "Assessing SARS-CoV-2 evolution through the analysis of emerging mutations", @@ -189128,125 +190065,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.10.23.22281414", - "rel_title": "Impact of vaccination on the presence and severity of symptoms of hospitalised patients with an infection by the Omicron variant (B.1.1.529) of the SARS-CoV-2 (subvariant BA.1).", - "rel_date": "2022-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.23.22281414", - "rel_abs": "ObjectivesThe emergence of SARS-CoV-2 variants raised questions over the extent to which vaccines designed in 2020 have remained effective. We aimed to assess whether vaccine status was associated with the severity of Omicron SARS-CoV-2 infection in hospitalised patients.\n\nMethodsWe conducted an international, multicentric, retrospective study in 14 centres (Bulgaria, Croatia, France, Turkey). We collected data on patients hospitalised [≥]24 hours between 01/12/2021 and 03/03/2022, with PCR-confirmed infection at a time of exclusive Omicron circulation, with hospitalisation related or not to the infection. Patients who had received prophylaxis by monoclonal antibodies were excluded. Patients were considered fully vaccinated if they had received at least 2 injections of either mRNA and/or ChAdOx1-S, or 1 injection of Ad26.CoV2-S vaccines.\n\nResultsAmong the 1215 patients (median [IQR] age 73.0 [57.0; 84.0]; 51.3% males), 746 (61.4%) were fully vaccinated. In multivariate analysis, being vaccinated was associated with lower 28-day mortality (RR=0.50 [0.32-0.77]), ICU admission (R=0.40 [0.26-0.62], and oxygen requirement (RR=0.34 [0.25-0.46]), independently of age and comorbidities. When co-analysing these Omicron patients with 948 Delta patients from a study we recently conducted, Omicron infection was associated with lower 28-day mortality (RR=0.53 [0.37-0.76]), ICU admission (R=0.19 [0.12-0.28], and oxygen requirements (RR=0.50 [0.38-0.67]), independently of age, comorbidities and vaccination status.\n\nConclusionsmRNA- and adenovirus-based vaccines have remained effective on severity of Omicron SARS-CoV-2 infection. Omicron is associated with a lower risk of severe forms, independently of vaccination and patient characteristics.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Guillaume Beraud", - "author_inst": "University Hospital of Poitiers" - }, - { - "author_name": "Laura Bouetard", - "author_inst": "APHP, Hopital Antoine Beclere, Service de Medecine Interne, Clamart, France and Universite Paris-Saclay, UVSQ, INSERM U1018, CESP, Le Kremlin-Bicetre, France." - }, - { - "author_name": "Rok Civljak", - "author_inst": "University Hospital for Infectious Diseases \"Dr. Fran Mihaljevic\", Zagreb, Croatia and University of Zagreb School of Medicine, Zagreb, Croatia." - }, - { - "author_name": "Jocelyn Michon", - "author_inst": "Department of Infectious diseases, University Hospital of Caen, Caen, France" - }, - { - "author_name": "Necla Tulek", - "author_inst": "Atilim University, Department of Infectious Diseases and Clinical Microbiology Ankara Training and Research Hospital, Turkey" - }, - { - "author_name": "Sophie Lejeune", - "author_inst": "Infectious diseases, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France" - }, - { - "author_name": "Romain Millot", - "author_inst": "Infectious disease department, University Hospital of Poitiers, Poitiers, France" - }, - { - "author_name": "Aurelie Garchet-Beaudron", - "author_inst": "Infectious Disease Department, CH, Le Mans, France" - }, - { - "author_name": "Maeva Lefebvre", - "author_inst": "Infectious Disease Department, Centre for Prevention of Infectious and Transmissible Diseases, CHU Nantes, Nantes, France and INSERM UIC 1413 Nantes University," - }, - { - "author_name": "Petar Velikov", - "author_inst": "Infectious Disease Hospital \"Prof. Ivan Kirov\", Medical University of Sofia, Bulgaria" - }, - { - "author_name": "Benjamin Festou", - "author_inst": "CHU Limoges, Department of Infectious Diseases and Tropical Medicine, Limoges France" - }, - { - "author_name": "Sophie Abgrall", - "author_inst": "APHP, Hopital Antoine Beclere, Service de Medecine Interne, Clamart, France and Universite Paris-Saclay, UVSQ, INSERM U1018, CESP, Le Kremlin-Bicetre, France." - }, - { - "author_name": "Ivan Kresimir Lizatovic", - "author_inst": "University Hospital for Infectious Diseases \"Dr. Fran Mihaljevic\", Zagreb, Croatia" - }, - { - "author_name": "Aurelie Baldolli", - "author_inst": "Department of Infectious diseases, University Hospital of Caen, Caen, France" - }, - { - "author_name": "Huseyin Esmer", - "author_inst": "Atilim University, Department of Infectious Diseases and Clinical Microbiology Ankara Training and Research Hospital, Turkey" - }, - { - "author_name": "Sophie Blanchi", - "author_inst": "Infectious Disease Department, CH, Le Mans, France" - }, - { - "author_name": "Gabrielle Froidevaux", - "author_inst": "Infectious Disease Department, Centre for Prevention of Infectious and Transmissible Diseases, CHU Nantes, Nantes, France" - }, - { - "author_name": "Nikol Kapincheva", - "author_inst": "Infectious Disease Hospital \"Prof. Ivan Kirov\", Medical University of Sofia, Bulgaria" - }, - { - "author_name": "Jean-Francois Faucher", - "author_inst": "CHU Limoges, Department of Infectious Diseases and Tropical Medicine, Limoges France and INSERM U1094, Limoges, France." - }, - { - "author_name": "Mario Duvnjak", - "author_inst": "Clinic for Infectious Diseases, University Hospital Centre Osijek, Osijek, Croatia and Faculty of Medicine Osijek, J. J. Strossmayer University of Osijek, Osije" - }, - { - "author_name": "Elcin Afsar", - "author_inst": "Atilim University, Vocational School of Health Services, Ankara, Turkey" - }, - { - "author_name": "Luka Svitek", - "author_inst": "Clinic for Infectious Diseases, University Hospital Centre Osijek, Osijek, Croatia and Faculty of Medicine Osijek, J. J. Strossmayer University of Osijek, Osije" - }, - { - "author_name": "Saliha Yarimoglu", - "author_inst": "Karaman Training and Research Hospital, Turkey" - }, - { - "author_name": "Rafet Yarimoglu", - "author_inst": "Karaman Training and Research Hospital, Turkey" - }, - { - "author_name": "Cecile Janssen", - "author_inst": "Infectious Disease Unit, Centre Hospitalier Annecy Genevois, Annecy, France" - }, - { - "author_name": "olivier EPAULARD", - "author_inst": "centre hospitalier universitaire Grenoble Alpes" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.24.513610", "rel_title": "Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the Spike protein from SARS-CoV-2", @@ -189646,6 +190464,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.24.513415", + "rel_title": "Vaccine- and BTI-elicited pre-Omicron immunity more effectively neutralizes Omicron sublineages BA.1, BA.2, BA.4 and BA.5 than pre-Omicron infection alone", + "rel_date": "2022-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.24.513415", + "rel_abs": "Since the emergence of SARS-CoV-2 Omicron BA.1 and BA.2, several Omicron sublineages have emerged, supplanting their predecessors. BA.5 is the current dominant sublineage. Here we compared the neutralization of Omicron sublineages BA.1, BA.2, BA.4 and BA.5 by human sera collected from individuals who were infected with the ancestral B.1 (D614G) strain, vaccinated (3 doses), or with hybrid immunity from vaccination (2 doses) followed by pre-Omicron breakthrough infection (BTI) with Gamma or Delta. All Omicron sublineages exhibited extensive escape from all sera compared to the ancestral B.1 strain and to Delta, albeit to different levels depending on the origin of the sera. Convalescent sera were unable to neutralize BA.1, and partly neutralized BA.2, BA.4 and BA.5. Vaccinee sera partly neutralized BA.2, but BA.1, BA.4 and BA.5 evaded neutralizing antibodies. BTI sera were either non-neutralizing or partially neutralizing. In this case, they had similar neutralizing ability against all Omicron sublineages. Despite similar levels of anti-Spike and anti-Receptor Binding Domain (RBD) antibody in all groups, BTI sera had the highest cross-neutralizing ability against all Omicron sublineages and convalescent sera were the least neutralizing. The NT50:antibody titer ratio, which reflects antibody avidity, was significantly higher in sera from BTI patients compared to convalescent sera, underscoring qualitative differences in antibodies elicited by infection alone and by vaccination. Together these findings highlight the importance of vaccination to trigger highly cross-reactive antibodies that neutralize phylogenetically and antigenically distant strains, and suggest that immune imprinting by first generation vaccines may restrict, but not abolish cross-neutralization.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Eveline Santos da Silva", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Jean-Yves Servais", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Michel Kohnen", + "author_inst": "Centre Hospitalier de Luxembourg" + }, + { + "author_name": "Victor Arendt", + "author_inst": "Centre Hospitalier de Luxembourg" + }, + { + "author_name": "Georges Gilson", + "author_inst": "Centre Hospitalier de Luxembourg" + }, + { + "author_name": "Therese Staub", + "author_inst": "Centre Hospitalier de Luxembourg" + }, + { + "author_name": "Carole Seguin-Devaux", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Danielle Perez-Bercoff", + "author_inst": "Luxembourg Institute of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.10.24.513517", "rel_title": "Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response", @@ -191134,29 +191999,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2022.10.18.22281063", - "rel_title": "Deep reinforcement learning framework for controlling infectious disease outbreaks in the context of multi-jurisdictions", - "rel_date": "2022-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281063", - "rel_abs": "In the absence of pharmaceutical interventions, social distancing and lockdown have been key options for controlling new or reemerging respiratory infectious disease outbreaks. The timely implementation of these interventions is vital for effectively controlling and safeguarding the economy.\n\nMotivated by the COVID-19 pandemic, we evaluated whether, when, and to what level lockdowns are necessary to minimize epidemic and economic burdens of new disease outbreaks. We formulated the question as a sequential decision-making Markov Decision Process and solved it using deep Q-network algorithm. We evaluated the question under two objective functions: a 2-objective function to minimize economic burden and hospital capacity violations, suitable for diseases with severe health risks but with minimal death, and a 3-objective function that additionally minimizes the number of deaths, suitable for diseases that have high risk of mortality. A key feature of the model is that we evaluated the above questions in the context of two-geographical jurisdictions that interact through travel but make autonomous and independent decisions, evaluating under cross-jurisdictional cooperation and non-cooperation.\n\nIn the 2-objective function under cross-jurisdictional cooperation, the optimal policy was to aim for shutdowns at 50% and 25% per day. Though this policy avoided hospital capacity violations, the shutdowns extended until a large proportion of the population reached herd immunity. Delays in initiating this optimal policy or non-cooperation from an outside jurisdiction required shutdowns at a higher level of 75% per day, thus adding to economic burdens. In the 3-objective function, the optimal policy under cross-jurisdictional cooperation was to aim for shutdowns of up to 75% per day to prevent deaths by reducing infected cases. This optimal policy continued for the entire duration of the simulation, suggesting that, until pharmaceutical interventions such as treatment or vaccines become available, contact reductions through physical distancing would be necessary to minimize deaths. Deviating from this policy increased the number of shutdowns and led to several deaths.\n\nIn summary, we present a decision-analytic methodology for identifying optimal lockdown strategy under the context of interactions between jurisdictions that make autonomous and independent decisions. The numerical analysis outcomes are intuitive and, as expected, serve as proof of the feasibility of such a model.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Seyedeh Nazanin khatami", - "author_inst": "MGH Institute for Technology Assessment, Harvard Medical School, Boston, MA 02114, , USA" - }, - { - "author_name": "Chaitra Gopalappa", - "author_inst": "University of Massachusetts Amherst" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.10.20.22281317", "rel_title": "The COVID-19 burnout scale: Development and initial validation", @@ -191368,6 +192210,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.19.22281286", + "rel_title": "Safety and effectiveness of COVID-19 mRNA vaccination and risk factors for hospitalisation caused by the omicron variant in 0.8 million adolescents: A nationwide cohort study in Sweden", + "rel_date": "2022-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.19.22281286", + "rel_abs": "BackgroundReal-world evidence on the safety and effectiveness of COVID-19 vaccination against severe disease caused by the omicron variant among adolescents is sparse. In addition, evidence on risk factors for severe COVID-19 disease, and whether vaccination is similarly effective in such risk groups, is unclear.\n\nMethods and findingsNationwide registers were used to examine the safety and effectiveness of COVID-19 mRNA vaccination against COVID-19 hospitalisation, and risk factors for COVID-19 hospitalisation in adolescents. The safety analysis included all individuals in Sweden born between 2003-2009 (aged 11.3-19.2 years) given at least one dose of mRNA vaccine (N=645,355), and never vaccinated controls (N=199,022). Outcomes evaluated included all hospitalisations until 5 June 2022. The vaccine effectiveness (VE) against COVID-19 hospitalisation and associated risk factors was evaluated in adolescents given two doses of mRNA vaccine (N=501,945), as compared to never vaccinated controls (N=170,083), during an omicron predominant period (1 January 2022 to 5 June 2022). The safety analysis showed that COVID-19 mRNA vaccination was not associated with an increased risk of any serious adverse events resulting in hospitalisation. During follow-up, 1.69% of the vaccinated individuals were hospitalised compared to 1.71% of the controls (P=0.29). In the VE analysis, there were 21 cases (0.004%) of COVID-19 hospitalisation among 2-dose recipients and 26 cases (0.015%) among controls, resulting in an estimated VE of 75% (95% CI, 54-86, P<0.001). Strong risk factors for COVID-19 hospitalisation included previous infections (odds ratio [OR], 14.3, 95% CI, 7.7-26.6, P<0.001), and cerebral palsy/development disorders (OR, 12.0, 95% CI, 6.4-22.6, P<0.001), with similar estimates of VE in these subgroups as in the total cohort. The number needed to vaccinate with two doses to prevent one case of COVID-19 hospitalisation was 9,007 in the total cohort and 1,031 in those with previous infections or developmental disorders. None of the individuals hospitalised due to COVID-19 died within 30 days.\n\nConclusionsIn this nationwide study, COVID-19 mRNA vaccination was not associated with an increased risk of any serious adverse event in adolescents. Two doses were associated with a lower risk of COVID-19 hospitalisation during the omicron predominant period, especially among those with certain predisposing conditions who should be prioritized for vaccination. However, COVID-19 hospitalisation among general adolescents was extremely rare, and additional doses in this population may not be warranted at this stage.\n\nWhy was this study doneO_ST_ABSEvidence before this studyC_ST_ABS[tpltrtarr] There is limited evidence on the effectiveness of COVID-19 vaccination against severe outcomes during the omicron era among adolescents. In addition, there is lack of data on whether certain groups of adolescents are at greater risk of severe COVID-19 and should be prioritized in vaccination programs, and whether vaccination is equally effective in such risk groups.\n[tpltrtarr]Regarding safety, some studies have indicated a link between COVID-19 mRNA vaccination and increased risk of myocarditis and pericarditis in young men, although the data appear inconsistent.\n\n\nWhat did the researchers do and find?[tpltrtarr] Using Swedish nationwide health registers, a cohort of 844,377 adolescents were followed until 5 June 2022 to evaluate the safety and effectiveness of COVID-19 mRNA vaccination against COVID-19 hospitalisation, and risk factors for COVID-19 hospitalisation.\n[tpltrtarr]COVID-19 mRNA vaccination in adolescents was not associated with an increased risk of any diagnoses resulting in hospitalisation. In contrast, two doses of vaccine had an associated 75% effectiveness against COVID-19 hospitalisation. However, only about 6 individuals in 100,000 were hospitalised due to COVID-19 during follow-up.\n[tpltrtarr]There were certain strong risk factors for COVID-19 hospitalisation, such as previous infections and different development disorders, which increased the risk of COVID-19 hospitalisation more than tenfold. Vaccine effectiveness among these individuals was similar as in the rest of the cohort.\n\n\nWhat do these findings mean?[tpltrtarr] Although COVID-19 mRNA vaccination appears safe and associated with reduced risk of COVID-19 hospitalisation, the risk of severe COVID-19 seems to be extremely low in general adolescents. Therefore, administration of additional doses to the general population of adolescents may not be warranted at this stage of the pandemic. In contrast, individuals with a high risk for severe COVID-19 should be prioritised for vaccination.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Peter Nordstr\u00f6m", + "author_inst": "Geriatrics" + }, + { + "author_name": "Marcel Ballin", + "author_inst": "Community medicine and rehabilitation" + }, + { + "author_name": "Anna Nordstr\u00f6m", + "author_inst": "Public health and clinical medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.19.22281254", "rel_title": "Socioeconomic inequalities of Long COVID: findings from a population-based survey in the United Kingdom", @@ -193196,81 +194065,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.18.22281172", - "rel_title": "Antibody-mediated protection against symptomatic COVID-19 can be achieved at low serum neutralizing titers", - "rel_date": "2022-10-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281172", - "rel_abs": "Multiple studies of vaccinated and convalescent cohorts have demonstrated that serum neutralizing antibody (nAb) titers correlate with protection against COVID-19. However, the induction of multiple layers of immunity following SARS-CoV-2 exposure has complicated the establishment of nAbs as a mechanistic correlate of protection (CoP) and hindered the definition of a protective nAb threshold. Here, we show that a half-life extended monoclonal antibody (adintrevimab) provides approximately 50% protection against symptomatic COVID-19 in SARS-CoV-2-naive adults at low serum nAb titers on the order of 1:30. Vaccine modeling supports a similar 50% protective nAb threshold, suggesting low levels of serum nAb can protect in both monoclonal and polyclonal settings. Extrapolation of adintrevimab pharmacokinetic data suggests that protection against susceptible variants could be maintained for approximately 3 years. The results provide a benchmark for the selection of next-generation vaccine candidates and support the use of broad, long-acting monoclonal antibodies as an alternative or supplement to vaccination in high-risk populations.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Pete Schmidt", - "author_inst": "Invivyd, Inc" - }, - { - "author_name": "Kristin Narayan", - "author_inst": "Invivyd, Inc." - }, - { - "author_name": "Yong Li", - "author_inst": "Invivyd, Inc" - }, - { - "author_name": "Chengzi Kaku", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Michael Brown", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Elizabeth Champney", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "James Geoghegan", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Maximiliano Vasquez", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Eric Krauland", - "author_inst": "Adimab, LLC" - }, - { - "author_name": "Thomas Yockachonis", - "author_inst": "Washington State University" - }, - { - "author_name": "Shuangyi Bai", - "author_inst": "Washington State University" - }, - { - "author_name": "Bronwyn Gunn", - "author_inst": "Washington State University" - }, - { - "author_name": "Anthony Cammarata", - "author_inst": "Institute for Clinical Pharmacodynamics" - }, - { - "author_name": "Chris Rubino", - "author_inst": "Institute for Clinical Pharmacodynamics" - }, - { - "author_name": "Laura M Walker", - "author_inst": "Invivyd, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.17.22281161", "rel_title": "Clinical antiviral efficacy of remdesivir and casirivimab/imdevimab against the SARS-CoV-2 Delta and Omicron variants", @@ -193722,6 +194516,109 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.18.512746", + "rel_title": "Regional epidemic dynamics and Delta variant diversity resulted in varying rates of spread of Omicron-BA.1 in Mexico", + "rel_date": "2022-10-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.18.512746", + "rel_abs": "The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In Mexico, this subvariant began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in the country. Unlike previous SARS-CoV-2 variants, BA.1 did not acquire local substitutions nor exhibited a geographically distinct circulation pattern in Mexico. However, a regional difference in the speed of the replacement of the Delta variant was observed, as some northern states showed persistence of Delta lineages well into February 2022. Mexican states were divided into four regions (North, Central North, Central South, and Southeast) based on the lineage circulation before the dominance of BA.1 to study possible causes for this difference. For each region, the time to fixation of BA.1, the diversity of Delta sublineages in the weeks preceding BA.1 entry, the population density, and the level of virus circulation during the inter-wave interval were determined. An association between a faster Omicron spread and lower Delta diversity, as well as fewer COVID-19 cases during the Delta-BA.1.x inter-wave period, was observed. For example, the North region exhibited the slowest spread but had the highest diversity of Delta sublineages and the greatest number of inter-wave cases relative to the maximum amount of the virus circulating in the region, whereas the Southeast region showed the opposite. Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics. Nonetheless, if there is a significant difference in the fitness of the variants or the time allowed for the competition is sufficient, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico.\n\nImpact statementThe surveillance of lineage circulation of SARS-CoV-2 has helped identify variants that have a transmission advantage and are of concern to public health and to track the virus dispersion accurately. However, many factors contributing to differences in lineage spread dynamics beyond the acquisition of specific mutations remain poorly understood. In this work, a description of BA.1 entry and dispersion within Mexico is presented, and which factors potentially affected the spread rates of the Omicron variant BA.1 among geographical regions in the country are analyzed, underlining the importance of population density, the proportion of active cases, and viral lineage diversity and identity before the entry of BA.1.\n\nData summaryThis work was carried out using data shared through the GISAID initiative. All sequences and metadate are available through GISAID with the accession EPI_SET_220927gw, accession numbers and metadata are also reported in the supplemental material of this article. Epidemiological data was obtained though the Secretaria de Salud website (https://www.gob.mx/salud/documentos/datos-abiertos-152127),", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Selene Z\u00e1rate", + "author_inst": "Posgrado en Ciencias Gen\u00f3micas, Universidad Aut\u00f3noma de la Ciudad de M\u00e9xico, Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "Blanca Taboada", + "author_inst": "Departamento de Gen\u00e9tica del Desarrollo y Fisiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cuernavaca, Morelos, M\u00e9xico" + }, + { + "author_name": "Mauricio Rosales-Rivera", + "author_inst": "Departamento de Gen\u00e9tica del Desarrollo y Fisiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cuernavaca, Morelos, M\u00e9xico" + }, + { + "author_name": "Rodrigo Garc\u00eda-L\u00f3pez", + "author_inst": "Departamento de Gen\u00e9tica del Desarrollo y Fisiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cuernavaca, Morelos, M\u00e9xico" + }, + { + "author_name": "Jose Esteban Mu\u0148oz-Medina", + "author_inst": "Coordinaci\u00f3n de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de M\u00e9xico, M\u00e9xico" + }, + { + "author_name": "Alejandro S\u00e1nchez-Flores", + "author_inst": "Unidad Universitaria de Secuenciaci\u00f3n Masiva y Bioinform\u00e1tica, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cuernavaca, Morelos, M\u00e9xico." + }, + { + "author_name": "Alfredo Herrera-Estrella", + "author_inst": "Laboratorio Nacional de Gen\u00f3mica para la Biodiversidad-Unidad de Gen\u00f3mica Avanzada, Centro de Investigaci\u00f3n y de Estudios Avanzados del IPN, Irapuato 36821, M\u00e9x" + }, + { + "author_name": "Bruno G\u00f3mez-Gil", + "author_inst": "Centro de Investigaci\u00f3n en Alimentaci\u00f3n y Desarrollo AC, Mazatl\u00e1n, Sinaloa, M\u00e9xico." + }, + { + "author_name": "Nelly Selem M\u00f3jica", + "author_inst": "Centro de Ciencias Matem\u00e1ticas, Universidad Nacional Aut\u00f3noma de Mexico, Morelia, Michoac\u00e1n, M\u00e9xico." + }, + { + "author_name": "Angel Gustavo Salas-Lais", + "author_inst": "Coordinaci\u00f3n de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de M\u00e9xico, M\u00e9xico" + }, + { + "author_name": "Joel Armando V\u00e1zquez-P\u00e9rez", + "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "David Alejandro Cabrera-Gayt\u00e1n", + "author_inst": "Coordinaci\u00f3n de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de M\u00e9xico, M\u00e9xico" + }, + { + "author_name": "Larissa Fernandes-Matano", + "author_inst": "Coordinaci\u00f3n de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de M\u00e9xico, M\u00e9xico" + }, + { + "author_name": "Luis Antonio Uribe-Noguez", + "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social, Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "Juan Bautista Chale-Dzul", + "author_inst": "Unidad de Investigaci\u00f3n M\u00e9dica Yucat\u00e1n, Instituto Mexicano del Seguro Social, M\u00e9rida, Yucat\u00e1n, M\u00e9xico." + }, + { + "author_name": "Brenda Irasema Maldonado Meza", + "author_inst": "Centro de Investigaci\u00f3n Biom\u00e9dica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, Nuevo Le\u00f3n, M\u00e9xico." + }, + { + "author_name": "Fidencio Mej\u00eda-Nepomuceno", + "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "Rogelio P\u00e9rez-Padilla", + "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cos\u00edo Villegas, Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "Rosa Mar\u00eda Guti\u00e9rrez-R\u00edos", + "author_inst": "Departamento de Microbiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cuernavaca, Morelos, M\u00e9xico." + }, + { + "author_name": "Antonio Loza", + "author_inst": "Departamento de Gen\u00e9tica del Desarrollo y Fisiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cuernavaca, Morelos, M\u00e9xico" + }, + { + "author_name": "Susana L\u00f3pez", + "author_inst": "Departamento de Gen\u00e9tica del Desarrollo y Fisiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cuernavaca, Morelos, M\u00e9xico" + }, + { + "author_name": "Carlos F. Arias", + "author_inst": "Departamento de Gen\u00e9tica del Desarrollo y Fisiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cuernavaca, Morelos, M\u00e9xico" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.18.512708", "rel_title": "Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.", @@ -195330,61 +196227,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.16.22281142", - "rel_title": "Making use of an App (Tawakkalna) to track and reduce COVID transmission in KSA", - "rel_date": "2022-10-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.16.22281142", - "rel_abs": "Since March 2020, the Kingdom of Saudi Arabia (KSA) has launched several digital applications to support the intervention response to reduce the spread of SARS-CoV-2. At the beginning of 2021, the KSA Government introduced a mandatory immunity passport to regulate access to public venues. The passport was part of the strategy of resuming public activities before reaching high vaccination coverage. The passport was implemented as a new service in the Tawakkalna mobile phone application (App). The immunity passport allowed access to public locations only for the users who recovered from COVID-19 or those who were double vaccinated. Our study aimed to evaluate the effectiveness of the immunity passport, implemented through the Tawakkalna App, on SARS-CoV-2 spread. We built a spatial-explicit individual-based model to represent the whole KSA population (IBM-KSA) and its dynamic on a national scale. The IBM-KSA was parameterized using country demographic, remote sensing, and epidemiological data. The model included non-pharmaceutical interventions and vaccination coverage. A social network was created to represent contact heterogeneity and interaction among age groups of the population. The IBM-KSA also simulated the movement of people across the country based on a gravity model. We used the IBM-KSA to evaluate the effect of the immunity passport on the COVID-19 epidemics outcomes. The IBM-KSA results showed that implementing the immunity passport through the Tawakkalna App mitigated the SARS-CoV2 spread. In a scenario without the immunity passport, the KSA could have reported 1,515,468 (95% confidence interval [CI]: 965,725-1,986,966) cases, and 30,309 (95% CI: 19,314-39,739) deaths from March 2021 to November 2021. The comparison of IBM-KSA results with COVID-19 official reporting estimated that the passport effectively reduced the number of cases, hospitalizations, and deaths by 8.7 times, 13.5 times, and 11.9 times, respectively. These results showed that the introduction of the immunity passport through the Tawakkalna App was able to control the spread of the SARS-COV-2 until vaccination reached high coverage. By introducing the immunity passport, The KSA was able to allow to resume most of public activities safely.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Donal Bisanzio", - "author_inst": "RTI International, Washington, D.C., USA." - }, - { - "author_name": "Richard Reithinger", - "author_inst": "RTI International, Washington, D.C., USA." - }, - { - "author_name": "Sami Almudarra", - "author_inst": "Saudi Ministry of Health, Riyadh, Saudi Arabia" - }, - { - "author_name": "Reem F Alsukait", - "author_inst": "Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Di Dong", - "author_inst": "World Bank, Washington, D.C., USA." - }, - { - "author_name": "Yi Zhang", - "author_inst": "World Bank, Washington, D.C., USA." - }, - { - "author_name": "Sameh El-Saharty", - "author_inst": "World Bank, Washington, D.C., USA." - }, - { - "author_name": "Hala Almossawi", - "author_inst": "RTI International, Washington, D.C., USA." - }, - { - "author_name": "Christopher H Herbst", - "author_inst": "World Bank, Washington, D.C., USA" - }, - { - "author_name": "Ada Alqunaibet", - "author_inst": "Saudi Public Health Authority, Riyadh, Saudi Arabia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.14.512325", "rel_title": "The impact of the ABO/Rh blood group on susceptibility and severity among COVID-19 patients in Luanda, Angola", @@ -195564,6 +196406,37 @@ "type": "confirmatory results", "category": "genomics" }, + { + "rel_doi": "10.1101/2022.10.16.512436", + "rel_title": "The Impact of Protein Dynamics on Residue-Residue Coevolution and Contact Prediction", + "rel_date": "2022-10-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.16.512436", + "rel_abs": "The need to maintain protein structure constrains evolution at the sequence level, and patterns of coevolution in homologous protein sequences can be used to predict their 3D structures with high accuracy. Our understanding of the relationship between protein structure and evolution has traditionally been benchmarked by computational models ability to predict contacts from a single representative, experimentally determined structure per protein family. However, proteins in vivo are highly dynamic and can adopt multiple functionally relevant conformations. Here we demonstrate that interactions that stabilize alternate conformations, as well those that mediate conformational changes, impose an underappreciated but significant set of evolutionary constraints. We analyze the extent of these constraints over 56 paralogous G protein coupled receptors (GPCRs), {beta}-arrestin and the human SARS-CoV2 receptor ACE2. Specifically, we observe that contacts uniquely found in molecular dynamics (MD) simulation data and alternate-conformation crystal structures are successfully predicted by unsupervised language models. In GPCRs, adding these contacts as positives increases the percentage of top contacts classified as true positives, as predicted by a state-of-the-art language model, from 69% to 87%. Our results show that protein dynamics impose constraints on molecular evolution and demonstrate the ability of unsupervised language models to measure these constraints.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Alexander Fung", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Antoine Koehl", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Milind Jagota", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Yun S. Song", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.10.15.512322", "rel_title": "Determinants and Mechanisms of the Low Fusogenicity and Endosomal Entry of Omicron Subvariants", @@ -197336,41 +198209,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.10.13.512053", - "rel_title": "SARS-CoV-2 infection in domestic rats after transmission from their infected owner", - "rel_date": "2022-10-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.13.512053", - "rel_abs": "We report the transmission of SARS-CoV-2 Omicron variant from a COVID-19 symptomatic individual to two domestic rats, one of which developed severe symptoms. Omicron carries several mutations which permit rodent infection. This report demonstrates that pet, and likely wild, rodents could therefore contribute to SARS-CoV-2 spread and evolution.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Xavier Montagutelli", - "author_inst": "Institut Pasteur, Universite Paris Cite, Mouse Genetics Laboratory, Paris, France" - }, - { - "author_name": "Berenice Decaudin", - "author_inst": "Service NAC, Centre Hospitalier Veterinaire Advetia, Velizy-Villacoublay, France" - }, - { - "author_name": "Maxime Beretta", - "author_inst": "Institut Pasteur, Universite Paris Cite, Laboratory of Humoral Immunology, Paris, France" - }, - { - "author_name": "Hugo Mouquet", - "author_inst": "Institut Pasteur, Universite Paris Cite, Laboratory of Humoral Immunology, Paris, France" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur, Universite Paris Cite, G5 Evolutionary Genomics of RNA Viruses, Paris, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.10.12.512011", "rel_title": "Laboratory evaluation of a quaternary ammonium compound (QAC)-based antimicrobial coating used in public transport during the COVID-19 pandemic", @@ -197674,6 +198512,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2022.10.10.22280933", + "rel_title": "Understanding mental health trends during COVID-19 pandemic in the United States using network analysis", + "rel_date": "2022-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.10.22280933", + "rel_abs": "The emergence of COVID-19 in the United States resulted in a series of federal and state-level lock-downs and COVID-19 related health mandates to manage the spread of the virus. These policies may negatively impact the mental health state of the population. This study focused on the trends in mental health indicators following the COVID-19 pandemic amongst four United States geographical regions, and political party preferences. Indicators of interest included feeling anxious, feeling depressed, and worried about finances. Survey data from Delphi Group in Carnegie Mellon University were analyzed using clustering algorithms and dynamic connectome obtained from sliding window analysis. United States maps were generated to observe spatial trends and identify communities with similar mental health and COVID-19 trends. Between March 3rd, 2021 and January 10th, 2022, states in the south geographic region showed similar trends for reported values of feeling anxious and worried about finances. There were no identifiable communities resembling geographical regions or political party affiliation for the feeling depressed indicator. We observed a high degree of correlation among southern states as well as within republican states, where the highest correlation values from the dynamic connectome analysis for feeling anxious and feeling depressed variables seemingly overlapped with an increase in COVID-19 related cases, deaths, hospitalizations, and rapid spread of the COVID-19 Delta variant.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Hiroko Kobayashi", + "author_inst": "University of Kansas" + }, + { + "author_name": "Raul Saenz-Escarcega", + "author_inst": "University of Kansas" + }, + { + "author_name": "Alexander Fulk", + "author_inst": "University of Kansas" + }, + { + "author_name": "Folashade Agusto", + "author_inst": "University of Kansas" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.13.22281024", "rel_title": "Atypical B cells and impaired SARS-CoV-2 neutralisation following booster vaccination in the elderly.", @@ -199342,29 +200211,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.10.22280683", - "rel_title": "Sensitivity of endemic behaviour of Covid-19 under a multi-dose vaccination regime, to various biological parameters and control variables", - "rel_date": "2022-10-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.10.22280683", - "rel_abs": "For an infectious disease such as Covid-19, we present a new four-stage vaccination model (un-vaccinated, dose 1+2, booster, repeated boosters), which examines the impact of vaccination coverage, vaccination rate, generation interval, control reproduction number, vaccine efficacies, and rates of waning immunity, upon the dynamics of infection. We derive a single equation that allows computation of equilibrium prevalence and incidence of infection, given knowledge about these parameter and variable values. Based upon a 20 compartment model, we develop a numerical simulation of the associated differential equations. The model is not a forecasting or even predictive one, given the uncertainty about several biological parameter values. Rather, it is intended to aid qualitative understanding of how equilibrium levels of infection may be impacted upon, by the parameters of the system. We examine one at a time sensitivity analysis around a base case scenario. The key finding which should be of interest to policy makers, is that while factors such as improved vaccine efficacy, increased vaccination rates, lower waning rates, and more stringent non-pharmaceutical interventions might be thought to improve equilibrium levels of infection, this might only be done to good effect, if vaccination coverage on a recurrent basis, is sufficiently high.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "John S Dagpunar", - "author_inst": "School of Mathematical Sciences, University of Southampton" - }, - { - "author_name": "Chenchen Wu", - "author_inst": "Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.09.22280878", "rel_title": "Associations Between Reported Post-COVID-19 Symptoms and Subjective Well-Being, Israel, July 2021 -April 2022", @@ -199736,6 +200582,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.08.22280836", + "rel_title": "GRAd-COV2 vaccine provides potent and durable immunity in a randomised placebo-controlled phase 2 trial (COVITAR)", + "rel_date": "2022-10-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.08.22280836", + "rel_abs": "BackgroundSARS-CoV-2 ongoing pandemic and heterologous immunization approaches implemented worldwide for booster doses call for diversified vaccines portfolio. We report safety and immunogenicity of GRAd-COV2, a novel gorilla adenovirus-based COVID-19 vaccine, in a phase 2 trial aimed at identifying the appropriate dose and schedule.\n\nMethod917 eligible adults aged 18 years or older, including participants with co-morbidities, were randomised to receive, 21 days apart, a single vaccine administration at 2x1011 viral particles (vp) followed by placebo, or repeated vaccine administration at 1x1011 vp, or two doses of placebo. Primary endpoints were the incidence of local and systemic solicited AEs for 7 days post each dose and the post-treatment (35 days after the first dose), geometric mean titers (GMTs) and geometric mean fold rise (GMFRs) of ELISA antibody responses to Spike protein. Additional humoral and cellular immune response parameters were monitored for up to six months.\n\nResultsThe safety profile of GRAd-COV2 was characterized by short-term, mild-to-moderate pain and tenderness at injection site, fatigue, headache, malaise, and myalgia. Neither related SAEs nor deaths were reported. Humoral (binding and neutralizing) Ab responses peaked at day 35 after a single administration, were boosted by a second vaccination, were sustained until day 57 to then decline at day 180. Potent, VOC cross-reactive T cell responses peaked already after first dose with high frequencies of long-lived CD8 T cells.\n\nConclusionGRAd-COV2 was safe, and induced robust immune responses after a single immunization; the second administration increased humoral but not cellular immune responses.\n\nTrial RegistrationClinicalTrials.gov NCT04791423.\n\nFundingReiThera Srl", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Stefania Capone", + "author_inst": "ReiThera srl, Rome, Italy" + }, + { + "author_name": "Francesco M Fusco", + "author_inst": "\"D. Cotugno\" Hospital, Azienda Specialistica dei Colli, Naples, Italy" + }, + { + "author_name": "Stefano Milleri", + "author_inst": "Centro Ricerche Cliniche di Verona- CRC, Verona, Italy" + }, + { + "author_name": "Silvio Borre'", + "author_inst": "ASL Vercelli Malattie Infettive, Vercelli, Italy" + }, + { + "author_name": "Sergio Carbonara", + "author_inst": "U.O.C. Malattie Infettive , P.O. V. Emanuele II, Bisceglie (BT), Italy" + }, + { + "author_name": "Sergio Lo Caputo", + "author_inst": "Malattie infettive, Dipartimento di Scienze Mediche e Chirurgiche, A.O. U. Policlinico Foggia, Italy" + }, + { + "author_name": "Sebastiano Leone", + "author_inst": "Division of Infectious Diseases, San Giuseppe Moscati Hospital, Avellino, Italy" + }, + { + "author_name": "Giovanni Gori", + "author_inst": "Centro di Farmacologia Clinica per la Sperimentazione dei Farmaci - Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy" + }, + { + "author_name": "Paolo Maggi", + "author_inst": "Universita' degli Studi della Campania Luigi Vanvitelli, Caserta, Italy;" + }, + { + "author_name": "Antonio Cascio", + "author_inst": "Department of Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy" + }, + { + "author_name": "Miriam Lichtner", + "author_inst": "Dept NESMOS Sapienza University of Rome, Infectious Disease Unit, SM Goretti Hospital, Latina, Italy" + }, + { + "author_name": "Roberto Cauda", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Sarah Dal Zoppo", + "author_inst": "UO Malattie Infettive, ASST Cremona, Italy" + }, + { + "author_name": "Maria V Cossu", + "author_inst": "I Divisione Malattie Infettive- ASST FBF SACCO, Milan, Italy" + }, + { + "author_name": "Andrea Gori", + "author_inst": "Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, University" + }, + { + "author_name": "Silvia Roda", + "author_inst": "U.O.C. Malattie Infettive - Fondazione IRCCS Policlinico San Matteo di Pavia, Italy" + }, + { + "author_name": "Paola Confalonieri", + "author_inst": "Struttura Complessa Pneumologia - Azienda Sanitaria Universitaria Giuliano-Isontina, Trieste, Italy" + }, + { + "author_name": "Stefano Bonora", + "author_inst": "Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Italy" + }, + { + "author_name": "Gabriele Missale", + "author_inst": "Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy. Department of Medicine and Surgery, University of Parma, P" + }, + { + "author_name": "Mauro Codeluppi", + "author_inst": "UOC di Malattie Infettive - Ospedale Guglielmo da Saliceto, AUSL Piacenza, Italy" + }, + { + "author_name": "Ivano Mezzaroma", + "author_inst": "UOC Malattie Infettive, AOU Policlinico Umberto 1; Dept of Translational and Precision Medicine, Sapienza University of Roma, Italy" + }, + { + "author_name": "Serena Capici", + "author_inst": "Phase 1 Research Unit, ASST Monza, Monza, Italy" + }, + { + "author_name": "Emanuele Pontali", + "author_inst": "Department of Infectious Diseases - E.O. Ospedali Galliera, Genova, Italy" + }, + { + "author_name": "Marco Libanore", + "author_inst": "Department Infectious Diseases St Anna Hospital and University Ferrara, Italy" + }, + { + "author_name": "Augusta Diani", + "author_inst": "Ospedale di Circolo e Fondazione Macchi, Varese, Italy" + }, + { + "author_name": "Simone Lanini", + "author_inst": "INMI Spallanzani Rome, Italy" + }, + { + "author_name": "Simone Battella", + "author_inst": "ReiThera srl, Rome, Italy" + }, + { + "author_name": "Alessandra M Contino", + "author_inst": "ReiThera srl, Rome, Italy" + }, + { + "author_name": "Eva Piano Mortari", + "author_inst": "B Cell Unit, Immunology Research Area, Bambino Gesu' Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Francesco Genova", + "author_inst": "ReiThera srl, Rome, Italy" + }, + { + "author_name": "Gessica Parente", + "author_inst": "ReiThera srl, Rome, Italy" + }, + { + "author_name": "Rosella Dragonetti", + "author_inst": "ReiThera srl, Rome, Italy" + }, + { + "author_name": "Stefano Colloca", + "author_inst": "ReiThera srl, Rome, Italy" + }, + { + "author_name": "Luigi Visani", + "author_inst": "Exom-Group Milan, Italy" + }, + { + "author_name": "Claudio Iannacone", + "author_inst": "SPARC Consulting , Milan, Italy" + }, + { + "author_name": "Rita Carsetti", + "author_inst": "B Cell Unit, Immunology Research Area, Bambino Gesu' Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Antonella Folgori", + "author_inst": "ReiThera srl, Rome, Italy" + }, + { + "author_name": "Roberto Camerini", + "author_inst": "ReiThera srl, Rome, Italy" + }, + { + "author_name": "- the COVITAR study group", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.09.22280826", "rel_title": "Time trends of mental health indicators in Germany's adult population before and during the COVID-19 pandemic", @@ -201136,41 +202153,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.10.04.510837", - "rel_title": "Community engagement through student-led science for dengue prevention during the COVID-19 pandemic in Cordoba, Argentina.", - "rel_date": "2022-10-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.04.510837", - "rel_abs": "BackgroundDuring 2019-2020 while COVID-19 pandemic, the Americas were facing the biggest dengue fever epidemic in recent history. Traditional vector control programs, based on insecticide application have been insufficient to control the spread of dengue fever. Several studies suggest refocusing on education with the aim of an integrated vector management strategy within the local ecological-community context. We aim to assess community perceptions, knowledge, attitude, preventive practice, and action through student-led science assignments regarding dengue fever, prevention, and socio-ecological factors in temperate Cordoba, Argentina.\n\nMethodsThe study was conducted during the COVID-19 quarantine when schools switched to online education for the first time. Several activities through Google Classroom platform included a survey to one students family member, and an outdoor activity to assess their attitudes and to clean the backyard and gardens.\n\nResultsSignificant number of respondents developed good preventive practices and increased their knowledge about the vector and disease highlighting that 75% of responders knew that dengue fever was transmitted by a mosquito, 81.96% declared having obtained knowledge regarding dengue and vector through television, 56% affirm that dengue is a severe illness, 67% of respondents admitted that individuals play an important role in the prevention of dengue. Regarding mosquito control activities, 90% of respondents reported turning containers.\n\nConclusionsThis highlights the need for school programs with curricula to address vector biology and the prevention of vector-borne diseases not only during activity periods when mosquitoes batter people but all year long to do real prevention.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Elizabet Lilia Estallo", - "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)" - }, - { - "author_name": "Magali Madelon", - "author_inst": "Instituto Jesus Maria" - }, - { - "author_name": "Elisabet Benitez", - "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)" - }, - { - "author_name": "Anna Maria Stewart-Ibarra", - "author_inst": "InterAmerican Institute for Global Change Research" - }, - { - "author_name": "Francisco Felipe Luduena-Almeida", - "author_inst": "Facultad de Ciencias Exactas, Fisicas y Naturales, Universidad Nacional de Cordoba." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2022.10.03.22280660", "rel_title": "Effectiveness and duration of a second COVID-19 vaccine booster", @@ -201474,6 +202456,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.10.04.22280700", + "rel_title": "Evaluation of the Abbott PanbioTM COVID-19 antigen detection rapid diagnostic test among healthcare workers in elderly care", + "rel_date": "2022-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.04.22280700", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) has been especially dangerous for elderly people. To reduce the risk of transmission from healthcare workers to elderly people, it is of utmost importance to detect possible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive healthcare workers as early as possible. We aimed to determine whether the Abbott Panbio COVID-19 antigen detection rapid diagnostic test (Ag-RDT) could be used as an alternative to reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The second aim was to compare the cycle threshold (Ct) in RT-qPCR with the results of the Ag-RDT.\n\nMethodsA prospective diagnostic evaluation of the Abbott Panbio COVID-19 Ag-RDT among healthcare workers across three elderly care facilities as well as home-based elderly care workers who met clinical criteria for COVID-19 during the second wave of the COVID-19 pandemic. Per healthcare worker, the first nasopharyngeal swab was obtained to perform the Ag-RDT and the second swab for RT-qPCR. A Ct-value of < 40 was interpreted as positive, [≥] 40 as negative.\n\nResultsA total of 683 healthcare workers with COVID-19 symptoms were sampled for detection of SARS-CoV-2 by both Ag-RDT and RT-qPCR. Sixty-three healthcare workers (9.2%) tested positive for SARS-CoV-2 by RT-qPCR. The overall sensitivity of Ag-RDT was 81.0% sensitivity (95%CI: 69.6-88.8%) and 100% specificity (95%CI: 99.4-100%). Using a cut-off Ct-value of 32, the sensitivity increased to 92.7% (95% CI: 82.7-97.1%). Negative Ag-RDT results were moderately associated with higher Ct-values (r = 0.62) compared to positive Ag-RDT results.\n\nConclusionThe Panbio COVID-19 Ag-RDT can be used to quickly detect positive SARS-CoV-2 healthcare workers. Negative Ag-RDT should be confirmed by RT-qPCR. In case of severe understaffing and with careful consideration, fully vaccinated healthcare workers with Ag-RDT negative results could work with a mask pending PCR results.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andrea Eikelenboom-Boskamp", + "author_inst": "Canisius Wilhelmina Hospital: Canisius Wilhelmina Ziekenhuis" + }, + { + "author_name": "Martijn den Ouden", + "author_inst": "Canisius Wilhelmina Hospital: Canisius Wilhelmina Ziekenhuis" + }, + { + "author_name": "Theun de Groot", + "author_inst": "Canisius Wilhelmina Hospital: Canisius Wilhelmina Ziekenhuis" + }, + { + "author_name": "Tim Stobernack", + "author_inst": "Radboudumc" + }, + { + "author_name": "Heiman Wertheim", + "author_inst": "Radboudumc" + }, + { + "author_name": "Andreas Voss", + "author_inst": "Universitair Medisch Centrum Groningen" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.05.511057", "rel_title": "Long-term passaging of replication competent pseudo-typed SARS-CoV-2 reveals the antiviral breadth of monoclonal and bispecific antibody cocktails", @@ -203190,41 +204211,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.10.03.22280646", - "rel_title": "Impact of Omicron Wave and Associated Infection Prevention and Control Measures in Shanghai on Health Management and Psychosocial Well-Being of Patients with Chronic Conditions", - "rel_date": "2022-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.03.22280646", - "rel_abs": "BackgroundCOVID-19 and associated controls may be particularly problematic in the context of chronic conditions. This study investigated health management, well-being, and pandemic-related perspectives in these patients in the context of stringent measures, and associated correlates.\n\nMethodsA self-report survey was administered via Wenjuanxing in Simplified Chinese between March-June 2022 during the Omicron wave lockdown in Shanghai, China. Items from the Somatic Symptom Scale (SSS) and Symptom Checklist-90 (SCL-90) were administered, as well as pandemic-related items created by a working group of the Chinese Preventive Medical Association. Chronic disease patients in this cross-sectional study were recruited through an associated community family physician group.\n\nResultsOverall, 1775 patients, mostly married females with hypertension, participated. Mean SSS scores were 36.1{+/-}10.5/80, with 41.5% scoring in the elevated range (i.e., above 36). In an adjusted model, female, diagnosis of coronary artery disease and arrhythmia, perceived impact of pandemic on life, duration can tolerate control measures, perception of future & control measures, impact of pandemic on health condition and change to exercise routine due to pandemic were significantly associated with greater distress. Approximately one-quarter (24.5%) perceived the pandemic had a permanent impact on their life, and 44.1% perceived at least a minor impact on their health. One-third (33.5%) discontinued exercise due to the pandemic. While 47.6% stocked up on their medications before the lockdown, their remaining supply was mostly only enough for a couple of weeks and 17.5% of participants discontinued use. Chief among their fears were inability to access healthcare (83.2%), and what they stated they most needed to manage their condition was medication access (65.6%).\n\nConclusionsSince 2020 when we assessed a similar cohort, distress and perceived impact of the pandemic has worsened. Greater access to cardiac rehabilitation in China could address these issues.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zhimin Xu", - "author_inst": "Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China" - }, - { - "author_name": "Gabriela Lima de Melo Ghisi", - "author_inst": "Cardiovascular Prevention and Rehabilitation Program, Toronto Rehabilitation Institute, University Health Network, University of Toronto, Toronto" - }, - { - "author_name": "Xia Liu", - "author_inst": "Chengdu Wanda UPMC Hospital, Chengdu, China" - }, - { - "author_name": "Lixian Cui", - "author_inst": "Division of Arts and Sciences, NYU Shanghai, Shanghai, China" - }, - { - "author_name": "Sherry Grace", - "author_inst": "Faculty of Health, York University, Toronto M3J 1P3, Canada; and KITE-Toronto Rehabilitation Institute & Peter Munk Cardiac Centre, University Health Network, U" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.10.02.22280627", "rel_title": "Dynamics of Vaccine-Hesitant Parents' Considerations Regarding Covid-19 Vaccination", @@ -203528,6 +204514,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.02.22280610", + "rel_title": "Protective effectiveness of prior SARS-CoV-2 infection and hybrid immunity against Omicron infection and severe disease: a systematic review and meta-regression", + "rel_date": "2022-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.02.22280610", + "rel_abs": "BackgroundWe aimed to systematically review the magnitude and duration of the protective effectiveness of prior infection (PE) and hybrid immunity (HE) against Omicron infection and severe disease.\n\nMethodsWe searched pre-print and peer-reviewed electronic databases for controlled studies from January 1, 2020, to June 1, 2022. Risk of bias (RoB) was assessed using the Risk of Bias In Non-Randomized Studies of Interventions (ROBINS-I)-Tool. We used random-effects meta-regression to estimate the magnitude of protection at 1-month intervals and the average change in protection since the last vaccine dose or infection from 3 months to 6 or 12 months. We compared our estimates of PE and HE to previously published estimates of the magnitude and durability of vaccine effectiveness (VE) against Omicron.\n\nFindingsEleven studies of prior infection and 15 studies of hybrid immunity were included. For prior infection, there were 97 estimates (27 at moderate RoB and 70 at serious RoB), with the longest follow up at 15 months. PE against hospitalization or severe disease was 82{middle dot}5% [71{middle dot}8-89{middle dot}7%] at 3 months, and 74{middle dot}6% [63{middle dot}1-83{middle dot}5%] at 12 months. PE against reinfection was 65{middle dot}2% [52{middle dot}9-75{middle dot}9%] at 3 months, and 24{middle dot}7% [16{middle dot}4-35{middle dot}5%] at 12 months. For HE, there were 153 estimates (78 at moderate RoB and 75 at serious RoB), with the longest follow up at 11 months for primary series vaccination and 4 months for first booster vaccination. Against hospitalization or severe disease, HE involving either primary series vaccination or first booster vaccination was consistently >95% for the available follow up. Against reinfection, HE involving primary series vaccination was 69{middle dot}0% [58{middle dot}9-77{middle dot}5%] at 3 months after the most recent infection or vaccination, and 41{middle dot}8% [31{middle dot}5-52{middle dot}8%] at 12 months, while HE involving first booster vaccination was 68{middle dot}6% [58{middle dot}8-76{middle dot}9%] at 3 months, and 46{middle dot}5% [36{middle dot}0-57{middle dot}3%] at 6 months. Against hospitalization or severe disease at 6 months, hybrid immunity with first booster vaccination (effectiveness 95{middle dot}3% [81{middle dot}9-98{middle dot}9%]) or with primary series alone (96{middle dot}5% [90{middle dot}2-98{middle dot}8%]) provided significantly greater protection than prior infection alone (80{middle dot}1% [70{middle dot}3-87{middle dot}2%]), first booster vaccination alone (76{middle dot}7% [72{middle dot}5-80{middle dot}4%]), or primary series alone (64{middle dot}6% [54{middle dot}5-73{middle dot}6%]). Results for protection against reinfection were similar.\n\nInterpretationPrior infection and hybrid immunity both provided greater and more sustained protection against Omicron than vaccination alone. All protection estimates waned quickly against infection but remained high for hospitalisation or severe disease. Individuals with hybrid immunity had the highest magnitude and durability of protection against all outcomes, reinforcing the global imperative for vaccination.\n\nFundingWHO COVID-19 Solidarity Response Fund and the Coalition for Epidemic Preparedness Innovations.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe global emergence and rapid spread of Omicron (B.1.1.529) variant of concern, characterized by their ability to escape immunity, has required scientists and policymakers to reassess the population protection against Omicron infection and severe disease. So far, few systematic reviews have incorporated data on Omicron, and none have examined the protection against Omicron conferred by hybrid immunity (i.e. the immunity gained from the combination of vaccination and prior infection) which is now widespread globally. While one preprint has recently reported protection from prior infection over time, no systematic review has systematically compared the magnitude and duration of vaccination, prior infection, and hybrid immunity. A large single-country study has reported that protection from either infection or hybrid immunity against Omicron infection wanes to low levels at 15 months, but is relatively stable against severe disease.\n\nAdded value of this studyPrior infection and hybrid immunity both provided greater and more sustained protection against Omicron than vaccination alone. Individuals with hybrid immunity had the highest magnitude and durability of protection against all outcomes; protection against severe disease remained above 95% until the end of available follow-up at 11 months after hybrid immunity with primary series and 4 months after hybrid immunity with booster vaccination, and was sustained at these high levels of protection in projections to 12 months and 6 months, respectively.\n\nImplications of all the available evidenceThese results may serve to tailor guidance on the optimal number and timing of vaccinations. At the public health level, these findings can be combined with data on local infection prevalence, vaccination rates, and their timing. In settings with high seroprevalence, limited resources, and competing health priorities, it may be reasonable to focus on achieving high coverage rates with primary series among individuals who are at higher risk of poor outcome, as this will provide a high level of protection against severe disease for at least one year among those with prior infection. Furthermore, given the waning protection for both infection-and vaccine induced immunity against infection or reinfection, mass vaccination could be timed for roll-out prior to periods of expected increased incidence, such as the winter season. At the individual level, these results can be combined with knowledge of a persons infection and vaccination history. A six-month delay in booster may be justified after the last infection or vaccination for individuals with a known prior infection and full primary series vaccination. Further follow-up of the protective effectiveness of hybrid immunity against hospitalization or severe disease for all vaccines is needed to clarify how much waning of protection might occur with longer duration since the last infection or vaccination. Producing estimates of protection for new variant-containing vaccines will be crucial for COVID-19 vaccine policy and decision-making bodies. Policy makers considering the use and timing of vaccinations should include the local extent of past infection, the protection conferred by prior infection or hybrid immunity, and the duration of this protection as key considerations to inform their decision-making.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Niklas Bobrovitz", + "author_inst": "Temerty Faculty of Medicine, University of Toronto, Canada. Department of Critical Care Medicine, University of Calgary, Canada. Centre for Health Informatics, " + }, + { + "author_name": "Harriet Ware", + "author_inst": "Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Canada." + }, + { + "author_name": "Xiaomeng Ma", + "author_inst": "Institute of Health Policy Management & Evaluation, University of Toronto, Canada." + }, + { + "author_name": "Zihan Li", + "author_inst": "Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Canada. Department of Bioengineering, University of California, Berkeley, USA." + }, + { + "author_name": "Reza Hosseini", + "author_inst": "Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Canada. School of Population and Public Health, University of British Columbia" + }, + { + "author_name": "Christian Cao", + "author_inst": "Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Canada. Temerty Faculty of Medicine, University of Toronto, Canada." + }, + { + "author_name": "Anabel Selemon", + "author_inst": "Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Canada." + }, + { + "author_name": "Mairead Whelan", + "author_inst": "Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Canada." + }, + { + "author_name": "Zahra Premji", + "author_inst": "Libraries, University of Victoria, Canada." + }, + { + "author_name": "Hanane Issa", + "author_inst": "Institute of Health Informatics, University College London, United Kingdom." + }, + { + "author_name": "Brianna Cheng", + "author_inst": "Temerty Faculty of Medicine, University of Toronto, Canada." + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine Qatar, Cornell University, Doha, Qatar." + }, + { + "author_name": "David L Buckeridge", + "author_inst": "Department of Epidemiology and Biostatistics, School of Population and Global Health, McGill University, Montreal, Canada." + }, + { + "author_name": "Maria Van Kerkhove", + "author_inst": "Health Emergency Program, World Health Organization, Geneva, Switzerland." + }, + { + "author_name": "Vanessa Piechotta", + "author_inst": "Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany." + }, + { + "author_name": "Melissa M Higdon", + "author_inst": "International Vaccine Access Center, Department of International Health, John Hopkins Bloomberg School of Public Health, Baltimore, MA, USA." + }, + { + "author_name": "Annelies Wilder-Smith", + "author_inst": "Department of Immunizations, Vaccines and Biologicals, World Health Organization, Geneva, Switzerland." + }, + { + "author_name": "Isabel Bergeri", + "author_inst": "Health Emergency Program, World Health Organization, Geneva, Switzerland." + }, + { + "author_name": "Daniel Feikin", + "author_inst": "Department of Immunizations, Vaccines and Biologicals, World Health Organization, Geneva, Switzerland." + }, + { + "author_name": "Rahul Krishan Arora", + "author_inst": "Centre for Health Informatics, Cumming School of Medicine, University of Calgary, Canada. Institute of Biomedical Engineering, University of Oxford, United King" + }, + { + "author_name": "Minal K Patel", + "author_inst": "Department of Immunizations, Vaccines and Biologicals, World Health Organization, Geneva, Switzerland." + }, + { + "author_name": "Lorenzo Subissi", + "author_inst": "Health Emergency Program, World Health Organization, Geneva, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.03.22280649", "rel_title": "Impact of vaccination on COVID-19-associated admissions to critical care in England: a population cohort study of linked data", @@ -205180,77 +206269,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.09.30.510287", - "rel_title": "Correlating the differences in the receptor binding domain of SARS-CoV-2 spike variants on their interactions with human ACE2 receptor", - "rel_date": "2022-09-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.30.510287", - "rel_abs": "Spike protein of SARS-CoV-2 variants play critical role in the infection and transmission through its interaction with hACE2 receptor. Prior findings using molecular docking and biomolecular studies reported varied findings on the difference in the interactions among the spike variants with hACE2 receptor. Hence, it is a prerequisite to understand these interactions in a more precise manner. To this end, firstly, we performed ELISA with trimeric spike proteins of Wild (Wuhan Hu-1), Delta, C.1.2 and Omicron variants. Further, to study the interactions in a more specific manner by mimicking the natural infection, we developed hACE2 receptor expressing HEK-293T cell line and evaluated binding efficiencies of the variants and competitive binding of spike variants with D614G spike pseudotyped virus. In lines with the existing findings, we observed that Omicron had higher binding efficiency compared to Delta in both ELISA and Cellular models. Intriguingly, we found that cellular models could differentiate the subtle differences between the closely related C.1.2 and Delta in their binding to hACE2. From the analysis in receptor binding domain (RBD) revealed that a single common modification, N501Y, present in both Omicron and C.1.2 is driving the enhanced spike binding to the receptor and showed two-fold superior competitive binding than Delta. Our study using cellular model provides a precise method to evaluate the binding interactions between spike sub-lineages to hACE2 receptors and signifies the role of single common modification N501Y in RBD towards imparting superior binding efficiencies. Our approach would be instrumental in understanding the disease progression and developing therapeutics.\n\nAuthor SummarySpike proteins of evolving SARS-CoV2 variants demonstrated their signature binding to hACE2 receptor, in turn contributed to driving the infection and transmission. Prior studies to scale the binding efficiencies between the spike variant and the receptor had consensus in distinct variants, but discrepancies in the closely related ones. To this end, we compared spike variants-receptor interactions with ELISA, from cells expressing hACE2 receptor. Intriguingly, we found that cellular models could differentiate the subtle differences between the closely related C.1.2 and Delta in their binding to hACE2. More importantly, competitive binding studies in presence of pseudovirus, demonstrated that a single common modification, N501Y, present in both Omicron and C.1.2 showed two fold superior competitive binding than Delta. Collectively, our study suggests a precise approach to evaluate the binding interactions between spike sub-lineages to hACE2 receptor. This would be instrumental in understanding the disease progression and developing therapeutics.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Gokulnath Mahalingam", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Porkizhi Arjunan", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Yogapriya Periasami", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Ajay Kumar Dhyani", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Nivedhitha Devaraju", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Vignesh Rajendiran", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Abhisha Crystal Christopher", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Ramya Devi KT", - "author_inst": "SRM University: SRM Institute of Science and Technology" - }, - { - "author_name": "Immanuel Darasingh", - "author_inst": "Vellore Institute of Technology: VIT University" - }, - { - "author_name": "Saravanabhavan Thangavel", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Mohankumar Murugesan", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Mahesh Moorthy", - "author_inst": "CMCH: Christian Medical College Vellore" - }, - { - "author_name": "Alok Srivastava", - "author_inst": "CSCR: Center for Stem Cell Research" - }, - { - "author_name": "Srujan Marepally", - "author_inst": "CSCR: Center for Stem Cell Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2022.09.28.22280472", "rel_title": "Covid-19: Qualitative Change in the Behavior of the \"Virus vs Human\" System - From Limit Cycle to Sustained Focus", @@ -205482,6 +206500,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.28.22280462", + "rel_title": "Trend and co-occurrence network study of symptoms through social media: an example of COVID-19", + "rel_date": "2022-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.28.22280462", + "rel_abs": "ImportanceCOVID-19 is a multi-organ disease with broad-spectrum manifestations. Clinical data-driven research can be difficult because many patients do not receive prompt diagnoses, treatment, and follow-up studies. Social medias accessibility, promptness, and rich information provide an opportunity for large-scale and long-term analyses, enabling a comprehensive symptom investigation to complement clinical studies.\n\nObjectivePresent an efficient workflow to identify and study the characteristics and co-occurrences of COVID-19 symptoms using social media.\n\nDesign, Setting, and ParticipantsThis retrospective cohort study analyzed 471,553,966 COVID-19-related tweets from February 1, 2020, to April 30, 2022. A comprehensive lexicon of symptoms was used to filter tweets through rule-based methods. 948,478 tweets with self-reported symptoms from 689,551 Twitter users were identified for analysis.\n\nMain Outcomes and MeasuresThe overall trends of COVID-19 symptoms reported on Twitter were analyzed (separately by the Delta strain and the Omicron strain) using weekly new numbers, overall frequency, and temporal distribution of reported symptoms. A co-occurrence network was developed to investigate relationships between symptoms and affected organ systems.\n\nResultsThe weekly quantity of self-reported symptoms has a high consistency (0.8528, P<0.0001) and one-week leading trend (0. 8802, P<0.0001) with new infections in four countries. We grouped 201 common symptoms (mentioned [≥] 10 times) into 10 affected systems. The frequency of symptoms showed dynamic changes as the pandemic progressed, from typical respiratory symptoms in the early stage to more musculoskeletal and nervous symptoms at later stages. When comparing symptoms reported during the Delta strain versus the Omicron variant, significant changes were observed, with dropped odd ratios of coma (95%CI 0.55-0.49, P<0.01) and anosmia (95%CI, 0.6-0.56), and more pain in the throat (95%CI, 1.86-1.96) and concentration problems (95%CI, 1.58-1.70). The co-occurrence network characterizes relationships among symptoms and affected systems, both intra-systemic, such as cough and sneezing (respiratory), and inter-systemic, such as alopecia (integumentary) and impotence (reproductive).\n\nConclusions and RelevanceWe found dynamic COVID-19 symptom evolution through self-reporting on social media and identified 201 symptoms from 10 affected systems. This demonstrates that social medias prevalence trends and co-occurrence networks can efficiently identify and study public health problems, such as common symptoms during pandemics.\n\nKey pointsO_ST_ABSQuestionsC_ST_ABSWhat are the epidemic characteristics and relationships of COVID-19 symptoms that have been extensively reported on social media?\n\nFindingsThis retrospective cohort study of 948,478 related tweets (February 2020 to April 2022) from 689,551 users identified 201 self-reported COVID-19 symptoms from 10 affected systems, mitigating the potential missing information in hospital-based epidemiologic studies due to many patients not being timely diagnosed and treated. Coma, anosmia, taste sense altered, and dyspnea were less common in participants infected during Omicron prevalence than in Delta. Symptoms that affect the same system have high co-occurrence. Frequent co-occurrences occurred between symptoms and systems corresponding to specific disease progressions, such as palpitations and dyspnea, alopecia and impotence.\n\nMeaningTrend and network analysis in social media can mine dynamic epidemic characteristics and relationships between symptoms in emergent pandemics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jiageng Wu", + "author_inst": "Zhejiang University" + }, + { + "author_name": "Lumin Wang", + "author_inst": "Zhejiang University" + }, + { + "author_name": "Yining Hua", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Minghui Li", + "author_inst": "Zhejiang University" + }, + { + "author_name": "Li Zhou", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "David W Bates", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Jie Yang", + "author_inst": "Zhejiang University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.09.28.22280476", "rel_title": "Binding and neutralizing IgG responses to SARS-CoV-2 after natural infection or vaccination", @@ -207098,97 +208159,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.26.22280364", - "rel_title": "Clinical Subphenotypes of Multisystem Inflammatory Syndrome in Children: An EHR-based cohort study from the RECOVER program", - "rel_date": "2022-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280364", - "rel_abs": "BackgroundMulti-system inflammatory syndrome in children (MIS-C) represents one of the most severe post-acute sequelae of SARS-CoV-2 infection in children, and there is a critical need to characterize its disease patterns for improved recognition and management. Our objective was to characterize subphenotypes of MIS-C based on presentation, demographics and laboratory parameters.\n\nMethodsWe conducted a retrospective cohort study of children with MIS-C from March 1, 2020 - April 30, 2022 and cared for in 8 pediatric medical centers that participate in PEDSnet. We included demographics, symptoms, conditions, laboratory values, medications and outcomes (ICU admission, death), and grouped variables into eight categories according to organ system involvement. We used a heterogeneity-adaptive latent class analysis model to identify three clinically-relevant subphenotypes. We further characterized the sociodemographic and clinical characteristics of each subphenotype, and evaluated their temporal patterns.\n\nFindingsWe identified 1186 children hospitalized with MIS-C. The highest proportion of children (44{middle dot}4%) were aged between 5-11 years, with a male predominance (61.0%), and non- Hispanic white ethnicity (40{middle dot}2%). Most (67{middle dot}8%) children did not have a chronic condition. Class 1 represented children with a severe clinical phenotype, with 72{middle dot}5% admitted to the ICU, higher inflammatory markers, hypotension/shock/dehydration, cardiac involvement, acute kidney injury and respiratory involvement. Class 2 represented a moderate presentation, with 4-6 organ systems involved, and some overlapping features with acute COVID-19. Class 3 represented a mild presentation, with fewer organ systems involved, lower CRP, troponin values and less cardiac involvement. Class 1 initially represented 51{middle dot}1% of children early in the pandemic, which decreased to 33{middle dot}9% from the pre-delta period to the omicron period.\n\nInterpretationMIS-C has a spectrum of clinical severity, with degree of laboratory abnormalities rather than the number of organ systems involved providing more useful indicators of severity. The proportion of severe/critical MIS-C decreased over time.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and preprint articles from December 2019, to July 2022, for studies published in English that investigated the clinical subphenotypes of MIS-C using the terms \"multi-system inflammatory syndrome in children\" or \"pediatric inflammatory multisystem syndrome\" and \"phenotypes\". Most previous research described the symptoms, clinical characteristics and risk factors associated with MIS-C and how these differ from acute COVID-19, Kawasaki Disease and Toxic Shock Syndrome. One single-center study of 63 patients conducted in 2020 divided patients into Kawasaki and non-Kawasaki disease subphenotypes. Another CDC study evaluated 3 subclasses of MIS-C in 570 children, with one class representing the highest number of organ systems, a second class with predominant respiratory system involvement, and a third class with features overlapping with Kawasaki Disease. However, this study evaluated cases from March to July 2020, during the early phase of the pandemic when misclassification of cases as Kawasaki disease or acute COVID-19 may have occurred. Therefore, it is not known from the existing literature whether the presentation of MIS-C has changed with newer variants such as delta and omicron.\n\nAdded value of this studyPEDSnet provides one of the largest MIS-C cohorts described so far, providing sufficient power for detailed analyses on MIS-C subphenotypes. Our analyses span the entire length of the pandemic, including the more recent omicron wave, and provide an update on the presentations of MIS-C and its temporal dynamics. We found that children have a spectrum of illness that can be characterized as mild (lower inflammatory markers, fewer organ systems involved), moderate (4-6 organ involvement with clinical overlap with acute COVID-19) and severe (higher inflammatory markers, critically ill, more likely to have cardiac involvement, with hypotension/shock and need for vasopressors).\n\nImplications of all the available evidenceThese results provide an update to the subphenotypes of MIS-C including the more recent delta and omicron periods and aid in the understanding of the various presentations of MIS-C. These and other findings provide a useful framework for clinicians in the recognition of MIS-C, identify factors associated with children at risk for increased severity, including the importance of laboratory parameters, for risk stratification, and to facilitate early evaluation, diagnosis and treatment.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Suchitra Rao", - "author_inst": "University of Colorado School of Medicine and Children's Hospital Colorado" - }, - { - "author_name": "Naimin Jing", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Xiaokang Liu", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Vitaly Lorman", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Mitchell Maltenfort", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Julia Schuchard", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Qiong Wu", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jiayi Tong", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Hanieh Razzaghi", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Asuncion Mejias", - "author_inst": "Nationwide Children's Hospital and The Ohio State University" - }, - { - "author_name": "Grace M. Lee", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Nathan M Pajor", - "author_inst": "Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine" - }, - { - "author_name": "Grant S. Schulert", - "author_inst": "Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine" - }, - { - "author_name": "Deepika Thacker", - "author_inst": "Nemours Children's Health" - }, - { - "author_name": "Ravi Jhaveri", - "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" - }, - { - "author_name": "Dimitri A. Christakis", - "author_inst": "Seattle Children's Hospital" - }, - { - "author_name": "L. Charles Bailey", - "author_inst": "Children's Hospital of Philadelphia and University of Pennsylvania" - }, - { - "author_name": "Christopher B. Forrest", - "author_inst": "Children's Hospital of Philadelphia and University of Pennsylvania" - }, - { - "author_name": "Yong Chen", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.09.22.22280262", "rel_title": "Development and validation of a methodology to measure exhaled carbon dioxide (CO2) and control indoor air renewal", @@ -207376,6 +208346,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.26.22280381", + "rel_title": "Nation-wide mammography screening participation in Denmark during the COVID-19 pandemic: An observational study", + "rel_date": "2022-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280381", + "rel_abs": "BackgroundIn most of the world, the mammography screening programmes were paused at the start of the pandemic, whilst mammography screening continued in Denmark. We examined the mammography screening participation during the COVID-19 pandemic in Denmark.\n\nMethodsThe study population comprised all women aged 50-69 years old invited to participate in mammography screening from 2016-2021 in Denmark based on data from the Danish Quality Database for Mammography Screening in combination with population-based registries. Using a generalised linear model, we estimated prevalence ratios (PR) and 95% confidence intervals (CI) of mammography screening participation within 90, 180 and 365 days since invitation during the pandemic in comparison with the previous years adjusting for age, year and month of invitation.\n\nResultsThe study comprised 1,828,791 invitations among 847,766 women. Before the pandemic, 80.2% of invitations resulted in participation in mammography screening within 90 days, 82.7% within 180 days and 83.1% within 365 days. At the start of the pandemic, the participation in screening within 90 days was reduced to 69.9% for those invited in pre-lockdown and to 76.5% for those invited in 1st lockdown. Extending the length of follow-up time to 365 days only a minor overall reduction was observed (PR=0.94; 95% CI: 0.93-0.95 in pre-lockdown and PR=0.97; 95% CI: 0.96-0.97 in 1st lockdown). A lower participation was; however, seen among immigrants and among women with a low income.\n\nConclusionsThe short-term participation in mammography screening was reduced at the start of the pandemic, whilst only a minor reduction in the overall participation was observed with longer follow-up time indicating that women postponed screening. Some groups of women; nonetheless, had a lower participation indicating that the social inequity in screening participation was exacerbated during the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tina Bech Olesen", + "author_inst": "The Danish Clinical Quality Program - National Clinical Registries" + }, + { + "author_name": "Henry Jensen", + "author_inst": "The Danish Clinical Quality Program - National Clinical Registries" + }, + { + "author_name": "Henrik M\u00f8ller", + "author_inst": "The Danish Clinical Quality Program - National Clinical Registries" + }, + { + "author_name": "Jens Winther Jensen", + "author_inst": "The Danish Clinical Quality Program - National Clinical Registries" + }, + { + "author_name": "Berit Andersen", + "author_inst": "Randers Regional Hospital" + }, + { + "author_name": "Ilse Vejborg", + "author_inst": "Copenhagen University Hospital" + }, + { + "author_name": "Sisse Helle Njor", + "author_inst": "Randers Regional Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.27.509682", "rel_title": "Wild red deer (Cervus elaphus) do not play a role as vectors or reservoirs of SARS-CoV-2 in north-eastern Poland.", @@ -209188,57 +210201,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.09.23.22280278", - "rel_title": "Impact of COVID-19 on lifestyle and mental wellbeing in a drought-affected rural Australian population: A mixed method approach", - "rel_date": "2022-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.23.22280278", - "rel_abs": "BackgroundThe Coronavirus disease 2019 (COVID-19) pandemic has caused unprecedented social and economic disruption, accompanied by the enactment of a multitude of public health measures to restrain disease transmission. These public health and social measures have had a considerable impact on lifestyle and mental wellbeing, which has been well-studied in metropolitan populations, but very little in rural populations. Additionally, the development and use of a standardised scoring system for an overall assessment of patient lifestyle management, and monitoring of changes in these, may be warranted in clinical practice.\n\nMethodsThe associations between psychological distress and changes in SNAPS health behaviours (smoking, nutrition, alcohol, physical activity, sleep) since the onset of COVID-19 in rural Australia were examined. A cross-sectional anonymous online survey was distributed among adults in the Western New South Wales Primary Health Network in August 2020. The survey included measures of psychological distress, income, disposition, lifestyle factors and behaviours during the pandemic, as well as changes in lifestyle due to COVID-19. A novel Global Lifestyle Score (GLS) was generated as a holistic assessment of lifestyle across multiple domains.\n\nResultsThe survey was completed by 308 individuals (modal age group: 45-54 years old, 86.4% female). High distress on the K5 scale was present in over one-third of respondents (n=98, 34.3%). Negative change was reported for sleep (24.4%), nutrition (14.3%), alcohol (17.8%), physical exercise (33.8%) and smoking (26.6%) since the onset of the pandemic. Additionally, changes in sleep, nutrition, physical activity and smoking were associated with distress. Respondents with a poor lifestyle (GLS) during the pandemic were significantly more distressed. Perceived COVID-19 impact was associated with high distress, level of drought impact and loss of income.\n\nConclusionHigh rates of distress amongst rural Australians during the COVID-19 pandemic was linked, worsening lifestyles as measured by the GLS and loss of income. Lifestyle promotion strategies should be considered by health professionals for the management of crisis-related distress. Further research may explore the impact of COVID-19 on a larger population, including a greater proportion of male respondents, and the impact of modifying lifestyle factors on the reduction of distress in the context of a stressor such as this pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jack Carlson", - "author_inst": "Western Sydney University - Campbelltown Campus" - }, - { - "author_name": "Kevin Chan", - "author_inst": "University of Western Sydney: Western Sydney University" - }, - { - "author_name": "Jonah Gray", - "author_inst": "Western Sydney University - Campbelltown Campus" - }, - { - "author_name": "Houston Xue", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Krista Reed", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Jannine K Bailey", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Tegan Dutton", - "author_inst": "Western Sydney University School of Medicine" - }, - { - "author_name": "Uchechukwu L. Osuagwu", - "author_inst": "Western Sydney University - Campbelltown Campus" - }, - { - "author_name": "Robyn Vines", - "author_inst": "Western Sydney University School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2022.09.23.22279458", "rel_title": "Pan-Canadian survey on the impact of the COVID-19 pandemic on cervical cancer screening and management", @@ -210010,6 +210972,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.09.24.22280310", + "rel_title": "Post-Concussion Assessment as a diagnostic and mechanistic framework for treating patients with Long COVID", + "rel_date": "2022-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.24.22280310", + "rel_abs": "IntroductionDespite first coming into view over two years ago, effective diagnostic and treatment pathways for Long COVID continue to evade the medical community. The overlap in neurological-based symptoms and neuroinflammatory origin indicates that the framework of post-concussion syndrome may provide insight into new diagnostics and treatment for patients with Long COVID. The objective of this investigation was to determine whether tools from the four common domains of concussion assessment were sensitive to differentiate between patients with Long COVID from a reference group who was infected with Sars-CoV-2 and does not have Long COVID.\n\nMethodsIn this prospective cohort design, each participant self reported their group (Acute, n=28) and Long COVID Group (n=33). Each participant underwent an examination in four assessment categories: symptoms, vestibular nystagmography, Automated Neuropsychological Assessment Metrics (ANAM), and a series of balance tasks.\n\nResultsTotal Symptom scores were separated into functional classifications and showed clear success as a tool to differentiate between Acute and Long COVID. Five of the 33 people in the Long COVID had detectable central lesions, which increases the risk of developing long COVID by 64% (Relative Risk=1.64). A wide variety of objective and quantitative measures from post-concussion care are sensitive to the Long COVID condition. Prolonged latency during random saccades eye tracking was present (p<0.01, d=0.87) in the Long COVID group corresponding to the King-Devick rapid reading test, which was highly sensitive to Long COVID (p<0.01, d=1.34). ANAM reaction time subtests had similarly large effects (p<0.01, d=0.93-1.09). Balance performance with corrupted sensory feedback was also sensitive (p<0.01, d=0.96).\n\nDiscussionOur results indicate that long-standing and validated post-concussion symptom questionnaires may be used for quantifying the severity of Long COVID. Some of the most sensitive measures (especially the King-Devick rapid reading test) are easy to implement clinically and may be effective at tracking patient progress in the context of Long COVID treatment. The results point to wide deficits in motor integration and provide a rationale for treating the subset of Long COVID patients with similar rehabilitation strategies as patients with post-concussion syndrome.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bradley Davidson", + "author_inst": "University of Denver" + }, + { + "author_name": "Lily Noteboom", + "author_inst": "University of Denver" + }, + { + "author_name": "Hannah Pierro", + "author_inst": "University of Denver" + }, + { + "author_name": "Cayce Kantor", + "author_inst": "University of Denver" + }, + { + "author_name": "Daniel Stoot", + "author_inst": "High Definition Physical Therapy" + }, + { + "author_name": "Fred Stoot", + "author_inst": "High Definition Physical Therapy" + }, + { + "author_name": "Daniel Linseman", + "author_inst": "University of Denver" + }, + { + "author_name": "Troy Hale", + "author_inst": "A.T. Still University" + }, + { + "author_name": "Kimberly Gorgens", + "author_inst": "University of Denver" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.09.19.22280101", "rel_title": "Adherence to and experiences of K-12 students in modified and standard home quarantine during the SARS-CoV-2 pandemic in Missouri", @@ -211562,145 +212575,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.09.22.509040", - "rel_title": "SARS-CoV-2 Omicron boosting induces de novo B cell response in humans", - "rel_date": "2022-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.22.509040", - "rel_abs": "The primary two-dose SARS-CoV-2 mRNA vaccine series are strongly immunogenic in humans, but the emergence of highly infectious variants necessitated additional doses of these vaccines and the development of new variant-derived ones1-4. SARS-CoV-2 booster immunizations in humans primarily recruit pre-existing memory B cells (MBCs)5-9. It remains unclear, however, whether the additional doses induce germinal centre (GC) reactions where reengaged B cells can further mature and whether variant-derived vaccines can elicit responses to novel epitopes specific to such variants. Here, we show that boosting with the original SARS- CoV-2 spike vaccine (mRNA-1273) or a B.1.351/B.1.617.2 (Beta/Delta) bivalent vaccine (mRNA-1273.213) induces robust spike-specific GC B cell responses in humans. The GC response persisted for at least eight weeks, leading to significantly more mutated antigen-specific MBC and bone marrow plasma cell compartments. Interrogation of MBC-derived spike-binding monoclonal antibodies (mAbs) isolated from individuals boosted with either mRNA-1273, mRNA-1273.213, or a monovalent Omicron BA.1-based vaccine (mRNA-1273.529) revealed a striking imprinting effect by the primary vaccination series, with all mAbs (n=769) recognizing the original SARS-CoV-2 spike protein. Nonetheless, using a more targeted approach, we isolated mAbs that recognized the spike protein of the SARS-CoV-2 Omicron (BA.1) but not the original SARS-CoV-2 spike from the mRNA-1273.529 boosted individuals. The latter mAbs were less mutated and recognized novel epitopes within the spike protein, suggesting a naive B cell origin. Thus, SARS-CoV-2 boosting in humans induce robust GC B cell responses, and immunization with an antigenically distant spike can overcome the antigenic imprinting by the primary vaccination series.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Wafaa B. Alsoussi", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sameer K. Malladi", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Julian Q. Zhou", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Zhuoming Liu", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Baoling Ying", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Wooseob Kim", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Aaron J. Schmitz", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Tingting Lei", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Stephen C. Horvath", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Alexandria J. Sturtz", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Katherine M. McIntire", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Birk Evavold", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Fangjie Han", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Suzanne M. Scheaffer", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Isabella F. Fox", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Luis Parra-Rodriguez", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Raffael Nachbagauer", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Biliana Nestorova", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Spyros Chalkias", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Christopher W. Farnsworth", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael K. Klebert", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Iskra Pusic", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Benjamin S. Strnad", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "William D. Middleton", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sharlene A. Teefey", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sean P.J. Whelan", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael S. Diamond", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Robert Paris", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Rachel M. Presti", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Jackson S. Turner", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Ali H. Ellebedy", - "author_inst": "Washington University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.09.22.508999", "rel_title": "Triple COVID-19 vaccination induces humoral and cellular immunity to SARS-CoV-2 with cross-recognition of the Omicron variant and IgA secretion", @@ -212032,6 +212906,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.20.22280170", + "rel_title": "Reconstructing the SARS-CoV-2 epidemic in eastern Uganda through longitudinal serosurveillance in a malaria cohort", + "rel_date": "2022-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.20.22280170", + "rel_abs": "ImportanceEstimating the true burden of SARS-CoV-2 infection has been difficult in sub-Saharan Africa due to asymptomatic infections and inadequate testing capacity. Antibody responses from serologic surveys can provide an estimate of SARS-CoV-2 exposure at the population level.\n\nObjectiveTo estimate SARS-CoV-2 seroprevalence, attack rates, and re-infection in eastern Uganda using serologic surveillance from 2020 to early 2022.\n\nDesignPlasma samples from participants in the Program for Resistance, Immunology, Surveillance, and Modeling of Malaria in Uganda (PRISM) Border Cohort were obtained at four sampling intervals: October-November 2020; March-April 2021; August-September 2021; and February-March 2022. Setting: Tororo and Busia districts, Uganda.\n\nParticipants1,483 samples from 441 participants living in 76 households were tested. Each participant contributed up to 4 time points for SARS-CoV-2 serology, with almost half of all participants contributing at all 4 time points, and almost 90% contributing at 3 or 4 time points. Information on SARS-CoV-2 vaccination status was collected from participants, with the earliest reported vaccinations in the cohort occurring in May 2021.\n\nMain Outcome(s) and Measure(s)The main outcomes of this study were antibody responses to the SARS-CoV-2 spike protein as measured with a bead-based serologic assay. Individual-level outcomes were aggregated to population-level SARS-CoV-2 seroprevalence, attack rates, and boosting rates. Estimates were weighted by the local age distribution based on census data.\n\nResultsBy the end of the Delta wave and before widespread vaccination, nearly 70% of the study population had experienced SARS-CoV-2 infection. During the subsequent Omicron wave, 85% of unvaccinated, previously seronegative individuals were infected for the first time, and [~]50% or more of unvaccinated, already seropositive individuals were likely re-infected, leading to an overall 96% seropositivity in this population. Our results suggest a lower probability of re-infection in individuals with higher pre-existing antibody levels. We found evidence of household clustering of SARS-CoV-2 seroconversion. We found no significant associations between SARS-CoV-2 seroconversion and gender, household size, or recent Plasmodium falciparum malaria exposure.\n\nConclusions and RelevanceFindings from this study are consistent with very high infection rates and re-infection rates for SARS-CoV-2 in a rural population from eastern Uganda throughout the pandemic.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jessica Briggs", + "author_inst": "UCSF" + }, + { + "author_name": "Saki Takahashi", + "author_inst": "UCSF" + }, + { + "author_name": "Patience Nayebare", + "author_inst": "IDRC" + }, + { + "author_name": "Gloria Cuu", + "author_inst": "IDRC" + }, + { + "author_name": "John Rek", + "author_inst": "IDRC" + }, + { + "author_name": "Maato Zedi", + "author_inst": "IDRC" + }, + { + "author_name": "Timothy Kizza", + "author_inst": "IDRC" + }, + { + "author_name": "Emmanuel Arinaitwe", + "author_inst": "IDRC" + }, + { + "author_name": "Joaniter I. Nankabirwa", + "author_inst": "IDRC" + }, + { + "author_name": "Moses Kamya", + "author_inst": "IDRC" + }, + { + "author_name": "Prasanna Jagannathan", + "author_inst": "Stanford" + }, + { + "author_name": "Karen Jacobson", + "author_inst": "Stanford" + }, + { + "author_name": "Philip J. Rosenthal", + "author_inst": "UCSF" + }, + { + "author_name": "Grant Dorsey", + "author_inst": "UCSF" + }, + { + "author_name": "Bryan Greenhouse", + "author_inst": "UCSF" + }, + { + "author_name": "Isaac Ssewanyana", + "author_inst": "IDRC" + }, + { + "author_name": "Isabel Rodriguez-Barraquer", + "author_inst": "UCSF" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.20.22279903", "rel_title": "Safety, Immunogenicity and Efficacy of NVX-CoV2373 in Adolescents in PREVENT-19: A Randomized, Phase 3 Trial", @@ -213564,77 +214521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.18.22280022", - "rel_title": "Liquid biomarkers of macrophage dysregulation and circulating spike protein illustrate the biological heterogeneity in patients with post-acute sequelae of COVID-19", - "rel_date": "2022-09-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.18.22280022", - "rel_abs": "Post-acute sequelae of COVID-19 (PASC) are long-term consequences of SARS-CoV-2 infection that can substantially impair quality of life. Underlying mechanisms ranging from persistent virus to innate and adaptive immune dysregulation have been discussed. Here, we profiled plasma of 181 individuals from the cohort study for digital health research in Germany (DigiHero) including individuals after mild to moderate COVID-19 with or without PASC and uninfected controls. We focused on soluble factors related to monocyte/macrophage biology and on circulating SARS-CoV-2 spike (S1) protein as potential biomarker for persistent viral reservoirs. At a median time of eight months after infection, we found pronounced dysregulation in almost all tested soluble factors including both pro-inflammatory and pro-fibrotic cytokines. These perturbations were remarkably independent of ongoing symptoms, but further correlation and regression analyses suggested PASC specific patterns involving CCL2/MCP-1 and IL-8 as well as long-term persistence of high IL-5 and IL-17F levels. None of the analyzed factors correlated with the detectability or levels of circulating S1 indicating that this represents an independent subset of patients with PASC. This data confirms prior evidence of immune dysregulation and persistence of viral protein in PASC and illustrates its biological heterogeneity that still awaits correlation with clinically defined PASC subtypes.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Christoph Schultheiss", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Edith Willscher", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Lisa Paschold", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Cornelia Gottschick", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Bianca Klee", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Lidia Bosurgi", - "author_inst": "I. Department of Medicine, University Medical Center Hamburg-Eppendorf; Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine" - }, - { - "author_name": "Jochen Dutzmann", - "author_inst": "Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Daniel Sedding", - "author_inst": "Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Thomas Frese", - "author_inst": "Institute of General Practice and Family Medicine, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Matthias Girndt", - "author_inst": "Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Jessica I. Hoell", - "author_inst": "Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Michael Gekle", - "author_inst": "Julius Bernstein-Institute of Physiology, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Rafael Mikolajczyk", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Mascha Binder", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.19.22280079", "rel_title": "The impact of prior COVID-19 on vaccine response and the resultant hybrid immunity are age-dependent", @@ -213950,6 +214836,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.16.22280017", + "rel_title": "Post-vaccination neutralization responses to Omicron sub-variants", + "rel_date": "2022-09-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.16.22280017", + "rel_abs": "BackgroundThe emergence of the Omicron variant (B.1.1.529) which correlated with dramatic losses in cross-neutralization capacity of post-vaccination sera raised concerns about the effectiveness of COVID-19 vaccines against infection and disease. Clinically relevant sub-variants (BA.1, BA.1.1, BA.2, BA.2.12.1, BA.3, and BA.4/5) subsequently emerged rapidly.\n\nMethodsWe evaluated published and pre-print studies reporting sub-variant specific reductions in cross-neutralization compared to the prototype strain of SARS-CoV-2 and between sub-variants. Median fold-reduction across studies was calculated by sub-variant and vaccine platform.\n\nResultsAmong 153 studies with post-vaccination data, after primary vaccination the sub-variant specific fold-reduction in neutralization capacity compared to the prototype antigen varied widely, from median 4.2-fold for BA.3 to 21.9-fold for BA.4/5; in boosted participants fold-reduction was similar for all sub-variants (5.9-fold to 7.1-fold) except for BA.4/5 which was 12.7-fold. Relative to BA.1, the other Omicron sub-variants had similar neutralization capacity post-primary vaccination (range median 0.8-fold to 1.1-fold) and post-booster (0.9-fold to 1.2-fold) except for BA.4/5 which was higher (2.0-fold). Omicron sub-variant specific responder rates were low post-primary vaccination (range median 33.5% to 56.7%) compared to the prototype (median 96.0%), but improved post-booster (range median 85.4% to 92.6%).\n\nConclusionFold-reductions in neutralization titers among Omicron sub-variants compared to the prototype strain varied widely post-primary vaccination but were comparable post-booster, except for BA.4/5 which had higher fold-reduction (2-fold relative to BA.1). Considering large fold-decreases in neutralization titers to the parental strain for all Omicron sub-variants, vaccine effectiveness is very likely to be reduced against all Omicron sub-variants, and probably more so against Omicron BA.4/5.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Henning Jacobsen", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Maeva Katzmarzyk", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Melissa M Higdon", + "author_inst": "International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Viviana Cobos Jimenez", + "author_inst": "Independent Consultant" + }, + { + "author_name": "Ioannis Sitaras", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Naor Bar-Zeev", + "author_inst": "International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Maria Deloria Knoll", + "author_inst": "International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.16.22279985", "rel_title": "Bayesian Prediction of Severe Outcomes in the LabMarCS: Laboratory Markers of COVID-19 Severity - Bristol Cohort", @@ -215542,25 +216471,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.09.10.22279806", - "rel_title": "Cognitive status and rehabilitation outcomes of patients in acute rehabilitation post Covid-19", - "rel_date": "2022-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.10.22279806", - "rel_abs": "ObjectiveThis study aims to 1) characterize cognitive functioning in patients admitted for inpatient rehabilitation due to Covid-19 diagnosis and 2) examine how cognitive status at admission is associated with rehabilitation outcomes.\n\nDesignRetrospective chart review.\n\nSettingAn inpatient rehabilitation center located in Chicago, Illinois.\n\nParticipants80 participants in acute rehabilitation due to Covid-19 disease\n\nInterventionNot applicable.\n\nMain Outcome MeasuresCognitive functioning as measured by the Montreal Cognitive Assessment (MoCA) and rehabilitation outcomes as measured by Functional Index Measure (FIM) and Section GG items for self-care and mobility (GG-SC and GG-M respectively).\n\nResultsOn average, our sample presented with mild cognitive impairment as assessed by the (MoCA). The most significant deficits were demonstrated in executive function, attention, language, and delayed free recall measures. Higher levels of overall cognitive function were associated with higher cognitive measures of rehabilitation outcomes. Weaker associations were observed with outcome measures of self-care and motor functioning.\n\nConclusionCognitive impairments are common in patients in acute rehabilitation due to Covid-19 and cognitive performance may help predict rehabilitation outcomes.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Madli Vahtra", - "author_inst": "Ascension St Alexius" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.09.09.22279763", "rel_title": "COVID-19 induced birth sex ratio changes in England and Wales", @@ -215916,6 +216826,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.12.507659", + "rel_title": "Fast bioluminescent nucleic acid detection using one-pot isothermal amplification and dCas9-based split luciferase complementation", + "rel_date": "2022-09-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.12.507659", + "rel_abs": "Nucleic acid detection methods based on isothermal amplification techniques show great potential for point-of-care diagnostic applications. However, most current methods rely on fluorescent or lateral flow assay readout, requiring external excitation or post-amplification reaction transfer. Here, we developed a bioluminescent nucleic acid sensor (LUNAS) platform in which target dsDNA is sequence-specifically detected by a pair of dCas9-based probes mediating split NanoLuc luciferase complementation. Whereas LUNAS itself features a detection limit of [~]1 pM for dsDNA targets, the LUNAS platform is easily integrated with recombinase polymerase amplification (RPA), providing attomolar sensitivity in a single-pot assay. We designed a one-pot RT-RPA-LUNAS assay for detecting SARS-CoV-2 RNA without the need for RNA isolation and demonstrated the diagnostic performance for COVID-19 patient nasopharyngeal swab samples using a digital camera to record the ratiometric signal. Detection of SARS-CoV-2 from samples with viral RNA loads of [~]200 cp/L was achieved within [~]20 minutes, showing that RPA-LUNAS is attractive for point-of-care diagnostic applications.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Harm J van der Veer", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Eva A van Aalen", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Claire M.S. Michielsen", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Eva T.L. Hanckmann", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Jeroen Deckers", + "author_inst": "Eindhoven University of Technology" + }, + { + "author_name": "Marcel M.G.J. van Borren", + "author_inst": "Rijnstate Hospital" + }, + { + "author_name": "Jacky Flipse", + "author_inst": "Rijnstate Hospital" + }, + { + "author_name": "Anne J.M. Loonen", + "author_inst": "Fontys University of Applied Sciences" + }, + { + "author_name": "Joost P.H. Schoeber", + "author_inst": "Fontys University of Applied Sciences" + }, + { + "author_name": "Maarten Merkx", + "author_inst": "Eindhoven University of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2022.09.15.507991", "rel_title": "A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2", @@ -217332,125 +218297,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.14.507842", - "rel_title": "Molecular engineering of a cryptic epitope in Spike RBD improves manufacturability and neutralizing breadth against SARS-CoV-2 variants", - "rel_date": "2022-09-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.14.507842", - "rel_abs": "There is a continued need for sarbecovirus vaccines that can be manufactured and distributed in low- and middle-income countries (LMICs). Subunit protein vaccines are manufactured at large scales at low costs, have less stringent temperature requirements for distribution in LMICs, and several candidates have shown protection against SARS-CoV-2. We previously reported an engineered variant of the SARS-CoV-2 Spike protein receptor binding domain antigen (RBD-L452K-F490W; RBD-J) with enhanced manufacturability and immunogenicity compared to the ancestral RBD. Here, we report a second-generation engineered RBD antigen (RBD-J6) with two additional mutations to a hydrophobic cryptic epitope in the RBD core, S383D and L518D, that further improved expression titers and biophysical stability. RBD-J6 retained binding affinity to human convalescent sera and to all tested neutralizing antibodies except antibodies that target the class IV epitope on the RBD core. K18-hACE2 transgenic mice immunized with three doses of a Beta variant of RBD-J6 displayed on a virus-like particle (VLP) generated neutralizing antibodies (nAb) to nine SARS-CoV-2 variants of concern at similar levels as two doses of Comirnaty. The vaccinated mice were also protected from challenge with Alpha or Beta SARS-CoV-2. This engineered antigen could be useful for modular RBD-based subunit vaccines to enhance manufacturability and global access, or for further development of variant-specific or broadly acting booster vaccines.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Sergio Andre Rodriguez-Aponte", - "author_inst": "MIT" - }, - { - "author_name": "Neil Chandra Dalvie", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ting Y. Wong", - "author_inst": "West Virginia University" - }, - { - "author_name": "Ryan S. Johnston", - "author_inst": "MIT" - }, - { - "author_name": "Christopher A. Naranjo", - "author_inst": "MIT" - }, - { - "author_name": "Sakshi Bajoria", - "author_inst": "University of Kansas" - }, - { - "author_name": "Ozan S. Kumru", - "author_inst": "University of Kansas" - }, - { - "author_name": "Kawaljit Kaur", - "author_inst": "University of Kansas" - }, - { - "author_name": "Brynnan P. Russ", - "author_inst": "West Virginia University" - }, - { - "author_name": "Katherine S. Lee", - "author_inst": "West Virginia University" - }, - { - "author_name": "Holly A. Cyphert", - "author_inst": "West Virginia University" - }, - { - "author_name": "Mariette Barbier", - "author_inst": "West Virginia University" - }, - { - "author_name": "Harish D. Rao", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Meghraj P. Rajurkar", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Rakesh R. Lothe", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Umesh Shaligram", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Saurabh Batwal", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Rahul Chandrasekaran", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Gaurav Nagar", - "author_inst": "Serum Institute of India" - }, - { - "author_name": "Harry Kleanthous", - "author_inst": "Bill & Melinda Gates Foundation" - }, - { - "author_name": "Sumi Biswas", - "author_inst": "Spybiotech Limited" - }, - { - "author_name": "Justin R. Bevere", - "author_inst": "West Virginia University" - }, - { - "author_name": "Sangeeta B. Joshi", - "author_inst": "University of Kansas" - }, - { - "author_name": "David B. Volkin", - "author_inst": "University of Kansas" - }, - { - "author_name": "Fredrick Heath Damron", - "author_inst": "West Virginia University" - }, - { - "author_name": "J. Christopher Love", - "author_inst": "Koch Institute at MIT" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.09.14.507985", "rel_title": "Analysis and comprehensive lineage identification for SARS-CoV-2 genomes through scalable learning methods", @@ -217678,6 +218524,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.12.507647", + "rel_title": "Humoral immunogenicity of a Coronavirus Disease 2019 (COVID-19) DNA Vaccine in Rhesus Macaques (Macaca mulatta) Delivered using Needle-free Jet Injection", + "rel_date": "2022-09-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.12.507647", + "rel_abs": "A SARS-CoV-2 DNA vaccine targeting the spike protein and delivered by jet injection, nCOV-S(JET), previously shown to protect wild-type and immunosuppressed Syrian hamsters (Mesocricetus auratus), was evaluated via two needle-free delivery methods in rhesus macaques (Macaca mulatta). The methods included intramuscular delivery of 2 mg per vaccination with the PharmaJet Stratis device and intradermal delivery of 0.4 mg per vaccination with the PharmaJet Tropis device. We hypothesized that the nCOV-S(JET) vaccine would mount detectable neutralizing antibody responses when delivered by needle-free jet injection by either the intradermal or intramuscular route. When delivered intramuscularly, the vaccines elicited neutralizing and variant (Beta, Gamma, and Delta) cross-neutralizing antibodies against SARS-CoV-2 in all six animals after three vaccinations. When delivered at a lower dose by the intradermal route, strong neutralizing antibody responses were only detected in two of six animals. This study confirms that a vaccine previously shown to protect in a hamster model can elicit neutralizing and cross-neutralizing antibodies against SARS-CoV-2 in nonhuman primates. We posit that nCOV-S(JET) has the potential for use as booster vaccine in heterologous vaccination strategies against COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alexandra Jay", + "author_inst": "USAMRIID: US Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Steven A Kwilas", + "author_inst": "USAMRIID: US Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Matthew Josleyn", + "author_inst": "USAMRIID: US Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Keersten Ricks", + "author_inst": "USAMRIID: US Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Jay W. Hooper", + "author_inst": "USAMRIID" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.12.507666", "rel_title": "Comparative multi-OMICS single-cell atlas of five COVID-19 (rAdVV and mRNA) vaccines describe unique and distinct mechanisms of action", @@ -219434,65 +220315,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.09.06.22279658", - "rel_title": "Persistence of a SARS-CoV-2 variant with a frameshifting deletion for the duration of a major outbreak", - "rel_date": "2022-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.06.22279658", - "rel_abs": "Australia experienced widespread COVID-19 outbreaks from infection with the SARS-CoV-2 Delta variant between June 2021 and February 2022. Whole-genome sequencing of virus from an early case revealed a sub-consensus level of sequencing reads supporting a 17-nucleotide frameshift-inducing deletion in ORF7a that truncated the peptide sequence. The variant rapidly became represented at the consensus level (Delta-ORF7a{Delta}17del) in most of the outbreak cases in Australia. Retrospective analysis of ORF7a deletions in all GISAID clade GK Delta genomes showed that of 4,018,216 genomes, 134,751 ([~]3.35%) possessed a deletion in ORF7a, with the ORF7a{Delta}17del mutation by far the most common. Approximately 99.05% of Delta-ORF7a{Delta}17del genomes on GISAID originated from the Australian Delta outbreak, and comprised 87% of genomes in the outbreak. In vitro comparison of lineages in cell culture showed a significantly greater proportion of cells were infected with Delta-ORF7a{Delta}17del than with a contemporaneous Delta variant without ORF7a{Delta}17del (Delta-ORF7aintact), and the proportion was also measurably higher than an early SARS-CoV-2 strain (A.2.2). These results showed that Delta-ORF7a{Delta}17del potentially has a slight growth advantage compared to Delta-ORF7aintact. Delta-ORF7a{Delta}17del viruses still produced ORF7a protein, but significantly less than A.2.2, in a different cellular distribution with a more diffuse expression throughout the cytoplasm of infected cells. These data suggest that the proliferation of Delta-ORF7a{Delta}17del genomes during the Australian Delta outbreak was likely not a result of an intrinsic benefit of the ORF7a{Delta}17del mutation, but rather a chance founder effect. Nonetheless, the abundance of different ORF7a deletions in genomes worldwide suggests these have some benefit to virus transmission.\n\nIMPORTANCEDeletions in the ORF7a region of SARS-CoV-2 have been noted since early in the COVID-19 pandemic, but are generally reported as transient mutations that are quickly lost in the population. Consequently, ORF7a deletions are considered disadvantageous to the virus through possible loss-of-function effects. In constrast to these earlier reports, we present the first report of a SARS-CoV-2 variant with an ORF7a deletion that dominated for the entirety of a protracted outbreak, and found no associated fitness disadvantage or advantage in cell culture. The relatively common rise and fall of ORF7a deletion variants over time likely represent chance founder events followed by proliferation until a more fit variant(s) is introduced to the population. Our global clade-level survey of ORF7a deletions will be a useful resource for future studies into this gene region.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Charles S.P. Foster", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Rowena Bull", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Nicodemus Tedla", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Fernando Santiago", - "author_inst": "University of New South Wales" - }, - { - "author_name": "David Agapiou", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Anurag Adhikari", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Gregory J Walker", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Lok Bahadur Shrestha", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Sebastiaan van Hal", - "author_inst": "Royal Prince Alfred Hospital" - }, - { - "author_name": "Ki Wook Kim", - "author_inst": "University of New South Wales" - }, - { - "author_name": "William D Rawlinson", - "author_inst": "Prince of Wales Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.09.08.22279729", "rel_title": "Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2", @@ -219932,6 +220754,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.05.22279620", + "rel_title": "Time trends between vaccination coverage and voting patterns before and during the COVID-19 pandemic: analysis of COVID-19 and flu surveys in the United States", + "rel_date": "2022-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.05.22279620", + "rel_abs": "BackgroundWe assessed the relationship between vaccination coverage and voting patterns: how has the association between COVID-19 vaccination and voting patterns changed during the pandemic, how does it compare to the association between flu vaccination coverage and voting patterns, and what can the time trends between flu vaccination and voting patterns tell us about the broader relationship between vaccination coverage and voting patterns.\n\nMethodsWe analyzed survey data on flu and COVID-19 vaccination coverage utilizing National Immunization Surveys for flu (NIS-FLU; years 2010-2021) and for COVID (NIS-ACM; 2021-2022), CDC surveillance of COVID-19 vaccination coverage (2021-2022) and US COVID-19 Trends and Impact Survey (CTIS; 2021-2022). We described the association between state-level COVID-19 and flu vaccination coverage and state-level voting patterns using Pearson correlation coefficient. We examined individual-level characteristics of people vaccinated for COVID-19 and for flu using logistic regression among responses in CTIS during April-June 2022. We analyzed flu vaccination coverage by age in NIS-FLU between 2010-2021, and its relationship with voting patterns to see whether there has been a departure from the secular pre-pandemic trend during the pandemic.\n\nResultsBetween May 2021 - June 2022 there was a strong and consistent correlation between state-level COVID-19 vaccination coverage and voting patterns for the Democratic party in the 2020 presidential elections. Pearson correlation coefficient was around 0.8 in NIS-ACM, CTIS and CDC surveillance with a range of 0.76-0.92. COVID-19 vaccination coverage in June 2022 was higher than flu vaccination coverage in all states and it had a stronger correlation with voting patterns (R=0.90 vs. R=0.60 in CTIS). There was a small reduction in the flu vaccination coverage between 2020-2021 and 2021-2022 flu seasons. In the individual-level logistic regression, vaccinated people were more likely to be living in a county where the majority voted for the Democratic candidate in 2020 elections both for COVID-19 (aOR .18, 95%CI 2.12-2.24) and for flu (aOR 1.38, 95%CI 1.36-1.41). We demonstrate a longstanding correlation between voting patterns and flu vaccination coverage. It varied by age with the strongest correlation in the youngest age groups. During the 2020-2021 flu season, all age groups, except for 5-12 years old, had a stronger correlation coefficient with voting patterns than in the previous years. However, the observed and predicted vaccination coverage show relatively modest differences in their correlation with vote share.\n\nConclusionsThere are existing pre-pandemic patterns between vaccination coverage and voting patterns as demonstrated by the flu vaccination coverage for 2010-2021. During the pandemic COVID-19 vaccination has been more strongly correlated with vote share than the correlation observed for flu during and before the pandemic. The findings align with other research that has identified an association between adverse health outcomes and the political environment in the United States.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Minttu M Ronn", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Nicolas A Menzies", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Joshua A Salomon", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.07.22279665", "rel_title": "An Early and Preliminary Assessment of the Clinical Severity of the Emerging SARS-CoV-2 Omicron Variants in Maharashtra, India", @@ -221476,57 +222325,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.09.08.507221", - "rel_title": "Use of the particle agglutination/particle agglutination-inhibition test for antigenic analysis of SARS-CoV-2", - "rel_date": "2022-09-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.08.507221", - "rel_abs": "The antigenicity of SARS-CoV-2 is a critical issue for the effectiveness of the vaccine, and thus it should be phenotypically evaluated by serological assays as new field isolates emerge. The hemagglutination/hemagglutination-inhibition (HA/HI) tests are well-known as a representative method for antigenic analysis of influenza viruses, but SARS-CoV-2 is unlikely to agglutinate to human or guinea pig red blood cells. Therefore, the antigenic analysis requires complicated enzyme-linked immunosorbent assay (ELISA) or cell-based assays such as the microneutralization assay. In this study, we developed the particle agglutination/particle agglutination-inhibition (PA/PAI) test to easily and rapidly quantify the virus and antibody using human angiotensin-converting enzyme 2 (hACE2)-bound latex beads. The PA titer was positively correlated with the plaque-forming units. The PAI titer using post-infection Syrian hamster antisera clearly revealed the antigenic difference between the omicron and previous variants. The results show the PAI test is useful for easy and rapid antigenic analysis of SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jun Kobayashi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shutoku Matsuyama", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Masayuki Shirakura", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Tomoko Arita", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Yasushi Suzuki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Hideki Asanuma", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shinji Watanabe", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Hideki Hasegawa", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kazuya Nakamura", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.09.09.507257", "rel_title": "Cellular stress modulates severity of the acute respiratory distress syndrome in COVID-19", @@ -221746,6 +222544,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.05.506640", + "rel_title": "Future COVID-19 surges prediction based on SARS-CoV-2 mutations surveillance", + "rel_date": "2022-09-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.05.506640", + "rel_abs": "COVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate, combined with high rates of transmission and fatality can cause a deadly world-wide pandemic in a matter of weeks.1 Apart from vaccines and post-infection treatment options, strategies for preparedness will be vital in responding to the current and future pandemics. Therefore, there is wide interest in approaches that allow predictions of increase in infections (\"surges\") before they occur. We describe here real time genomic surveillance particularly based on mutation analysis, of viral proteins as a methodology for a priori determination of surge in number of infection cases. The full results are available for SARS-CoV-2 at http://pandemics.okstate.edu/covid19/, and are updated daily as new virus sequences become available. This approach is generic and will also be applicable to other pathogens.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Fares Najar", + "author_inst": "Oklahoma State University" + }, + { + "author_name": "Evan Linde", + "author_inst": "Oklahoma State University" + }, + { + "author_name": "Chelsea Murphy", + "author_inst": "Oklahoma State University" + }, + { + "author_name": "Veniamin Borin", + "author_inst": "Oklahoma State University" + }, + { + "author_name": "Huan Wang", + "author_inst": "University College London" + }, + { + "author_name": "Shozeb Haider", + "author_inst": "University College London School of Pharmacy" + }, + { + "author_name": "Pratul Agarwal", + "author_inst": "Oklahoma State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.09.05.506698", "rel_title": "Atomistic Simulations and Network-Based Energetic Profiling of Binding and Allostery in the SARS-CoV-2 Spike Omicron BA.1, BA.1.1, BA.2 and BA.3 Subvariant Complexes with the Host Receptor: Revealing Hidden Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Long-Range Communication with Allosteric Pockets", @@ -223646,45 +224487,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.09.03.506470", - "rel_title": "Optimization and deoptimization of codons in SARS-CoV-2 and the implications for vaccine development", - "rel_date": "2022-09-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.03.506470", - "rel_abs": "The spread of Coronavirus Disease 2019 (COVID-19), caused by the SARS-CoV-2 coronavirus, has progressed into a global pandemic. To date, thousands of genetic variants have been identified across SARS-CoV-2 isolates from patients. Sequence analysis reveals that the codon usage of viral sequences decreased over time but fluctuated from time to time. In this study, through evolution modeling, we found that this phenomenon might result from the virus preference for mutations during transmission. Using dual luciferase assays, we further discovered that the deoptimization of codons on viruses might weaken protein expression during the virus evolution, indicating that the choice of codon usage might play important role in virus fitness. Finally, given the importance of codon usage in protein expression and particularly for mRNA vaccine, we designed several omicron BA.2.12.1 and BA.4/5 spike mRNA vaccine candidates based on codon optimization, and experimentally validated their high levels of expression. Our study highlights the importance of codon usage in virus evolution and mRNA vaccine development.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Xinkai Wu", - "author_inst": "Peking university" - }, - { - "author_name": "Kejia Shan", - "author_inst": "Peking University" - }, - { - "author_name": "Fuwen Zan", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Xiaolu Tang", - "author_inst": "Peking University" - }, - { - "author_name": "Zhaohui Qian", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Jian Lu", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.09.02.22279526", "rel_title": "Spatial determination of COVID-19 mortality", @@ -224008,6 +224810,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2022.09.02.22279556", + "rel_title": "A pattern shift in SARS-CoV-2 Omicron variant transmission after the city lockdown--observational study based upon daily reported addresses of infected cases", + "rel_date": "2022-09-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.02.22279556", + "rel_abs": "BackgroundVaried degrees of lockdown have been imposed for dozens of jurisdictions upon facing the SARS-CoV-2 epidemics during the past two years. Areal lockdown has been demonstrated effective to reduce the morbility and mortality of COVID-19. Even after the strict lockdown the peak of infection will appear around 9-25 days (median 18 days) thereafter. A wave of Omicron variant (BA.2 and BA.2.2) outbreak was seen from March to May 2022, in Shanghai, a megacity in China mainland. Aim To understand the sources of infection cases from outside or inside the isolated locations before and after the strict city lockdown.\n\nMethodsThe attributable addresses of SARS-CoV-2 infection were reported daily as well as the infected cases from March 18th, 2022 on through government website, which was publicly accessible. The address data and infected cases were collected until May 29th, 2022. The location (longitude and latitude) of these addresses were retrieved and the pattern of repeatedly reported addresses were analyzed. A tool of simple and meso-scale point-based (location-based) chronological graph was used to visualize and analyze the interactions of these locations.\n\nResultsFrom March 18th to May 29th 2022, 173,350 items representing 35,743 unique addresses and 636,279 infected cases were released. The infection cases peaked 16 days after the city lockdown and were highly clustered in much crowded districts. The proportion of repeatedly reported locations of the previous day increased from around 20% before lockdown to greater than 40% in the plateau and remained at this level for up to one third (20/62) of the lockdown phase. This significantly increased proportion of intra-address infection indicated a pattern shift from inter-addresses to intra-address (D=0.2954, p<0.0001), which might perpetuate to the growth of infection cases. Based upon the day-to-day nearest neighbour transmission assumption the connections between some frequently repeated locations might be complex and heterogeneous.\n\nInterpretationDuring the strict areal isolation the intra-address infection may contribute significantly to infected cases of SARS-CoV-2 Omicron variant, the infection might have easily spilled over the boundary of family(with averaged family size of 2.3-3.1 people and family were required stay-at-home compulsively). This significant inter-addresses to intra-address pattern shift necessitated the understanding of intra-location transmission routes and corresponding interventions. Areal isolation and close off with homogeneous assumption inside and outside the isolated areas should be modified and the quantifing of the elevated risk for previously less exposed but much vulnerable sub-population was in pressing need.\n\nResearch in contextEvidence before this study It is commonly observable that the infection cases will continue to increase and peaked in several weeks after the first day of imposing areal lockdown. The search syntax of [(SARS-CoV-2 OR COVID-19) AND (transmission OR infection) AND (post-lockdown OR \"during lockdown\" OR \"isolated area*\")] on PubMed hits 1372 records(on 2022-08-10). However, the viral transmission between the isolated locations or within them have not been studied thoroughly, maybe, due to the presumption that it would be stopped eventually by greatly reducing the inter-personal contact.The search syntax of [(SARS-CoV-2 OR COVID-19) AND (transmission OR infection) AND (post-lockdown OR \"during lockdown\" OR \"isolated area*\") AND (strict)] on PubMed hits 57 records. The populations of different ages with heterogeneous risks of exposure to viruses have been revealed.\n\nAdded values in this studyThe strict city lockdown of Shanghai in facing the Omicron outbreak provided a prototype to understand the sources of infection by using the daily reported address (isolated immediately) involving infected cases. A noticeable pattern shift was revealed in this study with significantly increased proportion of intra-location (small area) self-propagation after the city lockdown.\n\nImplication of all the available evidenceCounter measures should be provided to reduce the risk of transmmision within the small isolated areas; and the elevated risk for the much vulnerable sub-populations within the intra-location (small isolated areas) should be quantified and to trade off between the reduced inter-location risk and increased intra-location risk of infection in policy making.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Lihong Yin", + "author_inst": "Center for Disease Control and Prevention in Huangpu District, Shanghai" + }, + { + "author_name": "Guozhou Zhang", + "author_inst": "Fourth Rehabilitation Hospital of Shanghai" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.09.03.506425", "rel_title": "Plant production of high affinity nanobodies that block SARS-CoV-2 spike protein binding with its receptor, human angiotensin converting enzyme", @@ -225368,33 +226193,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.31.22279430", - "rel_title": "Periodic epidemic outbursts explained by local saturation of clusters", - "rel_date": "2022-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.31.22279430", - "rel_abs": "Adding the notion of spatial locality to the susceptible-infected-recovered (or SIR) model, allows to capture local saturation of an epidemic. The resulting minimum model of an epidemic, consisting of five ordinary differential equations with constant model coefficients, reproduces slowly decaying periodic outbursts, as observed in the COVID-19 or Spanish flu epidemic. It is shown that if immunity decays, even slowly, the model yields a fully periodic dynamics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Louis Gostiaux", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS, Laboratoire de Mecanique des Fluides et d'Acoustique, UMR 5509, 36 Avenue " - }, - { - "author_name": "Wouter Bos", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS, Laboratoire de Mecanique des Fluides et d'Acoustique, UMR 5509, 36 Avenue " - }, - { - "author_name": "Jean-Pierre Bertoglio", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS, Laboratoire de Mecanique des Fluides et d'Acoustique, UMR 5509, 36 Avenue " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.31.22279444", "rel_title": "Effectiveness of the COVID-19 vaccines against severe disease with Omicron sub-lineages BA.4 and BA.5 in England", @@ -225726,6 +226524,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.01.22279485", + "rel_title": "COVID-19 individual participant data meta-analyses. Can there be too many? Results from a rapid systematic review", + "rel_date": "2022-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.01.22279485", + "rel_abs": "BackgroundIndividual participant data meta-analyses (IPD-MAs), which include harmonising and analysing participant-level data from related studies, provide several advantages over aggregate data meta-analyses, which pool study-level findings. IPD-MAs are especially important for building and evaluating diagnostic and prognostic models, making them an important tool for informing the research and public health responses to COVID-19.\n\nMethodsWe conducted a rapid systematic review of protocols and publications from planned, ongoing, or completed COVID-19-related IPD-MAs to identify areas of overlap and maximise data request and harmonisation efforts. We searched four databases using a combination of text and MeSH terms. Two independent reviewers determined eligibility at the title-abstract and full-text stage. Data were extracted by one reviewer into a pretested data extraction form and subsequently reviewed by a second reviewer. Data were analysed using a narrative synthesis approach. A formal risk of bias assessment was not conducted.\n\nResultsWe identified 31 COVID-19-related IPD-MAs, including five living IPD-MAs and ten IPD-MAs that limited their inference to published data (e.g., case reports). We found overlap in study designs, populations, exposures, and outcomes of interest. For example, 26 IPD-MAs included RCTs; 17 IPD-MAs were limited to hospitalised patients. Sixteen IPD-MAs focused on evaluating medical treatments, including six IPD-MAs for antivirals, four on antibodies, and two that evaluated convalescent plasma.\n\nConclusionsCollaboration across related IPD-MAs can leverage limited resources and expertise by expediting the creation of cross-study participant-level data datasets, which can, in turn, fast-track evidence synthesis for the improved diagnosis and treatment of COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lauren Maxwell", + "author_inst": "Heidelberger Institut fur Global Health, Universitatsklinikum Heidelberg, Heidelberg, Germany" + }, + { + "author_name": "Priya Shreedhar", + "author_inst": "Heidelberger Institut fur Global Health, Universitatsklinikum Heidelberg, Heidelberg, Germany" + }, + { + "author_name": "Brooke Levis", + "author_inst": "Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada" + }, + { + "author_name": "Sayali Arvind Chavan", + "author_inst": "Institute of Tropical Medicine and Public Health, Charite, Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Shaila Akter", + "author_inst": "Heidelberger Institut fur Global Health, Universitatsklinikum Heidelberg, Heidelberg, Germany" + }, + { + "author_name": "Mabel Carabali", + "author_inst": "Departement de Medecine Sociale et Preventive, Ecole de Sante Publique, Universite de Montreal, Montreal, Canada" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.31.22279264", "rel_title": "Impact of COVID-19 and Effects of Vaccination with BNT162b2 on Patient-Reported Health-Related Quality of Life, Symptoms, and Work Productivity Among US Adult Outpatients with SARS-CoV-2", @@ -227130,77 +227967,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.08.29.505777", - "rel_title": "Can SARS-CoV-2 transmit from a dead body?", - "rel_date": "2022-08-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.29.505777", - "rel_abs": "Although it has been 2.5 years since the COVID-19 pandemic began, the transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a dead infected body remains unclear, and often, in Japan bereaved family members are not allowed to view in-person a loved one who has died from COVID-19. In this study, we analyzed the possibility of SARS-CoV-2 transmission from a dead body by using the hamster model. We also analyzed the effect of Angel-care--in which the pharynx, nostril, and rectum are plugged--and embalming on reducing transmissibility from dead bodies. We found that SARS-CoV-2 could be transmitted from the body of animals that died within a few days of infection; however, Angel-care and embalming were effective in preventing transmission from the dead body. These results suggest that protection from infection is essential when in contact with a SARS-CoV-2-infected dead body, and that sealing the cavities of a dead body is an important infection control step if embalming is not done.\n\nImportanceWe found that SARS-CoV-2 could be transmitted from a dead body presumably via postmortem gases. However, we also found that postmortem care, such as plugging the pharynx, nostrils, and rectum, or embalming could prevent transmission from the dead body. These results indicate that protection from infection is essential when handling infected corpses, and that appropriate care of SARS-CoV-2-infected corpses is important.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kiyoko Iwatsuki-Horimoto", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Hiroshi Ueki", - "author_inst": "The University of Tokyo Institute of Medical Science" - }, - { - "author_name": "Mutsumi Ito", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Sayaka Nagasawa", - "author_inst": "Graduate School of Medicine, Chiba University" - }, - { - "author_name": "Yuichiro Hirata", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kenichiro Hashizume", - "author_inst": "GSI Co., LTD" - }, - { - "author_name": "Kazuho Ushiwata", - "author_inst": "GSI Co., LTD" - }, - { - "author_name": "Hirotaro Iwase", - "author_inst": "Graduate School of Medicine, Chiba University" - }, - { - "author_name": "Yohsuke Makino", - "author_inst": "Graduate School of Medicine, University of Tokyo" - }, - { - "author_name": "Tetsuo Ushiku", - "author_inst": "Yokohama City University Hospital" - }, - { - "author_name": "Shinji Akitomi", - "author_inst": "Japan Medical Association Research Institute" - }, - { - "author_name": "Masaki Imai", - "author_inst": "The University of Tokyo Institute of Medical Science" - }, - { - "author_name": "Hisako Saitoh", - "author_inst": "Graduate School of Medicine, Chiba University" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin System" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.08.29.22279161", "rel_title": "Organizational impact of an ID NOW COVID-19 point-of-care testing for SARS-CoV2 detection in a maternity ward", @@ -227448,6 +228214,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.08.28.22279258", + "rel_title": "GHSI COVID-19 puzzle: did highly developed countries indeed fare worse?", + "rel_date": "2022-08-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.28.22279258", + "rel_abs": "Global Health Security Index (GHSI) categories are formulated to assess the capacity of world countries to deal with infectious disease risks. Thus, higher values of these indices were expected to translate to lower COVID-19 severity. However, it turned out to be the opposite, surprisingly suggesting that higher estimated country preparedness to epidemics may lead to higher disease mortality. To address this puzzle, we: i) use a model-derived measure of COVID-19 severity; ii) employ a range of statistical learning approaches, including non-parametric machine learning methods; iii) consider the overall excess mortality, in addition to official COVID-19 fatality counts. Our results suggest that the puzzle is, to a large extent, an artifact of oversimplified data analysis and a consequence of misclassified COVID-19 deaths, combined with the higher median age of the population and earlier epidemics onset in countries with high GHSI scores.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sofija Markovic", + "author_inst": "Quantitative Biology Group, Faculty of Biology, University of Belgrade, Serbia" + }, + { + "author_name": "Igor Salom", + "author_inst": "Institute of Physics Belgrade, National Institute of the Republic of Serbia, University of Belgrade, Serbia" + }, + { + "author_name": "Andjela Rodic", + "author_inst": "Quantitative Biology Group, Faculty of Biology, University of Belgrade, Serbia" + }, + { + "author_name": "Marko Djordjevic", + "author_inst": "Quantitative Biology Group, Faculty of Biology, University of Belgrade, Serbia" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.08.26.22279279", "rel_title": "SOCIAL INEQUITIES IN A PSYCHOLOGICAL DOMAIN OF FOOD INSECURITY AMONG MOTHERS FROM SOUTHERN BRAZIL DURING THE COVID-19 PANDEMIC", @@ -229096,49 +229893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.23.22279123", - "rel_title": "The Role of Modelling and Analytics in South African COVID-19 Planning and Budgeting", - "rel_date": "2022-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.23.22279123", - "rel_abs": "BackgroundThe South African COVID-19 Modelling Consortium (SACMC) was established in late March 2020 to support planning and budgeting for COVID-19 related healthcare in South Africa. We developed several tools in response to the needs of decision makers in the different stages of the epidemic, allowing the South African government to plan several months ahead of time.\n\nMethodsOur tools included epidemic projection models, several cost and budget impact models, and online dashboards to help government and the public visualise our projections, track case development and forecast hospital admissions. Information on new variants, including Delta and Omicron, were incorporated in real time to allow the shifting of scarce resources when necessary.\n\nResultsGiven the rapidly changing nature of the outbreak globally and in South Africa, the model projections were updated regularly. The updates reflected 1) the changing policy priorities over the course of the epidemic; 2) the availability of new data from South African data systems; and 3) the evolving response to COVID-19 in South Africa such as changes in lockdown levels and ensuing mobility and contact rates, testing and contact tracing strategies, and hospitalisation criteria. Insights into population behaviour required updates by incorporating notions of behavioural heterogeneity and behavioural responses to observed changes in mortality. We incorporated these aspects into developing scenarios for the third wave and developed additional methodology that allowed us to forecast required inpatient capacity. Finally, real-time analyses of the most important characteristics of the Omicron variant first identified in South Africa in November 2021 allowed us to advise policymakers early in the fourth wave that a relatively lower admission rate was likely.\n\nConclusionThe SACMCs models, developed rapidly in an emergency setting and regularly updated with local data, supported national and provincial government to plan several months ahead of time, expand hospital capacity when needed, allocate budgets, and procure additional resources where possible. Across four waves of COVID-19 cases, the SACMC continued to serve the planning needs of the government, tracking waves and supporting the national vaccine rollout.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gesine Meyer-Rath", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Rachel Hounsell", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Juliet Pulliam", - "author_inst": "University of Stellenbosch: Stellenbosch University" - }, - { - "author_name": "Lise Jamieson", - "author_inst": "University of the Witwatersrand Johannesburg" - }, - { - "author_name": "Brooke Nichols", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Harry Moultrie", - "author_inst": "NHLS: National Health Laboratory Service" - }, - { - "author_name": "Sheetal Prakash Silal", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.24.22279159", "rel_title": "Dynamics of anti-S IgG antibodies titers after the second dose of COVID 19 mRNA and non-mRNA vaccines in the manual and craft worker population of Qatar", @@ -229518,6 +230272,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.25.22279202", + "rel_title": "T cell responses to SARS-CoV-2 vaccination in people with multiple sclerosis differ between disease-modifying therapies", + "rel_date": "2022-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.25.22279202", + "rel_abs": "Immune responses in people with multiple sclerosis (pwMS) on disease-modifying therapies (DMTs) have been of significant interest throughout the COVID-19 pandemic. Lymphocyte-targeting immunotherapies including anti-CD20 treatments and sphingosine-1-phosphate receptor (S1PR) modulators attenuate antibody responses after vaccination. Evaluation of cellular responses after vaccination is therefore of particular importance in these populations. In this study, we analysed CD4 and CD8 T cell functional responses to SARS-CoV-2 spike peptides in healthy controls and pwMS on five different DMTs by flow cytometry. Although pwMS on anti-CD20 and S1PR therapies had low antibody responses after both 2 and 3 vaccine doses, T cell responses in pwMS on anti-CD20 therapies were preserved after a third vaccination, even when additional anti-CD20 treatment was administered between vaccine doses 2 and 3. PwMS taking S1PR modulators had low detectable T cell responses in peripheral blood. CD4 and CD8 T cell responses to SARS-CoV-2 variants of concern Delta and Omicron were lower than to the ancestral Wuhan-Hu-1 variant. Our results indicate the importance of assessing both cellular and humoral responses after vaccination and suggest that even in the absence of robust antibody responses vaccination can generate immune responses in pwMS.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Asia-Sophia Wolf", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Anthony Ravussin", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Marton K\u00f6nig", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "Mathias Herstad \u00d8ver\u00e5s", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "Guri Solum", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Ingrid Fadum Kj\u00f8nstad", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Adity Chopra", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "Trygve Holm\u00f8y", + "author_inst": "University of Oslo" + }, + { + "author_name": "Hanne F. Harbo", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "Silje Watterdal Syversen", + "author_inst": "Diakonhjemmet Hospital" + }, + { + "author_name": "Kristin Kaasen J\u00f8rgensen", + "author_inst": "Akershus University Hospital" + }, + { + "author_name": "Einar August H\u00f8gest\u00f8l", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "John Torgils Vaage", + "author_inst": "University of Oslo" + }, + { + "author_name": "Elisabeth G. Celius", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "Fridtjof Lund-Johansen", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "Ludvig A. Munthe", + "author_inst": "University of Oslo" + }, + { + "author_name": "Gro Owren Nygaard", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "Siri Mjaaland", + "author_inst": "Norwegian Institute of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.08.25.22279206", "rel_title": "Phenotypic evolution of SARS-CoV-2: a statistical inference approach", @@ -230790,185 +231631,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.22.22279080", - "rel_title": "Humoral and cellular response induced by a second booster of an inactivated SARS-CoV-2 vaccine in adults", - "rel_date": "2022-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.22.22279080", - "rel_abs": "The SARS-CoV-2 Omicron variant has challenged the control of the COVID-19 pandemic even in highly vaccinated countries. While a second booster of mRNA vaccines improved the immunity against SARS-CoV-2, the humoral and cellular responses induced by a second booster of an inactivated SARS-CoV-2 vaccine have not been studied. In the context of a phase 3 clinical study, we report that a second booster of CoronaVac(R) increased the neutralizing response against the ancestral virus yet showed poor neutralization against the Omicron variant. Additionally, isolated PBMCs displayed equivalent activation of specific CD4+ T cells and IFN-{gamma} production when stimulated with a mega-pool of peptides derived from the spike protein of the ancestral virus or the Omicron variant. In conclusion, a second booster dose of CoronaVac(R) does not improve the neutralizing response against the Omicron variant compared with the first booster dose, yet it helps maintaining a robust spike-specific CD4+ T cell response.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Felipe Melo-Gonzalez", - "author_inst": "Universidad Andres Bello, Santiago, Chile/Pontificia Universidad Catolica de Chile." - }, - { - "author_name": "Constanza Mendez", - "author_inst": "Pontificia Universidad Catolica de Chile." - }, - { - "author_name": "Hernan F Penaloza", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Barbara M Schultz", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alejandro Pina-Iturbe", - "author_inst": "Pontificia Universidad Catolica Chile" - }, - { - "author_name": "Mariana Rios", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Daniela Moreno-Tapia", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Patricia Pereira-Sanchez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Diane Leighton", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Claudia Orellana", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Consuelo Covarrubias", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Nicolas MS Galvez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Jorge A Soto", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "LUISA F DUARTE", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Daniela Rivera-Perez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Yaneisi Vazquez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alex Cabrera", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Sergio Bustos", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Carolina Iturriaga", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Marcela Urzua", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Maria S Navarrete", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alvaro Rojas", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Rodrigo Fasce", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Jorge Fernandez", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Judith Mora", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Eugenio Ramirez", - "author_inst": "Instituto de Salud Publica de Chile" - }, - { - "author_name": "Aracelly Gaete-Argel", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Monica Acevedo", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Fernando Valiente-Echeverria", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Ricardo Soto-Rifo", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute For Allergy & Immunology" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Allergy & Immunology" - }, - { - "author_name": "Gang Zeng", - "author_inst": "Sinovac Biotech" - }, - { - "author_name": "Weining Meng", - "author_inst": "Sinovac Biotech" - }, - { - "author_name": "- CoronaVac03CL Study Group", - "author_inst": "-" - }, - { - "author_name": "Jose V Gonzalez-Aramundiz", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Pablo A Gonzalez", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Katia Abarca", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Susan M Bueno", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Alexis M Kalergis", - "author_inst": "Pontificia Universidad Catolica de Chile" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.22.22279079", "rel_title": "Assessing Vulnerability to COVID-19 in High-Risk Populations: The Role of SARS-CoV-2 Spike-Targeted Serology", @@ -231284,6 +231946,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.22.22279097", + "rel_title": "\"All of the things to everyone everywhere\": A mixed methods analysis of community perspectives on equitable access to monoclonal antibody treatment for COVID-19", + "rel_date": "2022-08-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.22.22279097", + "rel_abs": "BackgroundNeutralizing monoclonal antibody (mAb) treatment for COVID-19 prevents hospitalization and death but is underused, especially in racial/ethnic minority and rural populations. The study assessed mAbs community awareness and opportunities for improving equitable mAb access.\n\nMethodsA concurrent mixed methods study including surveys and focus groups with adults with high-risk conditions or their proxy decision-makers. Surveys and focus group guides addressed diffusion of innovation theory factors. Descriptive statistics and Fishers exact method was used to report and compare survey findings by race and ethnicity. Rapid qualitative methods were used for focus group analysis.\n\nResultsSurveys from 515 individuals (460 English, 54 Spanish, 1 Amharic), and 8 focus groups (6 English, 2 Spanish) with 69 diverse participants, all completed between June 2021 and January 2022. Most survey respondents (75%) had heard little or nothing about mAbs, but 95% would consider getting mAb treatment. Hispanic/Latino and Non-Hispanic People of Color (POC) reported less awareness, greater concern about an intravenous infusion, and less trust in mAb safety and effectiveness than White, Non-Hispanic respondents. Focus group themes included little awareness but high interest in mAb treatment and concerns about cost and access, especially for those facing access barriers such as lacking an established source of care and travel from rural communities. Focus groups revealed preferences for broad-reaching but tailored messaging strategies using multiple media and trusted community leaders.\n\nConclusionsDespite unfamiliarity with mAb treatment, most respondents were willing to consider receiving mAbs or recommend mAbs to others. While mAb messaging should have broad reach \"to everyone everywhere,\" racial and geographic disparities in levels of awareness and trust about mAbs underscore the need for tailored messaging to promote equitable access. Care processes should address patient-level mAb barriers, such as transportation, insurance, or primary care access. COVID-19 treatment dissemination strategies should promote health equity.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Bethany M. Kwan", + "author_inst": "University of Colorado School of Medicine" + }, + { + "author_name": "Chelsea Sobczak", + "author_inst": "University of Colorado Anschutz Medical Campus: University of Colorado - Anschutz Medical Campus" + }, + { + "author_name": "Carol Gorman", + "author_inst": "University of Colorado Anschutz Medical Campus: University of Colorado - Anschutz Medical Campus" + }, + { + "author_name": "Samantha Roberts", + "author_inst": "Colorado School of Public Health" + }, + { + "author_name": "Vanessa Owen", + "author_inst": "University of Colorado Anschutz Medical Campus: University of Colorado - Anschutz Medical Campus" + }, + { + "author_name": "Matthew K. Wynia", + "author_inst": "University of Colorado Anschutz Medical Campus: University of Colorado - Anschutz Medical Campus" + }, + { + "author_name": "Adit A. Ginde", + "author_inst": "University of Colorado Anschutz Medical Campus: University of Colorado - Anschutz Medical Campus" + }, + { + "author_name": "Griselda Pena-Jackson", + "author_inst": "University of Colorado Anschutz Medical Campus: University of Colorado - Anschutz Medical Campus" + }, + { + "author_name": "Owen Ziegler", + "author_inst": "Z Cultural Services" + }, + { + "author_name": "Lisa Ross DeCamp", + "author_inst": "University of Colorado Anschutz Medical Campus: University of Colorado - Anschutz Medical Campus" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.08.23.22279112", "rel_title": "Prognostic accuracy of triage tools for adults with suspected COVID-19 in a middle-income setting: an observational cohort study", @@ -232648,93 +233365,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2022.08.21.22279029", - "rel_title": "Humoral and cellular immune correlates of protection against COVID-19 in kidney transplant recipients", - "rel_date": "2022-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.21.22279029", - "rel_abs": "As solid organ recipients are at high risk of severe COVID-19 and respond poorly to primary SARS-CoV-2 mRNA vaccination, they have been prioritized for booster vaccination. However, an immunological correlate of protection has not been identified in this vulnerable population. We conducted a prospective monocentric cohort study of 65 kidney transplant recipients who received three doses of SARS-CoV-2 BNT162b2 mRNA vaccination. Associations between symptomatic breakthrough infection (BTI) and vaccine responses, patient demographic and clinical characteristics were explored. Symptomatic COVID-19 was diagnosed in 32% of kidney transplant recipients during a period of six months after the administration of the third vaccine dose. During this period, SARS-CoV-2 delta and omicron were the dominant variants in the general population. Univariate analyzes identified avidity of SARS-CoV-2 receptor binding domain (RBD) binding IgG, neutralizing antibodies and SARS-CoV-2 S2 domain-specific IFN-{gamma} responses as correlates of protection against BTI. Some demographic and clinical parameters correlated with vaccine responses, but none correlated with the risk of BTI. In multivariate analysis, the risk of BTI was best predicted by neutralizing antibody and S2-specific IFN-{gamma} responses, adjusting for age, graft function and mycophenolate mofetil use. In conclusion, both antibody and T cell responses predict the risk of BTI in kidney transplant recipients who received three doses of SARS-CoV-2 mRNA vaccine. T cell responses may help compensate for the suboptimal antibody response to vaccination in this vulnerable population.\n\nOne Sentence SummaryAntibody and T cell responses to booster SARS-CoV-2 vaccination predict the risk of symptomatic breakthrough infection in kidney transplant recipients", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Delphine KEMLIN", - "author_inst": "Hopital Erasme, ULB, Bruxelles" - }, - { - "author_name": "Nicolas Gemander", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Stephanie Depickere", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Veronique Olislagers", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Daphnee Georges", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Alexandra Waegemans", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - }, - { - "author_name": "Pieter Pannus", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Anne Lemy", - "author_inst": "Department of Nephrology, Hopital Marie Curie, Charleroi, Belgium" - }, - { - "author_name": "Maria E Goossens", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Isabelle Desombere", - "author_inst": "Scientific Direction Infectious Diseases in Humans, Sciensano, Brussels, Belgium" - }, - { - "author_name": "Johan Michiels", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Marylene Vandevenne", - "author_inst": "Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liege, Liege, Belgium" - }, - { - "author_name": "Leo Heyndrickx", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Kevin K Arien", - "author_inst": "Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Andre Matagne", - "author_inst": "Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liege, Liege, Belgium" - }, - { - "author_name": "Margaret E Ackerman", - "author_inst": "Thayer School of Engineering, Dartmouth College, Hanover, NH, USA" - }, - { - "author_name": "Alain Le Moine", - "author_inst": "Department of Nephrology, Dialysis and Transplantation, Erasme Hospital, Universite Libre de Bruxelles (ULB), Bruxelles, Belgium" - }, - { - "author_name": "Arnaud Marchant", - "author_inst": "Institute for Medical Immunology and ULB Centre for Research in Immunology (U-CRI), Universite Libre de Bruxelles (ULB), Gosselies, Belgium" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "transplantation" - }, { "rel_doi": "10.1101/2022.08.20.22279023", "rel_title": "Brain microstructural changes and fatigue after COVID-19", @@ -232958,6 +233588,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.19.22277959", + "rel_title": "Pharmacokinetics of nirmatrelvir and ritonavir in COVID-19 patients with end stage renal disease on intermittent haemodialysis", + "rel_date": "2022-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.19.22277959", + "rel_abs": "BackgroundNirmatrelvir/ritonavir is an effective therapy against SARS-CoV-2. Patients with end-stage renal disease (ESRD) are at high risk for severe COVID-19 and show impaired vaccine responses underlining the importance of antiviral therapy. However, use of nirmatrelvir/ritonavir is not recommended in these patients due to lack of clinical and pharmacokinetic data.\n\nObjectiveTo investigate pharmacokinetics and hepatic tolerance of nirmatrelvir/ritonavir in patients with ESRD and haemodialysis (HD).\n\nPatients and methodsFour patients diagnosed with SARS-CoV-2 infection received nirmatrelvir/ritonavir 150/100mg twice daily as recommended for renal impairment; HD ran in two- to three-day intervals. Plasma and serum samples were drawn before and after each HD during the 5-day treatment and for ensuing 3-5 days.\n\nResultsMedian peak levels of nirmatrelvir obtained two hours after medication pre-HD in three patients were 7745ng/mL on day 3 and 6653ng/mL on day 5; median post-HD levels (C6h) declined to 5765ng/mL (74%) and 5521ng/mL (83%), on days 3 and 5 of treatment, respectively. Three days after end of treatment, median levels were 365ng/mL pre-HD and 30ng/mL post-HD. Measurements of the fourth patient, six hours after drug intake pre-HD showed nirmatrelvir-levels of 3704ng/mL on treatment day 3 which fell to 2308ng/mL post-HD, at one hour before intake of the next dose (Cmin).\n\nConclusionUse of nirmatrelvir/ritonavir in patients with ESRD results in high nirmatrelvir blood concentrations, which are still within the range known from patients without renal failure. No accumulation of nirmatrelvir took place and levels declined to zero within few days after end of treatment.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Tilman Lingscheid", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + }, + { + "author_name": "Martina Kinzig", + "author_inst": "IBMP Institute for Biomedical and Pharmaceutical Research, Paul Ehrlich Stra\u00dfe 19, 90562, N\u00fcrnberg Heroldsberg, Germany" + }, + { + "author_name": "Anne Kr\u00fcger", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + }, + { + "author_name": "Nils Benjamin M\u00fcller", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + }, + { + "author_name": "Georg B\u00f6lke", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + }, + { + "author_name": "Pinkus Tober-Lau", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + }, + { + "author_name": "Friederike M\u00fcnn", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + }, + { + "author_name": "Helene Kriedemann", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + }, + { + "author_name": "Martin Witzenrath", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + }, + { + "author_name": "Leif Erik Sander", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + }, + { + "author_name": "Fritz S\u00f6rgel", + "author_inst": "IBMP Institute for Biomedical and Pharmaceutical Research, Paul Ehrlich Stra\u00dfe 19, 90562, N\u00fcrnberg Heroldsberg, Germany" + }, + { + "author_name": "Florian Kurth", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Department of " + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.22.504760", "rel_title": "Airway epithelial cells and macrophages trigger IL-6-CD95/CD95L axis and mediate initial immunopathology of COVID-19", @@ -234334,117 +235027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.17.22278913", - "rel_title": "Field assessment of BinaxNOW antigen tests as COVID-19 treatment entry point at a community testing site in San Francisco during evolving omicron surges", - "rel_date": "2022-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.17.22278913", - "rel_abs": "BackgroundCOVID-19 oral treatments require initiation within 5 days of symptom onset. Although antigen tests are less sensitive than RT-PCR, rapid results could facilitate entry to treatment. As SARS-CoV-2 variants and host immunity evolve, it is important to characterize the use case for rapid antigen tests for treatment entry.\n\nMethodsWe collected anterior nasal swabs for BinaxNOW and RT-PCR testing and clinical data at a walk-up, community site in San Francisco, California between January and June 2022. SARS-CoV-2 genomic sequences were generated from positive samples and classified according to subtype and variant. Monte Carlo simulations were conducted to estimate the expected proportion of SARS-CoV-2 infected persons who would have been diagnosed within 5 days of symptom onset using RT-PCR versus BinaxNOW testing.\n\nResultsAmong 25,309 persons tested with BinaxNOW, 2,952 had concomitant RT-PCR. 1321/2952 (44.7%) were SARS-CoV-2 RT-PCR positive. We identified waves of predominant omicron BA.1, BA.2, BA.2.12, BA.4, and BA.5 among 720 sequenced samples. Among 1,321 RT-PCR positive samples, 938/1321 (71%) were detected by BinaxNOW; 95% (774/817) of those with Ct value <30 were detected by BinaxNOW. BinaxNOW detection was consistent over lineages. In analyses to evaluate entry to treatment, BinaxNOW detected 82.7% (410/496, 95% CI: 79-86%) of persons with COVID-19 within 5 days of symptom onset. In comparison, RT-PCR (24-hour turnaround) detected 83.1% (412/496 95% CI: 79-86%) and RT-PCR (48-hour turnaround) detected 66.3% (329/496 95% CI: 62-70%) of persons with COVID-19 within 5 days of symptom onset.\n\nConclusionsBinaxNOW detected high viral load from anterior nasal swabs consistently across omicron sublineages emerging between January and June of 2022. Simulations support BinaxNOW as an entry point for COVID-19 treatment in a community field setting.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "John Schrom", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Carina Marquez", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Chung-Yu Wang", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Aditi Saxena", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Anthea Mitchell", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Salustiano Ribeiro", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Genay Pilarowski", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Robert Nakamura", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Susana Rojas", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Douglas Black", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Maria Contreras Oseguera", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Edgar Castellanos Diaz", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Joselin Payan", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Susy Rojas", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Diane Jones", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Valerie Tulier-Laiwa", - "author_inst": "Unidos en Salud and Latino Task Force" - }, - { - "author_name": "Aleks Zavaleta", - "author_inst": "Unidos en Salud and Latino Task Force" - }, - { - "author_name": "Jacqueline Martinez", - "author_inst": "Unidos en Salud" - }, - { - "author_name": "Gabriel Chamie", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Carol Glaser", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Kathy Jacobson", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Maya Petersen", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Joseph DeRisi", - "author_inst": "CZ Biohub" - }, - { - "author_name": "Diane Havlir", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.17.22278893", "rel_title": "Uptake of Sotrovimab for prevention of severe COVID-19 and its safety in the community in England", @@ -234784,6 +235366,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.16.22278871", + "rel_title": "How Have Global Scientists Responded to Tackling COVID-19?", + "rel_date": "2022-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.16.22278871", + "rel_abs": "Since the outbreak of COVID-19, the global scientific communities across almost all countries have made urgent, intensive, and continuous effort on understanding, fighting and modeling the COVID-19 pandemic. COVID-19 research turns out to be the first overwhelming global scientific reaction to significant global crises and threats. This literature analysis report collects and summarizes the profiles, trends, quality and impact of this global scientific response. It collects and analyzes 346,267 scientific references in English, involving researchers from 189 countries and regions in 27 subject areas. The report generates a picture of how global scientists have responded to COVID-19 between Jan 2020 and Mar 2022 in terms of their publication quantity, impact, focused major problems, and research areas and methods over country/region, discipline and time and collaboratively. The report also captures broad-reaching distributions and trends of modeling COVID-19 by AI, data science, analytics, shallow and deep machine learning, epidemic modeling, applied mathematics, and social science methods, etc. We further show the correlations between publication quality and quantity and economic status and COVID-19 infections globally and in major countries and regions. The literature analysis results of this global scientific response to COVID-19 present a comprehensive global, regional and subject-specific picture of the significant cross-disciplinary, cross-country, cross-problem, and cross-technique profiles and differences of the COVID-19 publication quantity and quality. The report also discloses significant imbalances in the COVID-19 research across countries/regions, subject areas, problems, topics, methods, research collaborations, and economic statuses. We share the source and analytical data of this global literature analysis for further research on this unprecedented and future crises.\n\nMore Information about COVID-19 ModelingO_ST_ABSThe COVID-19 global scientists response datasetC_ST_ABSThe COVID-19 global scientists response dataset supporting this report can be found in Kaggle at: https://www.kaggle.com/datasets/datascienceslab/covid19-global-scientists-response, Dataset doi: 10.34740/kaggle/dsv/4077649.\n\nMore information about COVID-19 modelingInterested readers may refer to the following review on modeling COVID-19 which complements this global literature analysis: Longbing Cao and Qing Liu, COVID-19 Modeling: A Review, 1-103, 2022 (version 2). Accessible at medRxiv: https://www.medrxiv.org/content/10.1101/2022.08.22.22279022v1.\n\nMore information about COVID-19 modeling, including the analytical results of this report and data and review on COVID-19 can be found at: https://datasciences.org/covid19-modeling.\n\nCitation of this reportLongbing Cao and Wenfeng Hou. How have global scientists responded to tackling COVID-19? Full technical report, https://doi.org/10.1101/2022.08.16.22278871, Data Science Lab, University of Technology Sydney, 2022.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Longbing Cao", + "author_inst": "University of Technology Sydney" + }, + { + "author_name": "Wenfeng Hou", + "author_inst": "University of Technology Sydney" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.16.504128", "rel_title": "Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds", @@ -236068,49 +236673,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.08.11.503706", - "rel_title": "The P681H mutation in the Spike glycoprotein escapes IFITM restriction and is necessary for type I interferon resistance in the SARS-CoV-2 alpha variant", - "rel_date": "2022-08-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.11.503706", - "rel_abs": "The appearance of new dominant variants of concern (VOCs) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the COVID-19 pandemic. Of these, the alpha variant (also known as B.1.1.7) that appeared initially in the UK became the dominant variant in much of Europe and North America in the first half of 2021. The Spike (S) glycoprotein of alpha acquired seven mutations and two deletions compared to the ancestral virus, including the P681H mutation in the polybasic cleavage site that has been suggested to enhance S cleavage. Here, we show that the alpha S protein confers a level of resistance to the effects of interferon-{beta} (IFN{beta}) in human lung epithelial cells. This correlates with resistance to an entry restriction mediated by interferon-induced transmembrane protein 2 (IFITM2) and a pronounced infection enhancement by IFITM3. Furthermore, the P681H mutation is essential for resistance to IFN{beta} and context-dependent resistance to IFITMs in the alpha S. However, while this appears to confer changes in sensitivity to endosomal protease inhibition consistent with enhanced cell-surface entry, its reversion does not reduce cleaved S incorporation into particles, indicating a role downstream of furin cleavage. Overall, we suggest that, in addition to adaptive immune escape, mutations associated with VOCs may well also confer replication and/or transmission advantage through adaptation to resist innate immune mechanisms.\n\nIMPORTANCEThe emergence of Variants of Concern of SARS-CoV-2 has been a key challenge in the global response to the COVID-19 pandemic. Accumulating evidence suggests VOCs are being selected to evade the human immune response, with much interest focussed on mutations in the Spike protein that escape from neutralizing antibody responses. However, resistance to the innate immune response is essential for efficient viral replication and transmission. Here we show that the alpha (B.1.1.7) VOC of SARS-CoV-2 is substantially more resistant to type-1 interferons than the parental Wuhan-like virus. This correlates with resistance to the antiviral protein IFITM2, and enhancement by its paralogue IFITM3, that block virus entry into target cells. The key determinant of this is a proline to histidine change at position 681 in S adjacent to the furin-cleavage site that we have shown previously modulates IFITM2 sensitivity. Unlike other VOCs, in the context of the alpha spike, P681H modulates cell entry pathways of SARS-CoV-2, further reducing its dependence one endosomal proteases. Reversion of position 681 to a proline in viruses bearing the alpha spike is sufficient to restore interferon and IFITM2 sensitivity without reducing furin-mediated spike cleavage, suggesting post cleavage conformational changes in S are changing the viral entry pathway and therefore sensitivity to interferon. These data highlight the dynamic nature of the SARS CoV-2 S as it adapts to both innate and adaptive immunity in the human population.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Giuditta De Lorenzo", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Vanessa Cowton", - "author_inst": "MRC-University of Glasgow Centre For Virus Research" - }, - { - "author_name": "Wilhelm Furnon", - "author_inst": "MRC-University of Glasgow Centre For Virus Research" - }, - { - "author_name": "Nicol\u00e1s M. Su\u00e1rez", - "author_inst": "MRC-University of Glasgow Centre For Virus Research" - }, - { - "author_name": "Richard Orton", - "author_inst": "Medical Research Council - University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Massimo Palmirini", - "author_inst": "MRC-University of Glasgow Centre For Virus Research" - }, - { - "author_name": "Arvind H. Patel", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.08.12.503822", "rel_title": "The Spike protein of SARS-coV2 19B (S) clade mirrors critical features of viral adaptation and coevolution", @@ -236358,6 +236920,89 @@ "type": "new results", "category": "ecology" }, + { + "rel_doi": "10.1101/2022.08.15.504010", + "rel_title": "Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster", + "rel_date": "2022-08-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.15.504010", + "rel_abs": "It remains poorly understood how SARS-CoV-2 infection influences the physiological host factors important for aerosol transmission. We assessed breathing pattern, exhaled droplets, and infectious virus after infection with Alpha and Delta variants of concern (VOC) in the Syrian hamster. Both VOCs displayed a confined window of detectable airborne virus (24-48 h), shorter than compared to oropharyngeal swabs. The loss of airborne shedding was linked to airway constriction resulting in a decrease of fine aerosols (1-10{micro}m) produced, which are suspected to be the major driver of airborne transmission. Male sex was associated with increased viral replication and virus shedding in the air. Next, we compared the transmission efficiency of both variants and found no significant differences. Transmission efficiency varied mostly among donors, 0-100% (including a superspreading event), and aerosol transmission over multiple chain links was representative of natural heterogeneity of exposure dose and downstream viral kinetics. Co-infection with VOCs only occurred when both viruses were shed by the same donor during an increased exposure timeframe (24-48 h). This highlights that assessment of host and virus factors resulting in a differential exhaled particle profile is critical for understanding airborne transmission.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Julia R Port", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + }, + { + "author_name": "Dylan H Morris", + "author_inst": "Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA" + }, + { + "author_name": "Jade C Riopelle", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + }, + { + "author_name": "Claude Kwe Yinda", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + }, + { + "author_name": "Victoria A Avanzato", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + }, + { + "author_name": "Myndi G Holbrook", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + }, + { + "author_name": "Trenton Bushmaker", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + }, + { + "author_name": "Jonathan E Schulz", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + }, + { + "author_name": "Taylor A Saturday", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + }, + { + "author_name": "Kent Barbian", + "author_inst": "Genomics Research Section, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Instit" + }, + { + "author_name": "Collin A Russel", + "author_inst": "Department of Medical Microbiology | Amsterdam University Medical Center, University of Amsterdam" + }, + { + "author_name": "Rose Perry-Gottschalk", + "author_inst": "Rocky Mountain Visual and Medical Arts Unit, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Disease" + }, + { + "author_name": "Carl I Shaia", + "author_inst": "Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilto" + }, + { + "author_name": "Craig Martens", + "author_inst": "Genomics Research Section, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Instit" + }, + { + "author_name": "James O Lloyd-Smith", + "author_inst": "Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA" + }, + { + "author_name": "Robert J Fischer", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + }, + { + "author_name": "Vincent J Munster", + "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.13.503857", "rel_title": "Antisense oligonucleotide to SARS-Cov-2 trs gene: antiviral activity on an in vitro model and possibilities of vital and postmortem diagnosis of COVID-19.", @@ -238110,109 +238755,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.05.22278483", - "rel_title": "Antibody feedback regulation of memory B cell development in SARS-CoV-2 mRNA vaccination", - "rel_date": "2022-08-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.05.22278483", - "rel_abs": "Feedback inhibition of humoral immunity by antibodies was initially documented in guinea pigs by Theobald Smith in 1909, who showed that passive administration of excess anti-Diphtheria toxin inhibited immune responses1. Subsequent work documented that antibodies can enhance or inhibit immune responses depending on antibody isotype, affinity, the physical nature of the antigen, and engagement of immunoglobulin (Fc) and complement (C) receptors2, 3. However, little is known about how pre-existing antibodies might influence the subsequent development of memory B cells. Here we examined the memory B cell response in individuals who received two high-affinity IgG1 anti-SARS-CoV-2 receptor binding domain (RBD)-specific monoclonal antibodies, C144-LS and C135-LS, and subsequently two doses of a SARS-CoV-2 mRNA vaccine. The two antibodies target Class 2 and 3 epitopes that dominate the initial immune response to SARS-CoV-2 infection and mRNA vaccination4-8. Antibody responses to the vaccine in C144-LS and C135-LS recipients produced plasma antigen binding and neutralizing titers that were fractionally lower but not statistically different to controls. In contrast, memory B cells enumerated by flow cytometry after the second vaccine dose were present in higher numbers than in controls. However, the memory B cells that developed in antibody recipients differed from controls in that they were not enriched in VH3-53, VH1-46 and VH3-66 genes and predominantly expressed low-affinity IgM antibodies that carried small numbers of somatic mutations. These antibodies showed altered RBD target specificity consistent with epitope masking, and only 1 out of 77 anti-RBD memory antibodies tested neutralized the virus. The results indicate that pre-existing high-affinity antibodies bias memory B cell selection and have a profound effect on the development of immunological memory in humans that may in part explain the shifting target profile of memory antibodies elicited by the 3rd mRNA vaccine dose.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Dennis Schaefer-Babajew", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Zijun Wang", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Alice Cho", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Raphael Raspe", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Brianna Johnson", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Marie Canis", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Justin DaSilva", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Victor Ramos", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Martina Turroja", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Katrina Millard", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Fabian Schmidt", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Juan Dizon", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Irina Shimeliovich", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Kai-Hui Yao", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Thiago Oliveira", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Anna Gazumyan", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA & Howard Hughes Medical Institute, New York, NY, USA" - }, - { - "author_name": "Christian Gaebler", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Paul D. Bieniasz", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA & Howard Hughes Medical Institute, New York, NY, USA" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Marina Caskey", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA" - }, - { - "author_name": "Michel C. Nussenzweig", - "author_inst": "Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA & Howard Hughes Medical Institute, New York, NY, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.08.09.22274874", "rel_title": "Procalcitonin and High APACHE Scores are Associated with the Development of Acute Kidney Injury in Patients with SARS-CoV-2", @@ -238708,6 +239250,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.09.22278540", + "rel_title": "SARS-CoV-2 viral clearance and viral load kinetics in young children (1-6 years) compared to adults: Results of a longitudinal study in Germany", + "rel_date": "2022-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.09.22278540", + "rel_abs": "ObjectiveTo investigate SARS-COV-2 viral clearance and viral load kinetics in the course of infection in children aged 1-6 years in comparison with adults.\n\nMethodsProspective cohort study of infected daycare children and staff and their close contacts in households from 11/2020-06/2021, comprising serial (self) sampling of upper respiratory tract specimen and testing for SARS-CoV-2 via PCR. Data on symptoms and exposure were used to determine the date of probable infection for each participant. We determined (a) viral clearance, and (b) viral load dynamics over time. Samples were taken from day 4-6 to day 16-18 after diagnosis of the index case in the respective daycare group (5 samples per participant).\n\nResultsWe included 40 children (1-6 years) and 67 adults (18-77 years) with SARS-CoV-2 infection. Samples were available at a mean of 4.3 points of time per participant. Among the participants, the 12-day study period fell in different periods within the individual course of infection, ranging from day 5-17 to day 15-26 after assumed infection.\n\nChildren reached viral clearance at a median of 20 days after assumed infection (95% CI 17-21 days, Kaplan Meier Analysis), adults at 23 days (95% CI 20-25 days, difference not significant). In both children and adults, viral load decreased over time with trajectories of the mean viral load not being statistically different between groups. Only small proportions of those tested positive had a viral load of >1 million copies/ml, which is considered the threshold for infectivity. Kaplan-Meier calculations show that from day 15 (95% CI 13-15), 50% of all participants that had a viral load no longer infectious or were negative.\n\nConclusionChildren aged 1-6 and adults infected with SARS-CoV-2 (wild type and Alpha variant) did not differ significantly in terms of viral load kinetics and time needed to clear the virus. Therefore, containment measures are important also in the daycare settings as long as the pandemic continues.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Anna Elena Sandoni", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Angelika Schaffrath Rosario", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Janine Michel", + "author_inst": "Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Tim Kuttig", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Juliane Wurm", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute" + }, + { + "author_name": "Stefan Damerow", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Helena Iwanowski", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Bianca Finkel", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany," + }, + { + "author_name": "Livia Schrick", + "author_inst": "Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Udo Buchholz", + "author_inst": "Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Walter Haas", + "author_inst": "Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Gianni Varnaccia", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany," + }, + { + "author_name": "Ulrike Kubisch", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany," + }, + { + "author_name": "Susanne Jordan", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Anja Schienkiewitz", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Andreas Nitsche", + "author_inst": "Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany" + }, + { + "author_name": "Julika Loss", + "author_inst": "Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.09.22278452", "rel_title": "SARS-CoV-2 genomic diversity in households highlights the challenges of sequence-based transmission inference", @@ -240312,53 +240937,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.07.22278506", - "rel_title": "The prognostic value of transthoracic echocardiography findings in hospitalized adult patients with COVID-19: A single-center retrospective analysis", - "rel_date": "2022-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.07.22278506", - "rel_abs": "BackgroundCardiac involvement in coronavirus disease 2019 (COVID-19) is associated with poor outcomes. Transthoracic echocardiography (TTE) can be used to assess cardiac structure and function non-invasively, and has been shown to influence management in COVID-19.\n\nObjectivesWe aim to investigate the prognostic value of TTE findings in hospitalized adults with confirmed COVID-19.\n\nMethodsAll consecutive hospitalized adult patients with confirmed COVID-19 who underwent TTE assessment between 3rd April 2020 - 6th April 2021 were included. Comprehensive clinical data including TTE findings were collected from electronic medical records. Patients with mild-moderate and severe-critical COVID-19 were compared. Within the severe-critical group, patients who survived hospitalization and died were compared. Further analyses were conducted after matching for age >60 years, obesity, and diabetes.\n\nResultsA total of 488 COVID-19 patients were included in this study; 202 with mild-moderate and 286 severe-critical disease. All mild-moderate patients and 152 severe-critical patients survived hospitalization. In the matched cohorts, TTE findings associated with severe-critical COVID-19 included left ventricular (LV) hypertrophy (OR: 1.91; CI: 1.21 - 3.02), LV diastolic dysfunction (OR: 1.55; CI: 1.00 - 2.38), right ventricular (RV) dysfunction (OR: 3.86; CI: 1.06 - 14.08), wall motion abnormalities (WMAs) (OR: 2.76; CI: 1.28 - 5.96), and any TTE abnormalities (OR: 2.99; CI: 1.73 - 5.17). TTE findings associated with mortality included RV dysfunction (OR: 3.53; CI: 1.12 - 11.19) and WMAs (OR: 2.63; CI: 1.26 - 5.49).\n\nConclusionTTE is a non-invasive modality that can potentially be used for risk-stratification of hospitalized COVID-19 patients. These findings must be confirmed in larger prospective studies.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Hary Sakti Muliawan", - "author_inst": "Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Indonesia/ Universitas Indonesia Hospital" - }, - { - "author_name": "Raksheeth Agarwal", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Raka Aldy Nugraha", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - }, - { - "author_name": "Gatut Priyonugroho", - "author_inst": "Department of Pulmonology, Universitas Indonesia Hospital" - }, - { - "author_name": "Siti Hertine", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - }, - { - "author_name": "Sony Hilal Wicaksono", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - }, - { - "author_name": "Prima Almazini", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - }, - { - "author_name": "Dian Zamroni", - "author_inst": "Department of Cardiology and Vascular Medicine, Universitas Indonesia Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.08.07.22278510", "rel_title": "Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease: A COVID-19 Biobank study.", @@ -240698,6 +241276,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.08.09.22278587", + "rel_title": "Cyclical Student Shifting Models in a Limited Face-to-Face Learning Modality in the time of COVID-19 Pandemic in the Philippines", + "rel_date": "2022-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.09.22278587", + "rel_abs": "IntroductionA joint memorandum circular (JMC No. 2021-001) was released by the Commission on Higher Education (CHED) and the Department of Health (DOH) in the Philippines, outlining the guidelines on the gradual reopening of higher education campuses for limited face-to-face classes during the COVID-19 pandemic. Besides the strict enforcement of health protocols, the said circular recommended for the reduction of COVID-19 reproduction number by limiting the number of students present within the campus through the adoption of a cyclical student shifting model. This study evaluates 32 cyclical 2-shift models and how these schedules minimizes COVID-19 incidence in the campus.\n\nMethodA compartmental SEIRS model is used to simulate the number of infection for a 36-week period where the proposed 32 cyclical schedules and health protocols, such as the wearing of minimum personal protective gears and physical distancing, are inserted into the model.\n\nResultThe simulation has shown that all of the proposed schedules result to low disease transmission as long as there is strong adherence to health protocols among students or strict implementation of health policies for at least 18 weeks; otherwise, the 4-10 cycle model is recommended, or shifting schedules with 3-4 consecutive weeks of in-campus classes when health protocols are poorly implemented.\n\nConclusionThe results of this study will guide university administrators in crafting their COVID-19 academic plan, especially in the selection of a suitable cyclical shifting schedule for their institution.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alexander J Balsomo", + "author_inst": "West Visayas State University" + }, + { + "author_name": "Stephen G. Sabinay", + "author_inst": "West Visayas State University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.08.09.503302", "rel_title": "Spike-specific CXCR3+ TFH cells play a dominant functional role in supporting antibody responses in SARS-CoV-2 infection and vaccination", @@ -242358,37 +242959,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.04.22278431", - "rel_title": "Determining population-level allocation strategies for COVID-19 treatments in the United States using a quantitative framework, a case study using nirmatrelvir/ritonavir", - "rel_date": "2022-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278431", - "rel_abs": "BackgroundNew COVID-19 medications force decision makers to weigh limited evidence of efficacy and cost in determining which patient populations to target for treatment. A case in point is nirmatrelvir/ritonavir, a drug that has been recommended for elderly, high-risk individuals, regardless of vaccination status, even though clinical trials have only evaluated it in unvaccinated patients. A simple optimization framework might inform a more reasoned approach to the tradeoffs implicit in the treatment allocation decision.\n\nMethodsWe used a mathematical model to analyze the cost-effectiveness of four nirmatrelvir/ritonavir allocation strategies, stratified by vaccination status and risk for severe disease. We considered treatment effectiveness at preventing hospitalization ranging from 21% to 89%. Sensitivity analyses were performed on major parameters of interest. A web-based tool was developed to permit decision-makers to tailor the analysis to their settings and priorities.\n\nResultsProviding nirmatrelvir/ritonavir to unvaccinated patients at high-risk for severe disease was cost-saving when effectiveness against hospitalization exceeded 33% and cost-effective under all other data scenarios we considered. The cost-effectiveness of other allocation strategies, including those for vaccinated adults and those at lower-risk for severe disease, depended on willingness-to-pay thresholds, treatment cost and effectiveness, and the likelihood of severe disease.\n\nConclusionsPriority for nirmatrelvir/ritonavir treatment should be given to unvaccinated persons at high-risk of severe disease from COVID-19. Further priority may be assigned by weighing treatment effectiveness, disease severity, drug cost, and willingness to pay for deaths averted.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Alexandra Savinkina", - "author_inst": "Yale University" - }, - { - "author_name": "Gregg S. Gonsalves", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Joseph S. Ross", - "author_inst": "Yale University" - }, - { - "author_name": "A David Paltiel", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.08.05.22278466", "rel_title": "Performance of Screening for SARS-CoV-2 using Rapid Antigen Tests to Detect Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infection: findings from the Test Us at Home prospective cohort study", @@ -242836,6 +243406,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.04.22278415", + "rel_title": "Early Side Effects after Administration of the 1st Dose of Oxford-AstraZeneca Vaccine", + "rel_date": "2022-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278415", + "rel_abs": "Vaccines have played a central role in minimizing new infections, the rate of hospitalizations, and the overall burden on the health sector. Fear of side-effects is the biggest and commonest reason for avoiding getting vaccinated. It is, therefore, essential to maintain the clarity and consistency of message, to support and encourage people to get vaccinated. This study aims to contribute in that regard, by registering and quantifying the early side-effects of the Oxford-AstraZeneca COVID-19 vaccine in Pakistan. This study employs a non-random cross-sectional design. Data collected from 477 participants using a structured questionnaire was used to investigate the relationship between socio-demographic characteristics and side effect profiles of the participants. Binomial Logistic Regression was used to analyze the data. Odds Ratio (OR) gives the likelihood of having a side effect versus the reference group. Significance level () for the probability value (p-value) is set at 0.05. Fever (30.19%) was the most commonly experienced side effect, followed closely by fatigue (22.01%). 71.11% of those with fever experienced low grade fever (99-100F) while 62.69% of body aches experienced were moderate in intensity (Grades 4-6). In general, younger people are significantly more likely (p=0.023) to experience side effects (OR-1 = 1.023: interpreted as 1.023 times increase per unit decrease in age). Similarly, they are more likely (p= 0.029) to have a headache (OR-1 =1.039). Also, they are more likely (p= 0.007) to have a body ache (OR-1 =1.038). The Oxford-AstraZeneca COVID-19 vaccine side-effects seem to be more prevalent among younger age groups, which points to increased vaccine safety among older individuals that are usually more susceptible to severe COVID-19 infection. In addition, we found a substantially reduced number of side-effects, as compared to the clinical trials, which is an encouraging indicator for vaccine safety.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Pramod Singh", + "author_inst": "Punjab Medical College" + }, + { + "author_name": "Abdul Rafae Faisal", + "author_inst": "Punjab Medical College" + }, + { + "author_name": "M. Hassaan Shah", + "author_inst": "Qazi Hussain Ahmed Medical Complex" + }, + { + "author_name": "Ahmad Saeed", + "author_inst": "Punjab Medical College" + }, + { + "author_name": "Hadia Younas", + "author_inst": "Services Institute of Medical Sciences" + }, + { + "author_name": "Usamah Saeed Butt", + "author_inst": "King Edward Medical University" + }, + { + "author_name": "Sudip Pudasaini", + "author_inst": "Nepal Medical College" + }, + { + "author_name": "Abdul Rafay Pasha", + "author_inst": "Allama Iqbal Medical College" + }, + { + "author_name": "Umair Rehman", + "author_inst": "Punjab Medical College" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.04.502716", "rel_title": "Neutralization of Omicron BA.4/BA.5 and BA.2.75 by Booster Vaccination or BA.2 Breakthrough Infection Sera", @@ -244720,29 +245341,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.02.22278349", - "rel_title": "Geospatial disparities in federal COVID-19 test-to-treat program", - "rel_date": "2022-08-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.02.22278349", - "rel_abs": "BackgroundPaxlovid is authorized for the treatment of COVID-19 and must be used within the first 5 days of symptom onset. This limited window for initiating treatment makes rapid access critical. Federal Test-to-Treat programs provide tests, prescriptions, and medication in one visit3.\n\nObjectiveThe objective of this study was to map the location of and identify disparities in access to Test-to-Treat programs in the United States (U.S.).\n\nMethodsWe obtained location data for public providers of Paxlovid and Test-to-Treat programs in the contiguous U.S. and examined their spatial distribution at the zip code tabulation area level. We defined zip codes as underserved if there was no Test-to-Treat program located within the zip code or within 20 miles of its boundaries.\n\nResultsMore than 52,000,000 people--representing 16% of the continental U.S. population--do not have access to a Test-to-Treat program in their zip code or within 20 miles. The majority of zip codes representing metropolitan areas have a Test-to-Treat program within 20 miles (77%). In contrast, only 30% of small towns and 23% of rural areas have nearby access. Zip codes with a high proportion of Hispanic and Black residents were likely to have access to nearby Test-to-Treat programs (72%, 70%). In contrast, zip codes with a high proportion of Native American residents were likely to be underserved (70%). About half of high-poverty zip codes do not have access to a Test-to-Treat program within 20 miles.\n\nDiscussionDisparities in outcomes related to COVID-19 have been apparent since the beginning of the pandemic and continue to grow. While the multi-dimensional measure of social vulnerability was used to expand the federal Test-to-Treat program, some populations remain without access.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Emily R. Smith", - "author_inst": "George Washington University" - }, - { - "author_name": "Erin M Oakley", - "author_inst": "The George Washington University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.03.22278359", "rel_title": "COVID-19 convalescent plasma for the treatment of immunocompromised patients: a systematic review.", @@ -245010,6 +245608,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.02.22278277", + "rel_title": "Real-life evaluation of a rapid antigen test (DPP SARS-CoV-2 Antigen) for COVID-19 diagnosis of primary healthcare patients, in the context of the Omicron-dominant wave in Brazil", + "rel_date": "2022-08-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.02.22278277", + "rel_abs": "Rapid antigen tests play an important role in the monitoring and mitigation of the COVID-19 pandemic, as it provides an easy, fast and efficient diagnosis with minimum infrastructure requirements. However, as new variants of concern continue to emerge, mutations in the virus genome may impair the recognition of the mutated antigen by the tests. Therefore, it is essential to re-assess the tests sensitivity as the virus mutation profile undergoes significant changes. Here, we prospectively accessed the performance of the DPP(R) SARS-CoV-2 Antigen test in the context of an omicron-dominant real-life setting. We evaluated 347 unselected individuals (all-comers) from a public testing center in Brazil, performing the rapid antigen test diagnosis at point-of-care with fresh samples. The combinatory result from two distinct RT-qPCR methods was employed as reference and 13 samples with discordant PCR results were excluded. The assessment of the rapid test in 67 PCR-positive and 265 negative samples revealed an overall sensitivity of 80.5%, specificity of 99.2% and positive/negative predictive values higher than 95%. However, we observed that the sensitivity was dependent on the viral load (sensitivity in Ct<31 = 93.7%; Ct>31 = 47.4%). Furthermore, we were able to confirm that the positive samples evaluated in the study were Omicron (BA.1/BA.1.1) by whole-genome sequencing (n=40) and multiplex RT-qPCR (n=17). Altogether, the data obtained from a real-life prospective cohort supports that the rapid antigen test sensitivity for the Omicron remains high and underscores the reliability of the test for COVID-19 diagnosis in a setting with high disease prevalence and limited PCR testing capability.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Matheus Filgueira Bezerra", + "author_inst": "Instituto Aggeu Magalhaes, Fiocruz, Recife, Brazil" + }, + { + "author_name": "Lilian Caroliny Amorim Silva", + "author_inst": "Instituto Aggeu Magalhaes, Fiocruz, Recife, Brazil" + }, + { + "author_name": "Romulo Pessoa-e-Silva", + "author_inst": "Universidade Federal de Pernambuco, Recife Brazil" + }, + { + "author_name": "Gisele Lino", + "author_inst": "Gerencia de Vigilancia Epidemiologica, Secretaria Municipal de Saude, Caruaru, Brazil" + }, + { + "author_name": "Filipe Zimmer Dezordi", + "author_inst": "Instituto Aggeu Magalhaes, Fiocruz, Recife, Brazil" + }, + { + "author_name": "Gustavo Barbosa Lima", + "author_inst": "Instituto Aggeu Magalhaes, Fiocruz, Recife, Brazil" + }, + { + "author_name": "Raul Emidio de Lima", + "author_inst": "Instituto Aggeu Magalhaes, Fiocruz, Recife, Brazil" + }, + { + "author_name": "Tulio Campos", + "author_inst": "Instituto Aggeu Magalhaes, Fiocruz, Recife, Brazil" + }, + { + "author_name": "Cassia Docena", + "author_inst": "Instituto Aggeu Magalhaes, Fiocruz, Recife, Brazil" + }, + { + "author_name": "Anderson Oliveira", + "author_inst": "Gerencia de Vigilancia Epidemiologica, Secretaria Municipal de Saude, Caruaru, Brazil" + }, + { + "author_name": "Maira Galdino da Rocha Pitta", + "author_inst": "Universidade Federal de Pernambuco, Recife Brazil" + }, + { + "author_name": "Francisco de Assis Santos da Silva", + "author_inst": "Universidade Federal de Pernambuco, Caruaru, Brazil" + }, + { + "author_name": "Michelly Pereira", + "author_inst": "Universidade Federal de Pernambuco, Recife Brazil" + }, + { + "author_name": "Gabriel Luz Wallau", + "author_inst": "Instituto Aggeu Magalhaes, Fiocruz, Recife, Brazil" + }, + { + "author_name": "Marcelo Henrique Santos Paiva", + "author_inst": "Universidade Federal de Pernambuco, Caruaru, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.03.22278348", "rel_title": "Effects of allocation concealment and blinding in trials addressing treatments for COVID-19: A methods study", @@ -246394,101 +247067,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.07.31.500554", - "rel_title": "Memory B cells and memory T cells induced by SARS-CoV-2 booster vaccination or infection show different dynamics and efficacy to the Omicron variant.", - "rel_date": "2022-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.31.500554", - "rel_abs": "Although BNT162b2 vaccination was shown to prevent infection and reduce COVID-19 severity, and the persistence of immunological memory generated by the vaccination has not been well elucidated. We evaluated memory B and T cell responses to the SARS-CoV-2 spike protein before and after the third BNT162b2 booster. Although the antibody titer against the spike receptor-binding domain (RBD) decreased significantly 8 months after the second vaccination, the number of memory B cells continued to increase, while the number of memory T cells decreased slowly. Memory B and T cells from unvaccinated infected patients showed similar kinetics. After the third vaccination, the antibody titer increased to the level of the second vaccination, and memory B cells increased at significantly higher levels before the booster, while memory T cells recovered close to the second vaccination levels. In memory T cells, the frequency of CXCR5+CXCR3+CCR6- cTfh1 was positively correlated with RBD-specific antibody-secreting B cells. Furthermore, T cell-dependent antibody production from reactivated memory B cells in vitro was correlated to the Tfh-like cytokine levels. For the response to variant RBDs, although 60%-80% of memory B cells could bind to the Omicron RBD, their binding affinity was low, while memory T cells show an equal response to the Omicron spike. Thus, the persistent presence of memory B and T cells will quickly upregulate antibody production and T cell responses after Omicron strain infection, which prevents severe illness and death due to COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Setsuko Mise-Omata", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Mari Ikeda", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Masaru Takeshita", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Yoshifumi Uwamino", - "author_inst": "Keio Univeristy School of Medicine" - }, - { - "author_name": "Masatoshi Wakui", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Tomoko Arai", - "author_inst": "Keio University Hospital" - }, - { - "author_name": "Ayumi Yoshifuji", - "author_inst": "Tokyo Saiseikai Central Hospital" - }, - { - "author_name": "Kensaku Murano", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Haruhiko Siomi", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Kensuke Nakagawara", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Masaki Ohyagi", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Makoto Ando", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Naoki Hasegawa", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Hideyuki Saya", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Mitsuru Murata", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Koichi Fukunaga", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Ho Namkoong", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Xiuyuan Lu", - "author_inst": "Osaka University" - }, - { - "author_name": "Sho Yamasaki", - "author_inst": "Osaka University" - }, - { - "author_name": "Akihiko Yoshimura", - "author_inst": "Keio University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.07.29.502014", "rel_title": "Coronaviruses using different strategies to antagonize antiviral responses and pyroptosis", @@ -246788,6 +247366,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.07.28.22270513", + "rel_title": "Use of a Self-Care and Educational Mobile App to Improve Outcomes of Patients with Acute Decompensated Heart Failure during the COVID-19 Pandemic", + "rel_date": "2022-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.28.22270513", + "rel_abs": "IntroductionExpansion in digital health using mobile phone health applications has increased recently. We developed a mobile phone application (Aintree Heart Failure Passport-AHFP APP) for heart failure (HF) patient education, self-care and improved medication adherence.\n\nMethodsThis was a prospective observational study of patients with acute decompensated HF managed with day-case intravenous diuretics in a HF specialist nurse delivered Ambulatory Acute Heart Failure Unit (AAHFU) in a British university hospital during the ongoing COVID-19 pandemic (March 2020 to July 2021). We assessed self-care behaviour (European Heart Failure Self-care Behaviour scale - EHFSBs-9) and medication adherence (Medication Adherence Report Scale -MARS-5) at 2 weeks post-presentation in patients who utilised the AHFP APP and compared 30-day HF re-admissions with annual hospital HF data.\n\nResults148 out of 221 consecutive ADHF patients treated in the AAHFU downloaded the AHFP Mobile APP. 45% were women and mean age of the cohort 62 {+/-} 6.1 years. 55% patients had HF with reduced ejection fraction (HFrEF), 34% had HF with preserved EF (HFpEF) and 11% had HF with mildly reduced EF. Mean EHFSBs-9 was 19.1{+/-}6.7; mean MARS-5 score 23.3{+/-}1.HF 30 day re-hospitalisation incidence significantly lower (11%) in the APP cohort compared to the incidence of 19% amongst all patients with ADHF during the study period (p=0.02).\n\nConclusionsOur pilot feasibility study suggests that use of a HF educational self-care mobile phone APP in ADHF patients during the COVID pandemic, leads to high quality self-care behaviour, high medication adherence and also lower levels of 30-day HF re-hospitalisation. These results will need to be validated in a randomised controlled trial.\n\n3 Key PointsO_LIThe use of digital healthcare technologies such as mobile APPs, is rapidly increasing\nC_LIO_LIThis study analyses the role of our heart failure educational and self-care mobile APP, used by patients with acute decompensated heart failure during the COVID-19 pandemic\nC_LIO_LIOur results show that use of the mobile APP can lead to high levels of self-care, medication adherence and also reduced 30 day readmissions\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "hani abobakr essa", + "author_inst": "Aintree university hospital" + }, + { + "author_name": "Carolyn Jackson", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Siji Nyjo", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Annmarie Kelly", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Naomi Murphy", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Nick Hartshorne-Evans", + "author_inst": "The Pumping Marvellous Foundation Heart Failure Patient Charity" + }, + { + "author_name": "Lauren Walker", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Emeka Oguguo", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Homeyra Douglas", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Rajiv Sankaranarayanan", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2022.07.31.502203", "rel_title": "SARS-CoV-2-specific CD4+ and CD8+ T cell responses can originate from cross-reactive CMV-specific T cells", @@ -248228,45 +248861,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2022.07.26.22277958", - "rel_title": "Induction of poxviral immunity by synthetic MVA-based dual-antigen COVID-19 vaccine COH04S1", - "rel_date": "2022-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.26.22277958", - "rel_abs": "The recent outbreak of monkeypox (MPXV) outside its endemic boundaries has attracted global attention and prompted world leaders to reserve millions of doses of the only approved third-generation smallpox/MPXV vaccine, Jynneos, which is based on the highly attenuated modified vaccinia Ankara (MVA) vector. We previously developed COH04S1, a multiantigen SARS-CoV-2 vaccine built on a synthetic MVA (sMVA) platform. COH04S1 was extensively tested for efficacy and immunogenicity in animal models, including non-human primates (NHP), and was found to be safe and to induce SARS-CoV-2-specific immunity in a Phase 1 clinical trial in healthy adults. Here we demonstrate that one or two vaccinations of NHP with either COH04S1 or sMVA elicit robust othopoxvirus-specific binding and neutralizing antibody responses. Furthermore, healthy adults vaccinated with COH04S1 at different dose levels develop robust othopoxvirus-specific humoral and cellular immune responses that are durable for over six months post-vaccination. Importantly, both COH04S1 and sMVA vaccinations induce elevated and sustained antibody responses to MPXV-proteins that are major targets of protective neutralizing antibodies. These results demonstrate that COH04S1 and sMVA are valuable vaccine candidates to stimulate robust orthopox/MPXV-specific humoral and cellular immunity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Flavia Chiuppesi", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "John A Zaia", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "Sandra Ortega Francisco", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "Michael Ly", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "Felix Wussow", - "author_inst": "City of Hope National Medical Center" - }, - { - "author_name": "Don J Diamond", - "author_inst": "City of Hope National Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.24.22277784", "rel_title": "Efficacy of a patient isolation hood in reducing exposure to airborne infectious virus in a simulated healthcare setting", @@ -248542,6 +249136,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.26.22278056", + "rel_title": "Level of Compliance and Predictors with Personal COVID-19-preventive measures Among Office Government Employees Returning to work in the post-epidemic period in Western Ethiopia: A Multicenter Cross-sectional Study", + "rel_date": "2022-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.26.22278056", + "rel_abs": "BackgroundThe contemporary global issues, COVID-19 pandemic continued causing unprecedented impact on the public health, occupational health and the global economy. Keeping compliance with personal preventive measures is a vital tool for managing COVID-19 pandemic control and returning to work as no pharmaceutical treatments are currently available in Ethiopia. Although compliance with COVID -19 personal preventive measures (CPPMs) and predictors is well addressed in healthcare settings, data on the level of CPPMs and its determinants among government employees working in offices worldwide, including Ethiopia, is limited. This paper is aimed to fill this gaps.\n\nMethodsWe applied a cross-sectional study design from February to March, 2021. The participants were government workers working in offices who had resumed work. Stratified followed by simple random sampling technique was used to select 422 study participants from 30 government offices that had resumed work. Data were collected using a pre-tested and structured interviewer-administered questionnaires and analyzed by STATA 14 software. The significance of associations was established at p< 0.05 and adjusted odds ratio (AOR) with 95% confidence intervals (CI) in the multivariable model.\n\nResultsResponse rate 95.44% (N=394). The study found 22.3% (88) of study participants (95% CI = 18.5, 26.6) had high compliance with COVID -19 personal preventive measures during past month. Female workers were 2.80 times more likely than males to comply with COVID-19 personal preventive measures (AOR: 2.80, 95%CI (1.10, 7.12), favorable attitude towards COVID-19 prevention measures (AOR: 13.73, 95% CI (4.85, 38.83), high-risk perception of COVID-19 infections (AOR: 2.34; 95% CI (1.24, 4.41), and high misconception about COVID-19 (AOR : 3.92, 95% CI (1.45, 10.62) were predicted better compliance with COVID-19 PPMs (P < 0.05).\n\nConclusionsIn sum, little proportion of sampled study participants complied with COVID -19 personal preventive measures. Sex, attitudes, risk perception, and misconception have all been identified as significant risk factors. Actions are needed to strengthen COVID -19 personal preventive measures among government employees to maintain COVID -19 control following work resumption. In the future, its vital to work on government employees attitudes and perceptions in order to improve compliance.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Gebisa Guyasa Kabito", + "author_inst": "University of Gondar" + }, + { + "author_name": "Meskele Abreham", + "author_inst": "Labor and Social Affairs Office, Labor Inspector Nekemte town, Ethiopia" + }, + { + "author_name": "Amensisa Hailu Tesfaye", + "author_inst": "University of Gondar College of Medicine and Health Sciences" + }, + { + "author_name": "Tadesse Guadu", + "author_inst": "University of Gondar College of Medicine and Health Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.07.26.22277990", "rel_title": "The association between dysnatraemia during hospitalisation and post COVID-19 mental fatigue.", @@ -250130,49 +250755,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.20.22277848", - "rel_title": "Virtual care use among older immigrant adults in Ontario, Canada during the COVID-19 pandemic: a repeated cross-sectional analysis", - "rel_date": "2022-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.20.22277848", - "rel_abs": "The critical role of virtual care during the COVID-19 pandemic has raised concerns about the widening disparities to access by vulnerable populations including older immigrants. This paper aims to describe virtual care use in older immigrant populations residing in Ontario, Canada.\n\nIn this population-based, repeated cross-sectional study, we used linked administrative data to describe virtual care and healthcare utilization among immigrants aged 65 years and older before and during the COVID-19 pandemic. Visits were identified weekly from January 2018 to March 2021 among various older adult immigrant populations.\n\nAmong older immigrants, over 75% were high users of virtual care (had two or more virtual visits) during the pandemic. Rates of virtual care use increased for both older adult immigrant and non-immigrant populations. At the start of the pandemic, virtual care use was lower among immigrants compared to non-immigrants (weekly average of 77 vs 86 visits). As the pandemic progressed, the rates between these groups became similar (80 vs 79 visits). Virtual care use was consistently lower among immigrants in the family class (75 visits) compared to the economic (82 visits) or refugee (89 visits) classes, and was lower among those who only spoke French (69 visits) or neither French nor English (73 visits) compared to those who were fluent in English (81 visits).\n\nThis study found that use of virtual care was comparable between older immigrants and non-immigrants overall, though there may have been barriers to access for older immigrants early on in the pandemic. However, within older immigrant populations, immigration category and language ability were consistent differentiators in the rates of virtual care use throughout the pandemic.\n\nAuthor SummaryWhen the COVID-19 pandemic began, healthcare systems pivoted from in-person to virtual care to maintain physical distancing. Studies have shown that virtual care use became much more frequent during the pandemic as a result. What we do not know is whether virtual care is being used equitably, that is, whether everybody has fair access to the resource. This can be a big issue particularly amongst older adults, who are often battling several diseases and use healthcare frequently. Many older adults are immigrants who may face challenges in accessing healthcare due to reasons such as limited language fluency and resource support. Our study found that older adult immigrants aged 65 and above living in Ontario, Canada had lower use of virtual care initially, but their use eventually caught up with non-immigrants as the pandemic progressed. We also found that older adult immigrants from the family class had lower virtual care use compared to those from the economic, refugee, or other immigration classes. Additionally, immigrants who were not fluent in English had lower use compared to those who were fluent. These results show that virtual care access remains an issue for vulnerable minorities and steps should be taken to ensure these groups are receiving adequate care.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Janette Brual", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Cherry Chu", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Jiming Fang", - "author_inst": "Institute for Clinical Evaluative Sciences" - }, - { - "author_name": "Cathleen Fleury", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Vess Stamenova", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Onil Bhattacharyya", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Mina Tadrous", - "author_inst": "Women's College Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" - }, { "rel_doi": "10.1101/2022.07.26.22278045", "rel_title": "Effectiveness of the BNT162b2 vaccine against SARS-CoV-2 infection among children and adolescents in Qatar", @@ -250588,6 +251170,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.07.22.501212", + "rel_title": "SARS-CoV-2 Non-Structural Protein 1(NSP1) Mutation Virulence and Natural Selection: Evolutionary Trends in the Six Continents", + "rel_date": "2022-07-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.22.501212", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an unsegmented positivesense single-stranded RNA virus that belongs to the {beta}-coronavirus. This virus was the cause of a novel severe acute respiratory syndrome in 2019 (COVID-19) that emerged in Wuhan, China at the early stage of the pandemic and rapidly spread around the world. Rapid transmission and reproduction of SARS-CoV-2 threaten worldwide health with a high mortality rate from the virus. According to the significant role of non-structural protein 1 (NSP1) in inhibiting host mRNA translation, this study focuses on the link between amino acid sequences of NSP1 and alterations of them spreading around the world. The SARS-CoV-2 NSP1 protein sequences were analyzed and FASTA files were processed by Python language programming libraries. Reference sequences compared with each NSP1 sample to identify every mutation and categorize them were based on continents and frequencies. NSP1 mutations rate divided into continents were different. Based on continental studies, E87D in global vision and also in Europe notably increased. The E87D mutation has significantly risen especially in the last months of the study as the first frequent mutation observed. The remarkable mutations, H110Y and R24C, have the second and third frequencies, respectively. Based on this mutational information, despite NSP1 being a conserved sequence occurrence, these mutations change the rate of flexibility and stability of the NSP1 protein, which can eventually affect inhibiting the host translation.\n\nIMPORTANCEIn this study, we analyzed 6,510,947 sequences of non-structural protein 1 as a conserved region of SARS-CoV-2. According to the obtained results, 93.4819% of samples had no mutant regions on their amino acid sequences. Heat map data of mutational samples demonstrated high percentages of mutations that occurred in the region of 72 to 126 amino acids indicating a hot spot region of the protein. Increased rates of E87D, H110Y, and R24C mutations in the timeline of our study were reported as significant compared to available mutant samples. Analyzing the details of replacing amino acids in the most frequent E87D mutation reveals the role of this alteration in increasing molecule flexibility and destabilizing the structure of the protein.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Samira Salami Ghaleh", + "author_inst": "University of Guilan" + }, + { + "author_name": "Karim Rahimian", + "author_inst": "Tarbiat Modares University" + }, + { + "author_name": "Mohammadamin Mahmanzar", + "author_inst": "University of Hawaii John A. Burns School of Medicine" + }, + { + "author_name": "Bahar Mahdavi", + "author_inst": "Royan Institute" + }, + { + "author_name": "Samaneh Tokhanbigli", + "author_inst": "Islamic Azad University Pharmaceutical Sciences Branch" + }, + { + "author_name": "Mahsa Mollapour Sisakht", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Amin Farhadi", + "author_inst": "Payame Noor University" + }, + { + "author_name": "Mahsa Mousakhan Bakhtiari", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Donna Lee Kuehu", + "author_inst": "University of Hawaii John A. Burns School of Medicine" + }, + { + "author_name": "Youping Deng", + "author_inst": "University of Hawaii John A. Burns School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.07.24.22277975", "rel_title": "Highlighting the importance of semantics in COVID-19 fake news detection using a CNN hashmap color-based method", @@ -251936,53 +252573,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.23.22277948", - "rel_title": "Predicting intention to vaccinate against COVID-19 in older Syrian refugees in Lebanon: findings from a multi-wave study", - "rel_date": "2022-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.23.22277948", - "rel_abs": "IntroductionCOVID-19 vaccine acceptance among refugees in the Arab region remains low. This study aimed to examine the prevalence, reasons and predictors of COVID-19 vaccine refusal among older Syrian refugees in Lebanon.\n\nMethodA nested cross-sectional study among older Syrian refugees in Lebanon. The sampling frame was a complete listing of beneficiary households of a humanitarian organization with an adult aged 50 years or older. Telephone surveys were completed between September 2020 and May 2021. Logistic regression models were used to identify predictors of COVID-19 vaccine refusal. Models were internally validated using bootstrap methods and the models calibration and discrimination were presented.\n\nResultsOf 3,173 Syrian refugees, 61% intended to receive the COVID-19 vaccine, 31% refused and 7% were undecided. Reasons for vaccine refusal were: preference to follow preventive measures (27%) and belief that the vaccine is not essential (21%). Despite high vaccine acceptance, only 6% of older Syrian refugees were registered on the national platform to receive the vaccine. Reasons for not registering included: being unsure about how to register (36%), and not wanting to receive the vaccine (33%). Predictors of COVID-19 vaccine refusal included: sex (female), older age, education, living outside informal tented settlements, perceiving COVID-19 as not severe and vaccines as not safe or effective, and using social media for information on COVID-19. After adjusting for optimization, the final model showed moderate discrimination (C-statistic: 0.65 (95% CI:(0.63-0.67)) and good calibration (C-Slope: 0.93 (95% CI:0.82-1.06)).\n\nConclusionThis study developed predictive model for vaccination intention with a moderate discriminative ability and good calibration. Prediction models in humanitarian settings can help to identify refugees at higher risk of not intending to receive the COVID-19 vaccine for public health targeting.\n\nWhat is already known on this topicDespite global efforts towards more inclusive national deployment vaccination plans, vaccine coverage and uptake among migrants and refugees remains low. Refugees and migrants, the majority of whom live in low and middle income countries, bear the double burden of vaccine inequity and face several challenges and barriers to vaccination including low vaccine supply, inability to access health services, fear of arrest and deportation, lack of accessible information as well as other language, and economic barriers. Research on COVID-19 vaccine intentions among refugees in the region has been limited. Understanding intentions and predictors to vaccinate among refugees, and addressing barriers to vaccine acceptance and registration, is crucial to ensure equitable vaccination and coverage, reduce the spread of COVID-19 and achieve herd immunity.\n\nWhat this study addsThis study is one of the first to develop and internally validate a model of intention to refuse vaccination against COVID-19 in older Syrian refugees. Predictors of intention to refuse the vaccine include age, education, living outside informal tented settlements, sex, perceiving COVID-19 as not a serious infection and vaccines as not safe or effective, and using social media as a source of information on COVID-19. The primary reasons for vaccine refusal were: preference to follow preventive measures, concerns that the vaccine is too new, and belief that the vaccine is not essential. Registration on the national platform to receive the vaccine was low and the reasons for not registering included: being unsure about how to register, and not wanting to receive the vaccine.\n\nHow this study might affect research, practice or policyThis study highlights the need for targeted interventions to enhance vaccine acceptance and uptake among older Syrian refugees, and address barriers to vaccine registration. Predictors of COVID-19 vaccine refusal among older Syrian refugees will inform humanitarian programming and public health campaigns, and guide resource allocation and deployment planning. Findings inform future research to better understand the predictors of vaccine refusal.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Noura Joseph El Salibi", - "author_inst": "American University of Beirut Faculty of Health Sciences" - }, - { - "author_name": "Sawsan Abdulrahim", - "author_inst": "American University of Beirut" - }, - { - "author_name": "Maria El Haddad", - "author_inst": "American University of Beirut" - }, - { - "author_name": "Berthe Abi Zeid", - "author_inst": "American University of Beirut Faculty of Health Sciences" - }, - { - "author_name": "Marwan Alawieh", - "author_inst": "Norwegian Refugee Council" - }, - { - "author_name": "Zeinab Ramadan", - "author_inst": "Norwegian Refugee Council" - }, - { - "author_name": "Hala Ghattas", - "author_inst": "American University of Beirut Faculty of Health Sciences" - }, - { - "author_name": "Stephen J McCall", - "author_inst": "American University of Beirut" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.22.22277947", "rel_title": "High titre neutralizing antibodies in response to SARS-CoV-2 infection require RBD-specific CD4 T cells that include proliferative memory cells.", @@ -252310,6 +252900,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.21.22277910", + "rel_title": "A distinct symptom pattern emerges for COVID-19 Long-Haul: A nationwide study", + "rel_date": "2022-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.21.22277910", + "rel_abs": "Long-haul COVID-19, also called Post-Acute Sequelae of SARS-CoV-2 (PASC), is a new illness caused by SARS-CoV-2 infection and characterized by the persistence of symptoms. The purpose of this cross-sectional study was to identify a distinct and significant temporal pattern of PASC symptoms (symptom type and onset) among a nationwide sample of PASC survivors (n= 5,652). The sample was randomly sorted into two independent samples for exploratory (EFA) and confirmatory factor analyses (CFA). Five factors emerged from the EFA: (1) cold & flu-like symptoms, (2) change in smell and/or taste, (3) dyspnea and chest pain, (4) cognitive & visual problems, and (5) cardiac symptoms. The CFA had excellent model fit (x2 = 513.721, df= 207, p<0.01, TLI= 0.952, CFI= 0.964, RMSEA= 0.024). These findings demonstrate a novel symptom pattern for PASC. These findings can enable nurses in the identification of at-risk patients and facilitate early, systematic symptom management strategies for PASC.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Charles A Downs", + "author_inst": "University Of Miami" + }, + { + "author_name": "Melissa D Pinto", + "author_inst": "UCI Irvine" + }, + { + "author_name": "Yong Huang", + "author_inst": "UCI IRvine" + }, + { + "author_name": "Survivor Corps", + "author_inst": "SurvivorCorps" + }, + { + "author_name": "Sarach A El-Azab", + "author_inst": "Indiana University" + }, + { + "author_name": "Nathan S Ramrakhiani", + "author_inst": "Brown University" + }, + { + "author_name": "Anthony Barisano", + "author_inst": "Brown University" + }, + { + "author_name": "Lu Yu", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Kaityln Taylor", + "author_inst": "Indiana University" + }, + { + "author_name": "Alvaro Esperancas", + "author_inst": "Indiana University Purude" + }, + { + "author_name": "Heather Abrahim", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Thomas D Hughes", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Maria Giraldo Herrera", + "author_inst": "UCI Irvine" + }, + { + "author_name": "Amir Rahmani", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Nikil Dutt", + "author_inst": "UCI IRvine" + }, + { + "author_name": "Rana Chakraborty", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Christian Mendiola", + "author_inst": "Purdue School of Engineering & Technology, Computer, and Information Technology" + }, + { + "author_name": "Natalie J Lambert", + "author_inst": "Indiana University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.20.22277852", "rel_title": "Evaluation of trace elements analysis in Pediatric Patients with COVID-19\uff1aA report from Turkey", @@ -253554,81 +254231,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.07.19.22277248", - "rel_title": "COVID-19 could cause long term peripheral nerve demyelination and axonal loss: A One Year Prospective Cohort Study", - "rel_date": "2022-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.19.22277248", - "rel_abs": "BackgroundThere is a lack of studies on large-sample, medium-, or long-term follow-up data of peripheral neuropathy (PNP) in the COVID-19 survivors. This study evaluated the characteristics and related risk factors of PNP in the medium- and long-term rehabilitation, which provided real-world study data for the complete recovery of COVID-19 patients.\n\nMethodsThis study was a prospective cohort study of the COVID-19 survivors. We collected data on baseline characteristics, symptoms at onset and after discharge during the 6-month and 12-month follow-up. Peripheral nerves were measured by electromyography and inducible potentiometer. We used multivariable logistic regression to analyze the influencing factors of PNP. Additionally, we compared the difference between the two measurements among the population who completed both measurements.\n\nResults313 patients were included in the study and all of them underwent nerve conduction study. 67 patients completed two measurements at 6-month and 12-month follow-up. Commonly reported symptoms contained memory loss (86%), hair loss (28%), anxiety (24%), and sleep difficulties (24%). 232 patients (74%) were found with PNP, including 51 (16%) with mononeuropathy and 181 (58%) with generalized PNP. Patients with measurement at 12-month follow-up had a higher prevalence of generalized PNP (p=0.006). For pathological types, 64 (20%) patients had only axonal loss, 67 (21%) had only demyelination, and 101 (32%) had a mixed type. There was no significant difference in the prevalence of accompanying symptoms after discharge between the two groups with or without PNP. After adjustment, age was positively associated with PNP (OR=1.22 per 10-year increase of age, 95% CI, 1.05-1.41). Compared with less than the median amount of IgG at discharge, higher amount of IgG was associated with decreased risk of F-wave abnormality (OR=0.32, 95%CI, 0.11-0.82), but no significant difference in other types of PNP.\n\nConclusions and RelevanceSARS-CoV-2 could cause PNP in hospital survivors with COVID-19, which persisted and was associated with age, education, and IgG antibody at discharge, but had no significant correlation with symptoms after discharge.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Yubin Zhao", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Qian Yang", - "author_inst": "People's Hospital,Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Feng Sun", - "author_inst": "School of Public Health, Peking University" - }, - { - "author_name": "Meng Zhang", - "author_inst": "Peking university" - }, - { - "author_name": "Yanhui Lai", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Xuzhao Liu", - "author_inst": "North China University of Science and Technology" - }, - { - "author_name": "Fengshuang Liu", - "author_inst": "Hebei University of Chinese Medicine" - }, - { - "author_name": "Hongmin Zang", - "author_inst": "Hebei University of Chinese Medicine" - }, - { - "author_name": "Jinzhong Song", - "author_inst": "Hebei University of Chinese Medicine" - }, - { - "author_name": "Na Li", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Shuhua Cui", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Wei Shao", - "author_inst": "Peking university" - }, - { - "author_name": "Jiang Ma", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Zhibo Wang", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - }, - { - "author_name": "Ling Cui", - "author_inst": "People' Hospital Shijiazhuang,Hebei Province,China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.20.22277838", "rel_title": "National and regional prevalence of SARS-CoV-2 antibodies in primary and secondary school children in England: the School Infection Survey, a national open cohort study, November 2021", @@ -253908,6 +254510,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.07.19.500637", + "rel_title": "Vaccination shapes evolutionary trajectories of SARS-CoV-2", + "rel_date": "2022-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.19.500637", + "rel_abs": "The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, as well as anti-genic changes that reduce the cross-immunity induced by previous infections or vaccinations1-4. How this functional variation shapes the global evolutionary dynamics has remained unclear. Here we show that selection induced by vaccination impacts on the recent antigenic evolution of SARS-CoV-2; other relevant forces include intrinsic selection and antigenic selection induced by previous infections. We obtain these results from a fitness model with intrinsic and antigenic fitness components. To infer model parameters, we combine time-resolved sequence data5, epidemiological records6,7, and cross-neutralisation assays8-10. This model accurately captures the large-scale evolutionary dynamics of SARS-CoV-2 in multiple geographical regions. In particular, it quantifies how recent vaccinations and infections affect the speed of frequency shifts between viral variants. Our results show that timely neutralisation data can be harvested to identify hotspots of antigenic selection and to predict the impact of vaccination on viral evolution.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Matthijs Meijers", + "author_inst": "Institute for Biological Physics, University of Cologne, Cologne, Germany" + }, + { + "author_name": "Denis Ruchnewitz", + "author_inst": "Institute for Biological Physics, University of Cologne, Cologne, Germany" + }, + { + "author_name": "Marta Luksza", + "author_inst": "Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Michael L\u00e4ssig", + "author_inst": "Institute for Biological Physics, University of Cologne, Cologne, Germany" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.07.19.500631", "rel_title": "Regulation of mRNA transcripts, protein isoforms, glycosylation and spatial localization of ACE2 and other SARS-CoV-2-associated molecules in human airway epithelium upon viral infection and type 2 inflammation", @@ -255364,49 +255997,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2022.07.18.22276918", - "rel_title": "Drivers and prevalence of COVID-19 vaccine uptake among homeless and precariously housed people in France: a cross-sectional population-based study", - "rel_date": "2022-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22276918", - "rel_abs": "BackgroundFew global data exist regarding COVID-19 vaccine coverage in people experiencing homelessness (PEH) or precariously housed (PH) who are at high risk for COVID-19 infection, hospitalization, and death. Given the absence of documented French data, we aimed to determine COVID-19 vaccine coverage in PEH/PH in France, and its drivers.\n\nMethodsWe carried out a cross-sectional study following a two-stage cluster-sampling design in Ile-de-France and Marseille, France, in late 2021. Participants aged over 18 years were recruited where they slept the previous night, and then stratified for analysis into three housing groups (\"Streets\", \"Accommodated\", and \"Housed\"). Interviews were conducted face-to-face in the participants preferred language. Multilevel univariate and multivariable logistic regression models were built.\n\nFindings3,690 individuals were surveyed: 855 in the \"Housed\" stratum, 2,321 in the \"Accommodated\" stratum and 514 in the \"Streets\" stratum. 76{middle dot}2% (95%CI 74{middle dot}3-78{middle dot}1) reported receiving at least one COVID-19 vaccine dose. Vaccine uptake varied by stratum, with uptake highest (85.6%; reference) in \"Housed\", followed by \"Accommodated\" (75{middle dot}4%; AOR=0{middle dot}79 ; 95%CI 0{middle dot}51-1{middle dot}09 vs Housed) and lowest in \"Streets\" (42{middle dot}0%; AOR=0{middle dot}38 ; 95%CI 0{middle dot}25-0{middle dot}57 vs Housed). Use for vaccine certificate, socioeconomic drivers and vaccine hesitancy explained vaccine coverage.\n\nInterpretationIn France, PEH/PH are less likely than the general population likely to receive COVID-19 vaccines; with the most excluded being the least likely. The influence of both structural drivers and vaccine beliefs in PEH/PH reinforces the importance of targeted outreach, on-site vaccination and sensitisation activities to further vaccine uptake.\n\nFundingSante Publique France, Agence Nationale de Recherches sur le Sida/Capnet, Agence Regionale de Sante - Ile de France, Medecins Sans Frontieres, and Societe de Pathologie Infectieuse de Langue Francaise.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Thomas ROEDERER", - "author_inst": "Epicentre, Paris, France" - }, - { - "author_name": "Bastien MOLLO", - "author_inst": "Medecins Sans Frontieres, Paris, France" - }, - { - "author_name": "Charline VINCENT", - "author_inst": "Epicentre, Paris, France" - }, - { - "author_name": "Ghislain LEDUC", - "author_inst": "Epicentre, Paris, France" - }, - { - "author_name": "Jessica SAYYAD", - "author_inst": "Epicentre, Paris, France" - }, - { - "author_name": "Marine MOSNIER", - "author_inst": "Prospective et Cooperation, Marseille, France" - }, - { - "author_name": "Stephanie VANDENTORREN", - "author_inst": "Sante Publique France, Saint Maurice, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.16.22277716", "rel_title": "The association of typical and atypical symptoms on in-hospital mortality of older adults with COVID-19: a multicentre cohort study", @@ -255742,6 +256332,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.18.22277749", + "rel_title": "COVID-19 vaccine effectiveness against progression to in-hospital mortality -- Zambia, 2021-2022", + "rel_date": "2022-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22277749", + "rel_abs": "BackgroundCOVID-19 vaccines are highly effective for reducing severe disease and mortality. However, vaccine effectiveness data is limited from sub-Saharan Africa, where SARS-CoV-2 epidemiology has differed from other regions. We report COVID-19 vaccine effectiveness against progression to in-hospital mortality in Zambia.\n\nMethodsWe conducted a retrospective cohort study among admitted patients at eight COVID-19 treatment centers across Zambia during April 2021 through March 2022. Patient demographic and clinical information including vaccination status and hospitalization outcome (discharged or died) werecollected. Multivariable logistic regression was used to assess the odds of in-hospital mortality by vaccination status, adjusted for age, sex, number of comorbid conditions, disease severity, and COVID-19 treatment center. Vaccine effectiveness of [≥]1 vaccine dose was calculated from the adjusted odds ratio.\n\nResultsAmong 1,653 patients with data on their vaccination status and hospitalization outcome, 365 (22.1%) died. Overall, 236 (14.3%) patients had received [≥]1 vaccine dose before hospital admission. For patients who had received [≥]1 vaccine dose, 22 (9.3%) died compared with 343 (24.2%) among unvaccinated patients (p <0.01). The median time since receipt of a first vaccine dose was 52.5 days (IQR: 28-107). Vaccine effectiveness for progression to in-hospital mortality among hospitalized patients was 64.8% (95% CI: 42.3-79.4%).\n\nConclusionsAmong patients admitted to COVID-19 treatment centers in Zambia, COVID-19 vaccination was associated with lower progression to in-hospital mortality. These data are consistent with evidence from other countries demonstrating benefit of COVID-19 vaccination against severe complications. Vaccination is a critical tool for reducing the consequences of COVID-19 in Zambia.\n\nKey points- Receipt of [≥]1 COVID-19 vaccine dose reduced progression to in-hospital mortality in Zambia by 64.8%\n- Mortality benefit of COVID-19 vaccines was sustained during the period of omicron transmission in Zambia", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Duncan Chanda", + "author_inst": "University Teaching Hospital, Lusaka, Zambia; Ministry of Health, Lusaka, Zambia" + }, + { + "author_name": "Jonas Z. Hines", + "author_inst": "U.S. Centers for Disease Control and Prevention, Lusaka, Zambia" + }, + { + "author_name": "Megumi Itoh", + "author_inst": "U.S. Centers for Disease Control and Prevention, Lusaka, Zambia" + }, + { + "author_name": "Sombo Fwoloshi", + "author_inst": "University Teaching Hospital, Lusaka, Zambia; Ministry of Health, Lusaka, Zambia" + }, + { + "author_name": "Peter A Minchella", + "author_inst": "U.S. Centers for Disease Control and Prevention, Lusaka, Zambia" + }, + { + "author_name": "Khozya D. Zyambo", + "author_inst": "University Teaching Hospital, Lusaka, Zambia; Ministry of Health, Lusaka, Zambia" + }, + { + "author_name": "Suilanji Sivile", + "author_inst": "University Teaching Hospital, Lusaka, Zambia; Ministry of Health, Lusaka, Zambia" + }, + { + "author_name": "Davies Kampamba", + "author_inst": "Ministry of Health, Lusaka, Zambia" + }, + { + "author_name": "Bob Chirwa", + "author_inst": "Ministry of Health, Lusaka, Zambia" + }, + { + "author_name": "Raphael Chanda", + "author_inst": "University Teaching Hospital, Lusaka, Zambia" + }, + { + "author_name": "Katongo Mutengo", + "author_inst": "Livingstone Teaching Hospital, Livingstone, Zambia" + }, + { + "author_name": "Mazinga F. Kayembe", + "author_inst": "Kitwe Teaching Hospital, Kitwe, Zambia" + }, + { + "author_name": "Webster Chewe", + "author_inst": "University Teaching Hospital, Lusaka, Zambia" + }, + { + "author_name": "Peter Chipimo", + "author_inst": "Zambia National Public Health Institute, Lusaka, Zambia" + }, + { + "author_name": "Aggrey Mweemba", + "author_inst": "Levy Mwanawasa University Teaching Hospital, Lusaka, Zambia" + }, + { + "author_name": "Simon Agolory", + "author_inst": "U.S. Centers for Disease Control and Prevention, Lusaka, Zambia" + }, + { + "author_name": "Lloyd B. Mulenga", + "author_inst": "University Teaching Hospital, Lusaka, Zambia; Ministry of Health, Lusaka, Zambia" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.18.22277763", "rel_title": "Exploring Impacts to COVID-19 Herd Immunity Thresholds Under Demographic Heterogeneity that Lowers Vaccine Effectiveness", @@ -257314,41 +257987,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.12.22277450", - "rel_title": "Effect of Vitamin D3 supplementation vs. dietary-hygienic measures on SARS-COV-2 infection rates in hospital workers with 25-hydroxyvitamin D3 levels >20 ng/mL", - "rel_date": "2022-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.12.22277450", - "rel_abs": "BackgroundThere is scant information on the effect of supplementation with vitamin D3 in SARS-COV-2 infection cases when patient 25-hydroxyvitamin D3 [25(OH)D3] levels are between 20-100ng/mL. Our aim was to evaluate the effect of supplementation with vitamin D3 vs. dietary-hygienic measures on the SARS-COV-2 infection rate in participants with serum 25(OH)D3 levels [≥]20ng/mL.\n\nMethodsWe invited hospital workers with 25(OH)D3 levels between 20-100 ng/mL and no previous SARS-COV-2 infection; they were randomized as follows: treatment options were a) vitamin D3 supplementation (52,000 IU monthly, G1) or b) dietary-hygienic measures (G2). We conducted a 3- to 6-month follow-up of SARS-COV-2 infections. Participants with 25(OH)D3 levels <20 ng/mL were also analyzed. We divided these latter participants depending on whether they were supplemented (G3) or not (G4).\n\nResultsWe analyzed 198 participants, with an average age of 44.4 (SD 9) years, and 130 (65.7%) were women. G1 had less cases of SARS-COV-2 infection than G2 after a follow-up of 3- to 6-months (p<0.05). There were no differences between G3 and G4 at the 3- and 6-month follow-up cutoff points (p>0.05). Using mixed effect Cox regression analysis in 164 participants that completed six months of follow-up, vitamin D3 supplementation appeared to act as a protective factor against SARS-COV-2 infection (HR 0.21, p=0.008) in G1 and G2. None of the participants treated with the supplementation doses had serum 25(OH)D3 levels > 100ng/mL.\n\nConclusionVitamin D3 supplementation in participants with 25(OH)D3 levels between 20-100 ng/mL have a lower rate of SARS-COV-2 infection in comparison with the use of dietary-hygienic measures at six months follow-up.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Maria Elena Romero-Ibarguengoitia", - "author_inst": "Hospital Clinica Nova" - }, - { - "author_name": "Dalia Gutierrez-Gonzalez", - "author_inst": "Hospital Clinica Nova" - }, - { - "author_name": "Carlos Cantu-Lopez", - "author_inst": "Hospital Clinica Nova" - }, - { - "author_name": "Miguel Angel Sanz-Sanchez", - "author_inst": "Hospital Clinica Nova" - }, - { - "author_name": "Arnulfo Gonzalez-Cantu", - "author_inst": "Hospital Clinica Nova" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.12.22277518", "rel_title": "Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border", @@ -257820,6 +258458,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.07.12.22277533", + "rel_title": "Fully Quantitative Measurements of the Antibody Levels for SARS-CoV-2 Infections and Vaccinations calibrated against the NISTmAb Standard IgG Antibody", + "rel_date": "2022-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.12.22277533", + "rel_abs": "Humanised recombinant antibodies specific to the SARS-CoV-2 Spike protein were calibrated against the NISTmAb standard human antibody to produce a fully quantitative antibody assay. The assay allows comparative studies between patient cohorts to be performed from which common properties may be derived. Two cohorts comparing patient vaccine response to AstraZeneca ChAdOx1-S (AZ, 35 patients) and Pfizer/BioNTech BNT162b2 (Pfizer, 25 patients) shows close association of the 31st percentile of the AZ distribution (2.90 {+/-} 1.10 mg/L) and the 7th percentile of the Pfizer distribution (1.11 {+/-} 1.10 mg/L) corresponding to the efficacy of the vaccines at preventing infection. The AZ IgG response distribution varies from 0.6 mg/L-25.4 mg/L with an average (mode) of 3.3 {+/-} 1.0 mg/L; the Pfizer response distribution varies from 0.6 mg/L to 33.1 mg/L with a mode of 3.7 {+/-} 1.0 mg/L. A third patient cohort looked at the recovery of 195 SARS-CoV-2 RT-PCR-positive patient samples and 200 pre-pandemic patient samples. A fourth patient cohort reviewed the NIBSC Anti-SARS-CoV-2 Verification Panel. The diagnostic cut-off for RT-PCR-positive patient samples was 1.34 {+/-} 1.10 mg/L and the NIBSC panel separated seropositive and seronegative samples at 1.90 {+/-} 1.10 mg/L. The mean value of the two prevention and two recovery thresholds is 1.8 mg/L with 95% confidence limits of 0.2-3.4 mg/L. In recovery and, critically, infection prevention, an antibody concentration threshold estimate of 3.4 mg/L appears mechanistically important. An antibody immunity threshold predicting a mucosal concentration preventing SARS-CoV-2 colonisation of the nasopharyngeal cavity is discussed.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Philip H James-Pemberton", + "author_inst": "University of Exeter" + }, + { + "author_name": "Mark W Helliwell", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Rouslan V Olkhov", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Shivali Kohli", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Aaron C Westlake", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Benjamin M Farrar", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Andrew Shaw", + "author_inst": "University of Exeter" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.13.22277513", "rel_title": "Extreme differences in SARS-CoV-2 Omicron viral loads among specimen types drives poor performance of nasal rapid antigen tests for detecting presumably pre-infectious and infectious individuals, predicting improved performance of combination specimen antigen tests", @@ -259248,89 +259929,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.07.14.500039", - "rel_title": "SARS-CoV-2 BA.4 infection triggers more cross-reactive neutralizing antibodies than BA.1", - "rel_date": "2022-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.14.500039", - "rel_abs": "SARS-CoV-2 variants of concern (VOCs) differentially trigger neutralizing antibodies with variable cross-neutralizing capacity. Here we show that unlike SARS-CoV-2 Omicron BA.1, which triggered neutralizing antibodies with limited cross-reactivity, BA.4/5 infection triggers highly cross-reactive neutralizing antibodies. Cross-reactivity was observed both in the absence of prior vaccination and also in breakthrough infections following vaccination. This suggests that next-generation vaccines incorporating BA.4, which is spreading globally, might result in enhanced neutralization breadth.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Simone Richardson", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Thopisang Motlou", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Mieke van der Mescht", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Bronwen Lambson", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Josie Everatt", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Daniel Amoako", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Anne Van Gottberg", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Nicole Wolter", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Zelda de Beer", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Talita Roma de Villiers", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Annie Bodenstein", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Gretha van den Berg", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Theresa M. Rossouw", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Michael Boswell", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Veronica Ueckermann", - "author_inst": "University of Pretoria" - }, - { - "author_name": "Jinal Bhiman", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Penny Moore", - "author_inst": "University of the Witwatersrand" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.07.14.500068", "rel_title": "Ending transmission of SARS-CoV-2: sterilizing immunity using an intranasal subunit vaccine", @@ -259682,6 +260280,33 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2022.07.15.500170", + "rel_title": "Pangenome analysis of SARS-CoV2 strains to Identify Potential vaccine targets by Reverse Vaccinology", + "rel_date": "2022-07-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.15.500170", + "rel_abs": "BackgroundCoronavirus disease 2019 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) leads to respiratory failure and obstructive alveolar damage, which may be fatal in immunocompromised individuals. COVID-19 pandemic has severe global implications badly, and the situation in the world is depreciating with the emergence of novel variants. The aim of our study is to explore the genome of SARS-CoV2 followed by in silico reverse vaccinology analysis. This will help to identify the most putative vaccine candidate against the virus in a robust manner and enables cost-effective development of vaccines compared with traditional strategies.\n\nMethodsThe genomic sequencing data is retrieved from NCBI (Reference Sequence Number NC_045512.2). The sequences are explored through comparative genomics approaches by GENOMICS to find out the core genome. The comprehensive set of proteins obtained was employed in computational vaccinology approaches for the prediction of the best possible B and T cell epitopes through ABCpred and IEDB Analysis Resource, respectively. The multi-epitopes were further tested against human toll-like receptor and cloned in E. coli plasmid vector.\n\nFindingsThe designed Multiepitope Subunit Vaccine was non-allergenic, antigenic (0.6543), & non-toxic, with significant connections with the human leukocyte antigen (HLA) binding alleles, and collective global population coverage of 84.38%. It has 276 amino acids, consisting of an adjuvant with the aid of EAAAK linker, AAY linkers used to join the 4 CTL epitopes, GPGPG linkers used to join the 3 HTL epitopes and KK linkers used to join the 7 B-cell epitopes. MESV docking with human pathogenic toll-like receptors-3 (TLR3) exhibited a stable & high binding affinity. An in-silico codon optimization approach was used in the codon system of E. coli (strain K12) to obtain the GC-Content of Escherichia coli (strain K12): 50.7340272413779 and CAI-Value of the improved sequence: 0.9542834278823386. The multi-epitope vaccines optimized gene sequence was cloned in-silico in E. coli plasmid vector pET-30a (+), BamHI and HindIII restriction sites were added to the N and C-terminals of the sequence, respectively.\n\nConclusionThere is a pressing need to combat COVID-19 and we need quick and reliable approaches against Covid-19. By using In-silico approaches, we acquire an effective vaccine that could trigger adequate immune responses at the cellular and humoral level. The suggested sequences can be further validated through in vivo and in vitro experimentation.\n\nStatement of SignificanceCurrent developments in the immunological bioinformatics areas has resulted in different servers and tools that are cost and time efficient for the traditional vaccine development. Though for designing a multiple epitope vaccine the antigenic epitopes prediction of a relevant protein by immunoinformatic methods are very helpful.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Muhammad Haseeb Tariq", + "author_inst": "National Institute of Health, Islamabad, Pakistan" + }, + { + "author_name": "Afreenish Amir", + "author_inst": "National Institute of Health, Islamabad, Pakistan" + }, + { + "author_name": "Hamza Irshad", + "author_inst": "National Institute of Health, Islamabad, Pakistan" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.07.15.500185", "rel_title": "Lasting alterations in monocyte and dendritic cell subsets in individuals after hospitalization for COVID-19", @@ -260954,161 +261579,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.11.22277368", - "rel_title": "Structural epitope profiling identifies antibodies associated with critical COVID-19 and long COVID", - "rel_date": "2022-07-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.11.22277368", - "rel_abs": "Antibodies can have beneficial, neutral, or harmful effects so resolving an antibody repertoire to its target epitopes may explain heterogeneity in susceptibility to infectious disease. However, the three-dimensional nature of antibody-epitope interactions limits discovery of important targets. We describe and experimentally validated a novel computational method and synthetic biology pipeline for identifying epitopes that are structurally stable and functionally important and apply it to the SARS-CoV-2 proteome. We show patterns of epitope-binding antibodies associated with immunopathology, including a non-isotype switching IgM response to a Membrane protein epitope which is amongst the strongest immunological features associated with severe COVID-19 to date (adjusted OR 72.14, 95% CI: 9.71 - 1300.15). Consistent with a hypothesis that the mechanism driving the non-switching response was T independent B cell activation, we find that B cells secrete IgM and proliferate on exposure to virus-like particles lacking Spike. We also identified persistence (> 1 year) of this response in individuals with longCOVID particularly affected by fatigue and depression. These findings point to a previously unrecognized coronavirus host-pathogen interaction. We demonstrate that the Membrane epitope is a promising vaccine and monoclonal antibody target, which may complement spike-directed vaccination broadening immunological protection.\n\nOne-Sentence SummaryUsing a protein-structure-based B cell epitope discovery method with a wide range of possible applications, we have identified a novel host-pathogen signature associated with SARS-CoV-2 immunopathology and suggest the viral Membrane protein contains a pathological T independent antigen.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Patrick K.A. Kearns", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Charles Dixon", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Mihaly Badonyi", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Kim Lee", - "author_inst": "Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh; The King's Buildings, Ashworth Laboratories, Charlotte A" - }, - { - "author_name": "Rafal Czapiewski", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Olivia Fleming", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Lukas Gerasimivicous", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Rinal Sahputra", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "Bethany Potts", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "Sam Benton", - "author_inst": "Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh; The King's Buildings, Ashworth Laboratories, Charlotte A" - }, - { - "author_name": "Jacky Guy", - "author_inst": "Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh; CH Waddington Building, Kings Buildings, Mayfield Road, Edinbu" - }, - { - "author_name": "Scott Neilson", - "author_inst": "Edinburgh Genome Foundry, University of Edinburgh; Michael Swann Building, Max Born Crescent, Edinburgh, United Kingdom EH9 3BF" - }, - { - "author_name": "Helen Wise", - "author_inst": "Department of Clinical Biochemistry, Royal Infirmary of Edinburgh; 51 Little France Cres, Old Dalkeith Rd, Edinburgh, United Kingdom EH16 4SA" - }, - { - "author_name": "Sara Jenks", - "author_inst": "Department of Clinical Biochemistry, Royal Infirmary of Edinburgh; 51 Little France Cres, Old Dalkeith Rd, Edinburgh, United Kingdom EH16 4SA" - }, - { - "author_name": "Kate Templeton", - "author_inst": "Department of Clinical Biochemistry, Royal Infirmary of Edinburgh; 51 Little France Cres, Old Dalkeith Rd, Edinburgh, United Kingdom EH16 4SA" - }, - { - "author_name": "Christina Dold", - "author_inst": "Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford; Churchill Hospital Old Road, Headington, Oxford, United Kingd" - }, - { - "author_name": "Teresa Lambe", - "author_inst": "Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford; Churchill Hospital Old Road, Headington, Oxford, United Kingd" - }, - { - "author_name": "Alexander J. Mentzer", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom OX3 7BN" - }, - { - "author_name": "Julian Knight", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom OX3 7BN" - }, - { - "author_name": "- COMBAT", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, United Kingdom OX3 7BN" - }, - { - "author_name": "Andrew Pollard", - "author_inst": "Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford; Churchill Hospital Old Road, Headington, Oxford, United Kingd" - }, - { - "author_name": "Eleanor Barnes", - "author_inst": "Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, UK" - }, - { - "author_name": "Paul Klenerman", - "author_inst": "Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, UK" - }, - { - "author_name": "Susanna Dunachie", - "author_inst": "Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, UK" - }, - { - "author_name": "Tracy Hussell", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "- CIRCO", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "Laura McWhirter", - "author_inst": "Centre for Clinical Brain Sciences, University of Edinburgh; 49 Little France Crescent, Edinburgh, United Kingdom EH16 4SB" - }, - { - "author_name": "Alan Carson", - "author_inst": "Centre for Clinical Brain Sciences, University of Edinburgh; 49 Little France Crescent, Edinburgh, United Kingdom EH16 4SB" - }, - { - "author_name": "Rennos Fragkoudis", - "author_inst": "Edinburgh Genome Foundry, University of Edinburgh; Michael Swann Building, Max Born Crescent, Edinburgh, United Kingdom EH9 3BF" - }, - { - "author_name": "Susan Rosser", - "author_inst": "Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh; CH Waddington Building, Kings Buildings, Mayfield Road, Edinbu" - }, - { - "author_name": "David Cavanagh", - "author_inst": "Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh; The King's Buildings, Ashworth Laboratories, Charlotte A" - }, - { - "author_name": "Madhvi Menon", - "author_inst": "Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, University of Manchester; Oxford Rd, Manchester, United Kingdom M13 9PL" - }, - { - "author_name": "Joseph A. Marsh", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - }, - { - "author_name": "Dirk A. Kleinjan", - "author_inst": "Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh; CH Waddington Building, Kings Buildings, Mayfield Road, Edinbu" - }, - { - "author_name": "Nick Gilbert", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Western General Hospital. Crewe Road, Edinburgh EH4 2XU" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.12.22277538", "rel_title": "Dengue seroprevalence study during COVID-19 pandemic in Bali", @@ -261444,6 +261914,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.07.12.22277529", + "rel_title": "Comparative analysis of retracted pre-print and peer-reviewed articles on COVID-19", + "rel_date": "2022-07-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.12.22277529", + "rel_abs": "IntroductionDue to the accelerated pace and quantum of scientific publication during the COVID-19 pandemic, a large number of articles on COVID-19 have been retracted. Pre-prints though not peer-reviewed offer the advantage of rapid dissemination of new findings. In this study, we aim to systematically compare the article characteristics, time to retraction, social media attention, citations, and reasons for retraction between retracted pre-print and peer-reviewed articles on COVID-19.\n\nMethodsWe utilized the Retraction Watch database to identify retracted articles on COVID-19 published from 1st January 2020 to 10th March 2022. The articles were reviewed and metadata such as article characteristics (type, category), time to retraction, reasons for retraction, and Altmetric Attention Score (AAS) and citation count were collected.\n\nResultsWe identified 40 retracted pre-prints and 143 retracted peer-reviewed articles. The median (IQR) retraction time for pre-print and peer-reviewed articles was 29 (10-81.5) days and 139 (63-202) days (p = 0.0001). Pre-prints and peer-reviewed article had median (IQR) AAS of 26.5 (4-1155) and 8 (1-38.5), respectively (p = 0.0082). The median (IQR) citation count for pre-prints and peer-reviewed articles was 3 (0-14) and 3 (0-17), respectively (p = 0.5633). The AAS and citation counts were correlated for both pre-prints (r = 0.5200, p = 0.0006) and peer-reviewed articles(r = 0.5909, p = 0.0001). The commonest reason for retraction for pre-prints and peer-reviewed articles concerns about data and results.\n\nConclusionThe increased adoption of pre-prints results in faster identification of erroneous articles compared to the traditional peer-review process.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Manraj Singh Sra", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Mehak Arora", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Archisman Mazumder", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Ritik Mahaveer Goyal", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Giridara Gopal Parameswaran", + "author_inst": "Center for Disease Dynamics, Economics & Policy, New Delhi" + }, + { + "author_name": "Jitendra Kumar Meena", + "author_inst": "National Cancer Institute (NCI) Jhajjar, All India Institute of Medical Sciences, New Delhi" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.07.08.499374", "rel_title": "Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina", @@ -263316,89 +263825,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.08.22277388", - "rel_title": "Manifestations Associated with Post Acute Sequelae of SARS-CoV2 Infection (PASC) Predict Diagnosis of New-Onset Psychiatric Disease: Findings from the NIH N3C and RECOVER Studies", - "rel_date": "2022-07-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.08.22277388", - "rel_abs": "Acute COVID-19 infection can be followed by diverse clinical manifestations referred to as Post Acute Sequelae of SARS-CoV2 Infection (PASC). Studies have shown an increased risk of being diagnosed with new-onset psychiatric disease following a diagnosis of acute COVID-19. However, it was unclear whether non-psychiatric PASC-associated manifestations (PASC-AMs) are associated with an increased risk of new-onset psychiatric disease following COVID-19.\n\nA retrospective EHR cohort study of 1,603,767 individuals with acute COVID-19 was performed to evaluate whether non-psychiatric PASC-AMs are associated with new-onset psychiatric disease. Data were obtained from the National COVID Cohort Collaborative (N3C), which has EHR data from 65 clinical organizations. EHR codes were mapped to 151 non-psychiatric PASC-AMs recorded 28-120 days following SARS-CoV-2 diagnosis and before diagnosis of new-onset psychiatric disease. Association of newly diagnosed psychiatric disease with age, sex, race, pre-existing comorbidities, and PASC-AMs in seven categories was assessed by logistic regression.\n\nThere was a significant association between six categories and newly diagnosed anxiety, mood, and psychotic disorders, with odds ratios highest for cardiovascular (1.35, 1.27-1.42) PASC-AMs. Secondary analysis revealed that the proportions of 95 individual clinical features significantly differed between patients diagnosed with different psychiatric disorders.\n\nOur study provides evidence for association between non-psychiatric PASC-AMs and the incidence of newly diagnosed psychiatric disease. Significant associations were found for features related to multiple organ systems. This information could prove useful in understanding risk stratification for new-onset psychiatric disease following COVID-19. Prospective studies are needed to corroborate these findings.\n\nFundingNCATS U24 TR002306", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ben Coleman", - "author_inst": "The Jackson Laboratory, Genomic Medicine, Farmington 6032, CT, USA" - }, - { - "author_name": "Elena Casiraghi", - "author_inst": "AnacletoLab, Dipartimento di Informatica, Universita degli Studi di Milano, Italy" - }, - { - "author_name": "Tiffany J Callahan", - "author_inst": "University of Colorado Anschutz Medical Campus, Center for Health AI, Aurora 80045, CO, USA" - }, - { - "author_name": "Hannah Blau", - "author_inst": "The Jackson Laboratory, Genomic Medicine, Farmington 6032, CT, USA" - }, - { - "author_name": "Lauren Chan", - "author_inst": "College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA" - }, - { - "author_name": "Bryan Laraway", - "author_inst": "University of Colorado Anschutz Medical Campus, Center for Health AI, Aurora 80045, CO, USA" - }, - { - "author_name": "Kevin B Clark", - "author_inst": "Cures Within Reach, Chicago, IL, USA" - }, - { - "author_name": "Yochai Re'em", - "author_inst": "Weill Cornell Medicine, Department of Psychiatry, New York, NY, USA" - }, - { - "author_name": "Ken R Gersing", - "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland." - }, - { - "author_name": "Ken Wilkins", - "author_inst": "Biostatistics Program, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland" - }, - { - "author_name": "Nomi Harris", - "author_inst": "Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA" - }, - { - "author_name": "Giorgio Valentini", - "author_inst": "AnacletoLab, Dipartimento di Informatica, Universita degli Studi di Milano, Italy" - }, - { - "author_name": "Melissa A Haendel", - "author_inst": "University of Colorado Anschutz Medical Campus, Center for Health AI, Aurora 80045, CO, USA" - }, - { - "author_name": "Justin Reese", - "author_inst": "Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA" - }, - { - "author_name": "Peter N Robinson", - "author_inst": "The Jackson Laboratory, Genomic Medicine, Farmington 6032, CT, USA" - }, - { - "author_name": "- N3C Consortium", - "author_inst": "" - }, - { - "author_name": "- RECOVER Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.08.22276768", "rel_title": "Healthcare utilization following SARS-CoV-2 infection in children and adolescents with chronic conditions: An EHR-based Cohort Study from the RECOVER Program", @@ -263738,6 +264164,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.06.22277014", + "rel_title": "Genomic Surveillance Identifies SARS-CoV-2 Transmission Patterns in Local University Populations, Wisconsin, USA, 2020-2022", + "rel_date": "2022-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.06.22277014", + "rel_abs": "Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the current coronavirus disease 2019 (COVID-19) pandemic extends into its third year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in a higher education setting that will inform pubic health policy during pandemics. In this study, we performed whole-genome sequencing of 537 of 1,717 SARS-CoV-2 positive nasopharyngeal/nasal swab samples collected for nearly 20 months from the two university populations in Wisconsin, United States. We observed that the viral sequences were distributed into 57 lineages/sub-lineages belonging to 15 clades of which the majority were from 21K (Omicron, 36.13%) and 21J (Delta, 30.91%). Nearly 40% (213) of the sequences were Omicron of which BA.1 and its eight descendent lineages account for 91%, while the remaining belong to BA.2 and its six descendent lineages. The independent analysis of these two universities sequences revealed significant differences in circulating the SARS-CoV-2 variants. The genome-based analysis of closely-related strains along with phylogenetic clusters had identified that potential virus transmission occurred within as well as between universities, and between the university and local community. Although this study improves our understanding of distinct transmission patterns of circulating variants in local universities, expanding the genomic surveillance capacity will aid local jurisdictions in identifying emerging SARS-CoV-2 variants like BA.4 and BA.5, and improve data-driven public health mitigation and policy efforts.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Arunachalam Ramaiah", + "author_inst": "City of Milwaukee Health Department" + }, + { + "author_name": "Manjeet Khubbar", + "author_inst": "City of Milwaukee Health Department" + }, + { + "author_name": "Amy Bauer", + "author_inst": "City of Milwaukee Health Department" + }, + { + "author_name": "Katherine Akinyemi", + "author_inst": "City of Milwaukee Health Department" + }, + { + "author_name": "Josh Weiner", + "author_inst": "City of Milwaukee Health Department" + }, + { + "author_name": "Sanjib Bhattacharyya", + "author_inst": "City of Milwaukee Health Department" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.07.499204", "rel_title": "Correlation of Alpha-1 Antitrypsin Levels and Exosome Associated Neutrophil Elastase Endothelial Injury in Subjects with SARS-CoV2 Infection", @@ -265374,53 +265839,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.07.04.22277239", - "rel_title": "Drivers of Mortality in COVID ARDS Depend on Patient Sub-Type", - "rel_date": "2022-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.04.22277239", - "rel_abs": "BackgroundThe most common cause of death in people with COVID-19 is acute respiratory distress syndrome (ARDS). ARDS is a heterogeneous syndrome, however, subgroups that have been identified among non-COVID-19 ARDS patients do not clearly apply to COVID-19 ARDS patients. Additionally, studies of COVID-19 ARDS have been limited by sample size.\n\nMethodsWe applied an iterative clustering and machine learning framework to electronic health record data from thousands of hospitalized COVID-19 ARDS patients with the goal of defining and characterizing clinically-relevant COVID-19 ARDS subgroups (phenoclusters). We then applied a supervised model to identify risk factors for hospital mortality for each phenocluster and compared these between phenoclusters and the entire cohort.\n\nFindingsRisk factors that predict mortality in the overall cohort of COVID-19 ARDS patients do not necessarily predict mortality in phenoclusters. In fact, some risk factors increase the risk of hospital mortality in some phenoclusters, but decrease mortality in others.\n\nInterpretationThese phenocluster-specific risk factors would not have been observed with a single predictive model. Heterogeneity in phenoclusters of COVID-19 ARDS as well as drivers of mortality may partially explain challenges in finding effective treatments when applied to all patients with ARDS.\n\nFundingThis work was supported by philanthropic funds to the Feinstein Institutes for Medical Research. The funding source did not control any aspect of the study and did not review the results. All authors had full access to the full data in the study and accept responsibility to submit for publication.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Helen Cheyne", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Amir Gandomi", - "author_inst": "Feinstein Institutes for Medical Research" - }, - { - "author_name": "Shahrzad Hosseini Vajargah", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Victoria M Catterson", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Travis Mackoy", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Lauren Mccullagh", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Gabriel Musso", - "author_inst": "BioSymetrics, Inc" - }, - { - "author_name": "Negin Hajizadeh", - "author_inst": "Feinstein Institutes for Medical Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.07.04.22277193", "rel_title": "Reductions in stillbirths and preterm birth in COVID-19 vaccinated women: a multi-center cohort study of vaccination uptake and perinatal outcomes", @@ -265792,6 +266210,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.05.498881", + "rel_title": "Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors", + "rel_date": "2022-07-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.05.498881", + "rel_abs": "Antiviral therapeutics to treat SARS-CoV-2 are much desired for the on-going pandemic. A well-precedented viral enzyme is the main protease (MPro), which is now targeted by an approved drug and by several investigational drugs. With the inevitable liabilities of these new drugs, and facing viral resistance, there remains a call for new chemical scaffolds against MPro. We virtually docked 1.2 billion non-covalent and a new library of 6.5 million electrophilic molecules against the enzyme structure. From these, 29 non-covalent and 11 covalent inhibitors were identified in 37 series, the most potent having an IC50 of 29 M and 20 M, respectively. Several series were optimized, resulting in inhibitors active in the low micromolar range. Subsequent crystallography confirmed the docking predicted binding modes and may template further optimization. Together, these compounds reveal new chemotypes to aid in further discovery of MPro inhibitors for SARS-CoV-2 and other future coronaviruses.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Elissa A Fink", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Conner Bardine", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Stefan Gahbauer", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Isha Singh", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Kris White", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Shuo Gu", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Xiaobo Wan", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Beatrice Ary", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Isabelle Glenn", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Pavla Fajtova", + "author_inst": "Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, San Diego, CA, USA" + }, + { + "author_name": "Jiankun Lyu", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Seth Vigneron", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Nicholas J Young", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Ivan S Kondratov", + "author_inst": "Enamine Ltd. Kyiv, Ukraine" + }, + { + "author_name": "Yurii Moroz", + "author_inst": "Chemspace LLC, Kyiv, Ukraine" + }, + { + "author_name": "Jack Taunton", + "author_inst": "Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Adam R Renslo", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "John J Irwin", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Brian K Shoichet", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Charles S Craik", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.07.05.498883", "rel_title": "Post-vaccination Omicron infections induce broader immunity across antigenic space than prototype mRNA COVID-19 booster vaccination or primary infection", @@ -268644,57 +269161,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.28.22276786", - "rel_title": "Hybrid immunity expands the functional humoral footprint of both mRNA and vector-based SARS-CoV-2 vaccines", - "rel_date": "2022-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.28.22276786", - "rel_abs": "The COVID-19 pandemic catalyzed a revolution in vaccine development, leading to the testing and approval of several global vaccine platforms that have shown tremendous promise in curbing the pandemic. Yet, despite these successes, waning immunity, and the emergence of variants of concern linked to rising breakthrough infections among vaccinees, have begun to highlight opportunities to improve vaccine platforms and deployment. Real-world vaccine efficacy has highlighted the reduced risk of breakthrough infection and disease among individuals infected and vaccinated, otherwise referred to as hybrid immunity. Hybrid immunity points to the potential for more vigorous or distinct immunity primed by the infection and may confer enhanced protection from COVID-19. Beyond augmented hybrid induced neutralizing antibody and T cell immune responses, here we sought to define whether hybrid immunity may shape the functional humoral immune response to SARS-CoV-2 following Pfizer/BNT162b2 and Moderna mRNA1273 mRNA-based, and ChadOx1/AZ1222 and Ad26.COV2.S vector-based SARS-CoV-2 vaccination. Each vaccine exhibited a unique functional humoral immune profile in the setting of naive or hybrid immunity. However, hybrid immunity showed a unique augmentation in S2-domain specific functional humoral immunity that was poorly induced in the setting of naive immune response. These data highlight the immunodominant effect of the S1-domain in the setting of natural immunity, which is highly variable during viral evolution, and the importance of natural infection in breaking this immunodominance in driving immunity to the S2 region of the SARS-CoV-2 S2 domain that is more conserved across variants of concern.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Paulina Kaplonek", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Yixiang Deng", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Jessica Shih-Lu Lee", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Heather Zar", - "author_inst": "Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Dace Zavadska", - "author_inst": "Childrens Clinical University Hospital, Riga, Latvia" - }, - { - "author_name": "Marina Johnson", - "author_inst": "Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London, UK" - }, - { - "author_name": "Douglas A Lauffenburger", - "author_inst": "MIT" - }, - { - "author_name": "David Goldblatt", - "author_inst": "University College London Institute of Child Health" - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.02.495455", "rel_title": "SARS-CoV-2 3CLpro mutations confer resistance to Paxlovid (nirmatrelvir/ritonavir) in a VSV-based, non-gain-of-function system", @@ -268946,6 +269412,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, + { + "rel_doi": "10.1101/2022.06.30.22277052", + "rel_title": "Impact of SARS-Cov-2 on Clinical Trial Unit workforce in the United Kingdom; An observational study", + "rel_date": "2022-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.30.22277052", + "rel_abs": "ObjectiveThe clinical trial unit (CTU) workforce in the UK have been delivering COVID-19 research since the inception of the pandemic. Challenges associated with COVID-19 research have impacted the global healthcare communities differently. Thus, the overall objective of the study was to determine the mental health impact among CTU staff working during the COVID-19 pandemic.\n\nDesignA mixed-methods based observational study was designed using a new workforce impact questionnaire using validated mental health assessments of Vancouver Index of Acculturation (VIA), Hospital Anxiety and Depression Scale (HADS), Insomnia Severity Index (ISI), Pandemic Stress Index (PSI), Burnout Assessment Too-12 (BAT-12), General Self Efficacy Scale (GSE) and The Everyday Discrimination Scale (EDS).\n\nSettingThe Qualtrics platform was used to deploy the questionnaire where a quantitative analysis was conducted. The qualitative part of the study used the Microsoft Teams digital application to complete the interviews.\n\nParticipantsAll participants were CTU staff within the United Kingdom.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Gayathri Delanerolle", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jingtong Hu", + "author_inst": "Southern University of Science and Technology" + }, + { + "author_name": "Heitor Cavalini", + "author_inst": "Southern Health NHS Foundation Trust" + }, + { + "author_name": "Lucy Yardley", + "author_inst": "University of Southampton" + }, + { + "author_name": "Katharine Barnard-Kelly", + "author_inst": "4Southern Health NHS Foundation Trust" + }, + { + "author_name": "Katheryn Elliot", + "author_inst": "Southern Health NHS Foundation Trust" + }, + { + "author_name": "Vanessa Raymont", + "author_inst": "University of Oxford" + }, + { + "author_name": "Shanaya Rathod", + "author_inst": "Southern Health NHS Foundation Trust" + }, + { + "author_name": "Jian Qing Shi", + "author_inst": "Southern University of Science and Technology" + }, + { + "author_name": "Peter Phiri", + "author_inst": "Southern Health NHS Foundation" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2022.07.01.22277058", "rel_title": "Hydroxychloroquine pre-exposure prophylaxis to prevent SARS-CoV-2 among health care workers at risk for SARS-CoV-2 exposure: A nonrandomized controlled trial", @@ -270262,81 +270783,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.29.498158", - "rel_title": "Vitamin D and the ability to produce 1,25(OH)2D are critical for protection from viral infection of the lungs.", - "rel_date": "2022-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.29.498158", - "rel_abs": "Vitamin D supplementation has been linked to improved outcomes from respiratory virus infection, and the COVID19 pandemic has renewed interest in understanding the potential role of vitamin D in protecting the lung from viral infections. Therefore, we evaluated the role of Vitamin D using animal models of pandemic H1N1 influenza and SARS-CoV-2 infection. In mice, dietary induced vitamin D deficiency resulted in lung inflammation that was present prior to infection. Vitamin D sufficient (D+) and deficient (D-) wildtype (WT) and D+ and D-Cyp27B1 (Cyp) knockout (KO, cannot produce 1,25(OH)2D) mice were infected with pandemic H1N1. D- WT, D+ Cyp KO, and D- Cyp KO mice all exhibited significantly reduced survival compared to D+ WT mice. Importantly, survival was not the result of reduced viral replication as influenza M gene expression in the lungs was similar for all animals. Based on these findings, additional experiments were performed using the mouse and hamster models of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. In these studies, high dose vitamin D supplementation reduced lung inflammation in mice but not hamsters. A trend to faster weight recovery was observed in 1,25(OH)2D treated mice that survived SARS-CoV-2 infection. There was no effect of vitamin D on SARS-CoV-2 N gene expression in the lung of either mice or hamsters. Therefore, vitamin D deficiency enhanced disease severity, while vitamin D sufficient/supplementation reduced inflammation following infections with H1N1 influenza and SARS-CoV-2.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Juhi Arora", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Devanshi R Patel", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "McKayla J Nicol", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Cassandra J Field", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Katherine H Restori", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Jinpeng Wang", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Nicole E Froelich", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Bhuvana Katkere", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Josey A Terwilliger", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Veronika Weaver", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Erin Luley", - "author_inst": "Animal Diagnostic Laboratory, Pennsylvania State University" - }, - { - "author_name": "Kathleen Kelly", - "author_inst": "Animal Diagnostic Laboratory, Pennsylvania State University" - }, - { - "author_name": "Girish S Kirimanjeswara", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Troy C Sutton", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Margherita Teresa-Anna Cantorna", - "author_inst": "Pennsylvania State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.06.29.498191", "rel_title": "Inhibitory effects of GT0918 on acute lung injury and the molecular mechanisms of anti-inflammatory response", @@ -270588,6 +271034,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.30.22277089", + "rel_title": "Influenza and pneumococcal vaccination and the risk of COVID-19: A systematic review and meta-analysis", + "rel_date": "2022-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.30.22277089", + "rel_abs": "A number of studies have investigated the potential non-specific effects of some routinely administered vaccines (e.g. influenza, pneumococcal) on COVID-19 related outcomes, with contrasting results. In order to elucidate this discrepancy, we conducted a systematic review and meta-analysis to assess the association between seasonal influenza vaccination and pneumococcal vaccination with SARS-CoV-2 infection and its clinical outcomes. PubMed and medRxiv databases were searched, up until November 2021. Random effects model was used in the meta-analysis to pool odds ratio (OR) and adjusted estimates with their 95% confidence intervals (CIs). Heterogeneity was quantitatively assessed using the Cohrans Q and the I2 index. Sub-group analysis, sensitivity analysis and assessment of publication bias were performed for all outcomes. In total 38 observational studies were included in the meta-analysis and there was substantial heterogeneity. Influenza and pneumococcal vaccination were associated with lower risk of SARS-Cov-2 infection (OR: 0.80, 95% CI: 0.75-0.86 and OR: 0.70, 95% CI: 0.57-0.88, respectively). Regarding influenza vaccination, it seems that the majority of studies did not properly adjust for all potential confounders, so when the analysis was limited to studies that adjusted for age, sex, comorbidities and socioeconomic indices, the association diminished. This is not the case regarding the pneumococcal vaccination, for which even after adjustment for such factors the association persisted. Regarding harder endpoints such as ICU admission and death, current data do not support the association. Possible explanations are discussed, including trained immunity, inadequate matching for socioeconomic indices and possible coinfection.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Georgia V Kapoula", + "author_inst": "General Hospital of Lamia" + }, + { + "author_name": "Konstantina E Vennou", + "author_inst": "University of Thessaly" + }, + { + "author_name": "Pantelis G Bagos", + "author_inst": "University of Thessaly" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.30.498305", "rel_title": "Inactivated SARS-CoV-2 Reprograms the Tumor Immune Microenvironment and Improves Murine Cancer Outcomes", @@ -272068,49 +272541,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "urology" }, - { - "rel_doi": "10.1101/2022.06.27.22276790", - "rel_title": "BNT162b2 effectiveness against Delta & Omicron variants in teens by dosing interval and duration", - "rel_date": "2022-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.27.22276790", - "rel_abs": "Background and ObjectivesTwo- and three-dose BNT162b2 (Pfizer-BioNTech) mRNA vaccine effectiveness (VE) against SARS-CoV-2 infection, including Delta and Omicron variants, was assessed among adolescents in two Canadian provinces where first and second doses were spaced longer than the manufacturer-specified 3-week interval.\n\nMethodsTest-negative design estimated VE against laboratory-confirmed SARS-CoV-2 infection among 12-17-year-olds in Quebec and British Columbia, Canada between September 5, 2021 (epi-week 36), and April 30, 2022 (epi-week 17). Delta-dominant and Omicron-dominant periods spanned epi-weeks 36-47 and 51-17, respectively. VE was assessed from 14 days and explored by interval between first and second doses, time since second dose, and with administration of a third dose.\n\nResultsMedian first-second dosing-interval was [~]8 weeks and second-third dosing-interval was [~]29-31 weeks. Median follow-up post-second dose was [~]10-11 weeks for Delta-dominant and [~]21-22 weeks for Omicron-dominant periods, and [~]2-7 weeks post-third dose. VE against Delta was [≥]90% to at least the 5th month post-second dose. VE against Omicron declined from [~]65-75% at 2-3 weeks to [≤]50% by the 3rd month post-vaccination, restored to [~]65% shortly following a third dose. VE exceeded 90% against Delta regardless of dosing-interval but appeared improved against Omicron with [≥]8 weeks between first and second doses.\n\nConclusionIn adolescents, two BNT162b2 doses provided strong and sustained protection against Delta but reduced and rapidly-waning VE against Omicron. Longer interval between first and second doses and a third dose improved Omicron protection. Updated vaccine antigens, increased doses and/or dosing-intervals may be needed to improve adolescent VE against immunological-escape variants.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Iulia G Ionescu", - "author_inst": "Centre Hospitalier Universitaire (CHU) de Qu\u00e9bec-Universit\u00e9 Laval Research Center" - }, - { - "author_name": "Danuta M Skowronski", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services" - }, - { - "author_name": "Chantal Sauvageau", - "author_inst": "Institut national de sant\u00e9 publique du Qu\u00e9bec, Biological and Occupational Risks" - }, - { - "author_name": "Erica Chuang", - "author_inst": "BC Centre for Disease Control, Data and Analytics Services" - }, - { - "author_name": "Manale Ouakki", - "author_inst": "Institut national de sant\u00e9 publique du Qu\u00e9bec, Biological and Occupational Risks" - }, - { - "author_name": "Shinhye Kim", - "author_inst": "BC Centre for Disease Control, Communicable Diseases and Immunization Services" - }, - { - "author_name": "Gaston De Serres", - "author_inst": "Institut national de sant\u00e9 publique du Qu\u00e9bec, Biological and Occupational Risks" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.28.22276851", "rel_title": "The COVID-19 pandemic sparked off a large-scale outbreak of carbapenem-resistant Acinetobacter baumannii from the endemic strains of an Italian hospital", @@ -272602,6 +273032,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.06.27.497883", + "rel_title": "The Staphylococcus aureus iron-regulated surface determinant A (IsdA) increases SARS CoV-2 replication by modulating JAK-STAT signaling", + "rel_date": "2022-06-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.27.497883", + "rel_abs": "The emergence and spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) and the associated Coronavirus disease (COVID-19) pandemic have affected millions globally. Like other respiratory viruses, a significant complication of COVID-19 infection is secondary bacterial co-infection, which is seen in approximately 25% of severe cases. The most common organism isolated from co-infection is the Gram-positive bacterium Staphylococcus aureus. Here, we developed an in vitro co-infection model where both CoV-2 and S. aureus replication kinetics can be examined. We demonstrate CoV-2 infection does not alter how S. aureus attaches to or grows in host epithelial cells. In contrast, the presence of replicating S. aureus enhances the replication of CoV-2 by 10-15-fold. We identify this pro-viral activity is due to the S. aureus iron-regulated surface determinant A (IsdA) and this effect is mimicked across different SARS CoV-2 permissive cell lines infected with multiple viral variants. Analysis of co-infected cells demonstrated an IsdA dependent modification of host transcription. Using chemical inhibition, we determined S. aureus IsdA modifies host Janus Kinase - Signal Transducer and Activator of Transcription (JAK-STAT) signalling, ultimately leading to increased viral replication. These findings provide key insight into the molecular interactions that occur between host cells, CoV-2 and S. aureus during co-infection.\n\nImportanceBacterial co-infection is a common and significant complication of respiratory viral infection, including in patients with COVID-19, and leads to increased morbidity and mortality. The relationship between virus, bacteria and host is largely unknown, which makes it difficult to design effective treatment strategies. In the present study we created a model of co-infection between SARS CoV-2 and Staphylococcus aureus, the most common species identified in COVID-19 patients with co-infection. We demonstrate that the S. aureus protein IsdA enhances the replication of SARS CoV-2 in vitro by modulating host cell signal transduction pathways. The significance of this finding is in identifying a bacterial component that enhances CoV-2 pathogenesis, which could be a target for the development of co-infection specific therapy in the future. In addition, this protein can be used as a tool to decipher the mechanisms by which CoV-2 manipulates the host cell, providing a better understanding of COVID-19 virulence.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mariya I. Goncheva", + "author_inst": "Western University" + }, + { + "author_name": "Richard Gibson", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Ainslie C Shouldice", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Jimmy D. Dikeakos", + "author_inst": "The University of Western Ontario Schulich School of Medicine and Dentistry" + }, + { + "author_name": "David E Heinrichs", + "author_inst": "University of Western Ontario" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.28.22276926", "rel_title": "Increasing SARS-CoV2 cases, hospitalizations and deaths among the vaccinated elderly populations during the Omicron (B.1.1.529) variant surge in UK.", @@ -273762,65 +274227,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.26.22276861", - "rel_title": "The burden of respiratory conditions in the emergency department of Muhimbili National Hospital in Tanzania in the first two years of the COVID-19 pandemic", - "rel_date": "2022-06-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.26.22276861", - "rel_abs": "BackgroundGlobally, respiratory diseases cause 10 million deaths every year. With the COVID-19 pandemic, the burden of respiratory illness increased and led to significant morbidity and mortality in both high- and low-income countries. This study assessed the burden and trend of respiratory conditions among patients presenting to the emergency department of Muhimbili National Hospital in Tanzania and compared with national COVID-19 data to determine if this knowledge may be useful for the surveillance of disease outbreaks in settings of limited specific diagnostic testing.\n\nMethodsThe study used routinely collected data from the electronic information system in the Emergency Medical Department (EMD) of Muhimbili National Hospital in Tanzania. All patients presenting to the EMD in a 2-year period, 2020 and 2021 with respiratory conditions were included. Descriptive statistics and graphical visualizations were used to describe the burden of respiratory conditions and the trends over time and to compare to national Tanzanian COVID-19 data during the same period.\n\nResultsOne in every four patients who presented to the EMD of the Muhimbili National Hospital had a respiratory condition - 1039 patients per month. Of the 24,942 patients, 52% were males, and the median age (IQR) was 34.7 (21.7, 53.7) years. The most common respiratory diagnoses were pneumonia (52%), upper respiratory tract infections (31%), asthma (4.8%) and suspected COVID-19 (2.5%). There were four peaks of respiratory conditions coinciding with the four waves in the national COVID-19 data.\n\nConclusionsThere is a high burden of respiratory conditions among patients presenting to the EMD of Muhimbili National Hospital. The trend shows four peaks of respiratory conditions in 2020-2021 seen to coincide with the four waves in the national COVID-19 data. Real-time hospital-based surveillance tools may be useful for early detection of respiratory disease outbreaks and other public health emergencies in settings with limited diagnostic testing.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Harrieth Peter Ndumwa", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Erick A Mboya", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Davis Elias Amani", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Ramadhani Mashoka", - "author_inst": "Muhimbili National Hospital" - }, - { - "author_name": "Paulina Nicholaus", - "author_inst": "Muhimbili National Hospital" - }, - { - "author_name": "Rashan Haniffa", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit" - }, - { - "author_name": "Abi Beane", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit" - }, - { - "author_name": "Juma Mfinanga", - "author_inst": "Muhimbili National Hospital" - }, - { - "author_name": "Bruno Sunguya", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Hendry R. Sawe", - "author_inst": "Muhimbili University of Health and Allied Sciences" - }, - { - "author_name": "Tim Baker", - "author_inst": "Muhimbili University of Health and Allied Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.06.27.22276736", "rel_title": "An Economic Evaluation of a virtual Covid Ward in Leicester, Leicestershire, and Rutland", @@ -274084,6 +274490,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.06.26.22276919", + "rel_title": "Predicting Hand, Foot, and Mouth Disease in Japan Using Google Trends: Infodemiology Study", + "rel_date": "2022-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.26.22276919", + "rel_abs": "BackgroundCOVID-19 pandemic affected common disease infections, while the impact on hand, foot, and mouth disease (HFMD) is unclear. Google Trends data is beneficial in approximately real-time statistics and easily accessed, expecting to be used for infection explanation from information-seeking behavior perspectives. We aimed to explain HFMD cases before and during COVID-19 using Google Trends data.\n\nMethodsHFMD cases were obtained from the National Institute of Infectious Disease, and Google search data from 2009 to 2021 was downloaded using Google Trends in Japan. Pearson correlation coefficients were calculated between HFMD cases and the search topic \"HFMD\" from 2009 to 2021. Japanese tweets containing \"HFMD\" were retrieved to select search terms for further analysis. Search terms were retained with counts larger than 1000 and belonging to ranges of infection sources, susceptible sites, susceptible populations, symptoms, treatment, preventive measures, and identified diseases. Cross-correlation analyses were conducted to detect lag changes between HFMD cases and HFMD search terms before and during COVID-19. Multiple linear regressions with backward elimination processing were used to identify the most significant terms for HFMD explanation.\n\nResultsHFMD cases and Google search volume peaked around July in most years without 2020 and 2021. The search topic \"HFMD\" presented strong correlations with HFMD cases except in 2020 when COVID-19 outbroke. In addition, differences in lags for 73 (72.3%) search terms were negative, might indicating increasing public awareness of HFMD infections during the COVID-19 pandemic. Results of multiple linear regression demonstrated that significant search terms contained the same meanings but expanded informative search content during COVID-19.\n\nConclusionsSignificant terms for HFMD cases explanation before and during COVID-19 were different. The awareness of HFMD infection in Japan may improve during the COVID-19 pandemic. Continuous monitoring is important to promote public health and prevent resurgence. Public interest reflected in information-seeking behavior can be helpful for public health surveillance.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Qian Niu", + "author_inst": "Kyoto University" + }, + { + "author_name": "Junyu Liu", + "author_inst": "Kyoto University" + }, + { + "author_name": "Zixi Zhao", + "author_inst": "Kyoto University" + }, + { + "author_name": "Miyu Onishi", + "author_inst": "Kyoto University" + }, + { + "author_name": "Asuka Kawaguchi", + "author_inst": "Kyoto University" + }, + { + "author_name": "Anuradhi Bandara", + "author_inst": "Kyoto University" + }, + { + "author_name": "Keiko Harada", + "author_inst": "Kyoto University" + }, + { + "author_name": "Tomoki Aoyama", + "author_inst": "Kyoto University" + }, + { + "author_name": "Momoko Nagai-Tanima", + "author_inst": "Kyoto University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.06.24.497555", "rel_title": "A statistical, reference-free algorithm subsumes myriad problems in genome science and enables novel discovery", @@ -275532,29 +275989,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.22.22276298", - "rel_title": "Mathematical modelling of COVID-19 with periodic transmission: The case of South Africa", - "rel_date": "2022-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276298", - "rel_abs": "The data on SARS-CoV-2 (COVID-19) in South Africa shows seasonal transmission patterns to date, with the peaks having occurred in winter and summer since the out-breaks began. The transmission dynamics have mainly been driven by variations in environmental factors and virus evolution, and the two are at the center of driving the different waves of the disease. It is thus important to understand the role of seasonality in the transmission dynamics of COVID-19. In this paper a compartmental model with a time dependent transmission rate is formulated and the stabilities of the steady states analysed. We note that if R0 < 1, the disease-free equilibrium is globally asymptotically stable, and the disease completely dies out and when R0 > 1, the system admits a positive periodic solution, and the disease is uniformly or periodically persistent. The model is fitted to data on new cases in South Africa for the first four waves. The model results clearly indicate the need to consider seasonality in the transmission dynamics of COVID-19 and its importance in modelling fluctuations in the data for new cases. The potential impact of seasonality in the transmission patterns of COVID-19 and the public health implications are discussed.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Farai Nyabadza", - "author_inst": "University of Johannesburg" - }, - { - "author_name": "Belthasara Assan", - "author_inst": "University of Johannesburg" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.22.22276362", "rel_title": "Immune Correlates Analysis of the PREVENT-19 COVID-19 Vaccine Efficacy Clinical Trial", @@ -275994,6 +276428,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.22.22276072", + "rel_title": "A Multi-Institutional Study Benchmarking Cycle Threshold Values for Major Clinical SARS-CoV-2 RT-PCR Assays", + "rel_date": "2022-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276072", + "rel_abs": "Real-time, reverse transcriptase PCR assays are a pervasive technology used for diagnosis of SARS-CoV-2 infection. These assays produce a cycle threshold value (Ct) corresponding to the first amplification cycle in which reliable amplification is detected. (1)Such Ct values have been used by clinicians and in public health settings to guide treatment, monitor disease progression, assess prognosis, and inform isolation practices. To understanding the risk of reporting out uncalibrated Ct values and potential for instead reporting out calibrated viral load values, we performed a multi-institutional study to benchmark major clinical platforms against a calibrated standard. We found that for any given Ct value, corresponding viral loads varied up to 1000-fold among the different tests. In contrast, when these different assays were calibrated against a common standard and then used to test unknown de-identified specimens at several dilutions, viral load values showed high precision between methods (standard deviation and range of 0.36 and 1.1 log10 genome copies) and high accuracy compared with droplet digital PCR (ddPCR) determinations (difference between mean CDC N2 and Sarbeco E ddPCR determinations and mean determinations by calibrated RT-PCR assays examined in our study of 0.044 log10 genome copies). We, therefore, find strong support for calibration of SARS-CoV-2 RT-PCR tests to allow conversion of cycle thresholds to accurate and precise viral load values that are reproducible across major clinical systems. Implementation of calibrated assays will provide more reliable information for clinical decision making and allow more rigorous interpretation of SARS-CoV-2 laboratory data in clinical and laboratory investigation.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "James E Kirby", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Annie Cheng", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Megan H Cleveland", + "author_inst": "National Institute of Standards and Technology" + }, + { + "author_name": "E Degli-Angeli", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "C Todd DeMarco", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine" + }, + { + "author_name": "M Faron", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Torrey L Gallagher", + "author_inst": "Dartmouth-Hitchcock Medical Center" + }, + { + "author_name": "Russell K Garlick", + "author_inst": "LGC SeraCare" + }, + { + "author_name": "E Goecker", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "R W Coombs", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Catherine Huang", + "author_inst": "LGC SeraCare" + }, + { + "author_name": "Raul Louzao", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine" + }, + { + "author_name": "Thomas N Denny", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine" + }, + { + "author_name": "Eric Morreale", + "author_inst": "LGC SeraCare" + }, + { + "author_name": "Gerard Oakley", + "author_inst": "Eli Lilly and Company" + }, + { + "author_name": "G Reymann", + "author_inst": "Wisconsin Diagnostics Laboratories" + }, + { + "author_name": "Andrew Schade", + "author_inst": "Eli Lilly and Company" + }, + { + "author_name": "Salvatore Scianna", + "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine" + }, + { + "author_name": "Gregory J Tsongalis", + "author_inst": "Dartmouth-Hitchcock Medical Center" + }, + { + "author_name": "Peter M Vallone", + "author_inst": "National Institute of Standards and Technology" + }, + { + "author_name": "Jim Huggett", + "author_inst": "LGC National Measurement Lab" + }, + { + "author_name": "Nathan A Ledeboer", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Joel A Lefferts", + "author_inst": "Dartmouth-Hitchcock Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.22.22276760", "rel_title": "COVID-19 vaccine booster strategies in light of emerging viral variants: Frequency, timing, and target groups", @@ -277442,45 +277983,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.06.22.497134", - "rel_title": "Mutational insights among the structural proteins of SARS-CoV-2: frequencies and evolutionary trends in American countries", - "rel_date": "2022-06-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.22.497134", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a role in the mortality of more than 6 million people worldwide. This virus owns the genome, which contains four structural proteins, including spike (S), envelope (E), membrane (M), and nucleocapsid (N). The occurrence of structural mutations can induce the emergence of new variants. Depending on the mutations, the variants may display different patterns of infectivity, mortality, and sensitivity toward drugs and vaccines. In this study, we analyzed samples of amino-acid sequences (AASs) for structural proteins from the coronavirus 2019 (COVID-19) declaration as a pandemic to April 2022 among American countries. The analysis process included considering mutations frequencies, locations, and evolutionary trends utilizing sequence alignment to the reference sequence. In the following, the results were compared with the same analyses among the samples of the entire world. Results displayed that despite samples of North America and international countries that own the region of 508 to 635 with the highest mutation frequency among S AASs, the region with the same characteristic was concluded as 1 to 127 in South America. Besides, the most frequent mutations in S, E, M, and N proteins from North America and worldwide samples were concluded as D614G, T9I, I82T, and R203M. In comparison, R203K was the first frequent mutation in N samples in South America. Widely comparing mutations between North America and South America and between the Americas and the world can help scientists introduce better drug and vaccine development strategies.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mohammad Abavisani", - "author_inst": "mashhad universiy of medical sciences" - }, - { - "author_name": "Karim Rahimian", - "author_inst": "Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran." - }, - { - "author_name": "Reza Khayami", - "author_inst": "Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran." - }, - { - "author_name": "Mahsa Mollapour Sisakht", - "author_inst": "ErasmusMC" - }, - { - "author_name": "Mohammadamin Mahmanzar", - "author_inst": "Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran" - }, - { - "author_name": "Zahra Meshkat", - "author_inst": "Antimicrobial Resistance Research Center & Department of Medical Bacteriology and Virology, Bu-Ali Research Institute & Ghaem University Hospital, Faculty of Me" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.06.21.497047", "rel_title": "Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection", @@ -277892,6 +278394,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.06.22.22276765", + "rel_title": "COVID-19 vaccine breakthrough infections among fully vaccinated Health Care Workers in Lagos, Nigeria", + "rel_date": "2022-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276765", + "rel_abs": "BackgroundAccess to vaccines has contributed to the control of COVID-19. However, evaluation of the effectiveness of the vaccines in a setting where the vaccines were not originally tested is critically important. This study evaluates the clinical and laboratory characteristics of COVID-19 vaccine breakthrough infections among healthcare workers (HCWs).\n\nMethodsA multicentre prospective study among HCWs who had two doses of the Oxford/AstraZeneca ChAdOx1-S [recombinant] (AZD1222) vaccine were followed up 24 weeks. Nasopharyngeal and oropharyngeal specimens were tested using RT-PCR for SARS-CoV-2 and positive samples were subjected to whole genome sequencing for variant assignment.\n\nResultA total of 369 HCWs were enrolled; of which 24 (6.5%) had breakthrough infections. There was equal sex distribution among the breakthrough cases. The majority were aged between 30 to 39years (37.5%), and had mild symptoms of cough, fever, headache, and nausea/vomiting (58%), with no hospitalization. Among the 24 breakthrough cases whose whole genomes were successfully sequenced, three were confirmed to be Delta B.1.617.2 variant during the 3rd wave and an additional three were confirmed as omicron B.1.1.529 variant during the 4th wave.\n\nConclusionWe reported vaccine breakthrough cases among fully vaccinated HCWs with the majority presenting with mild illness. Both delta and omicron variants were identified during the different epidemiologic spectrums of SARS-CoV-2. Therefore, there is a need to scale up vaccination for all front-line health workers and high-risk populations in developing countries.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "David Ayoola Oladele", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Abideen Salako", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "James Ayorinde", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Chika Onwuamah", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Olagoke Usman", + "author_inst": "Federal Medical Centre Ebute-Metta" + }, + { + "author_name": "Rufai Abubakar", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Gideon Liboro", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Oluwatosin Odubela", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Sunday Mogaji", + "author_inst": "Federal Medical Centre Ebute-Metta" + }, + { + "author_name": "Fehintola Ige", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Gregory Ohihoin", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Oliver Ezechi", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Rosemary Audu", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Richard A. Adegbola", + "author_inst": "Nigerian Institute of Medical Research" + }, + { + "author_name": "Adedamola Dada", + "author_inst": "Federal Medical Centre Ebute-Metta" + }, + { + "author_name": "Tunde Salako", + "author_inst": "Nigerian Institute of Medical Research" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.20.496903", "rel_title": "Probing the biophysical constraints of SARS-CoV-2 spike N-terminal domain using deep mutational scanning", @@ -279284,85 +279865,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.20.22275994", - "rel_title": "Characterising patterns of COVID-19 and long COVID symptoms: Evidence from nine UK longitudinal studies", - "rel_date": "2022-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22275994", - "rel_abs": "Multiple studies across global populations have established the primary symptoms characterising COVID-19 (Coronavirus Disease 2019) and long COVID. However, as symptoms may also occur in the absence of COVID-19, a lack of appropriate controls has often meant that specificity of symptoms to acute COVID-19 or long COVID could not be examined. We aimed to characterise patterns of COVID-19 and long COVID symptoms across nine UK longitudinal studies, totalling over 42,000 participants. Conducting latent class analyses separately in three groups ( no COVID-19, COVID-19 in last 12 weeks, COVID-19 > 12 weeks ago), the data did not support the presence of more than two distinct symptom patterns, representing high and low symptom burden, in each group. Comparing the high symptom burden classes between the COVID-19 in last 12 weeks and no COVID-19 groups we identified symptoms characteristic of acute COVID-19, including loss of taste and smell, fatigue, cough, shortness of breath and muscle pains or aches. Comparing the high symptom burden classes between the COVID-19 > 12 weeks ago and no COVID-19 groups we identified symptoms characteristic of long COVID, including fatigue, shortness of breath, muscle pain or aches, difficulty concentrating and chest tightness. The identified symptom patterns among individuals with COVID-19 > 12 weeks ago were strongly associated with self-reported length of time unable to function as normal due to COVID-19 symptoms, suggesting that the symptom pattern identified corresponds to long COVID. Building the evidence base regarding typical long COVID symptoms will improve diagnosis of this condition and the ability to elicit underlying biological mechanisms, leading to better patient access to treatment and services.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ruth C E Bowyer", - "author_inst": "King's College London" - }, - { - "author_name": "Charlotte Huggins", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Renin Toms", - "author_inst": "University of Bristol" - }, - { - "author_name": "Richard John Shaw", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Bo Hou", - "author_inst": "Bradford Institute for Health Research" - }, - { - "author_name": "Ellen J Thompson", - "author_inst": "King's College London" - }, - { - "author_name": "Alex Siu Fung Kwong", - "author_inst": "University of Bristol" - }, - { - "author_name": "Dylan M Williams", - "author_inst": "UCL" - }, - { - "author_name": "Milla Kibble", - "author_inst": "King's College London" - }, - { - "author_name": "George B Ploubidis", - "author_inst": "University College London" - }, - { - "author_name": "Nicholas J Timpson", - "author_inst": "University of Bristol" - }, - { - "author_name": "Jonathan A C Sterne", - "author_inst": "University of Bristol" - }, - { - "author_name": "Nishi Chaturvedi", - "author_inst": "University College London" - }, - { - "author_name": "Claire J Steves", - "author_inst": "King's College London" - }, - { - "author_name": "Kate Tilling", - "author_inst": "University of Bristol" - }, - { - "author_name": "Richard J Silverwood", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.17.22276229", "rel_title": "Low level of knowledge about COVID-19 among a sample of Deaf persons in Ghana.", @@ -279602,6 +280104,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.17.496635", + "rel_title": "Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1", + "rel_date": "2022-06-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.17.496635", + "rel_abs": "The Omicron BA.1 variant emerged in late 2021 and quickly spread across the world. Compared to the ancestral Wuhan Hu-1 strain and other pre-Omicron SARS-CoV-2 variants, BA.1 has many mutations, a number of which are known to enable antibody escape 1-3. Many of these antibody-escape mutations individually decrease the spike receptor-binding domain (RBD) affinity for ACE2 in the background of early SARS-CoV-2 variants 4, but BA.1 still binds ACE2 with high affinity 5,6. The fitness and evolution of the BA.1 lineage is therefore driven by the combined effects of numerous mutations. Here, we systematically map the epistatic interactions between the 15 mutations in the RBD of BA.1 relative to the Wuhan Hu-1 strain. Specifically, we measure the ACE2 affinity of all possible combinations of these 15 mutations (2 15 = 32,768 genotypes), spanning all possible evolutionary intermediates from the ancestral Wuhan Hu-1 strain to BA.1. We find that immune escape mutations in BA.1 individually reduce ACE2 affinity but are compensated by epistatic interactions with other affinity-enhancing mutations, including Q498R and N501Y. Thus, the ability of BA.1 to evade immunity while maintaining ACE2 affinity is contingent on acquiring multiple interacting mutations. Our results implicate compensatory epistasis as a key factor driving substantial evolutionary change for SARS-CoV-2 and are consistent with Omicron BA.1 arising from a chronic infection.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Alief Moulana", + "author_inst": "Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA 02138" + }, + { + "author_name": "Thomas Dupic", + "author_inst": "Harvard" + }, + { + "author_name": "Angela M. Phillips", + "author_inst": "Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA 02138" + }, + { + "author_name": "Jeffrey Chang", + "author_inst": "Department of Physics, Harvard University, Cambridge, MA 02138" + }, + { + "author_name": "Serafina Nieves", + "author_inst": "Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138" + }, + { + "author_name": "Anne A. Roffler", + "author_inst": "Biological and Biomedical Sciences, Harvard Medical School, Boston MA 02115" + }, + { + "author_name": "Allison J. Greaney", + "author_inst": "Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; Department of Genome Sciences, University " + }, + { + "author_name": "Tyler N. Starr", + "author_inst": "Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109" + }, + { + "author_name": "Jesse D. Bloom", + "author_inst": "Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; Department of Genome Sciences, University " + }, + { + "author_name": "Michael M. Desai", + "author_inst": "Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA 02138" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2022.06.17.496600", "rel_title": "Efficient direct and limited environmental transmission of SARS-CoV-2 lineage B.1.22 in domestic cats", @@ -281222,49 +281779,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.15.22276427", - "rel_title": "Efficacy and Safety of Nebulized Ethanol Inhalation in COVID-19 Treatment. A Randomized, Clinical Trial", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.15.22276427", - "rel_abs": "BackgroundConsidering anti coronavirus effects of ethanol, the efficacy of its administration was evaluated in this research. Because of respiratory tract entrance of virus in COVID-19, this study was done by inhalation of nebulized ethanol.\n\nMethodsNinety-nine positive SARS-CoV-2-PCR patients who had been admitted at a respiratory clinic were included in this study. Patients were randomly assigned to the control (distilled water spray) and intervention (35% ethanol spray) group. Both groups were instructed to inhale 3 puffs of spray and inhale it, every six hours for a week. Global symptomatic score (GSS), clinical status scale,0020Blood Oxygenation, and C-Reactive Protein (CRP) at the first visit and days 3, 7, 14 were measured and compared between groups.\n\nResultsThe GSS decreased more and faster in the intervention group (ethanol) (1.4+1.4 vs 2.3+1.7, P=0.035) two weeks after starting intervention. On day 14, the odds of intervention group to have better clinical status was 5.715 times (95% CI, 2.47 to 13.19) than of control group a statistically significant effect, Wald {chi}2 (1) =16.67, P =0.001. Blood oxygen saturation also improved earlier in the ethanol group but without statistical significance difference. The readmission rate was lower in the intervention group (zero vs 10.9%, P=0.02).\n\nConclusionInhaled ethanol seems to be effective in improvement, mitigating clinical symptoms and reducing the need to repeat treatment. Considering the low cost, availability and no significant adverse events of ethanol, research and additional efforts are recommended to evaluate its curative effects in the early stages of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ali Amoushahi", - "author_inst": "Department of Anesthesiology and Intensive Care Unit, Isabn-e- Maryam Hospital, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Elham Moazam", - "author_inst": "Isabn-e-Maryam Hospital, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Amin Reza Tabatabaei", - "author_inst": "Isabn-e-Maryam Hospital, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Golnaz Ghasimi", - "author_inst": "Isabn-e-Maryam Hospital, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Pietro Salvatori", - "author_inst": "Formerly, ENT Department, Humanitas San Pio X Hospital, Milan, Italy" - }, - { - "author_name": "Ian Grant-Whyte", - "author_inst": "Diplomat of the American Board of family practice, Canada" - }, - { - "author_name": "Ahmed Ragab Ezz", - "author_inst": "Mansoura University, Dakahlia Governorate, Egypt" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.15.22276466", "rel_title": "Effectiveness of mRNA COVID-19 vaccine boosters against infection, hospitalization and death: a target trial emulation in the omicron (B.1.1.529) variant era", @@ -281464,6 +281978,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.16.22276479", + "rel_title": "Mental health of healthcare workers in England during the COVID-19 pandemic: a longitudinal cohort study", + "rel_date": "2022-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.16.22276479", + "rel_abs": "ObjectiveTo examine variations in impact of the COVID-19 pandemic on the mental health of all types of healthcare workers (HCWs) in England over the first 17 months of the pandemic.\n\nMethodWe undertook a prospective cohort study of 22,501 HCWs from 18 English acute and mental health NHS Trusts, collecting online survey data on common mental disorders (CMDs), depression, anxiety, alcohol use, and PTSD, from April 2020 to August 2021. We analysed these data cross-sectionally by time period (corresponding to periods the NHS was under most pressure), and longitudinally. Data were weighted to better represent Trust population demographics.\n\nResultsThe proportion of those with probable CMDs was greater during periods when the NHS was under most pressure (measured by average monthly deaths). For example, 55% (95%CI 53%, 58%) of participants reported symptoms of CMDs in April-June 2020 versus 47% (95%CI 46%, 48%) July-October 2020. Contrary to expectation, there were no major differences between professional groups (i.e. clinical and non-clinical staff). Younger, female, lower paid staff, who felt poorly supported by colleagues/managers, and who experienced potentially morally injurious events were most at risk of negative mental health outcomes.\n\nConclusionAmong HCWs, the prevalence of probable CMDs increased during periods of escalating pressure on the NHS, suggesting staff support should be increased at such points in the future, and staff should be better prepared for such situations via training. All staff, regardless of role, experienced poorer mental health during these periods, suggesting that support should be provided for all staff groups.\n\nKey messagesO_ST_ABSWhat is already known on this topicC_ST_ABSExisting evidence about the mental health of healthcare workers (HCWs) through the COVID-19 pandemic comes mainly from cross-sectional studies using unrepresentative convenience samples, typically focussing on clinical staff rather than all HCWs. Such studies show high prevalence of symptoms of mental disorders, but the strength of this evidence is uncertain.\n\nWhat this study addsUsing a defined sampling frame, with longitudinal, weighted data, we show that during periods of greater pressure on the NHS (as indicated by average monthly national COVID-19 death rates), prevalence of mental disorder symptoms increased, and, importantly, that this effect was seen in non-clinical as well as clinical staff.\n\nHow this study might affect research, practice or policyThese findings indicate that provision of support for HCWs should not only focus on those providing clinical care, but also on non-clinical staff such as porters, cleaners, and administrative staff, and additional support should be provided during higher pressure periods. Better preparation of staff for such situations is also suggested.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Danielle Lamb", + "author_inst": "UCL" + }, + { + "author_name": "Rafael Gafoor", + "author_inst": "University College London" + }, + { + "author_name": "Hannah Scott", + "author_inst": "King's College London" + }, + { + "author_name": "Ewan Carr", + "author_inst": "King's College London" + }, + { + "author_name": "Sharon Stevelink", + "author_inst": "King's College London" + }, + { + "author_name": "Rosalind Raine", + "author_inst": "University College London" + }, + { + "author_name": "Matthew Hotopf", + "author_inst": "King's College London" + }, + { + "author_name": "Neil Greenberg", + "author_inst": "King's College London" + }, + { + "author_name": "Siobhan Hegarty", + "author_inst": "King's College London" + }, + { + "author_name": "Ira Madan", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Paul Moran", + "author_inst": "University of Bristol" + }, + { + "author_name": "Richard Morriss", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Dominic Murphy", + "author_inst": "Combat Stress" + }, + { + "author_name": "Anne Marie Rafferty", + "author_inst": "King's College London" + }, + { + "author_name": "Scott Weich", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Sarah Dorrington", + "author_inst": "King's College London" + }, + { + "author_name": "Simon Wessely", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.06.16.22276487", "rel_title": "Capturing the experiences of UK healthcare workers during the COVID-19 pandemic: A structural topic modelling analysis of 7,412 free-text survey responses", @@ -283476,81 +284073,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.13.22276312", - "rel_title": "Quantifying Inequities in COVID-19 Vaccine Distribution Over Time by social vulnerability, race and ethnicity, and location: A Population-Level Analysis in St. Louis and Kansas City, Missouri", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276312", - "rel_abs": "BACKGROUNDEquity in vaccination coverage is a cornerstone to a successful public health response to COVID-19. To deepen understand of the extent to which vaccination coverage compared to initial strategies for equitable vaccination, we explore primary vaccine series and booster rollout over time and by race/ethnicity, social vulnerability, and geography.\n\nMETHODS AND FINDINGSWe analyzed data from the Missouri State Department of Health and Senior Services on all COVID-19 vaccinations administered across 7 counties in the St. Louis region and 4 counties in the Kansas City Region. We compared rates of receiving the primary COVID-19 vaccine series and boosters relative to time, race/ethnicity, zip code-level social vulnerability index (SVI), vaccine location type, and COVID-19 disease burden. We adapted a well-established tool for measuring inequity--the Lorenz curve--to quantify inequities in COVID-19 vaccination relative to these key metrics. Between 12/15/2020 and 2/15/2022, 1,762,508 individuals completed the primary series and 871,896 had received a booster. During early phases of the primary series rollout, Black and Hispanic individuals from high SVI zip codes were vaccinated at less than half the rate of White individuals, but rates increased over time until they were higher than rates in White individuals after June 2021; Asian individuals maintained high levels of vaccination throughout. Increasing vaccination rates in Black and Hispanic communities corresponded with periods when more vaccinations were offered at small community-based sites such as pharmacies rather than larger health systems and mass vaccination sites. Using Lorenz curves, zip codes in the quartile with the lowest rates of primary series completion accounted for 19.3%, 18.1%, 10.8%, and 8.8% of vaccinations but represented 25% of either the total population, cases, deaths, or population-level SVI, respectively. When tracking Gini coefficients, these disparities were greatest earlier during rollout, but improvements were slow and modest and vaccine disparities remained across all metrics even after one year. Patterns of disparities for boosters were similar but often of much greater magnitude during rollout in Fall 2021. Study limitations include inherent limitations in vaccine registry dataset such as missing and misclassified race/ethnicity and zip code variables and potential changes in zip code population sizes since census enumeration.\n\nCONCLUSIONSRacial inequity in the initial COVID-19 vaccination and booster rollout in two large U.S. metropolitan areas were apparent across racial/ethnic communities, across levels of social vulnerability, over time, and across types of vaccination administration sites. Disparities in receipt of the primary vaccine series attenuated over time during a period in which sites of vaccination administration diversified, but were recapitulated during booster rollout. These findings highlight how public health strategies from the outset must directly target these deeply embedded structural and systemic determinants of disparities and track equity metrics over time to avoid perpetuating inequities in health care access.\n\nAUTHOR SUMMARYO_ST_ABSWhy Was This Study Done?C_ST_ABSO_LIEquitable vaccine strategies are critical for the public health response to COVID-19, but there is limited understanding of how vaccination campaigns compared to different metrics for equity.\nC_LIO_LIMany initial approaches to vaccine allocation sought to acknowledge the known disparities in exposure risk, disease burden, needs, and access by formally considering social vulnerability or race/ethnicity in plans to prioritize vaccinations, but there is limited empirical evaluation of how actual primary vaccine series and subsequent booster efforts aligned with the initial goals set out for equity.\nC_LIO_LIWe quantify COVID-19 vaccine-related inequities in receipt of the primary vaccine series and booster across key equity metrics including race/ethnicity, social vulnerability, location, and time using a novel application of Lorenz curves and Gini coefficients--tools from economics to measure inequalities--in the St. Louis and Kansas City regions of Missouri.\nC_LI\n\nWhat Did the Researchers Do and Find?O_LIWe analyzed data from the Missouri State Department of Health and Senior Services on all COVID-19 vaccinations administered in the St. Louis region and Kansas City Regions. We compared rates of receiving the primary COVID-19 vaccine series and boosters relative to time, race/ethnicity, zip code-level social vulnerability index (SVI), vaccine location type, and COVID-19 disease burden. We adapted Lorenz curves and Gini coefficients to quantify the inequities in COVID-19 vaccination relative to these key metrics and examined how they changed over time.\nC_LIO_LIBlack and Hispanic individuals from high SVI zip codes completed the primary series at less than half the rate of White individuals during early phases of the primary series rollout, but surpassed rates in White individuals after June 2021. These relative increases in primary series completion rates in Black and Hispanic communities corresponded to periods when vaccinations became more available at small community-based sites.\nC_LIO_LILorenz curves demonstrated that zip codes in the quartile with the lowest rates of primary series completion accounted for 19.3%, 18.1%, 10.8%, and 8.8% of vaccinations but represented 25% of either the total population, cases, deaths, or population-level SVI, respectively. Tracking Gini coefficients over time demonstrated that these disparities were greatest earlier during rollout, but only improved slowly and modestly over time.\nC_LIO_LIPatterns of disparities for boosters were similar but often of much greater magnitude that those seen with completion of the primary vaccine series. patterns of disparities were similar but often of greater magnitude during booster rollout in Fall 2021.\nC_LI\n\nWhat Do These Findings Mean?O_LIVaccination coverage for both the primary series and boosters demonstrated substantial disparities across race/ethnicity, levels of social vulnerability, types of vaccine administration sites, and over time.\nC_LIO_LIDespite well-documented inequities for COVID-19 and need for equitable vaccine approaches, the strategies employed did not overcome deeply entrenched systemic inequities in health care and society.\nC_LIO_LIPublic health strategies must proactively target these deeply embedded structural determinants of disparities from the outset and should systematically track equity metrics over time to avoid perpetuating inequities in health care access.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Aaloke Mody", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Cory Bradley", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Salil Redkar", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Branson Fox", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Ingrid Eshun-Wilson", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Matifadza G. Hlatshwayo", - "author_inst": "St. Louis City Department of Health" - }, - { - "author_name": "Anne Trolard", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Khai Hoan Tram", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Lindsey Filiatreau", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Franda Thomas", - "author_inst": "St. Louis City Department of Health" - }, - { - "author_name": "Matt Haslam", - "author_inst": "St. Louis City Department of Health" - }, - { - "author_name": "George Turabelidze", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Vetta Sanders-Thompson", - "author_inst": "Washington University in St Louis George Warren Brown School of Social Work" - }, - { - "author_name": "William G. Powderly", - "author_inst": "Washington University in St Louis School of Medicine" - }, - { - "author_name": "Elvin H. Geng", - "author_inst": "Washington University in St Louis School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.14.22276393", "rel_title": "Nirmatrelvir plus ritonavir for early COVID-19 and hospitalization in a large US health system", @@ -283902,6 +284424,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.06.12.22276290", + "rel_title": "Impact of non-pharmaceutical interventions targeted at the COVID-19 pandemic on influenza cases in the UK Armed Forces", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.12.22276290", + "rel_abs": "IntroductionNon-pharmaceutical interventions (NPIs) such as lockdown, social distancing and use of face coverings was adopted by the United Kingdom (UK) Armed Forces (AF) during the COVID-19 pandemic. This study assessed the impact of the use of NPIs on influenza activity in the UK AF.\n\nMethodsA longitudinal study design was adopted, and secondary data was analysed retrospectively. Clinical Read codes for influenza-like illness (ILI) was used to generate data for flu seasons before and during the COVID-19 pandemic (September 2017 to April 2021).\n\nResultsBefore the COVID-19 pandemic, the rate of reporting ILI was [~] 4% across all flu seasons. The count of ILI was 2.9%, 2.2% and 3.1% during 2017-18, 2018-19 and 2019-20 flu seasons respectively. During the COVID-19 pandemic, both the rate of reporting ILI (0.6%) and the count of ILI (0.5%) were significantly smaller (p < .001). The rate of reporting ILI was positively correlated with the count of ILI (r (2) = .97, p = .014). Influenza vaccination rate increased by 1.3% during the COVID-19 pandemic. vaccination rate was negatively correlated with the rate of reporting ILI (r (2) = -.52, p = 0.24) and the count of ILI (r (2) = -.61, p = 0.19). However, this correlation was not significant. The use of NPIs was negatively correlated with the rate of reporting ILI (r (2) = -.99, p = < .001) and the count of ILI (r (2) = -.95, p = 0.026). The overall multiple regression performed was statistically significant (R2 = 0.94, F (1, 2) = 33.628, p = 0.028). The rate of reporting ILI significantly predicted the count of ILI ({beta} = 0.609, p = 0.028) while vaccination rate did not significantly predict the count of ILI ({beta} = -0.136, p = 0.677).\n\nConclusionsInfluenza activity in the UK AF was significantly reduced during the COVID-19 pandemic. The use of NPIs and the rate of reporting ILI significantly reduced the count of ILI. Being vaccinated for influenza did not significantly reduce the count of ILI.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ngwa Niba Rawlings", + "author_inst": "CORE Africa" + }, + { + "author_name": "George Otieno", + "author_inst": "UKAF" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.11.22276272", "rel_title": "Impaired Neutralization of SARS-CoV-2 Including Omicron Variants after COVID-19 mRNA Booster Immunization under Methotrexate Therapy.", @@ -285386,41 +285931,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.09.22276209", - "rel_title": "Blood biomarkers representing maternal-fetal interface tissues used to predict early-and late-onset preeclampsia but not COVID-19 infection", - "rel_date": "2022-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276209", - "rel_abs": "BackgroundA well-known blood biomarker (soluble fms-like tyrosinase-1 [sFLT-1]) for preeclampsia, i.e., a pregnancy disorder, was found to predict severe COVID-19, including in males. True biomarker may be masked by more-abrupt changes related to endothelial instead of placental dysfunction. This study aimed to identify blood biomarkers that represent maternal-fetal interface tissues for predicting preeclampsia but not COVID-19 infection.\n\nMethodsThe surrogate transcriptome of the tissues was determined by that in maternal blood, utilizing four datasets (n=1,354) which were collected before the COVID-19 pandemic. Applying machine learning, a preeclampsia prediction model was chosen between those using blood transcriptome (differentially expressed genes [DEGs]) and the blood-derived surrogate for the tissues. We selected the most predictive model by the area under receiver operating characteristic (AUROC) using a dataset for developing the model, and well-replicated in datasets either with or without intervention. To identify eligible blood biomarkers that predicted any-onset preeclampsia from the datasets but did not predict positives in the COVID-19 dataset (n=47), we compared several methods of predictor discovery: (1) the best prediction model; (2) gene sets by standard pipelines; and (3) a validated gene set for predicting any-onset preeclampsia during the pandemic (n=404). We chose the most predictive biomarkers from the best method with the significantly largest number of discoveries by a permutation test. The biological relevance was justified by exploring and reanalyzing low- and high-level, multi-omics information.\n\nResultsA prediction model using the surrogates developed for predicting any-onset preeclampsia (AUROC of 0.85, 95% confidence interval [CI] 0.77 to 0.93) was the only that was well-replicated in an independent dataset with no intervention. No model was well-replicated in datasets with a vitamin D intervention. None of the blood biomarkers with high weights in the best model overlapped with blood DEGs. Blood biomarkers were transcripts of integrin-5 (ITGA5), interferon regulatory factor-6 (IRF6), and P2X purinoreceptor-7 (P2RX7) from the prediction model, which was the only method that significantly discovered the eligible blood biomarkers (n=3/100 combinations, 3.0%; P=.036). Most of the predicted events (73.70%) among any-onset preeclampsia were cluster A as defined by ITGA5 (Z-score [≥]1.1), but were only a minority (6.34%) among positives in the COVID-19 dataset. The remaining were the predicted events (26.30%) among any-onset preeclampsia or those among COVID-19 infection (93.66%) if IRF6 Z-score was [≥]-0.73 (clusters B and C), in which none was the predicted events among either late-onset preeclampsia (LOPE) or COVID-19 infection if P2RX7 Z-score was <0.13 (cluster B). Greater proportion of predicted events among LOPE were cluster A (82.85% vs. 70.53%) compared to early-onset preeclampsia (EOPE). The biological relevance by multi-omics information explained the biomarker mechanism, polymicrobial infection in any-onset preeclampsia by ITGA5, viral co-infection in EOPE by ITGA5-IRF6, a shared prediction with COVID-19 infection by ITGA5-IRF6-P2RX7, and non-replicability in datasets with a vitamin D intervention by ITGA5.\n\nConclusionsIn a model that predicts preeclampsia but not COVID-19 infection, the important predictors were maternal-blood genes that were not extremely expressed, including the proposed blood biomarkers. The predictive performance and biological relevance should be validated in future experiments.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Herdiantri Sufriyana", - "author_inst": "Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taiwan; Department of Medical Physiology, Fa" - }, - { - "author_name": "Hotimah Masdan Salim", - "author_inst": "Department of Molecular Biology, Faculty of Medicine, Universitas Nahdlatul Ulama Surabaya, Indonesia." - }, - { - "author_name": "Akbar Reza Muhammad", - "author_inst": "Faculty of Medicine, Universitas Nahdlatul Ulama Surabaya, Indonesia." - }, - { - "author_name": "Yu-Wei Wu", - "author_inst": "Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taiwan; Clinical Big Data Research Center, T" - }, - { - "author_name": "Emily Chia-Yu Su", - "author_inst": "Graduate Institute of Biomedical Informatics, College of Medical Science and Technology and Research Center for Artificial Intelligence in Medicine, Taipei Medi" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2022.06.08.22276134", "rel_title": "Implementation of a digital early warning score (NEWS2) in a cardiac specialist and general hospital settings in the COVID-19 pandemic: A qualitative study.", @@ -285904,6 +286414,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.06.13.22276327", + "rel_title": "The prevalence of mental ill-health in women during pregnancy and after childbirth during the Covid-19 pandemic: a Systematic review and Meta-analysis", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276327", + "rel_abs": "BackgroundSevere Acute Respiratory Syndrome Coronavirus (SARS-CoV) is a respiratory disease causing coronavirus. SARS-CoV has caused the Middle East Respiratory Syndrome (MERS), SARS-CoV in Hong King and SARS-CoV-2 (COVID-19). COVID-19, to date, have had the highest mortality and morbidity globally, thus reaching the pandemic status. In comparison to research conducted to explore the impact of pandemics on the general wellbeing, there appears to be a paucity on its association with womens mental health. Many pregnant women have reported that the pandemic negatively impacted their mental health.\n\nAimThis study aimed is to explore the prevalence of the impact of the COVID-19, MERS and SARS pandemics on the mental health of pregnant women.\n\nMethodA study protocol was developed and published in PROSPERO (CRD42021235356) to explore a number of key objectives. For the purpose of this study PubMed, Science direct, Ovid PsycINFO and EMBASE databases were searched from December 2000 - July 2021. The search results were screened, first by title, and then by abstract. A meta-analysis was conducted to report the findings.\n\nResultsThere were no studies reporting the mental health impact due to MERS and SARS. We systematically identified 316 studies that reported on the mental health of women that were pregnant and soon after birth. The meta-analysis indicated 24.9% (21.37%-29.02%) of pregnant women reported symptoms of depression, 32.8% (29.05% to 37.21%) anxiety, 29.44% (18.21% - 47.61%) stress, 27.93% (9.05%-86.15 %) PTSD, and 24.38% (11.89%-49.96%) sleep disorders during the COVID-19 pandemic. Furthermore, the I2 test showed a high heterogeneity value.\n\nConclusionThe importance of managing the mental health during pregnancy and after-delivery improves the quality of life and wellbeing of mothers. Developing an evidence based mental health framework as part of pandemic preparedness to help pregnant women would improve the quality of care received during challenging times.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gayathri Delanerolle", + "author_inst": "University of Oxford" + }, + { + "author_name": "Mary McCauley", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Martin Hirsch", + "author_inst": "University of College London NHS Foundation Trust" + }, + { + "author_name": "Yutian Zeng", + "author_inst": "Southern University of Science and Technology" + }, + { + "author_name": "Xu Cong", + "author_inst": "Southern University of Science and Technology" + }, + { + "author_name": "Heitor Cavalini", + "author_inst": "Southern Health NHS Foundation Trust" + }, + { + "author_name": "Ashish Shetty", + "author_inst": "University College London NHS Foundation Trust" + }, + { + "author_name": "shanaya rathod", + "author_inst": "Southern Health NHS Foundation Trust" + }, + { + "author_name": "Jian Qing Shi", + "author_inst": "Southern University of Science and Technology" + }, + { + "author_name": "Dharani K Hapangama", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Peter Phiri", + "author_inst": "Southern Health NHS Foundation" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "sexual and reproductive health" + }, { "rel_doi": "10.1101/2022.06.10.22276268", "rel_title": "Disentangling the common genetic architecture and causality of rheumatoid arthritis and systemic lupus erythematosus with COVID-19 outcomes: genome-wide cross trait analysis and bi-directional Mendelian randomization study", @@ -287120,69 +287689,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.10.495677", - "rel_title": "The Fc-effector function of COVID-19 convalescent plasma contributes to SARS-CoV-2 treatment efficacy in mice", - "rel_date": "2022-06-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.10.495677", - "rel_abs": "COVID-19 convalescent plasmas (CCPs) are chosen for plasma therapy based on neutralizing titers and anti-Spike immunoglobulin levels. However, specific CCP characteristics that promote SARS-CoV-2 control in recipients are complex and incompletely defined. Using an in vivo imaging approach, we demonstrate that CCPs with low neutralizing and high Fc-effector activity, in contrast to those with poor Fc-function, afford effective prophylaxis and therapy in K18-hACE2 mice lethally challenged with SARS-CoV-2-nLuc. Macrophages and neutrophils significantly contributed to CCP effects during therapy but to a reduced extent under prophylaxis. Both IgG and Ig(M+A) were required during therapy, but the IgG fraction alone was sufficient during prophylaxis. Finally, despite neutralizing poorly, SARS-CoV-2 Wuhan-elicited CCPs delayed Delta and Beta variants of concern (VOC)-induced mortality in mice illustrating the contribution of polyclonal Fc-effector functions in immunity against VOCs. Thus, in addition to neutralization, Fc-effector activity is a significant criterion for CCP selection for therapeutic applications.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Irfan Ullah", - "author_inst": "Yale University" - }, - { - "author_name": "Guillaume Beaudoin-Bussieres", - "author_inst": "CRCHUM" - }, - { - "author_name": "Kelly Symmes", - "author_inst": "Yale University" - }, - { - "author_name": "Marc Cloutier", - "author_inst": "Hema-Quebec, Affaires Medicales et Innovation" - }, - { - "author_name": "Eric Ducas", - "author_inst": "Hema-Quebec" - }, - { - "author_name": "Alexandra Tauzin", - "author_inst": "Centre de Recherche du CHUM" - }, - { - "author_name": "Annemarie Laumaea", - "author_inst": "Universite de Montreal" - }, - { - "author_name": "Philippe Begin", - "author_inst": "CHUM-MED" - }, - { - "author_name": "Walther Mothes", - "author_inst": "Yale University" - }, - { - "author_name": "Renee Bazin", - "author_inst": "Hema-Quebec" - }, - { - "author_name": "Andres Finzi", - "author_inst": "Universite de Montreal" - }, - { - "author_name": "Pradeep D Uchil", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.06.10.22276252", "rel_title": "Ivermectin for Treatment of Mild-to-Moderate COVID-19 in the Outpatient Setting: A Decentralized, Placebo-controlled, Randomized, Platform Clinical Trial", @@ -287378,6 +287884,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.06.08.22276091", + "rel_title": "Environmental circulation of adenovirus 40/41 and SARS-CoV-2 in the context of the emergence of acute hepatitis of unknown origin", + "rel_date": "2022-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.08.22276091", + "rel_abs": "The recent surge of hepatitis of unknown origin in children is hypothesized to be caused by adenovirus 41 and/or SARS-CoV-2 infections. A relatively high proportion of patients testing positive for these viruses concomitantly with the development of acute hepatitis supports this hypothesis. To formally incriminate these viral infections as causative agents of hepatitis, both a plausible physiopathological pathway and supporting epidemiological dynamics in the community need demonstration. In this study, we measured the level of circulation of adenovirus 40/41 and SARS-CoV-2 in the general population of the city of Leuven in Belgium using wastewater monitoring between December 2020 and May 2022 and indoor air sampling in day care centers between November 2021 and May 2022. We also retrospectively analyzed medical records of 12.672 children attending a tertiary hospital draining the same region between January 2019 and April 2022. Our results demonstrate a recent but modest increase in hepatitis of unknown origin concomitant with a surge of circulating adenovirus 41 and SARS-CoV-2 in the general population, including in children under 5.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Elke Wollants", + "author_inst": "KU Leuven Rega Institute" + }, + { + "author_name": "Els Keyaerts", + "author_inst": "KU Leuven / UZ Leuven" + }, + { + "author_name": "Lize Cuypers", + "author_inst": "UZ Leuven" + }, + { + "author_name": "Mandy Bloemen", + "author_inst": "KU Leuven" + }, + { + "author_name": "Marijn Thijssen", + "author_inst": "KU Leuven" + }, + { + "author_name": "Sien Ombelet", + "author_inst": "UZ Leuven" + }, + { + "author_name": "Joren Raymenants", + "author_inst": "KU Leuven" + }, + { + "author_name": "Kurt Beuselinck", + "author_inst": "UZ Leuven" + }, + { + "author_name": "Lies Laenen", + "author_inst": "UZ Leuven" + }, + { + "author_name": "Lore Budts", + "author_inst": "UZ Leuven" + }, + { + "author_name": "Bram Pussig", + "author_inst": "KU Leuven" + }, + { + "author_name": "Katrien Lagrou", + "author_inst": "UZ Leuven" + }, + { + "author_name": "Marc Van Ranst", + "author_inst": "UZ / KU Leuven" + }, + { + "author_name": "Emmanuel Andre", + "author_inst": "UZ /KU Leuven" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.08.22276169", "rel_title": "Out-of-hospital Cardiac Arrest Before and During the COVID-19 Pandemic in the South Bronx", @@ -288750,25 +289327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.05.22276023", - "rel_title": "Modeling the Omicron Dynamics and Development in China: with a Deep Learning Enhanced Compartmental Model", - "rel_date": "2022-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.05.22276023", - "rel_abs": "BackgroundCompartmental models dominate epidemic modeling. Estimations of transmission parameters between compartments are typically done through stochastic parameterization processes that depend upon detailed statistics on transmission characteristics, which are economically and resource-wide expensive to collect.\n\nObjectivesWe apply deep learning techniques as a lower data dependency alternative to estimate transmission parameters of a customized compartmental model, for the purpose of simulating the dynamics of the Omicron phase of the COVID-19 epidemics and projecting its further development in China and subregions within the country.\n\nMethodsWe construct a compartmental model, and develop a multivariate, multistep deep learning methodology to estimate the models transmission parameters. We then feed the estimated transmission parameters to the compartmental model to predict the development of the COVID-19 epidemics in China and subregions within the country for 28 days.\n\nResultsIn China (excluding Hong Kong and Taiwan), the daily Omicron infection increase is between 60 and 260 in the 28-day forecast period between June 4 and July 1, 2022. On July 1, 2022, there would be 768,622 cumulative confirmed cases and 591 cumulative deceased cases. The CFR would stabilize at 0.077%{+/-}0.00025%. Assuming a 25% infection rate, the total deaths with Omicron would be up to 280,000 without non-pharmaceutical intervention (NPI).\n\nConclusionsCurrent compartmental models require stochastic parameterization to estimate the transmission parameters. These models effectiveness depends upon detailed statistics on transmission characteristics. As an alternative, deep learning techniques are effective in estimating these stochastic parameters with greatly reduced dependency on data particularity.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "QI DENG", - "author_inst": "Zhejiang Normal University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.07.22275493", "rel_title": "Precarious employment and associations with health during COVID-19: a nationally representative survey in Wales, UK", @@ -289116,6 +289674,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.06.07.494579", + "rel_title": "GABA-receptors are a new druggable target for limiting disease severity, lung viral load, and death in SARS-CoV-2 infected mice", + "rel_date": "2022-06-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.07.494579", + "rel_abs": "GABA-receptors (GABA-Rs) are well-known neurotransmitter receptors in the central nervous system. GABA-Rs are also expressed by immune cells and lung epithelial cells and GABA-R agonists/potentiators reduce inflammatory immune cell activities and limit acute lung injuries. Notably, plasma GABA levels are reduced in hospitalized COVID-19 patients. Hence, GABA-R agonists may have therapeutic potential for treating COVID-19. Here, we show that oral GABA treatment initiated just after SARS-CoV-2 infection, or 2 days later near the peak of lung viral load, reduced disease severity, lung coefficient index, and death rates in K18-hACE2 mice. GABA-treated mice had a reduced viral load in their lungs and displayed shifts in their serum cytokine and chemokine levels that are associated with better outcomes in COVID-19 patients. Thus, GABA-R activation had multiple beneficial effects in this mouse model which are also desirable for the treatment of COVID-19. A number of GABA-R agonists are safe for human use and can be readily tested in clinical trials with COVID-19 patients. We also discuss their potential for limiting COVID-19-associated neuroinflammation.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jide Tian", + "author_inst": "University of California, Los Angeles, California, California" + }, + { + "author_name": "Barbara Dillion", + "author_inst": "University of California, Los Angeles, California, California" + }, + { + "author_name": "Jill Henley", + "author_inst": "University of Southern California" + }, + { + "author_name": "Lucio Comai", + "author_inst": "University of Southern California" + }, + { + "author_name": "Daniel Kaufman", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.07.495142", "rel_title": "Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks", @@ -290888,33 +291481,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.06.05.494906", - "rel_title": "Implications of Spike Protein Interactions with Zn-bound form of ACE2: A Computational Structural Study", - "rel_date": "2022-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.05.494906", - "rel_abs": "The COVID-19 pandemic has generated a major interest in designing inhibitors to prevent SARS-CoV-2 binding on host cells to protect against infection. One promising approach to such research utilizes molecular dynamics (MD) to identify potential inhibitors that can prevent the interaction between spike (S) protein on the virus and angiotensin converting enzyme 2 (ACE2) receptor on the host cells. In these studies, many groups have chosen to exclude a zinc (Zn) ion bound to the ACE2 molecule which is critical for enzymatic activity. While the relatively distant location of Zn ion from the S protein binding site (S1 domain), combined with the difficulties in modeling this ion have motivated the decision of exclusion, Zn can potentially contribute to the structural stability of the entire protein, and thus, may have implications on spike protein interaction. In this study, we explored the effects of excluding Zn on the structural stability and binding free energy of the ACE2-S1 protein complex. We generated two versions of an experimentally-derived structure of the ACE2-S1 protein complex: one with Zn and one without. Examining the differences between these two complexes during MD simulation, we found that the Zn-bound complex exhibited greater instability at nearly all residues except for the interacting residues, which were more stable in the Zn-bound complex. Additionally, the Zn-bound complex had a stronger binding free energy at all internal dielectric constants greater than one. Since binding free energy is often used to score inhibitors performances, excluding Zn could potentially have implications on inhibitor selection and performance, both in the ACE2-S1 protein system and other protein complexes that include the Zn ion.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Peter R. Fatouros", - "author_inst": "Clarkson University" - }, - { - "author_name": "Urmi Roy", - "author_inst": "Clarkson University" - }, - { - "author_name": "Shantanu Sur", - "author_inst": "Clarkson University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.06.06.22276040", "rel_title": "Transcriptomics Meta-Analysis Predicts Two Robust Human Biomarkers for Severe Infection with SARS-CoV-2", @@ -291170,6 +291736,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.06.06.494494", + "rel_title": "SARS-CoV-2 S protein antagonizes type I interferon downstream signal pathway through interacting and attenuating phosphorylation of STAT1/STAT2", + "rel_date": "2022-06-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.06.494494", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may keep patients in a clinically asymptomatic state by blocking cellular innate antiviral immunity, but the molecular mechanism remains unclear. Here, we screened the viral proteins of SARS-CoV-2 and found that the spike (S) protein inhibits the activation of interferon-stimulated genes (ISGs) and even reduces the expression of these genes to below background values. Mechanistically, the S protein interacted with STAT1, STAT2, and IRF9 and impedes the phosphorylation of STAT1/STAT2, thus preventing the formation of the interferon-stimulating gene factor 3 (ISGF3) complex and inhibiting the downstream production of Interferon-stimulated genes (ISGs). Remarkably, we also have found that the inhibitory mechanism of the S protein was conservative among SARS-CoV-2 variants and other human coronaviruses, including SARS-CoV, MERS-CoV, HCoV-229E, HCoV-NL63, and HCoV-HKU1. Truncation studies indicated that the most conserved S2 domain played a major inhibitory role. Altogether, our findings unveil a new mechanism by which SARS-CoV-2 S protein attenuated the hosts antiviral immune response and provide new insights into the pathogenic mechanism of coronavirus.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Wenjia Ni", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Wenkang Li", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Zeng Cai", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China; Institute for Vaccine Research, Animal Biosafety Level 3" + }, + { + "author_name": "Wenhua Guo", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Yucheng Zheng", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Yongliang Zhao", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Zhixuan Wu", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Simeng Liang", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Jiajie Ye", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Xiao Guo", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Dan Zhou", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Xiaoying Wu", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Chanjuan Zhou", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Mingliang Tang", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Yu Chen", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China; Institute for Vaccine Research, Animal Biosafety Level 3" + }, + { + "author_name": "Ke Lan", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China; Institute for Vaccine Research, Animal Biosafety Level 3" + }, + { + "author_name": "Li Zhou", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China; Institute for Vaccine Research, Animal Biosafety Level 3" + }, + { + "author_name": "Ke Xu", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China; Institute for Vaccine Research, Animal Biosafety Level 3" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.03.22275891", "rel_title": "A More Accurate Measurement of the Burden of COVID-19 Hospitalizations", @@ -292646,29 +293299,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.06.02.22275908", - "rel_title": "Asymptotic Analysis of Optimal Vaccination Policies", - "rel_date": "2022-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.02.22275908", - "rel_abs": "Targeted vaccination policies can have a significant impact on the number of infections and deaths in an epidemic. However, optimising such policies is complicated and the resultant solution may be difficult to explain to policy-makers and to the public. The key novelty of this paper is a derivation of the leading order optimal vaccination policy under multi-group SIR (Susceptible-Infected-Recovered) dynamics in two different cases. Firstly, it considers the case of a small vulnerable subgroup in a population and shows that (in the asymptotic limit) it is optimal to vaccinate this group first, regardless of the properties of the other groups. Then, it considers the case of a small vaccine supply and transforms the optimal vaccination problem into a simple knapsack problem by linearising the final size equations. Both of these cases are then explored further through numerical examples which show that these solutions are also directly useful for realistic parameter values. Moreover, the findings of this paper give some general principles for optimal vaccination policies which will help policy-makers and the public to understand the reasoning behind optimal vaccination programs in more generic cases.\n\nAuthor summaryThe COVID-19 pandemic has illustrated the importance of vaccination programs in preventing infections and deaths from an epidemic. A common feature of vaccination programs across the world has been a prioritisation of different groups within each countrys population, particularly those who are more vulnerable to the disease. Finding the best priority order is crucial, but may be complicated and difficult to justify to policy-makers and the public. In this paper, we consider two extreme cases where the best prioritisation order can be mathematically derived. Firstly, we consider the case of a population with a very small, very vulnerable group and show that this group should always be vaccinated first. Then, we consider the case of a small supply of vaccines and derive an equation which gives the best prioritisation order. Understanding these extreme cases is important, as it highlights general principles of optimal policies which will be useful when understanding the solution in more complicated settings.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Matthew J Penn", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christl A. Donnelly", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.31.22275835", "rel_title": "One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants", @@ -293036,6 +293666,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.06.01.22275882", + "rel_title": "Longitudinal profiles of plasma gelsolin, cytokines and antibody expression predict COVID-19 severity and hospitalization outcomes", + "rel_date": "2022-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.01.22275882", + "rel_abs": "BackgroundPrognostic markers for COVID-19 disease outcome are currently lacking. Plasma gelsolin (pGSN) is an actin-binding protein and an innate immune marker involved in disease pathogenesis and viral infections. Here, we demonstrate the utility of pGSN as a prognostic marker for COVID-19 disease outcome; a test performance that is significantly improved when combined with cytokines and antibodies compared to other conventional markers such as CRP and ferritin.\n\nMethodsBlood samples were longitudinally collected from hospitalized COVID-19 patients as well as COVID-19 negative controls and the levels of pGSN in g/mL, cytokines and anti-SARS-CoV-2 spike protein antibodies assayed. Mean{+/-}SEM values were correlated with clinical parameters to develop a prognostic platform.\n\nResultspGSN levels were significantly reduced in COVID-19 patients compared to healthy individuals. Additionally, pGSN levels combined with plasma IL-6, IP-10 and M-CSF significantly distinguished COVID-19 patients from healthy individuals. While pGSN and anti-spike IgG titers together strongly predict COVID-19 severity and death, the combination of pGSN and IL-6 was a significant predictor of milder disease and favorable outcomes.\n\nConclusionTaken together, these findings suggest that multi-parameter analysis of pGSN, cytokines and antibodies could predict COVID-19 hospitalization outcomes with greater certainty compared with conventional clinical laboratory markers such as CRP and ferritin. This research will inform and improve clinical management and health system interventions in response to SARS-CoV-2 infection.\n\nTrial RegistrationN/A\n\nFundingThe Ottawa Hospital Department of Medicine - Special Pandemic Agile Research Competition", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Meshach Asare-Werehene", + "author_inst": "Ottawa Hospital Research Institute" + }, + { + "author_name": "Michaeline McGuinty", + "author_inst": "The Ottawa Hospital" + }, + { + "author_name": "Agatha Vranjkovic", + "author_inst": "Ottawa Hospital Research Institute" + }, + { + "author_name": "Yannick Galipeau", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Juthaporn Cowan", + "author_inst": "The Ottawa Hospital" + }, + { + "author_name": "Bill Cameron", + "author_inst": "The Ottawa Hospital" + }, + { + "author_name": "Curtis L Cooper", + "author_inst": "The Ottawa Hospital" + }, + { + "author_name": "Marc-Andre Langlois", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Angela M Crawley", + "author_inst": "Ottawa Hospital Research Institute" + }, + { + "author_name": "Benjamin K Tsang", + "author_inst": "Ottawa Hospital Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.02.22275901", "rel_title": "Iron status and the risk of sepsis and severe COVID-19: A two-sample Mendelian randomization study", @@ -294360,89 +295045,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.05.31.22275802", - "rel_title": "SARS-CoV-2 genomic surveillance in Rwanda: Introductions and local transmission of the B.1.617.2 (Delta) variant of concern", - "rel_date": "2022-05-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22275802", - "rel_abs": "The emergence of the SARS-CoV-2 Delta variant of concern (lineage B.1.617.2) in late 2020 resulted in a new wave of infections in many countries across the world, where it often became the dominant lineage in a relatively short amount of time. We here report on a novel genomic surveillance effort in Rwanda in the time period from June to September 2021, leading to 201 SARS-CoV-2 genomes being generated, the majority of which were identified as the Delta variant of concern. We show that in Rwanda, the Delta variant almost completely replaced the previously dominant A.23.1 and B.1.351 (Beta) lineages in a matter of weeks, and led to a tripling of the total number of COVID-19 infections and COVID-19-related fatalities over the course of only three months. We estimate that Delta in Rwanda had an average growth rate advantage of 0.034 (95% CI 0.025-0.045) per day over A.23.1, and of 0.022 (95% CI 0.012-0.032) over B.1.351. Phylogenetic analysis reveals the presence of at least seven local Delta transmission clusters, with two of these clusters occurring close to the border with the Democratic Republic of the Congo, and another cluster close to the border with Tanzania. A smaller Delta cluster of infections also appeared close to the border with Uganda, illustrating the importance of monitoring cross-border traffic to limit the spread between Rwanda and its neighboring countries. We discuss our findings against a background of increased vaccination efforts in Rwanda, and also discuss a number of breakthrough infections identified during our study. Concluding, our study has added an important collection of data to the available genomes for the Eastern Africa region, with the number of Delta infections close to the border with neighboring countries highlighting the need to further strengthen genomic surveillance in the region to obtain a better understanding of the impact of border crossings on lowering the epidemic curve in Rwanda.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Yvan Butera", - "author_inst": "Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda; Rwanda National Joint Task Force COVID-19, Rwanda Biom" - }, - { - "author_name": "Samuel L. Hong", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Muhammed Semakula", - "author_inst": "Center for Excellence in Data Science, University of Rwanda, Kigali, Rwanda; Centre for Statistics, Hasselt Biostatistics and Statistical Bioinformatics Center," - }, - { - "author_name": "Nena Bollen", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Verity Hill", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland" - }, - { - "author_name": "Aine O'Toole", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland" - }, - { - "author_name": "Barney I. Potter", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Dieudonne Mutangana", - "author_inst": "Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda; School of Science, College of Science and Technology, " - }, - { - "author_name": "Reuben Sindayiheba", - "author_inst": "National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda" - }, - { - "author_name": "Robert Rutayisire", - "author_inst": "Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda; National Reference Laboratory, Rwanda Biomedical Center" - }, - { - "author_name": "Maria Artesi", - "author_inst": "Laboratory of Human Genetics, GIGA Research Institute, Liege, Belgium" - }, - { - "author_name": "Vincent Bours", - "author_inst": "Laboratory of Human Genetics, GIGA Research Institute, Liege, Belgium; Department of Human Genetics, University Hospital of Liege, Liege, Belgium" - }, - { - "author_name": "Nadine Rujeni", - "author_inst": "Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda; School of Health Sciences, College of Medicine and Heal" - }, - { - "author_name": "Simon Dellicour", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium; Spatial Epidemiology Laboratory, University Libre de Bru" - }, - { - "author_name": "Keith Durkin", - "author_inst": "Laboratory of Human Genetics, GIGA Research Institute, Liege, Belgium" - }, - { - "author_name": "Leon Mutesa", - "author_inst": "Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda; Rwanda National Joint Task Force COVID-19, Rwanda Biom" - }, - { - "author_name": "Guy Baele", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.05.31.22275814", "rel_title": "Heterogeneous evolution of SARS-CoV-2 seroprevalence in school-age children: Results from the Ciao Corona study in November-December 2021 in the canton of Zurich", @@ -294666,6 +295268,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.31.494162", + "rel_title": "The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity", + "rel_date": "2022-05-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.31.494162", + "rel_abs": "Oral and upper respiratory microbiota play important roles in modulating host immune responses to viral infection. As emerging evidence suggests the host microbiome may be involved in the pathophysiology of COVID-19, we aimed to investigate associations between the oral and nasopharyngeal microbiome and COVID-19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID-19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID-19 symptoms, and blood cytokines. SARS-CoV-2 infection status, but not COVID-19 severity, was associated with community-level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Several bacterial genera were differentially abundant by COVID-19 severity, including oral Bifidobacterium, Lactobacillus, and Solobacterium, all of which were depleted in patients with severe COVID-19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID-19. Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID-19 biomarkers interleukin 17F (IL-17F) and monocyte chemoattractant protein-1 (MCP-1). In conclusion, our results suggest COVID-19 disease severity is associated with the relative abundance of certain bacterial taxa.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Josh G Kim", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Ai Zhang", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Adriana M Rauseo", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Charles William Goss", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Philip A Mudd", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Leyao Wang", + "author_inst": "Washington University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.05.31.493925", "rel_title": "Comprehensive characterization of the transcriptional response to COVID-19 in multiple organs reveals shared signatures across tissues", @@ -295998,25 +296639,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2022.05.24.22275504", - "rel_title": "The connection between COVID-19 vaccine abundance, vaccination coverage, and public trust in government across the globe", - "rel_date": "2022-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.24.22275504", - "rel_abs": "This study investigates that how the number of COVID-19 vaccines secured correlates with the vaccination coverage (full and booster) depending on whether there is trust in national government or not across 47 countries. The data are based on global figures as of Nov. 2021 and Feb. 2022 while measures for confidence in government is according to Gallup World Poll, Oct. 2021. The model includes an interaction term of the two key variables, also controls for a range of socio-economic factors and country specific variables. The results indicate a non-linear and mixed relationship between the number secured, the public trust, and the vaccination rate. In Feb. 2022, with confidence in government, securing number of vaccines to cover 200% of the population (or more) increased the full vaccination rate by 12.26% (95% CI: 11.70 - 12.81); where number secured was 300% (or more), the coverage increased by 7.46% (95% CI: 6.95 - 7.97). Under similar scenarios, rate of booster shots increased by 13.16% (95% CI: 12.62 - 13.70; p < 0.01) and 14.36% (95% CI: 13.86 - 14.85; p < 0.01), respectively. Where the number secured fell below 200%, confidence in government had a revers relationship with the rate of full vaccination (-2.65; 95% CI: -3.32 - -1.99), yet positive with the rate of booster shots (1.65; 95% CI: 1.18 - 2.12). These results indicate that better success can be achieved by a combination of factors including securing sufficient number of vaccines and also ensuring the public trust. Vaccine abundance, however, cannot be translated into greater success in vaccination coverage. This study highlights the importance of efficiency in acquiring vaccine resources and need for improvement in public belief in immunization programmes rather than stock piling.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ida G. Monfared", - "author_inst": "Georg-August-Universitat Gottingen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.27.22275708", "rel_title": "Identifying COVID-19 phenotypes using cluster analysis and assessing their clinical outcomes", @@ -296288,6 +296910,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2022.05.27.22275673", + "rel_title": "CMV seropositivity in older adults changes T cell functionality, but does not prevent antibody or cellular SARS-CoV-2 vaccine responses", + "rel_date": "2022-05-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.27.22275673", + "rel_abs": "Chronic infection with human cytomegalovirus (CMV) may contribute to poor vaccine efficacy in older adults. We assessed effects of CMV serostatus on antibody quantity and quality, as well as cellular memory recall responses, after 2 and 3 SARS-CoV-2 mRNA vaccine doses, in older adults in assisted living facilities. CMV serostatus did not affect anti-Spike and anti-RBD IgG antibody levels, nor neutralization capacity against wildtype or beta variants of SARS-CoV-2 several months after vaccination. CMV seropositivity altered T cell expression of senescence-associated markers and increased TEMRA cell numbers, as has been previously reported; however, this did not impact Spike-specific CD4+ T cell memory recall responses. CMV seropositive individuals did not have a higher incidence of COVID-19, though prior infection influenced humoral immunity. Therefore, CMV seropositivity may alter T cell composition but does not impede the durability of humoral protection or cellular memory responses after SARS-CoV-2 mRNA vaccination in older adults.\n\nKey PointsCMV seropositive older adults have more EMRA and terminally differentiated T cells CMV seropositivity does not prevent antibody maintenance after SARS-CoV-2 vaccination CMV seropositivity does not impede SARS-CoV-2 vaccine T cell memory recall responses", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Jessica A. Breznik", + "author_inst": "McMaster University" + }, + { + "author_name": "Angela Huynh", + "author_inst": "McMaster University" + }, + { + "author_name": "Ali Zhang", + "author_inst": "McMaster University" + }, + { + "author_name": "Lucas Bilaver", + "author_inst": "McMaster University" + }, + { + "author_name": "Hina Bhakta", + "author_inst": "McMaster University" + }, + { + "author_name": "Hannah D. Stacey", + "author_inst": "McMaster University" + }, + { + "author_name": "Jann C. Ang", + "author_inst": "McMaster University" + }, + { + "author_name": "Jonathan L. Bramson", + "author_inst": "McMaster University" + }, + { + "author_name": "Ishac Nazy", + "author_inst": "McMaster University" + }, + { + "author_name": "Matthew S Miller", + "author_inst": "McMaster University" + }, + { + "author_name": "Judah Denburg", + "author_inst": "McMaster University" + }, + { + "author_name": "Andrew P Costa", + "author_inst": "McMaster University" + }, + { + "author_name": "Dawn M. E. Bowdish", + "author_inst": "McMaster University" + }, + { + "author_name": "- COVID-in-LTC Study Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.05.27.22275706", "rel_title": "A pharmacoepidemiological study of myocarditis and pericarditis following mRNA COVID-19 vaccination in Europe", @@ -297940,33 +298633,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.05.27.493693", - "rel_title": "Development of a Novel SARS-CoV-2 Immune Complex Vaccine Candidate (CRCx) with Broad Immune Responses: A Preclinical Trial in Animal Model", - "rel_date": "2022-05-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.27.493693", - "rel_abs": "BackgroundThe ongoing pandemic of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a serious threat to global public health and imposes a severe burden on the entire human population. Faced with a virus that can mutate its structure while immunity is incapacitated, a need to develop a universal vaccine that can boost immunity to coronaviruses is highly needed.\n\nDesignFive formulations of two types (CRCx2 and CRCx3) of immune complexes with an immunogen adjuvant were evaluated in a mouse model as candidate SARS CoV-2 vaccines in a pretrial prior to clinical trials in humans. CRCx3 comprises 3 different formulas and CRCx2 comprises 2. Balb/c mice were vaccinated intraperitoneally on days 0/7 with a high or low dose of CRCx2 or on days 0/7/14 with a high, medium, or low dose of CRCx3 series, and their blood was sampled for serum antibody measurements. Mice were challenged with live virus after immunization with either vaccine to evaluate prophylaxis ability or treated with them after challenge to evaluate therapeutic ability on day 15. Immunological markers and histopathological studies as well as titration of neutralizing antibodies to the vaccines were evaluated and analyzed.\n\nResultsCRCx 3 and CRCx 2 vaccine candidates induced elevated levels of positive neutralizing antibodies as well as a cellular immune response with safety, efficient productivity, and good genetic stability for vaccine manufacturing to provide protection against SARS-CoV-2 with relatively higher levels with the high dose CRCx2 candidate combination.\n\nConclusionsHighly efficient protection and therapeutic effect against SARS-CoV-2 were obtained with a double-dose immunization schedule spaced at 7-day intervals using injections 0.25 of or 0.40 ml of CRCx2 vaccine formulations with a 25-mm needle. These results support further evaluation of CRCx in a clinical trial on humans.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Khalid Mahmoud El Sayed Zayed", - "author_inst": "Ain Shams University" - }, - { - "author_name": "Sherif Salah Abdulaziz", - "author_inst": "Cairo University" - }, - { - "author_name": "Khaled Omar Abdallah", - "author_inst": "Ain Shams University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.05.24.22275478", "rel_title": "Effective antiviral regimens to reduce COVID-19 hospitalizations: a systematic comparison of randomized controlled trials", @@ -298774,6 +299440,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.25.22275592", + "rel_title": "COVID-19 pandemic impact on preterm birth and stillbirth rates associated with socioeconomic disparities: A quasi-experimental study", + "rel_date": "2022-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.25.22275592", + "rel_abs": "BackgroundConflicting evidence exists on the impact of the COVID-19 pandemic restrictions on preterm birth (PTB) and stillbirth rates. We aimed to evaluate changes in PTB and stillbirth rates before and during the pandemic period and assess the potential effect modification of socioeconomic status (SES).\n\nMethodsUsing the linked administrative health databases from Manitoba, Canada, we conducted a quasi-experimental study among all pregnant women, comparing 3.5 years pre-pandemic (1 October 2016 to 29 February 2020) to the first year of the pandemic (1 March 2020 to 31 March 2021). We used interrupted time series analysis using autoregressive integrated moving average models to assess the quarterly rates of PTB (<37 weeks) and stillbirths. We calculated the predicted trends based on pre-pandemic period data. Finally, we evaluated the lower and higher SES (average annual household income) using subgroup analysis and interaction models.\n\nResultsWe examined 70,931 pregnancies in Manitoba during the study period. Following the implementation of COVID-19 restrictions in March 2020, there were no statistically significant changes in the rates of both PTB (p=0.094) and stillbirths (p=0.958). However, over the pandemic, the PTB rate significantly decreased as a rebound effect by 0.63% per quarter(p=0.005); whereas the stillbirth rate did not change significantly (p=0.878) compared to pre-pandemic period. During the first quarter of 2021, the absolute differences in the observed and expected PTB and stillbirth percentages were 2.05% and 0.04%, respectively. We observed a statistically significant effect modification by SES for PTB rates (p=0.047).\n\nConclusionWhile the onset of COVID-19 pandemic restrictions was not associated with significant effects on PTB and stillbirth rates, we observed a statistically significant rebound effect on PTB rates. The impact of COVID-19 on preterm birth was dependent on SES, with higher influence on families with lower SES. Further studies are needed to detect future trend changes during pandemic waves after 2021 and assess potential underlying mechanisms.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Laila Aboulatta", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Kaarina Kowalec", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Christine Leong", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Joseph Delaney", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Jamie Falk", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Silvia Alessi-Severini", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Dan Chateau", + "author_inst": "College of Health and Medicine, Australian National University, Australia." + }, + { + "author_name": "Qier Tan", + "author_inst": "Manitoba Centre for Health Policy" + }, + { + "author_name": "Katherine Kearns", + "author_inst": "College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Christina Raimondi", + "author_inst": "College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Alekhya Lavu", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Lara Haidar", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Christine Vaccaro", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + }, + { + "author_name": "Sherif Eltonsy", + "author_inst": "College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Canada." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.25.22275586", "rel_title": "Noninvasive ventilation strategies for patients with severe or critical COVID-19: A rapid review of clinical outcomes", @@ -300214,81 +300951,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.24.493187", - "rel_title": "Hemin shows antiviral activity in vitro, possibly through suppression of viral entry mediators.", - "rel_date": "2022-05-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.24.493187", - "rel_abs": "Heme oxygenase-1 (HO-1) is a stress-induced enzyme that catalyzes the breakdown of heme into biliverdin, carbon monoxide, and iron. Targeting HO-1 to treat severe COVID-19 has been suggested by several groups, yet the role of HO-1 in SARS-CoV-2 infection remains unclear. Based on this, we aimed to investigate the antiviral activity of Hemin, an activator of HO-1. Infectivity of SARS-CoV-2 was decreased in Vero E6 cells treated with Hemin. Hemin also decreased TMPRSS2 and ACE2 mRNA levels in non-infected cells, possibly explaining the observed decrease in infectivity. TMPRSS2 protein expression and proteolytic activity were decreased in Vero E6 cells treated with Hemin. Besides that, experimental studies supported with in silico calculations. Overall, our study supports further exploration of Hemin as a potential antiviral and inflammatory drug for the treatment of COVID-19.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Mehmet Altay UNAL", - "author_inst": "Ankara University Stem Cell" - }, - { - "author_name": "Ceylan Verda BITIRIM", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Julia SOMERS", - "author_inst": "Oregon Health & Science Univerity" - }, - { - "author_name": "Gokce Yagmur SUMMAK", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Omur BUL BESBINAR", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Ebru KOCAKAYA", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Cansu GURCAN", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Hasan NAZIR", - "author_inst": "Ankara University Faculty of Science Department of Chemistry" - }, - { - "author_name": "Zeynep Busra Aksoy Ozer", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Sibel Aysil OZKAN", - "author_inst": "Ankara University Faculty of Pharmacy" - }, - { - "author_name": "Sidar BEREKETOGLU", - "author_inst": "Ankara University Faculty of Science" - }, - { - "author_name": "Aykut OZKUL", - "author_inst": "Ankara University Faculty of Veterinary Medicine" - }, - { - "author_name": "Emek DEMIR", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Kamil Can AKCALI", - "author_inst": "Ankara Universiy Faculty of Medicine Depatment of Biophysics" - }, - { - "author_name": "Acelya YILMAZER", - "author_inst": "Ankara University Faculty of Engineering Department of Biomedical Engineering" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2022.05.24.22275529", "rel_title": "Depressive and anxiety symptoms during the COVID-19 pandemic: A two-year follow-up", @@ -300656,6 +301318,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.05.23.22275458", + "rel_title": "Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States", + "rel_date": "2022-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.23.22275458", + "rel_abs": "Covid-19 has caused more than 1 million deaths in the US, including at least 1,204 deaths among children and young people (CYP) aged 0-19 years, with 796 occurring in the one year period April 1, 2021 - March 31, 2022. Deaths among US CYP are rare in general, and so we argue here that the mortality burden of Covid-19 in CYP is best understood in the context of all other causes of CYP death. Using publicly available data from CDC WONDER on NCHSs 113 Selected Causes of Death, and comparing to mortality in 2019, the immediate pre-pandemic period, we find that Covid-19 mortality is among the 10 leading causes of death in CYP aged 0-19 years in the US, ranking 8th among all causes of deaths, 5th in disease-related causes of deaths (excluding accidents, assault and suicide), and 1st in deaths caused by infectious or respiratory diseases. Covid-19 deaths constitute 2.3% of the 10 leading causes of death in this age group. Covid-19 caused substantially more deaths in CYP than major vaccine-preventable diseases did historically in the period before vaccines became available. Various factors including underreporting and Covid-19s role as a contributing cause of death from other diseases mean that our estimates may understate the true mortality burden of Covid-19. Our findings underscore the public health relevance of Covid-19 to CYP. In the likely future context of sustained SARS-CoV-2 circulation, pharmaceutical and non-pharmaceutical interventions will continue to play an important role in limiting transmission of the virus in CYP and mitigating severe disease.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Seth Flaxman", + "author_inst": "Oxford" + }, + { + "author_name": "Charles Whittaker", + "author_inst": "Imperial College London" + }, + { + "author_name": "Elizaveta Semenova", + "author_inst": "AstraZeneca" + }, + { + "author_name": "Theo Rashid", + "author_inst": "Imperial College London" + }, + { + "author_name": "Robbie Parks", + "author_inst": "Columbia University" + }, + { + "author_name": "Alexandra Blenkinsop", + "author_inst": "Imperial College London" + }, + { + "author_name": "H Juliette T Unwin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Swapnil Mishra", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Samir Bhatt", + "author_inst": "University of Copenhagen, Imperial College London" + }, + { + "author_name": "Deepti Gurdasani", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Oliver Ratmann", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.24.493347", "rel_title": "Subcutaneous delivery of an antibody against SARS-CoV-2 from a supramolecular hydrogel depot", @@ -302120,57 +302841,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.21.22275368", - "rel_title": "Variant-specific symptoms of COVID-19 among 1,542,510 people in England", - "rel_date": "2022-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.21.22275368", - "rel_abs": "Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Matthew Whitaker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Joshua Elliott", - "author_inst": "Imperial College London" - }, - { - "author_name": "Barbara Bodinier", - "author_inst": "Imperial College London" - }, - { - "author_name": "Wendy S Barclay", - "author_inst": "Imperial College London" - }, - { - "author_name": "Helen Ward", - "author_inst": "Imperial College London" - }, - { - "author_name": "Graham Cooke", - "author_inst": "Imperial College London" - }, - { - "author_name": "Christl A Donnelly", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marc Chadeau-Hyam", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paul Elliott", - "author_inst": "Imperial College London School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.21.492928", "rel_title": "Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccines", @@ -302694,6 +303364,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.21.492922", + "rel_title": "Using a reverse genetics system to generate recombinant SARS-CoV-2 expressing robust levels of reporter genes", + "rel_date": "2022-05-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.21.492922", + "rel_abs": "Reporter-expressing recombinant virus represents an excellent option and a powerful tool to investigate, among others, viral infection, pathogenicity, and transmission, as well as to identify therapeutic compounds that inhibit viral infection and prophylactic vaccines. To combat the still ongoing coronavirus disease 2019 (COVID-19) pandemic, we have established a robust bacterial artificial chromosome (BAC)-based reverse genetics (RG) system to rapidly generate recombinant severe acute respiratory syndrome coronavirus 2 (rSARS-CoV-2) to study the contribution of viral proteins in viral pathogenesis. In addition, we have also engineered reporter-expressing recombinant viruses in which we place the reporter genes upstream of the viral nucleocapsid (N) gene to promote high levels of reporter gene expression that facilitates the study of SARS-CoV-2 in vitro and in vivo. Although successful, the genetic manipulation of the BAC containing the entire SARS-CoV-2 genome of [~]30,000 nucleotides, is challenging. Herein, we depict the technical details to engineer rSARS-CoV-2 expressing reporter genes using the BAC-based RG approach. We describe i) assembly of the full-length (FL) SARS-CoV-2 genome sequences into the empty pBeloBAC, ii) verification of the pBeloBAC-FL, iii) cloning of a Venus reporter gene into the pBeloBAC-FL, and iv) recovery of the Venus-expressing rSARS-CoV-2. By following this protocol, researchers with basic molecular biology and gene engineering techniques knowledge will be able to generate wild-type and reporter-expressing rSARS-CoV-2.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.05.23.492800", "rel_title": "Predictions of immunogenicity reveal potent SARS-CoV-2 CD8+ T-cell epitopes", @@ -304202,57 +304895,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2022.05.19.22275339", - "rel_title": "Covid-19 Vaccine Acceptance Among People Incarcerated in Connecticut State Jails", - "rel_date": "2022-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275339", - "rel_abs": "ObjectiveTo assess the Connecticut Department of Corrections (DOC) COVID-19 vaccine program within jails.\n\nMethodsWe conducted a retrospective cohort analysis among people who were incarcerated in a DOC-operated jail between February 2 and November 8, 2021, and were eligible for vaccination at the time of incarceration (intake). We compared the vaccination rates before and after incarceration using an age-adjusted survival analysis with a time-varying exposure of incarceration and an outcome of vaccination.\n\nResultsDuring the study period, 3,716 people spent [≥]1 night in jail and were eligible for vaccination at intake. Of these residents, 136 were vaccinated prior to incarceration, 2,265 had a recorded vaccine offer, and 476 were vaccinated while incarcerated. The age-adjusted hazard of vaccination following incarceration was significantly higher than prior to incarceration (12.5; 95% CI: 10.2-15.3).\n\nConclusionsWe found that residents were more likely to become vaccinated in jail than the community. Though these findings highlight the utility of vaccination programs within jails, the low level of vaccination in this population speaks to the need for additional program development within jails and the community.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Margaret Lind", - "author_inst": "Yale University" - }, - { - "author_name": "Byron S Kennedy", - "author_inst": "Connecticut Department of Correction" - }, - { - "author_name": "Murilo Dorion Nieto", - "author_inst": "Yale University" - }, - { - "author_name": "Amy J Houde", - "author_inst": "Connecticut Department of Corrections" - }, - { - "author_name": "Peri Sosensky", - "author_inst": "Yale University" - }, - { - "author_name": "Ryan Borg", - "author_inst": "Yale University" - }, - { - "author_name": "Derek A.T. Cummings", - "author_inst": "University of Florida" - }, - { - "author_name": "Albert Ko", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Robert P Richeson", - "author_inst": "Connecticut Department of Corrections" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.20.492819", "rel_title": "Revealing druggable cryptic pockets in the Nsp-1 of SARS-CoV-2 and other \u03b2-coronaviruses by simulations and crystallography", @@ -304556,6 +305198,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.05.20.492815", + "rel_title": "Structural basis for substrate selection by the SARS-CoV-2 replicase", + "rel_date": "2022-05-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.20.492815", + "rel_abs": "The SARS-CoV-2 RNA-dependent RNA polymerase coordinates viral RNA synthesis as part of an assembly known as the replication-transcription complex (RTC)1. Accordingly, the RTC is a target for clinically approved antiviral nucleoside analogs, including remdesivir2. Faithful synthesis of viral RNAs by the RTC requires recognition of the correct nucleotide triphosphate (NTP) for incorporation into the nascent RNA. To be effective inhibitors, antiviral nucleoside analogs must compete with the natural NTPs for incorporation. How the SARS-CoV-2 RTC discriminates between the natural NTPs, and how antiviral nucleoside analogs compete, has not been discerned in detail. Here, we use cryo-electron microscopy to visualize the RTC bound to each of the natural NTPs in states poised for incorporation. Furthermore, we investigate the RTC with the active metabolite of remdesivir, remdesivir triphosphate (RDV-TP), highlighting the structural basis for the selective incorporation of RDV-TP over its natural counterpart ATP3,4. Our results elucidate the suite of interactions required for NTP recognition, informing the rational design of antivirals. Our analysis also yields insights into nucleotide recognition by the nsp12 NiRAN, an enigmatic catalytic domain essential for viral propagation5. The NiRAN selectively binds GTP, strengthening proposals for the role of this domain in the formation of the 5 RNA cap6.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Brandon F. Malone", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Jason K. Perry", + "author_inst": "Gilead Sciences" + }, + { + "author_name": "Paul Dominic B. Olinares", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "James Chen", + "author_inst": "New York University" + }, + { + "author_name": "Todd K. Appleby", + "author_inst": "Gilead Sciences" + }, + { + "author_name": "Joy Y. Feng", + "author_inst": "Gilead Sciences" + }, + { + "author_name": "John P. Bilello", + "author_inst": "Gilead Sciences" + }, + { + "author_name": "Honkit Ng", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Johanna Sotiris", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Mark Ebrahim", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Eugene Y.D. Chua", + "author_inst": "New York Structural Biology Center" + }, + { + "author_name": "Joshua H. Mendez", + "author_inst": "New York Structural Biology Center" + }, + { + "author_name": "Edward T. Eng", + "author_inst": "New York Structural Biology Center" + }, + { + "author_name": "Robert Landick", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Brian T. Chait", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Elizabeth A. Campbell", + "author_inst": "The Rockefeller Univeristy" + }, + { + "author_name": "Seth A. Darst", + "author_inst": "The Rockefeller University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.05.20.492779", "rel_title": "Omicron breakthrough infections in vaccinated or previously infected hamsters", @@ -306104,73 +306829,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2022.05.19.22275053", - "rel_title": "Evaluating the impact on health outcomes of an event that resulted in a delay in contact tracing of COVID-19 cases", - "rel_date": "2022-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275053", - "rel_abs": "ObjectiveIn September 2020, records of 15,861 SARS-CoV-2 cases failed to upload from the Second Generation Laboratory Surveillance System (SGSS) to the Contact Tracing Advisory Service (CTAS) tool, resulting in a delay in the contact tracing of these cases. This study used CTAS data to determine the impact of this delay on health outcomes: transmission events, hospitalisations, and mortality. Previously, a modelling study had suggested a substantial impact.\n\nDesignObservational study\n\nSettingEngland.\n\nPopulationIndividuals testing positive for SARS-CoV-2 and their reported contacts.\n\nMain outcome measuresSecondary attack rates (SARs), hospitalisations, and deaths amongst primary and secondary contacts were calculated, compared to all other concurrent, unaffected cases. SGSS records affected by the event were matched to CTAS records and successive contacts and cases were identified.\n\nResultsThe initiation of contact tracing was delayed by 3 days on average in the primary cases in the delay group (6 days) compared to the control group (3 days). This was associated with lower completion of contact tracing of primary cases in the delay group: 80% (95%CI: 79-81%) in the delay group and 83% (95%CI: 83-84%) in the control group. There was some evidence to suggest an increase in transmission to non-household contacts amongst those affected by the delay. The SAR for non-household contacts was higher amongst secondary contacts in the delay group than the control group (delay group: 7.9%, 95%CI:6.4% to 9.2%; control group: 5.9%, 95%CI: 5.3% to 6.6%). There was no evidence of a difference between the delay and control groups in the odds of hospitalisation (crude odds ratio: 1.1 (95%CI: 0.9 to 1.2) or death (crude odds ratio: 0.7 (0.1 to 4.0)) amongst secondary contacts.\n\nConclusionsThe delay in contact tracing had a limited impact on population health outcomes.\n\nStrengths and limitations of the studyO_LIShows empirical data on the health impact of an event leading to a delay in contact tracing so can test hypotheses generated by models of the potential impact of a delay in contact tracing\nC_LIO_LIEstimates the extent of further transmission and odds of increased mortality or hospitalisation in up to the third generation of cases affected by the event\nC_LIO_LIThe event acts as a natural experiment to describe the possible impact of contact tracing, comparing a group affected by chance by delayed contact tracing to a control group who experienced no delay\nC_LIO_LIContact tracing was not completed for all individuals, so the study might not capture all affected contacts or transmissions\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Lucy Findlater", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Livia Pierotti", - "author_inst": "University of Bristol" - }, - { - "author_name": "Charlie Turner", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Adrian Wensley", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Cong Chen", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Shaun Seaman", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Pantelis Samartsidis", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Andre Charlett", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Charlotte Anderson", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Gareth Hughes", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Matthew Hickman", - "author_inst": "University of Bristol" - }, - { - "author_name": "Obaghe Edeghere", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Isabel Oliver", - "author_inst": "UK Health Security Agency" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.19.22275055", "rel_title": "How Should COVID-19 Vaccines be Distributed between the Global North and South? A Discrete Choice Experiment in Six European Countries", @@ -306350,6 +307008,173 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.15.22275051", + "rel_title": "Infectious viral shedding of SARS-CoV-2 Delta following vaccination: a longitudinal cohort study", + "rel_date": "2022-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.15.22275051", + "rel_abs": "The impact of vaccination on SARS-CoV-2 infectiousness is not well understood. We compared longitudinal viral shedding dynamics in unvaccinated and fully vaccinated adults. SARS-CoV-2-infected adults were enrolled within 5 days of symptom onset and nasal specimens were self-collected daily for two weeks and intermittently for an additional two weeks. SARS-CoV-2 RNA load and infectious virus were analyzed relative to symptom onset stratified by vaccination status. We tested 1080 nasal specimens from 52 unvaccinated adults enrolled in the pre-Delta period and 32 fully vaccinated adults with predominantly Delta infections. While we observed no differences by vaccination status in maximum RNA levels, maximum infectious titers and the median duration of viral RNA shedding, the rate of decay from the maximum RNA load was faster among vaccinated; maximum infectious titers and maximum RNA levels were highly correlated. Furthermore, amongst participants with infectious virus, median duration of infectious virus detection was reduced from 7.5 days (IQR: 6.0-9.0) in unvaccinated participants to 6 days (IQR: 5.0-8.0) in those vaccinated (P=0.02). Accordingly, the odds of shedding infectious virus from days 6 to 12 post-onset were lower among vaccinated participants than unvaccinated participants (OR 0.42 95% CI 0.19-0.89). These results indicate that vaccination had reduced the probability of shedding infectious virus after 5 days from symptom onset.\n\nSignificance statementWe present longitudinal data on the magnitude, duration and decay rate of viral RNA and the magnitude and duration of infectious virus in nasal specimens from vaccinated and unvaccinated participants. On average, vaccinated participants (infected with the highly transmissible Delta variant) showed a lower probability of having infectious virus after 5 days of symptoms compared to unvaccinated participants (infected with mostly pre-delta viral lineages), even though both groups had a similar magnitude of infectious virus at or near the peak. These data help improve our understanding of the duration of the infectious period when infection occurs following vaccination and serves as a reference for future studies of shedding dynamics following infections with novel variants of concern.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Miguel A Garcia-Knight", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Khamal Anglin", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Michel Tassetto", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Scott Lu", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Amethyst Zhang", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Sarah A Goldberg", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Adam Catching", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Michelle C Davidson", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Joshua R Shak", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Mariela Romero", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jesus Pineda-Ramirez", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Ruth Diaz-Sanchez", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Paulina Rugart", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Kevin Donohue", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jonathan Massachi", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Hannah M Sans", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Manuella Djomaleu", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Sujata Mathur", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Venice Servellita", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "David McIlwain", + "author_inst": "Stanford University" + }, + { + "author_name": "Brice Gaudiliere", + "author_inst": "Stanford University" + }, + { + "author_name": "Jessica Chen", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Enrique O Martinez", + "author_inst": "Medical College of Wisconsin" + }, + { + "author_name": "Jacqueline M Tavs", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Grace Bronstone", + "author_inst": "Wellesley College" + }, + { + "author_name": "Jacob Weiss", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "John T Watson", + "author_inst": "Centers for Disease Control" + }, + { + "author_name": "Melissa Briggs-Hagen", + "author_inst": "Centers for Disease Control" + }, + { + "author_name": "Glen R Abedi", + "author_inst": "Centers for Disease Control" + }, + { + "author_name": "George W Rutherford", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Steven G Deeks", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Charles Chiu", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Sharon Saydah", + "author_inst": "Centers for Disease Control" + }, + { + "author_name": "Michael J Peluso", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Claire M Midgley", + "author_inst": "Centers for Disease Control" + }, + { + "author_name": "Jeffrey N Martin", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Raul Andino", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "J Daniel Kelly", + "author_inst": "University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.17.22275188", "rel_title": "COMPARISON OF SARS-COV-2 WUHAN AND ALPHA VARIANTS: CLINICAL AND LABORATORY HIGHLIGHTS", @@ -307506,57 +308331,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.05.17.492198", - "rel_title": "SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to downregulate MHC-I surface expression", - "rel_date": "2022-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.17.492198", - "rel_abs": "Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small protein {beta}2-microglobulin ({beta}2m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8+ T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that downregulate MHC-I expression to avoid CD8+ T cell recognition. Here we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, downregulate MHC-I expression using distinct mechanisms. One, ORF3a, a viroporin, reduces global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of {beta}2m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a novel and specific mechanism that allows immune evasion by SARS-CoV-2.\n\nSignificance StatementViruses may down-regulate MHC class I expression on infected cells to avoid elimination by cytotoxic T cells. We report that the accessory proteins ORF7a and ORF3a of SARS-CoV-2 mediate this function and delineate the two distinct mechanisms involved. While ORF3a inhibits global protein trafficking to the cell surface, ORF7a acts specifically on MHC-I by competing with {beta}2m for binding to the MHC-I heavy chain. This is the first account of molecular mimicry of {beta}2m as a viral mechanism of MHC-I down-regulation to facilitate immune evasion.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Najla Arshad", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Maudry Laurent-Rolle", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Wesam S Ahmed", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Jack Chun-Chieh Hsu", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Susan M Mitchell", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Joanna Pawlak", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Debrup Sengupta", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Kabir Hassan Biswas", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Peter Cresswell", - "author_inst": "Yale University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.05.15.22275086", "rel_title": "Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals", @@ -307828,6 +308602,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.12.22274990", + "rel_title": "Post COVID-19 condition of the Omicron variant of SARS-CoV-2", + "rel_date": "2022-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.12.22274990", + "rel_abs": "BackgroundNo epidemiological data on post coronavirus disease (COVID-19) condition due to Omicron variant has been reported yet.\n\nMethodsThis was as a single-center, cross-sectional study, that interviewed via telephone the patients who recovered from Omicron COVID-19 infection (Omicron group), and surveyed via self-reporting questionnaire those patients infected with other strains (control group). Data on patients characteristics, information regarding the acute-phase COVID-19, as well as presence and duration of COVID-19-related symptoms were obtained. Post COVID-19 condition in this study was defined as a symptom that lasted at least 2 months within 3 months since the onset of COVID-19. We investigated and compared the prevalence of post COVID-19 condition in both groups after performing propensity score matching.\n\nResultsWe conducted interviews for 53 out of 128 patients with Omicron, and obtained 502 responses in the control group. After matching, 18 patients each in Omicron and control group had improved covariate balance of the older adult, female sex, obese patients, and vaccination status. There were no significant differences in the prevalence of each post-acute COVID-19 symptoms between the two groups. The numbers of patients with at least one post-acute COVID-19 symptom in the Omicron and the control group were 1 (5.6%) and 10 (55.6%) (p=0.003), respectively.\n\nConclusionThe prevalence of post Omicron COVID-19 conditions was less than that of the other strains. Further research with more participants is needed to investigate the precise epidemiology of post COVID-19 condition of Omicron, and its impact on health-related quality of life and social productivity.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Shinichiro Morioka", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Shinya Tsuzuki", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Michiyo Suzuki", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Mari Terada", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Masako Akashi", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Yasuyo Osanai", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Chika Kuge", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Mio Sanada", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Keiko Tanaka", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Taketomo Maruki", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Kozue Takahashi", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Sho Saito", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Kayoko Hayakawa", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Katsuji Teruya", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Masayuki Hojo", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.13.22275054", "rel_title": "Self-Reported SARS-CoV-2 Vaccination is Consistent with Electronic Health Record Data among the COVID-19 Community Research Partnership", @@ -309144,33 +309997,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2022.05.16.22275147", - "rel_title": "Quantifying the information in noisy epidemic curves", - "rel_date": "2022-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22275147", - "rel_abs": "Reliably estimating the dynamics of transmissible diseases from noisy surveillance data is an enduring problem in modern epidemiology. Key parameters, such as the instantaneous reproduction number, Rt at time t, are often inferred from incident time series, with the aim of informing policymakers on the growth rate of outbreaks or testing hypotheses about the effectiveness of public health interventions. However, the reliability of these inferences depends critically on reporting errors and latencies innate to those time series. While studies have proposed corrections for these issues, methodology for formally assessing how these sources of noise degrade Rt estimate quality is lacking. By adapting Fisher information and experimental design theory, we develop an analytical framework to quantify the uncertainty induced by under-reporting and delays in reporting infections. This yields a novel metric, defined by the geometric means of reporting and cumulative delay probabilities, for ranking surveillance data informativeness. We apply this metric to two primary data sources for inferring Rt: epidemic case and death curves. We find that the assumption of death curves as more reliable, commonly made for acute infectious diseases such as COVID-19 and influenza, is not obvious and possibly untrue in many settings. Our framework clarifies and quantifies how actionable information about pathogen transmissibility is lost due to surveillance limitations.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kris V Parag", - "author_inst": "Imperial College London" - }, - { - "author_name": "Christl A. Donnelly", - "author_inst": "Imperial College London" - }, - { - "author_name": "Alexander E Zarebski", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.15.22273842", "rel_title": "Summaries, Analysis and Simulations of Recent COVID-19 Epidemic in Shanghai", @@ -309458,6 +310284,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.10.22274892", + "rel_title": "Acceptability of a behavioural intervention to mitigate the psychological impacts of COVID-19 restrictions in older people with long-term conditions: a qualitative study", + "rel_date": "2022-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.10.22274892", + "rel_abs": "ObjectivesThe COVID-19 pandemic has heightened the need to address loneliness and social isolation (and associated incidence of depression) amongst older adults. Between June and October 2020, the Behavioural Activation in Social IsoLation (BASIL) pilot study investigated the acceptability and feasibility of a remotely delivered brief psychological intervention (Behavioural Activation, BA) to prevent and reduce loneliness and depression in older people with long term conditions (LTCs) during the COVID-19 pandemic.\n\nDesignAn embedded qualitative study was conducted with semi-structured interviews to generate data that was first analysed inductively using thematic analysis and then deductively using the Theoretical Framework of Acceptability (TFA).\n\nSettingNational Health Service and third sector organisations in England.\n\nParticipantsSixteen older adults and 9 Support Workers (BSWs) participating in the BASIL pilot trial.\n\nResultsOlder adults and BSWs described a positive affective attitude towards the intervention linked to altruism, however the activity planning aspect of the intervention was limited due to COVID-19 restrictions. The intervention was understood by older adults & BSWs, although less understanding in older adults without low mood. A manageable burden was involved with delivering and participating in the intervention. For ethicality, older adults valued social contact and making changes, BSWs valued being able to observe those changes. Opportunity cost was low for BSWs & older adults. BA was perceived to be useful in the pandemic and likely to achieve its aims, (Perceived Effectiveness) especially if tailored to people with both low mood and LTCs. Self-efficacy developed over time and with experience for both BSWs and older adults.\n\nConclusionsOverall, the BASIL pilot study processes and BA intervention were found to be acceptable. Use of the TFA provided valuable insights into how the intervention was experienced and how the acceptability of study processes and the BA intervention could be enhanced ahead of the larger definitive trial (BASIL+).\n\nStrengths & LimitationsO_LIThe use of TFA in both informing the topic guide and conducting the analysis, demonstrating a systematic enquiry into acceptability, and contributing to the wider field as well as the topic area.\nC_LIO_LIThe length of the interviews facilitated an in-depth exploration of older adults and BASIL Support Workers experiences.\nC_LIO_LIConducting the interviews by telephone whilst discussing feasibility of telephone delivery may have enabled contextual cues to be discussed that may have been missed in a face-to-face interview set up, however may have led to a self-selecting sample of people who were comfortable with the telephone.\nC_LIO_LIA limitation is that the short timescale for the study meant that participants had to be interviewed as they completed 3m outcome measures, rather than using strategic sampling.\nC_LI", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Leanne Shearsmith", + "author_inst": "University of Leeds" + }, + { + "author_name": "Peter Coventry", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "Claire Sloan", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "Andrew Henry", + "author_inst": "University of York" + }, + { + "author_name": "Lauren Burke", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "Eloise Ryde", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "Elizabeth Newbronner", + "author_inst": "University of York" + }, + { + "author_name": "Della Bailey", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "Samantha Gascoyne", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "Rebecca Woodhouse", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "Dean McMillan", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "David Ekers", + "author_inst": "University of York Department of Health Sciences" + }, + { + "author_name": "Simon Gilbody", + "author_inst": "Mental Health and Addictions Research Group" + }, + { + "author_name": "Carolyn A. Chew-Graham", + "author_inst": "Keele University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.05.11.22274932", "rel_title": "The preliminary safety and immunogenicity results of a randomized, double-blind, placebo-controlled Phase I trial for a recombinant two-component subunit SARS-CoV-2 vaccine ReCOV", @@ -310830,61 +311727,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.09.22274769", - "rel_title": "COVID-19 vaccination in pregnancy: views and vaccination uptake rates in pregnancy, a mixed methods analysis from the Born In Wales study", - "rel_date": "2022-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274769", - "rel_abs": "BackgroundVaccine hesitancy amongst pregnant women has been found to be a concern during past epidemics.\n\nObjectivesThe aims of this study were to 1) estimate COVID-19 vaccination rates among pregnant women in Wales and their association with age, ethnicity, and area of deprivation, using electronic health records (EHR) linkage, and 2) explore pregnant womens views on receiving the COVID-19 vaccine during pregnancy using data from a survey recruiting via social media (Facebook, Twitter), through midwives, and posters in hospitals (Born in Wales Cohort).\n\nDesignA mixed methods study utilising routinely collected linked data from the Secure Anonymised Information Linkage (SAIL) (Objective 1) and the Born In Wales Birth Cohort participants (Objective 2). SAIL combines data from general practice, hospital admissions, the national community child health dataset, maternal indicators dataset, and COVID-19 vaccination databases.\n\nSetting and participantsObjective 1) All women documented as being pregnant on or after 13th April 2021, aged 18 years or older, and eligible for COVID-19 vaccination were identified in routine health care. They were linked to the vaccination data up to and including 31st December 2021. Objective 2) Separately, a cross-section of pregnant women in Wales were invited to complete an online survey via social media advertising. The survey asked what their views were on having the COVID-19 vaccination during pregnancy, and if they had already received, or intended to receive, the COVID-19 vaccination during their pregnancies. They were also asked to give reasons for their decisions.\n\nOutcomes1 (a). Rate of vaccination uptake per month during pregnancy among women eligible for vaccination. 1 (b). Survival analysis was utilised to examine and compare the length of time to vaccination uptake in pregnancy, and variation in uptake by; age, ethnicity, and deprivation area was examined using hazard ratios (HR) from Cox regression. 2.Expectant mothers views of the COVID-19 vaccination during pregnancy.\n\nResults\n\nPopulation-level data linkage (objective 1)Within the population cohort, 32.7% (n = 8,203) were vaccinated (at least one dose of the vaccine) during pregnancy, 34.1% (n = 8,572) remained unvaccinated throughout follow-up period, and 33.2% (n = 8,336) received the vaccine postpartum. Younger women (<30 years) were less likely to have the vaccine and those living in areas of high deprivation were also less likely to have the vaccine (HR=0.88, 95% CI 0.82 to 0.95). Asian and other ethnic groups were 1.12 and 1.18 times more likely to have the vaccine in pregnancy compared to women of White ethnicity (HR=1.12, 95% CI 1.00 to 1.25) and (HR=1.18, 95% CI 1.03 to 1.37) respectively.\n\nSurvey responses (objective 2)69% of participants stated that they would be happy to have the vaccine during pregnancy (n = 207). The remainder, 31%, indicated that they would not have the vaccine during pregnancy (n = 94). Reasons for having the vaccine related to protecting self and baby, perceived risk level, and receipt of sufficient evidence and advice. Reasons for vaccine refusal included lack of research about long-term outcomes for the baby, anxiety about vaccines, inconsistent advice/information, and preference to wait until after the pregnancy.\n\nConclusionPotentially only 1 in 3 pregnant women would have the COVID-19 vaccine during pregnancy, even though 2 in 3 reported they would have the vaccination, thus it is critical to develop tailored strategies to increase its acceptance rate and to decrease vaccine hesitancy. A targeted approach to vaccinations may be required for groups such as younger people and those living in higher deprivation level areas.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mohamed Mhereeg", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK" - }, - { - "author_name": "Hope Jones", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Jonathan Kennedy", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Michael Seaborne", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Michael Parker", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Natasha Kennedy", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Sarah Beeson", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK." - }, - { - "author_name": "Luisa Zuccolo", - "author_inst": "Bristol Medical School, University of Bristol, Bristol, England, UK." - }, - { - "author_name": "Alisha Davies", - "author_inst": "Public Health Wales, UK" - }, - { - "author_name": "Sinead Brophy", - "author_inst": "Swansea University Medical School, Swansea, Wales, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.09.22274776", "rel_title": "Early detection of fraudulent COVID-19 products from Twitter chatter", @@ -311152,6 +311994,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.03.22274607", + "rel_title": "A New Paper Framework to Increase Reproducibility: Example Relating to Web Pharmacovigilance During COVID-19 in Italy", + "rel_date": "2022-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.03.22274607", + "rel_abs": "Reproducibility and transparency represent some of the main problems of scientific publishing. Currently, the editorial requests of academic journals and peer reviewers can divert the authors attention from an accurate description of the methods adopted, thus compromising these fundamental scientific aspects. This paves the way for the voluntary falsification of data to obtain striking results. Furthermore, the excessive expansion of introduction and discussion sections increases the likelihood of introducing evaluation bias. Since peer reviewers are generally unpaid for their work, they are not required to reproduce the analysis of the studies they review but only to assess methodological accuracy, reproducibility, and plausibility. Therefore, this paper aims to emphasize that the methods and results sections are the central parts of quantitative analysis. In this regard, we firmly believe that the peer review process should, whenever possible, reproduce the analysis from scratch. Consequently, authors must be required to provide a simple and straightforward tutorial to reproduce the analysis as it was conceived both methodologically and chronologically. Ideas, insights, and discussions among the authors must also be reported. This complete description can be provided as integrative material published with the main manuscript, which is nothing more than a summary of methods and results. Such a procedure would represent the first step to improving the quality of scientific publications, waiting for unscientific concepts such as \"publish or perish\" to be eradicated from the academic world. In this manuscript, we provide a framework that can serve as a fully reproducible and transparent example of analysis. The aim is to investigate the Italian netizens web interest in paracetamol, ibuprofen, and nimesulide from 2015 to 2022, searching for causal associations with the fever symptom and COVID-19. The infodemiological tool \"Google Trends\" has been used to collect the data. Correlational analysis showed plausible causal associations between paracetamol, ibuprofen, and fever due to seasonal flu and COVID-19 and, although to a minor extent, COVID-19 vaccines side effects. Paracetamol was the most historically searched substance. However, the trend of ibuprofen has caught up with that of paracetamol in 2022. Interest in paracetamol, ibuprofen, and nimesulide increased substantially during the COVID-19 pandemic period. We conclude that web pharmacovigilance via Google Trends can provide relevant evidence for monitoring drug intake in relation to epidemiologically significant events such as epidemics and mass vaccination campaigns.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alessandro Rovetta", + "author_inst": "R&C Research, Bovezzo (BS), Italy" + }, + { + "author_name": "Lucia Castaldo", + "author_inst": "R&C Research, Bovezzo (BS), Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.08.491108", "rel_title": "Imprinted antibody responses against SARS-CoV-2 Omicron sublineages", @@ -312920,49 +313785,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.10.22274918", - "rel_title": "Unrealistic optimism in the eye of the storm: Positive bias towards the consequences of COVID-19 during the second and third waves of the pandemic.", - "rel_date": "2022-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.10.22274918", - "rel_abs": "Research conducted at the outset of the pandemic shows that people are vulnerable to unrealistic optimism (UO). However, the Weinstein model suggests that this tendency may not persist as the pandemic progresses. Our research aimed at verifying whether UO persists during the second (Study 1) and the third wave (Study 2) of the pandemic in Poland, whether it concerns the assessment of the chances of COVID-19 infection (Study 1 and Study 2), the chances of severe course of the disease and adverse vaccine reactions (Study 2). We show that UO towards contracting COVID-19 persists throughout the pandemic. However, in situations where we have little influence on the occurrence of the event, the participants do not show UO. The exceptions are those who have known personally someone who has died from a coronavirus infection. These results are discussed in terms of self-esteem protection and the psychological threat reduction mechanism.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ada Maksim", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "S\u0142awomir \u015apiewak", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Natalia Lipp", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Natalia Du\u017cma\u0144ska-Misiarczyk", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Krzysztof R\u0119bilas", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Grzegorz Gustaw", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - }, - { - "author_name": "Pawe\u0142 Strojny", - "author_inst": "Jagiellonian University: Uniwersytet Jagiellonski w Krakowie" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.09.491201", "rel_title": "COVID-19 mRNA third dose induces a unique hybrid immunity-like antibody response", @@ -313314,6 +314136,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.05.06.22274584", + "rel_title": "Substance abuse and the risk of severe COVID-19: Mendelian randomization confirms the causal role of opioids but hints a negative causal effect for cannabinoids.", + "rel_date": "2022-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274584", + "rel_abs": "Since the start of the COVID-19 global pandemic, our understanding of the underlying disease mechanism and factors associated with the disease severity has dramatically increased. A recent report investigated the relationship between substance use disorders (SUD) and the risk of severe COVID-19 in the United States and concluded that the risk of hospitalization and death due to COVID-19 is directly correlated with substance abuse, including opioid use disorder (OUD) and cannabis use disorder (CUD). While we found this analysis fascinating, we believe this observation may be biased due to comorbidities (such as hypertension, diabetes, and cardiovascular disease) confounding the direct impact of SUD on severe COVID-19 illness. To objectively answer this question, we sought to investigate the causal relationship between substance abuse and medication-taking history (as a proxy trait for comorbidities) with the risk of COVID-19 adverse outcomes. Our Mendelian randomization analysis confirms the causal relationship between SUD and severe COVID-19 illness but hints at a negative causal effect for cannabinoids. Given that a great deal of COVID-19 mortality is attributed to disturbed immune regulation, the possible modulatory impact of cannabinoids in alleviating cytokine storms merits further investigation.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "M.Reza Jabalameli", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Zhengdong D Zhang", + "author_inst": "Albert Einstein College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2022.05.06.22274613", "rel_title": "Exploratory data on the clinical efficacy of monoclonal antibodies against SARS-CoV-2 Omicron Variant of Concern", @@ -314758,25 +315603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.04.22274677", - "rel_title": "A statistical definition of epidemic waves", - "rel_date": "2022-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.04.22274677", - "rel_abs": "The timely identification of expected surges of cases during infectious disease epidemics is essential for allocating resources and preparing interventions. This study describes a simple way to evaluate whether an epidemic wave is likely to be present based on daily new case count data. The proposed measure compares two models that assume exponential or linear dynamics, respectively. Technically, the output of two regression analyses is used to approximate a Bayes factor, which quantifies the support for the exponential over the linear model and can be used for epidemic wave detection. The trajectory of the coronavirus epidemic in three countries is analyzed and discussed for illustration. The proposed measure detects epidemic waves at an early stage, which are otherwise visible only by inspecting the development of case count data retrospectively. In addition to informing public health decision making, the outlined approach may serve as a starting point for scientific discussions on epidemic waves.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Levente Kriston", - "author_inst": "University Medical Center Hamburg-Eppendorf" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.06.22274701", "rel_title": "COVID-19 vaccine effectiveness during a prison outbreak when the Omicron was the dominant circulating variant, Zambia, December 2021", @@ -315180,6 +316006,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.03.22274517", + "rel_title": "Escape of SARS-CoV-2 variant Omicron to mucosal immunity in vaccinated subjects.", + "rel_date": "2022-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.03.22274517", + "rel_abs": "Omicron s escape to vaccine-induced systemic antibody responses has been shown in several studies in Omicron-infected patients and vaccine controls.\n\nIn the present study we compared mucosal antibody response to Omicron to mucosal antibody response to ancestral strain and Delta variant. This was done on nasal epithelial lining fluid (NELF) prospectively collected in 84 otherwise healthy healthcare workers who had never exhibited PCR-documented COVID-19 and had received three doses of the Pfizer-BioNTech COVID-19 mRNA vaccine. NELF was collected prior to Omicron detection in the geographical area of inclusion.\n\nWe show that NELF antibodies from vaccinated individuals were less efficient at inhibiting the binding of the Omicron Spike protein to ACE-2 compared to those of Delta or the ancestral strain.\n\nThese findings may explain the increased risk of onward transmission of Omicron, consistent with its successful global displacement of Delta in countries with a high vaccination coverage.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Emanuela MARTINUZZI", + "author_inst": "Universite Cote d'Azur, CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, Valbonne, France" + }, + { + "author_name": "Jacques BOUTROS", + "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Department of Pulmonary Medicine and Thoracic Oncology, FHU Oncoage, Nice, France Universite C" + }, + { + "author_name": "Jonathan BENZAQUEN", + "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Department of Pulmonary Medicine and Thoracic Oncology, FHU Oncoage, Nice, France Universite C" + }, + { + "author_name": "Nicolas GLAICHENHAUS", + "author_inst": "Universite Cote d'Azur, CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, Valbonne, France" + }, + { + "author_name": "Paul HOFMAN", + "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Laboratory of Clinical and Experimental Pathology, Biobank (BB-0033-00025), FHU OncoAge, Centr" + }, + { + "author_name": "Charles Hugo MARQUETTE", + "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Department of Pulmonary Medicine and Thoracic Oncology, FHU Oncoage, Nice, France Universite C" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.05.490805", "rel_title": "ACE2 nanoparticles prevent cell entry of SARS-CoV-2", @@ -316668,61 +317533,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.04.22274647", - "rel_title": "Protection against omicron severe disease 0-7 months after BNT162b2 booster", - "rel_date": "2022-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.04.22274647", - "rel_abs": "Following a rise in cases due to the delta variant and evidence of waning immunity after 2 doses of the BNT162b2 vaccine, Israel began administering a third BNT162b2 dose (booster) in July 2021. Recent studies showed that the 3rd dose provides a much lower protection against infection with the omicron variant compared to the delta variant and that this protection wanes quickly. In this study, we used data from Israel to estimate the protection of the 3rd dose against severe disease up to 7 months from receiving the booster dose. The analysis shows that protection conferred by the 3rd dose against omicron did not wane over a 7-month period and that a 4th dose further increased protection, with a severe disease rate approximately 3-fold lower than in the 3-dose cohorts.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ofra Amir", - "author_inst": "Technion - Israel Institute of Technology, Israel" - }, - { - "author_name": "Yair Goldberg", - "author_inst": "Technion - Israel Institute of Technology, Israel" - }, - { - "author_name": "Micha Mandel", - "author_inst": "The Hebrew University of Jerusalem, Israel" - }, - { - "author_name": "Yinon M. Bar-On", - "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" - }, - { - "author_name": "Omri Bodenheimer", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Laurence Freedman", - "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" - }, - { - "author_name": "Sharon Alroy-Preis", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Nachman Ash", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Amit Huppert", - "author_inst": "The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" - }, - { - "author_name": "Ron Milo", - "author_inst": "Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.04.490614", "rel_title": "SARS-CoV-2 variants do not evolve to promote further escape from MHC-I recognition", @@ -317002,6 +317812,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.05.01.22274548", + "rel_title": "Immunogenicity and reactogenicity of a third dose of BNT162b2 vaccine for COVID-19 after a primary regimen with BBIBP-CorV or BNT162b2 vaccines in Lima, Peru.", + "rel_date": "2022-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.01.22274548", + "rel_abs": "BackgroundThe administration of a third (booster) dose of COVID-19 vaccines in Peru initially employed the BNT162b2 (Pfizer) mRNA vaccine. The national vaccination program started with healthcare workers (HCW) who received BBIBP-CorV (Sinopharm) vaccine as primary regimen and elderly people previously immunized with BNT162b2. This study evaluated the reactogenicity and immunogenicity of the \"booster\" dose in these two groups in Lima, Peru.\n\nMethodsWe conducted a prospective cohort study, recruiting participants from November to December of 2021 in Lima, Peru. We evaluated immunogenicity and reactogenicity in HCW and elderly patients previously vaccinated with either two doses of BBIBP-CorV (heterologous regimen) or BTN162b2 (homologous regimen). Immunogenicity was measured by anti-SARS-CoV-2 IgG antibody levels immediately before boosting dose and 14 days later. IgG geometric means (GM) and medians were obtained, and modeled using ANCOVA and quantile regressions.\n\nResultsThe GM of IgG levels increased significantly after boosting: from 28.5{+/-}5.0 AU/mL up to 486.6{+/-}1.2 AU/mL (p<0.001) which corresponds to a 17-fold increase. The heterologous vaccine regimen produced higher GM of post-booster anti-SARS-CoV-2 IgG levels, eliciting a 13% fold increase in the geometric mean ratio (95%CI: 1.02-1.27) and a median difference of 92.3 AU/ml (95%CI: 24.9-159.7). Both were safe and well tolerated. Previous COVID-19 infection was also associated with higher pre and post-booster IgG GM levels.\n\nConclusionAlthough both boosting regimens were highly immunogenic, two doses of BBIBP-CorV boosted with BTN162b2 produced a stronger IgG antibody response than the homologous BNT162b2 regimen in the Peruvian population. Additionally, both regimens were mildly reactogenic and well-tolerated.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Natalia Gladys Vargas Herrera", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Manuel Fern\u00e1ndez-Navarro", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "N\u00e9stor Cabezudo-Pillpe", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Percy Soto-Becerra", + "author_inst": "Seguro Social Peru" + }, + { + "author_name": "Gilmer Sol\u00eds-Sanchez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Stefan Escobar-\u00c1greda", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Javier Silva-Valencia", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Luis Pampa-Espinoza", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Ricardo Bado-P\u00e9rez", + "author_inst": "Peruvian State Ministry of Health: Estado Peruano Ministerio de Salud" + }, + { + "author_name": "Lely Solari", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Roger V Araujo-Castillo", + "author_inst": "Instituto Nacional de Salud" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.02.22274478", "rel_title": "An Early Return-to-Work Program for COVID-19 Close Contacts in Healthcare During the Omicron Wave in Japan", @@ -318894,29 +319763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.29.22274494", - "rel_title": "Forecast Intervals for Infectious Disease Models", - "rel_date": "2022-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.29.22274494", - "rel_abs": "Forecast intervals for infectious disease transmission and mortality have long been overconfident -- i.e., the advertised coverage probabilities of those intervals fell short of their subsequent performances. Further, there was no apparent relation between how good models claimed to be (as measured by their purported forecast uncertainties) and how good the models really were (as measured by their actual forecast errors). The main cause of this problem lies in the misapplication of textbook methods for uncertainty quantification. A solution lies in the creative use of predictive tail probabilities to obtain valid interval coverages. This approach is compatible with all probabilistic predictive models whose forecast error behavior does not change \"too quickly\" over time.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rick Picard", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Dave Osthus", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.29.22274485", "rel_title": "Human behaviour, NPI and mobility reduction effects on COVID-19 transmission in different countries of the world", @@ -319152,6 +319998,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.04.29.22274486", + "rel_title": "How did the COVID-19 pandemic affect access to condoms, chlamydia and HIV testing, and cervical cancer screening at a population level in Britain? (Natsal-COVID)", + "rel_date": "2022-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.29.22274486", + "rel_abs": "ObjectivesTo investigate how differential access to key interventions to reduce sexually transmitted infections (STI), HIV, and their sequelae changed during the COVID-19 pandemic.\n\nMethodsBritish participants (18-59y) completed a cross-sectional web survey one year (March to April 2021) after the initial lockdown in Britain. Quota-based sampling and weighting resulted in a quasi-representative population sample. We compared Natsal-COVID data with Natsal-3, a household-based probability sample cross-sectional survey (16-74y) conducted in 2010-12. Reported unmet need for condoms because of the pandemic and uptake of chlamydia testing/HIV testing/cervical cancer screening were analysed among sexually-experienced participants (18-44y) (n=2869, Natsal-COVID; n=8551, Natsal-3). Odds ratios adjusted for age (aOR) and other potential confounders (AOR) describe associations with demographic and behavioural factors.\n\nResultsIn 2021, 6.9% of women and 16.2% of men reported unmet need for condoms because of the pandemic. This was more likely among participants: aged 18-24 years, of Black or Black British ethnicity, and reporting same-sex sex (past five years) or one or more new relationships (past year). Chlamydia and HIV testing were more commonly reported by younger participants, those reporting condomless sex with new sexual partners, and men reporting same-sex partners; a very similar distribution to 10 years previously (Natsal-3). However, there were differences during the pandemic, including stronger associations with chlamydia testing for men reporting same-sex partners; with HIV testing for women reporting new sexual partners; and with cervical screening among smokers.\n\nConclusionsOur study suggests differential access to key primary and secondary STI/HIV prevention interventions continued during the first year of the COVID-19 pandemic. However, the available evidence does not suggest substantial changes in inequalities in since 2010-12. While the pandemic might not have exacerbated inequalities in access to primary and secondary prevention, it is clear that large inequalities persisted, typically among those at greatest STI/HIV risk.\n\nKey MessagesO_LIMany MSM, people of Black ethnicity and young people (i.e. groups most impacted by STIs) reported unmet need for condoms because of the pandemic\nC_LIO_LIWe compared inequalities in access to key interventions using Natsal-COVID (2021) and Natsal-3 (2010-12).\nC_LIO_LIDuring the pandemic (Natsal-COVID), there were stronger associations with chlamydia testing for MSM and with HIV testing for women reporting new sexual partners.\nC_LIO_LIThere were stronger associations with cervical screening among smokers during the pandemic compared to 2010-12 (Natsal-3).\nC_LIO_LIHowever, we did not find strong evidence that vulnerable groups were at additional risk during the pandemic when compared to 2010-12.\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Emily Dema", + "author_inst": "University College London" + }, + { + "author_name": "Pam Sonnenberg", + "author_inst": "University College London" + }, + { + "author_name": "Jo Gibbs", + "author_inst": "University College London" + }, + { + "author_name": "Anne Conolly", + "author_inst": "NatCen Social Research, University College London" + }, + { + "author_name": "Malachi Willis", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Julie Riddell", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Raquel Boso Perez", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Andrew J Copas", + "author_inst": "University College London" + }, + { + "author_name": "Clare Tanton", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Chris Bonell", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Clarissa Oeser", + "author_inst": "University College London" + }, + { + "author_name": "Soazig Clifton", + "author_inst": "NatCen Social Research, University College London" + }, + { + "author_name": "Magnus Unemo", + "author_inst": "Orebro University" + }, + { + "author_name": "Catherine H Mercer", + "author_inst": "University College London" + }, + { + "author_name": "Kirstin R Mitchell", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Nigel Field", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "sexual and reproductive health" + }, { "rel_doi": "10.1101/2022.04.29.22274396", "rel_title": "Immune responses following 3rd and 4th doses of heterologous and homologous COVID-19 vaccines in kidney transplant recipients", @@ -320608,33 +321533,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.04.26.22274273", - "rel_title": "COVID-19 third wave experience in India, a survey of 5971 adults", - "rel_date": "2022-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274273", - "rel_abs": "BackgroundThe third wave of the pandemic in India lasted from January till March 2022, and breakthrough infections were common. Third dose of vaccine was rolled out to priority groups in the beginning of 2022. There is no published information available about the clinical outcomes in this context.\n\nAimsO_LITo assess the community level experience of the pandemic, with focus on the third wave and vaccination in India.\nC_LIO_LITo describe the experience of the boosted and non-boosted population during the 3rd wave.\nC_LIO_LITo study the public perception about the precautionary (3rd) dose in India.\nC_LI\n\nResultsAmong 5971 respondents, 98.6% were vaccinated, 40% of whom had also received the 3rd dose. Age range: 24% were below 40, 50% were 40-59, 26% were >60 years.\n\n45% were women, 53% were healthcare workers.\n\nCOVID-19 was reported by 3361 (56%) respondents. Among those who reported COVID-19, 2311 (70%) were infected during the third wave. Severe symptoms occurred in <1%, while moderate severity was reported by 42%. Repeated bouts of infection were common; 15% of those with a history of COVID-19 had been infected at least twice. 44% of the respondents (2610/5971) did not report a history of COVID-19.\n\nThe third dose was taken by 2383 individuals, of whom 30% reported COVID-19 during the 3rd wave. The boosted group also had higher N95 use, and a greater proportion of healthcare workers. Among those who did not take a 3rd dose, 45% reported COVID-19 in the 3rd wave. COVID-19 incidence was lower at 27% among those in this group who had recently received their second dose. Longer gap after the second dose correlated with higher chance of infection during 3rd wave. Giving a 3rd dose before a 6-month gap since the second dose did not make a difference in infection rate.\n\nCovaxin and Covishield recipients had the same incidence of COVID-19 during the third wave.\n\nWhile 35% of the respondents believed it was helpful, 65% of the respondents were either uncertain or disapproving of the benefit of a 3rd dose.\n\nConclusionsO_LI30% of respondents who received a 3rd dose went on to get COVID-19 during the 3rd wave.\nC_LIO_LIYounger adults were more likely to be affected during 3rd wave.\nC_LIO_LIAlthough severe disease was rare, 42% reported having symptoms of moderate severity that could temporarily incapacitate people, affecting their routine and productivity.\nC_LIO_LIThe proportion of different grades of severity was similar among all vaccinated people, regardless of whether they received a 3rd dose.\nC_LIO_LIReinfections occurred in 15%, and were not always milder.\nC_LIO_LIAmong those who did not receive a 3rd dose, 45% reported COVID-19 in the 3rd wave. However, this group had lower use of N95 masks (50%) than the 3rd dose group (68%) which may have reduced the overall protection.\nC_LIO_LIThe longer the gap after the second dose, the greater was the chance of reporting COVID-19.\nC_LIO_LIPeople who received their second dose recently had the same incidence of third wave COVID-19 as following a 3rd dose.\nC_LIO_LIThe 3rd dose, given too close to the second dose, made no difference in the infection rate.\nC_LIO_LICovaxin and Covishield recipients had the same rate of COVID-19 in the third wave.\nC_LIO_LIAlthough the respondents were 98.6% vaccinated at baseline, there was considerable uncertainty (65%) amongst them about the benefit of a 3rd dose.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rajeev Jayadevan", - "author_inst": "Sunrise Hospital" - }, - { - "author_name": "Ramesh Shenoy", - "author_inst": "Lisie Hospital Cochin India" - }, - { - "author_name": "Anithadevi TS", - "author_inst": "Little Flower Hospital Angamaly Kerala India" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.26.22274301", "rel_title": "Trends in non-COVID-19 hospitalizations prior to and during the COVID-19 pandemic period, United States, 2017-2021", @@ -321098,6 +321996,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.04.27.22274377", + "rel_title": "Which countries need COVID-19 vaccines the most? Development of a prioritisation tool", + "rel_date": "2022-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.27.22274377", + "rel_abs": "BackgroundAssessing relative needs for COVID-19 vaccines across countries has been challenging. The objective of this study was to identify the most important factors for assessing countries needs for vaccines, and to weight each, generating a scoring tool for prioritising countries.\n\nMethodsThe study was conducted between March and November 2021. The first stage involved a Delphi survey with a purposive and snowball sample of public health experts, to reach consensus on country-level factors for assessing relative needs for COVID-19 vaccines. The second stage involved a discrete choice experiment (DCE) to determine weights for the factors.\n\nResultsThe study included 28 experts working across 13 different countries and globally. The Delphi survey found 37 factors related to needs. Nine of the most important factors were included in the DCE. Among these, the most important factor was the proportion of overall population not fully vaccinated with a mean weight of 19.5, followed by proportion of high-risk population not fully vaccinated (16.1), health system capacity (14.2), capacity to purchase vaccines (11.9) and the proportion of the population clinically vulnerable (11.3).\n\nConclusionsBy assessing relative needs, this scoring tool can build on existing methods to further the role of equity in global COVID-19 vaccine allocation.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vageesh Jain", + "author_inst": "University College London" + }, + { + "author_name": "Rifat Atun", + "author_inst": "Harvard University" + }, + { + "author_name": "Paul Hansen", + "author_inst": "University of Otago" + }, + { + "author_name": "Paula Lorgelly", + "author_inst": "University of Auckland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.27.22274369", "rel_title": "High-Dimensional Multinomial Multiclass Severity Scoring of COVID-19 Pneumonia Using CT Radiomics Features and Machine Learning Algorithms", @@ -322698,37 +323627,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.25.22274291", - "rel_title": "Epidemiological behavior of the contamination curve by COVID-19 in Brazil: a time series study", - "rel_date": "2022-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.25.22274291", - "rel_abs": "The Brazil is experiencing the greatest episode of sanitary collapse ever known in the countrys history. Therefore, the relevance of this study is highlighted for the scientific advance on the epidemiological behavior of the virus in Brazil, enabling the development of analyses and discussions on the factors that influenced the high rates of contamination by SARS-CoV-2 in the country. Given the above, the study in question aims to analyze the epidemiological behavior of the contamination curve by COVID-19 by epidemiological week (EW), in the years 2020-2021, in Brazil. This is an ecological study of time series, prepared using information collected through secondary means. The country of origin of the study is Brazil, and its main theme is the number of those infected during the pandemic of COVID-19, this being the dependent variable of the study. The data been analyzed from February 23, 2020, when the first case was confirmed in Brazil, to January 1, 2022. In 2021, the countrys graph shows an exorbitant growth, reaching a peak of approximately 250 new cases per 100,000 inhabitants in the 12th EW. This data became the highest rate of the pandemic in Brazil, and did not vary significantly for the next twelve weeks. Thus, it was identified that Brazil was severely impacted by the new coronavirus, considering the high rates of confirmed cases of the virus in the country, the low adhesion of the population to preventive measures, the late start of mass vaccination in the Brazilian population, and the lack of structure in the health system, which was not properly prepared for the high demand generated by COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Thiffany Nayara Bento de Morais", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - }, - { - "author_name": "Ketyllem Tayanne da Silva Costa", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - }, - { - "author_name": "Gustavo Nepomuceno Capistrano", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - }, - { - "author_name": "F\u00e1bia Barbosa de Andrade", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.25.22273197", "rel_title": "Clinical characteristics and outcome of immunocompromised patients with COVID-19 caused by the Omicron variant: a prospective observational study", @@ -323024,6 +323922,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.04.25.22274251", + "rel_title": "Long-COVID post-viral chronic fatigue syndrome and affective symptoms are associated with oxidative damage, lowered antioxidant defenses and inflammation: a proof of concept and mechanism study.", + "rel_date": "2022-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.25.22274251", + "rel_abs": "The immune-inflammatory response during the acute phase of COVID-19, as assessed using peak body temperature (PBT) and peripheral oxygen saturation (SpO2), predicts the severity of chronic fatigue, depression and anxiety (\"physio-affective\") symptoms three to four months later. The present study was performed to characterize whether the effects of SpO2 and PBT on the physio-affective phenome of Long COVID are mediated by immune, oxidative and nitrosative stress (IO&NS) pathways. This study assayed SpO2 and PBT during acute COVID-19, and C-reactive protein (CRP), malondialdehyde (MDA), protein carbonyls (PCs), myeloperoxidase (MPO), nitric oxide (NO), zinc, and glutathione peroxidase (Gpx) in 120 Long COVID individuals and 36 controls. Cluster analysis showed that 31.7% of the Long COVID patients had severe abnormalities in SpO2, body temperature, increased oxidative toxicity (OSTOX) and lowered antioxidant defenses (ANTIOX), and increased total Hamilton Depression (HAMD) and Anxiety (HAMA) and Fibromylagia-Fatigue (FF) scores. Around 60% of the variance in the physio-affective phenome of Long COVID (a factor extracted from HAMD, HAMA and FF scores) was explained by OSTOX/ANTIOX ratio, PBT and SpO2. Increased PBT predicted increased CRP and lowered ANTIOX and zinc levels, while lowered SpO2 predicted lowered Gpx and increased NO production. Both PBT and SpO2 strongly predict OSTOX/ATIOX during Long COVID. In conclusion, the impact of acute COVID-19 on the physio-affective symptoms of Long COVID is partly mediated by OSTOX/ANTIOX, especially lowered Gpx and zinc, increased MPO and NO production and lipid peroxidation-associated aldehyde formation. Post-viral physio-affective symptoms have an inflammatory origin and are partly mediated by neuro-oxidative toxicity.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hussein K Al-Hakeim", + "author_inst": "University of Kufa" + }, + { + "author_name": "Haneen Al-Rubaye", + "author_inst": "Imam Ja'afar Al-Sadiq University" + }, + { + "author_name": "Dhurgham Al-Hadrawi", + "author_inst": "Al-Najaf Center for Cardiac Surgery and Transcatheter Therapy" + }, + { + "author_name": "Abbas Almulla", + "author_inst": "Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq" + }, + { + "author_name": "Michael Maes", + "author_inst": "Chulalongkorn University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.25.22274280", "rel_title": "The prevalence of SARS-CoV-2 antibodies within the community of a private tertiary university in the Philippines: a serial cross sectional study", @@ -324308,25 +325241,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.22.22274198", - "rel_title": "Estimation of the Ascertainment Bias in Covid Case Detection During the Omicron Wave", - "rel_date": "2022-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.22.22274198", - "rel_abs": "Covid cases in the general population have been historically underreported due to a variety of reasons including limited access to PCR testing at the start of the pandemic, lack of nation-wide surveillance testing, and discouraged testing unless symptomatic. Concerns about underreporting have increased during the Omicron surge due to the expanded use of at-home rapid tests which are not required to be officially reported. For the state of Illinois, we have found that reported cases constituted only 50%-70% of the actual cases during the pre-Omicron waves (August 2020-December 2021). During the first Omicron (BA1) wave, this fraction dropped to 20-29% (i.e., only 1 in 4 to 1 in 5 cases are reported). During the ongoing second Omicron (BA2) surge, this fraction has further decreased to 12-18% (i.e., only 1 in 6 to 1 in 8 cases are reported). These estimates have important implications on understanding the extent of the Omicron surge at the state and national levels.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ahmed Elbanna", - "author_inst": "University of Illinois Urbana Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.19.22274030", "rel_title": "Estimating the distribution of COVID-19-susceptible, -recovered, and -vaccinated individuals in Germany up to April 2022", @@ -324698,6 +325612,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.04.20.488933", + "rel_title": "A Quantum Dot Biomimetic for SARS-CoV-2 to Interrogate Dysregulation of the Neurovascular Unit Relevant to Brain Inflammation", + "rel_date": "2022-04-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.20.488933", + "rel_abs": "Despite limited evidence for competent infection and viral replication of SARS-CoV-2 in the central nervous system (CNS), neurologic dysfunction is a common post-acute medical condition reported in \"recovered\" COVID-19 patients. To identify a potential noninfectious route for SARS-CoV-2-mediated neurological damage, we constructed colloidal nanocrystal quantum dots linked to micelles decorated with spike protein (COVID-QDs) as a biomimetic to interrogate how blood-brain barrier (BBB) dysregulation may subsequently induce neuroinflammation in the absence of infection. In transwell co-culture of endothelial bEnd.3 monolayers and primary neuroglia, we exposed only the bEnd.3 monolayers to COVID-QDs and examined by fluorescence microscopy whether such treatment led to (i) increased inflammation and leakage across the bEnd.3 monolayers, (ii) permeability of the COVID-QDs across the monolayers, and (iii) induction of neuroinflammation in neuroglial cultures. The results of our study provide evidence of neuroinflammatory hallmarks in cultured neurons and astrocytes without direct exposure to SARS-CoV-2-like nanoparticles. Additionally, we found that pre-treatment of our co-cultures with a small-molecule, broad-spectrum inhibitor of mixed lineage and leucine rich repeat kinases led to reversal of the observed dysregulation in endothelial monolayers and resulted in neuroglial protection. The results reported here may serve to guide future studies into the potential mechanisms by which SARS-CoV-2 mediates neurologic dysfunction.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Wesley Chiang", + "author_inst": "University of Rochester Medical Center" + }, + { + "author_name": "Angela Litzburg", + "author_inst": "University of Rochester Medical Center" + }, + { + "author_name": "Francine Yanchik-Slade", + "author_inst": "University of Rochester" + }, + { + "author_name": "Herman Li", + "author_inst": "University of Rochester Medical Center" + }, + { + "author_name": "Bradley L. Nilsson", + "author_inst": "University of Rochester" + }, + { + "author_name": "Harris A Gelbard", + "author_inst": "University of Rochester Medical Center" + }, + { + "author_name": "Todd D Krauss", + "author_inst": "University of Rochester" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2022.04.21.489072", "rel_title": "Impaired immune response drives age-dependent severity of COVID-19", @@ -326046,153 +327003,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.20.22274046", - "rel_title": "Elevated plasma Complement Factor H Regulating Protein 5 is associated with venous thromboembolism and COVID-19 severity", - "rel_date": "2022-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.20.22274046", - "rel_abs": "Venous thromboembolism (VTE), comprising both deep vein thrombosis (DVT) and pulmonary embolism (PE) is a common, multi-causal disease with potentially serious short- and long-term complications. In clinical practice, there is a need for improved plasma biomarker-based tools for VTE diagnosis and risk prediction. We used multiplex proteomics profiling to screen plasma from patients with suspected acute VTE, and a case-control study of patients followed up after ending anticoagulant treatment for a first VTE. With replication in 5 independent studies, together totalling 1137 patients and 1272 controls, we identify Complement Factor H Related Protein (CFHR5), a regulator of the alternative pathway of complement activation, as a novel VTE associated plasma biomarker. Using GWAS analysis of 2967 individuals we identified a genome-wide significant pQTL signal on chr1q31.3 associated with CFHR5 levels. We showed that higher CFHR5 levels are associated with increased thrombin generation in patient plasma and that recombinant CFHR5 enhances platelet activation in vitro. Thrombotic complications are a frequent feature of COVID-19; in hospitalised patients we found CFHR5 levels at baseline were associated with short-time prognosis of disease severity, defined as maximum level of respiratory support needed during hospital stay. Our results indicate a clinically important role for regulation of the alternative pathway of complement activation in the pathogenesis of VTE and pulmonary complications in acute COVID-19. Thus, CFHR5 is a potential diagnostic and/or risk predictive plasma biomarker reflecting underlying pathology in VTE and acute COVID-19.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Laura Sanchez-Rivera", - "author_inst": "Science for Life Laboratory, KTH Royal Institute of Technology" - }, - { - "author_name": "Maria Jesus Iglesias", - "author_inst": "Science for Life Laboratory, KTH Royal Institute of Technology" - }, - { - "author_name": "Manal Ibrahim-Kosta", - "author_inst": "Aix-Marseille Univ, INSERM, INRAE, C2VN, - Hopitaux de Marseille." - }, - { - "author_name": "Julia Barbara Kral- Pointner", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Sebastian Havervall", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Louisa Goumidi", - "author_inst": "Aix-Marseille Univ, INSERM, INRAE, C2VN, - Hopitaux de Marseille." - }, - { - "author_name": "Maria Farm", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Gaelle Munsch", - "author_inst": "University of Bordeaux, Inserm" - }, - { - "author_name": "Marine Germain", - "author_inst": "University of Bordeaux, Inserm" - }, - { - "author_name": "Philip Smith", - "author_inst": "Karolinska Institute and Karolinska University Hospital" - }, - { - "author_name": "Mun-Gwan Hong", - "author_inst": "Science for Life Laboratory, KTH Royal Institute of Technology" - }, - { - "author_name": "Pierre Suchon", - "author_inst": "Aix-Marseille Univ, INSERM, INRAE- Hopitaux de Marseille" - }, - { - "author_name": "Clement Naudin", - "author_inst": "Science for Life Laboratory, KTH Royal Institute of Technology," - }, - { - "author_name": "Anne Boland", - "author_inst": "Universite Paris-Saclay" - }, - { - "author_name": "David M Smadja", - "author_inst": "Universite de Paris" - }, - { - "author_name": "Margareta Holmstrom", - "author_inst": "Karolinska University Hospital" - }, - { - "author_name": "Maria Magnusson", - "author_inst": "Karolinska Institute and Karolinska University Hospital" - }, - { - "author_name": "Angela Silveira", - "author_inst": "Karolinska Institutet and Karolinska University Hospital" - }, - { - "author_name": "Mathias Uhlen", - "author_inst": "KTH - Royal Institute of Technology" - }, - { - "author_name": "Thomas Renne", - "author_inst": "University Medical Centre Hamburg-Eppendorf" - }, - { - "author_name": "Angel Martinez-Perez", - "author_inst": "Research Institute Hospital de la Santa Creu" - }, - { - "author_name": "Joseph Emmerich", - "author_inst": "University of Paris Cite" - }, - { - "author_name": "Jean-Fran\u00e7ois Deleuze", - "author_inst": "Centre national de recherche en g\u00e9nomique humaine" - }, - { - "author_name": "Jovan Antovic", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Alice Assinger", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Jose Manuel Soria Fernandez", - "author_inst": "Hospital de la Santa Creu i Sant Pau." - }, - { - "author_name": "Charlotte Thalin", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jochen M Schwenk", - "author_inst": "KTH" - }, - { - "author_name": "Juan Carlos Souto Andres", - "author_inst": "Hospital de la Santa Creu i Sant Pau." - }, - { - "author_name": "Pierre-Emmanuel Morange", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Lynn M Butler", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "David Alexandre Tregouet", - "author_inst": "University of Bordeaux, Inserm" - }, - { - "author_name": "Jacob Odeberg", - "author_inst": "SciLifeLab KTH" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.04.19.22274026", "rel_title": "A Platform for Data-centric, Continuous Epidemiological Analyses", @@ -326472,6 +327282,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.19.22274047", + "rel_title": "COVID-19 outcomes by cancer status, type, treatment, and vaccination", + "rel_date": "2022-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.19.22274047", + "rel_abs": "BackgroundObservational studies have identified patients with cancer as a potential subgroup of individuals at elevated risk of severe SARS-CoV-2 (COVID-19) disease and mortality. Early studies showed an increased risk of COVID-19 mortality for cancer patients, but it is not well understood how this association varies by cancer site, cancer treatment, and vaccination status.\n\nMethodsUsing electronic health record data from an academic medical center, we identified 259,893 individuals who were tested for or diagnosed with COVID-19 from March 10, 2020, to February 2, 2022. Of these, 41,218 tested positive for COVID-19 of whom 10,266 had a past or current cancer diagnosis. We conducted Firth-corrected, covariate-adjusted logistic regression to assess the association of cancer status, cancer type, and cancer treatment with four COVID-19 outcomes: hospitalization, intensive care unit (ICU) admission, mortality, and a composite \"severe COVID-19\" outcome which is the union of the first three outcomes. We examine the effect of the timing of cancer diagnosis and treatment relative to COVID diagnosis, and the effect of vaccination.\n\nResultsCancer status was associated with higher rates of severe COVID-19 infection [OR (95% CI): 1.18 (1.08, 1.29)], hospitalization [OR (95% CI): 1.18 (1.06, 1.28)], and mortality [OR (95% CI): 1.22 (1.00, 1.48)]. These associations were driven by patients whose most recent initial cancer diagnosis was within the past three years. Chemotherapy receipt was positively associated with all four COVID-19 outcomes (e.g., severe COVID [OR (95% CI): 1.96 (1.73, 2.22)], while receipt of either radiation or surgery alone were not associated with worse COVID-19 outcomes. Among cancer types, hematologic malignancies [OR (95% CI): 1.62 (1.39, 1.88)] and lung cancer [OR (95% CI): 1.81 (1.34, 2.43)] were significantly associated with higher odds of hospitalization. Hematologic malignancies were associated with ICU admission [OR (95% CI): 1.49 (1.11, 1.97)] and mortality [OR (95% CI): 1.57 (1.15, 2.11)], while melanoma and breast cancer were not associated with worse COVID-19 outcomes. Vaccinations were found to reduce the frequency of occurrence for the four COVID-19 outcomes across cancer status but those with cancer continued to have elevated risk of severe COVID [cancer OR (95% CI) among those fully vaccinated: 1.69 (1.10, 2.62)] relative to those without cancer even among vaccinated.\n\nConclusionOur study provides insight to the relationship between cancer diagnosis, treatment, cancer type, vaccination, and COVID-19 outcomes. Our results indicate that it is plausible that specific diagnoses (e.g., hematologic malignancies, lung cancer) and treatments (e.g., chemotherapy) are associated with worse COVID-19 outcomes. Vaccines significantly reduce the risk of severe COVID-19 outcomes in individuals with cancer and those without, but cancer patients are still at higher risk of breakthrough infections and more severe COVID outcomes even after vaccination. These findings provide actionable insights for risk identification and targeted treatment and prevention strategies.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Maxwell Salvatore", + "author_inst": "University of Michigan" + }, + { + "author_name": "Miriam M Hu", + "author_inst": "University of Michigan" + }, + { + "author_name": "Lauren J Beesley", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Alison Mondul", + "author_inst": "University of Michigan" + }, + { + "author_name": "Celeste Leigh Pearce", + "author_inst": "University of Michigan" + }, + { + "author_name": "Christopher R Friese", + "author_inst": "University of Michigan" + }, + { + "author_name": "Lars G. Fritsche", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Bhramar Mukherjee", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.19.22274053", "rel_title": "Public attitudes towards COVID-19 vaccines in Africa: a systematic review", @@ -329504,85 +330361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.18.22273978", - "rel_title": "Effectiveness of BBIBP-CorV, BNT162b2 and mRNA-1273 vaccines against hospitalisations among children and adolescents during the Omicron outbreak in Argentina", - "rel_date": "2022-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22273978", - "rel_abs": "BackgroundAlthough paediatric clinical presentations of COVID-19 are usually less severe than in adults, serious illness and death have occurred. Many countries started the vaccination rollout of children in 2021; still, information about effectiveness in the real-world setting is scarce. The aim of our study was to evaluate vaccine effectiveness (VE) against COVID-19-associated-hospitalisations in the 3-17-year population during the Omicron outbreak.\n\nMethodsWe conducted a retrospective cohort study including individuals aged 3-17 registered in the online vaccination system of the Buenos Aires Province, Argentina. mRNA-1273 and BNT162b2 were administered to 12-17-year subjects; and BBIBP-CorV to 3-11- year subjects. Vaccinated group had received a two-dose scheme by 12/1/2021. Unvaccinated group did not receive any COVID-19 vaccine between 12/14/2021-3/9/2022, which was the entire monitoring period. Vaccine effectiveness (VE) against COVID-19-associated hospitalisations was calculated as (1-OR) x100.\n\nFindingsBy 12/1/2021, 1,536,435 individuals aged 3-17 who had received zero or two doses of SARS-CoV-2 vaccines were included in this study. Of the latter, 1,440,389 were vaccinated and 96,046 not vaccinated. VE were 78{middle dot}0% [68{middle dot}7-84{middle dot}2], 76{middle dot}4%[62{middle dot}9-84{middle dot}5] and 80{middle dot}0%[64{middle dot}3-88{middle dot}0] for the entire cohort, 3-11 subgroup and 12-17 subgroup, respectively. VE for the entire population was 82{middle dot}7% during the period of Delta and Omicron overlapping circulation and decreased to 67{middle dot}7% when Omicron was the only variant present.\n\nInterpretationThis report provides evidence of high vaccine protection against associated-hospitalisations in the paediatric population during the Omicron outbreak but suggests a decrease of protection when Omicron became predominant. Application of a booster dose in children aged 3-11 warrants further consideration.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThere is limited evidence on the effectiveness of vaccines in the pediatric population, particularly in children aged 3-11 years after the SARS-CoV-2 B.1.1.529 (Omicron) variants emergence.\n\nWe searched preprint and peer-reviewed published articles in PubMed, medRxiv, and SSRN for observational studies, with no language restrictions, using the term \"COVID-19 OR SARS-CoV-2\" AND \"vaccine effectiveness\" OR \"vaccine impact\" AND \"children\" OR \"pediatric\" AND \"Omicron\" published between December 1, 2021, and April 1, 2022. We found 4 studies that included subjects in the 3-17-year population who received a two-dose-scheme of any of the available vaccines-according to each countrys authorisation. Three studies were from the US; two were test-negative-case-control studies and one was a retrospective non-peer-reviewed cohort study. The reported vaccine effectiveness (VE) for 2-doses of BNT162b2-mRNA (Pfizer-BioNTech) in preventing hospitalisations during Omicron predominance was 48-78%; and it was 40-92% for 5-11 and 12-17-year subgroups, respectively. The fourth was a cohort study still in preprint form conducted in Chile and utilized an inactivated vaccine, CoronaVac (SinoVac), widely used in Latin-America. VE for two doses of CoronaVac in the 3-5-year subgroup against hospitalisations was 64% and 69% against ICU admissions.\n\nAdded value of this studyUp to date, there are no published studies about the effectiveness of the BBIBP-CorV vaccine against hospitalisation in the pediatric population. Additionally, there are no real-world studies from low and middle-income countries about VE in the 12-17 aged population during the Omicron outbreak.\n\nThis study shows that VE after 14 days or more from two-dose-scheme was 78{middle dot}0% [68{middle dot}7-84{middle dot}2], 76{middle dot}4% [62{middle dot}9-84{middle dot}5] and 80{middle dot}0% [64{middle dot}3-88{middle dot}0] for the 3-17-year entire group, and for 3-11-year (BBIBP-CorV) and 12-17-year (mRNA vaccines) subgroups, respectively. VE for the 3-17-year entire group was 82{middle dot}7% during the period of Delta and Omicron overlapping circulation and decreased to 67{middle dot}7% when Omicron was the only variant present. These effects were consistent across all subgroups.\n\nImplications of all the available evidenceOur results provide evidence of high vaccine protection against COVID-19 associated-hospitalisations in the pediatric population during the Omicron outbreak, but suggest a decrease of protection when Omicron became predominant. Application of a booster dose in children aged 3-11 warrants further consideration.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Soledad Estrella Gonzalez", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Santiago Olszevicki", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Alejandra Gaiano", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Ana Nina Varela Baino", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Lorena Regairaz", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Martin Salazar", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Santiago Pesci", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Lupe Marin", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Veronica Gonzalez", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Teresa Varela", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Leticia Ceriani", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Enio Garcia", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Nicolas Kreplak", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Alexia Navarro", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Elisa Estenssoro", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Franco L. Marsico", - "author_inst": "Calculus Institute, University of Buenos Aires" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.18.22271936", "rel_title": "Anti-nucleocapsid antibodies following SARS-CoV-2 infection in the blinded phase of the mRNA-1273 Covid-19 vaccine efficacy clinical trial", @@ -329818,6 +330596,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.19.22273034", + "rel_title": "Pathogen- and type-specific changes in invasive bacterial disease epidemiology during the first year of the COVID-19 pandemic in the Netherlands", + "rel_date": "2022-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.19.22273034", + "rel_abs": "The COVID-19 control measures have resulted in a decline in invasive bacterial disease caused by Neisseria meningitidis (IMD), Streptococcus pneumoniae (IPD), and Haemophilus influenzae (Hi-D). The species comprise different serogroups and serotypes that impact transmissibility and virulence. We evaluated type- and pathogen-specific changes in invasive bacterial disease epidemiology in the Netherlands during the first year of the SARS-CoV-2 pandemic. Cases were based on nationwide surveillance for five bacterial species with either respiratory (IMD, IPD, Hi-D) or non-respiratory (controls) transmission routes and compared between the pre-COVID period (April 2015-March 2020) and the first COVID-19 year (April 2020-March 2021). IMD, IPD, and Hi-D cases decreased by 78%, 67%, and 35%, respectively, in the first COVID-19 year compared to the pre-COVID period although effects differed per age group. Serogroup B-IMD declined by 61%, while serogroup W and Y-IMD decreased >90%. IPD caused by serotypes 7F, 15A, 12F, 33F, and 8 showed the most pronounced decline ([≥]76%). In contrast to an overall decrease in Hi-D cases, vaccine-preventable serotype b (Hib) increased by 51%. COVID-19 control measures had pathogen- and type-specific effects related to invasive infections. Continued surveillance is critical to monitor potential rebound effects once restriction measures are lifted and transmission is resumed.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Anneke Steens", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Mirjam J Knol", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Wieke Freudenburg-de Graaf", + "author_inst": "Amsterdam UMC, location University of Amsterdam" + }, + { + "author_name": "Hester E de Melker", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Arie van der Ende", + "author_inst": "Amsterdam UMC, location University of Amsterdam" + }, + { + "author_name": "Nina M. van Sorge", + "author_inst": "Amsterdam UMC, location University of Amsterdam" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.15.487518", "rel_title": "V\u03b39V\u03b42 T cells are potent inhibitors of SARS-CoV-2 replication and exert effector phenotypes in COVID-19 patients", @@ -331162,29 +331979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.17.22273854", - "rel_title": "Characterization of SARS-CoV-2 vaccine waning in Mexico", - "rel_date": "2022-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.17.22273854", - "rel_abs": "1.We use survival analysis to analyze the decay in the protection induced by eight vaccines using data from 44, 006 patients from the IMSS public health system in Mexico, including only previously vaccinated, confirmed SARS-CoV-2 positive with a PCR test. We analyze three groupings: all data, complete vs. incomplete dose and less than 60 years or older. We found that a Weibull distribution fits very well the complete dose data. Only three vaccines still had 30% of their initial strength after 32 weeks. In two-dose vaccines, we found that the average protection time of a complete dose increases 2 to 3 times compared to that of an incomplete dose.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "CARLOS M HERNANDEZ-SUAREZ", - "author_inst": "Universidad Francisco Gavidia" - }, - { - "author_name": "Efren Murillo-Zamora", - "author_inst": "Instituto Mexicano del Seguro Social" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.18.22273961", "rel_title": "Clonal diversity determines persistence of SARS-CoV-2 epitope-specific T cell response", @@ -331512,6 +332306,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2022.04.17.22273938", + "rel_title": "Permissive Omicron breakthrough infections in individuals with binding or neutralizing antibodies to ancestral SARS-CoV-2", + "rel_date": "2022-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.17.22273938", + "rel_abs": "BackgroundBreakthrough infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529) has occurred in populations with high vaccination rates. These infections are due to sequence variation in the spike protein leading to a reduction in protection afforded by the current vaccines, which are based on the original Wuhan-Hu-1 strain, or by natural infection with pre-Omicron strains.\n\nMethodsIn a longitudinal cohort study, pre-breakthrough infection sera for Omicron breakthroughs (n=12) were analyzed. Assays utilized include a laboratory-developed solid phase binding assay to recombinant spike protein, a commercial assay to the S1 domain of the spike protein calibrated to the World Health Organization (WHO) standard, and a commercial solid-phase surrogate neutralizing activity (SNA) assay. All assays employed spike protein preparations based on sequences from the Wuhan-Hu-1 strain. Participant demographics and clinical characteristics were captured.\n\nResultsPre-breakthrough binding antibody (bAB) titers ranged from 1:800-1:51,200 for the laboratory-developed binding assay, which correlated well and agreed quantitatively with the commercial spike S1 domain WHO calibrated assay. SNA was detected in 10/12 (83%) samples.\n\nConclusionsNeither high bAB nor SNA were markers of protection from Omicron infection/re-infection. Laboratory tests with antigen targets based on Wuhan-Hu-1 may not accurately reflect the degree of immune protection from variants with significant spike protein differences. Omicron breakthrough infections are likely due to high sequence variation of the spike protein and reflect incomplete immune protection from previous infection with strains that preceded Omicron or with vaccinations based on the original Wuhan-Hu-1 strain.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Erin Williams", + "author_inst": "University of Miami" + }, + { + "author_name": "Jordan D Colson", + "author_inst": "University of Miami Miller School of Medicine" + }, + { + "author_name": "Ranjini Valiathan", + "author_inst": "University of Miami Miller School of Medicine" + }, + { + "author_name": "Juan Manuel Carreno Quiroz", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Michael E Hoffer", + "author_inst": "University of Miami Miller School of Medicine" + }, + { + "author_name": "Suresh Pallikkuth", + "author_inst": "University of Miami Miller School of Medicine" + }, + { + "author_name": "Savita Pahwa", + "author_inst": "University of Miami Miller School of Medicine" + }, + { + "author_name": "David Andrews", + "author_inst": "University of Miami Miller School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.12.22273745", "rel_title": "Duration of COVID-19 mRNA Vaccine Effectiveness against Severe Disease", @@ -333028,41 +333873,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.08.22273513", - "rel_title": "SARS-CoV-2 spike 340 and 337 mutations in Omicron variants are selected after Sotrovimab infusion in immunocompromised patients", - "rel_date": "2022-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.08.22273513", - "rel_abs": "After monoclonal antibody sotrovimab implementation, Rockett et al have warned on March 9th about two resistant mutations in the spike at position 337 and 340 occurring within the first week in four immunocompromised patients infected by a Delta variant and resulting in viable infection up to 25 days. As sotrovimab is currently the only effective treatment against BA.1 lineage of Omicron variant, we investigated the presence of these mutations in our 22,908 Omicron sequences performed from December 2021 to March 2022.\n\nAmong 25 Omicron sequences with S:337 and S:340 substitutions, 9 were reported in six patients who had available clinical data and a follow up. All were immunicompromised, and presented a rapid selection of these mutations after sotrovimab monotherapy infusion.\n\nWith these findings, we underscore that although these mutations are rare, they have been exclusively reported in immunocompromised patients treated with sotrovimab. We urge to consider monoclonal antibody as monotherapy in immunocompromised patients as a risk for escape mutants selection.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "gregory destras", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - }, - { - "author_name": "antonin bal", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - }, - { - "author_name": "bruno simon", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - }, - { - "author_name": "bruno lina", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - }, - { - "author_name": "laurence josset", - "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Hospices Civils de Lyon, France" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.08.22273532", "rel_title": "Heterologous Gam-COVID-Vac (Sputnik V) / mRNA-1273 (Moderna) vaccination induces a stronger humoral response than homologous Sputnik V in a real-world data analysis", @@ -333246,6 +334056,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.12.22273589", + "rel_title": "Profile of Brazilian inpatients with COVID-19 vaccine breakthrough infection and risk factors for unfavorable outcome", + "rel_date": "2022-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.12.22273589", + "rel_abs": "ObjectiveTo characterize the epidemiological and clinical profile of individuals more likely to become infected by SARS-CoV-2 after the fully vaccination schedule in order to profile priority groups to receive a booster dose in situations of vaccine doses shortage as well as for maintenance of personal protective care.\n\nMethodsData from hospitalized COVID-19 patients who had been fully vaccinated and had a SARS-CoV-2 infection positive diagnosis were collected from the SIVEP-Gripe database (Influenza Epidemiological Surveillance Information System) from January 18, 2021 to September 15, 2021. Demographic data, clinical symptoms/signs and preexisting medical conditions (comorbidities) were analyzed. The primary outcome was in-hospital death.\n\nResultsThe majority of hospitalized patients with vaccine breakthrough infection were elderly [≥] 60 years old, male, with critical or severe COVID-19. The fatality rate was extremely high (50.27%) and more pronounced in elderly groups. The most prevalent symptoms were cough, dyspnoea, respiratory distress, and low blood oxygen saturation. The most frequent comorbidities were heart disease and diabetes. High fatality rates were observed among patients admitted to the intensive care units (72.88%) and those who required invasive mechanical ventilation (87.82%). The main risk factors for an unfavorable outcome were older age, respiratory compromise, inactivated virus vaccine immunization, and preexisting medical conditions.\n\nConclusionsWe characterize the profile of hospitalized Brazilian patients with COVID-19 vaccine breakthrough infection and the risk factors for an unfavorable outcome. These data have made it possible to identify priority groups to receive a booster dose, in addition to not neglecting personal protection.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Matheus Alexandre Santos de Jesus", + "author_inst": "Federal University of S\u00e3o Jo\u00e3o del-Rei" + }, + { + "author_name": "Nat\u00e1lia Satchiko Hojo-Souza", + "author_inst": "OswaldoCruz Foundation" + }, + { + "author_name": "Thiago Rocha de Moraes", + "author_inst": "Federal University of S\u00e3o Jo\u00e3o del-Rei" + }, + { + "author_name": "Daniel Ludovico Guidoni", + "author_inst": "Federal University of Ouro Preto" + }, + { + "author_name": "Fernanda Sumika Hojo Souza", + "author_inst": "Federal University of Ouro Preto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.15.22273925", "rel_title": "COVID-19 relevant genetic variants confirmed in an admixed population", @@ -334510,121 +335355,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2022.04.14.22272888", - "rel_title": "Anti-inflammatory therapy with nebulised dornase alfa in patients with severe COVID-19 pneumonia", - "rel_date": "2022-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.14.22272888", - "rel_abs": "BackgroundCell-free (cf)-DNA, from cellular sources, including Neutrophil Extracellular Traps (NETs), is found in the circulation of COVID-19 patients and may contribute to immune dysregulation. This study determined whether pulmonary administration of the endonuclease, dornase alfa, reduced systemic inflammation by degrading local and systemic cf-DNA.\n\nMethodsEligible patients were randomized (3:1) to receive twice-daily nebulised dornase alfa in addition to best available care (BAC) or BAC alone for seven days or until discharge. A 2:1 ratio of matched contemporary controls (CC-BAC) provided additional comparators. The primary endpoint was improvement in C-reactive protein (CRP) over time, analysed using a repeated-measures mixed model, adjusted for baseline factors.\n\nResultsBetween June 2020-October 2021 we recruited 39 evaluable patients: 30 randomised to dornase alfa (R-BAC+DA); 9 randomised to BAC (R-BAC); with the addition of 60 CC-BAC participants. Dornase alfa was well tolerated and reduced CRP by 33% compared to combined BAC groups (T-BAC). Least squares (LS) mean post-dexamethasone CRP fell from 101.9mg/L to 23.23 mg/L in the BAC+ dornase alfa group versus a fall from 99.5mg/L to 34.82 mg/L in the T-BAC group at 7 days; P=0.01. This effect of dornase alfa on CRP was confirmed with subgroup and sensitivity analyses that mitigated potential biases associated with the use of the CC-BAC group. Dornase alfa increased the chance of live discharge by 63% (HR 1.63, 95% CI 1.01 to 2.61, P=0.03), increased lymphocyte counts (LS mean: 1.08 vs 0.87, P=0.02) and reduced circulating cf-DNA and the coagulopathy marker D-dimer (LS mean: 570.78 vs 1656.96 g/mL, P=0.004).\n\nConclusionWe provide proof-of-concept evidence that dornase alfa reduces pathogenic inflammation in hospitalised patients with COVID-19 pneumonia, suggesting that best available care can be improved by the inclusion of anti-inflammatory treatments that target damage-associated molecules.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Joanna Porter", - "author_inst": "UCL Respiratory, University College London, UK" - }, - { - "author_name": "Jamie Inshaw", - "author_inst": "Exploristics, Belfast, N. Ireland" - }, - { - "author_name": "Vincente Joel Solis", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Emma Denneny", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Rebecca Evans", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Mia I. Temkin", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Nathalia De Vasconcelos", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Iker Valle Aramburu", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Dennis Hoving", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Donna Basire", - "author_inst": "UCL Respiratory, University College London, UK" - }, - { - "author_name": "Tracey Crissell", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Jesusa Guinto", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Alison Webb", - "author_inst": "University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Hanif Esmail", - "author_inst": "National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK" - }, - { - "author_name": "Victoria Johnston", - "author_inst": "National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK" - }, - { - "author_name": "Anna Last", - "author_inst": "Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Thomas Rampling", - "author_inst": "National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK" - }, - { - "author_name": "Elisa Theresa Helbig", - "author_inst": "Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany" - }, - { - "author_name": "Lena Lippert", - "author_inst": "Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany" - }, - { - "author_name": "Florian Kurth", - "author_inst": "Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany" - }, - { - "author_name": "Bryan Williams", - "author_inst": "National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK" - }, - { - "author_name": "Aiden Flynn", - "author_inst": "Exploristics, Belfast, N. Ireland" - }, - { - "author_name": "Pauline Lukey", - "author_inst": "Target to Treatment Consulting Ltd, Stevenage, UK" - }, - { - "author_name": "Veronique Birault", - "author_inst": "Translation, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Venizelos Papayannopoulos", - "author_inst": "Antimicrobial Defence lab, The Francis Crick Institute, London, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.13.22273835", "rel_title": "Evaluation of machine learning for predicting COVID-19 outcomes from a national electronic medical records database", @@ -334868,6 +335598,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.13.486321", + "rel_title": "Relative infectivity of the SARS-CoV-2 Omicron variant in human alveolar cells", + "rel_date": "2022-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.13.486321", + "rel_abs": "With the emergence of multiple highly transmissible SARS-CoV-2 variants during the recent pandemic, the comparison of their infectivity has become a substantially critical issue for public health. However, a direct assessment of these viral characteristics has been challenging due to the lack of appropriate experimental models and efficient methods. Here, we integrated human alveolar organoids and single-cell transcriptome sequencing techniques to facilitate the evaluation. In a proof-of-concept study using the assay with four highly transmissible SARS-CoV-2 variants, including GR (B.1.1.119), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.1), a rapid evaluation of the relative infectivity was possible. Our results demonstrate that the Omicron (BA.1) variant is 3-5-fold more infectious to human alveolar cells than the other SARS-CoV-2 variants at the early phase of infection. To our knowledge, this study provides the first direct measurement of the infectivity of the Omicron variant and new experimental procedures that can be applied for monitoring newly emerging viral variants.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Taewoo Kim", + "author_inst": "Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea" + }, + { + "author_name": "Kyoung Il Min", + "author_inst": "Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea" + }, + { + "author_name": "Jeong-Sun Yang", + "author_inst": "Division of Emerging Virus & Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Che" + }, + { + "author_name": "Jun Won Kim", + "author_inst": "Division of Emerging Virus & Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Che" + }, + { + "author_name": "Junhyung Cho", + "author_inst": "Division of Emerging Virus & Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Che" + }, + { + "author_name": "Yun Ho Kim", + "author_inst": "Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul National University Cancer Research Institute, Seoul 03080, Republi" + }, + { + "author_name": "Jeong Seok Lee", + "author_inst": "Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea, GENOME INSIGHT Inc., D" + }, + { + "author_name": "Young Tae Kim", + "author_inst": "Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul National University Cancer Research Institute, Seoul 03080, Republi" + }, + { + "author_name": "Kyung-Chang Kim", + "author_inst": "Division of Emerging Virus & Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Che" + }, + { + "author_name": "Jeong Yeon Kim", + "author_inst": "GENOME INSIGHT Inc., Daejeon 34051, Republic of Korea" + }, + { + "author_name": "Kwon Joong Na", + "author_inst": "Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul National University Cancer Research Institute, Seoul 03080, Republi" + }, + { + "author_name": "Joo-Yeon Lee", + "author_inst": "Division of Emerging Virus & Vector Research, Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Che" + }, + { + "author_name": "Young Seok Ju", + "author_inst": "Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea, GENOME INSIGHT Inc., D" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.04.07.22273595", "rel_title": "Epidemiology of infections with SARS-CoV-2 Omicron BA.2 variant in Hong Kong, January-March 2022", @@ -336163,73 +336960,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.12.487379", - "rel_title": "Evolution of nasal and olfactory infection characteristics of SARS-CoV-2 variants", - "rel_date": "2022-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.12.487379", - "rel_abs": "SARS-CoV-2 infection of the upper airway and the subsequent immune response are early, critical factors in COVID-19 pathogenesis. By studying infection of human biopsies in vitro and in a hamster model in vivo, we demonstrated a transition in tropism from olfactory to respiratory epithelium as the virus evolved. Analyzing each variants revealed that SARS-CoV-2 WA1 or Delta infects a proportion of olfactory neurons in addition to the primary target sustentacular cells. The Delta variant possesses broader cellular invasion capacity into the submucosa, while Omicron displays longer retention in the sinonasal epithelium. The olfactory neuronal infection by WA1 and the subsequent olfactory bulb transport via axon is more pronounced in younger hosts. In addition, the observed viral clearance delay and phagocytic dysfunction in aged olfactory mucosa is accompanied by a decline of phagocytosis related genes. Furthermore, robust basal stem cell activation contributes to neuroepithelial regeneration and restores ACE2 expression post-infection. Together, our study characterized the nasal tropism of SARS-CoV-2 strains, immune clearance, and regeneration post infection. The shifting characteristics of viral infection at the airway portal provides insight into the variability of COVID-19 clinical features and may suggest differing strategies for early local intervention.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Mengfei Chen", - "author_inst": "Johns Hopkins University-School of Medicine" - }, - { - "author_name": "Andrew Pekosz", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Jason Villano", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Wenjuan Shen", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Ruifeng Zhou", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Heather Kulaga", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Zhexuan Li", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Sarah E. Beck", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Kenneth W Witwer", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Joseph Mankowski", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Murugappan Ramanathan Jr.", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Nicholas Rowan", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Andrew Lane", - "author_inst": "Johns Hopkins University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2022.04.12.487988", "rel_title": "An ACAT inhibitor regulates SARS-CoV-2 replication and antiviral T cell activity", @@ -336649,6 +337379,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.04.11.487970", + "rel_title": "Discrimination of SARS-CoV-2 Omicron sub-lineages BA.1 and BA.2 using a high-resolution melting-based assay: A pilot study", + "rel_date": "2022-04-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.11.487970", + "rel_abs": "The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. As of March 2022, Omicron variant BA.2 is rapidly replacing variant BA.1. As variant BA.2 may cause more severe disease than variant BA.1, variant BA.2 requires continuous monitoring. The current study aimed to develop a novel high-resolution melting (HRM) assay for variants BA.1 and BA.2 and to determine the sensitivity and specificity of our method using clinical samples. Here, we focused on the mutational spectra at three regions in the spike receptor-binding domain (RBD; R408, G446/L452, and S477/T478) for the variant-selective HRM analysis. Each variant was identified based on the mutational spectra as follows: no mutations (Alpha variant); L452R and T478K (Delta variant); G446S and S477N/T478K (Omicron variant BA.1); and R408S and S477N/T478K (Omicron variant BA.2). Upon analysis of mutation-coding RNA fragments, the melting peaks of the wild-type fragments were distinct from those of the mutant fragments. The sensitivity and specificity of this method were determined as 100% and more than 97.5%, respectively, based on 128 clinical samples (40 Alpha, 40 Delta, 40 Omicron variants BA.1/BA.1.1, and 8 Omicron BA.2). These results suggest that this HRM-based assay is a promising screening method for monitoring the transmission of Omicron variants BA.1 and BA.2.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Akira Aoki", + "author_inst": "Meijo University" + }, + { + "author_name": "Hirokazu Adachi", + "author_inst": "Aichi Prefectural Institute of Public Health" + }, + { + "author_name": "Yoko Mori", + "author_inst": "Meijo University" + }, + { + "author_name": "Miyabi Ito", + "author_inst": "Aichi Prefectural Institute of Public Health" + }, + { + "author_name": "Katsuhiko Sato", + "author_inst": "Aichi Prefectural Institute of Public Health" + }, + { + "author_name": "Kenji Okuda", + "author_inst": "Aichi Prefectural Institute of Public Health" + }, + { + "author_name": "Toru Sakakibara", + "author_inst": "Aichi Prefectural Institute of Public Health" + }, + { + "author_name": "Yoshinori Okamoto", + "author_inst": "Meijo University" + }, + { + "author_name": "Hideto Jinno", + "author_inst": "Meijo University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.04.12.488010", "rel_title": "Genome wide screen of RNAi molecules against SARS-CoV-2 creates a broadly potent prophylaxis", @@ -337722,33 +338503,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.04.09.487739", - "rel_title": "Disrupting ACE2 Dimerization Mitigates the Infection by SARS-COV-2", - "rel_date": "2022-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.09.487739", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has caused over 6 million death and 460 million reported cases globally. More effective antiviral medications are needed to curb the continued spread of this disease. The infection by SARS-COV-2 virus is initiated via the interaction between the receptor binding domain (RBD) of the viral glycoprotein Spike (S protein) and the N-term peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE2) expressed on host cell membrane. ACE2 forms protein homodimer primarily through its ferredoxin-like fold domain (aka. Neck-domain). We investigated whether the dimerization of ACE2 receptor plays a role in SARS-COV-2 virus infection. We report here that the ACE2 receptor dimerization enhances the recognition of SARS-COV-2 S protein. A 43 amino acid peptide based on the N-term of Neck-domain could block the ACE2 dimerization and the interaction between RBD and ACE2, and mitigate the SARS-COV-2/host cell interaction. Our study illustrated a new route to develop potential therapeutics for the prevention and treatment of SARS-COV-2 viral infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jiaqi Zhu", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Yue Su", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Young Tang", - "author_inst": "University of Connecticut" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.04.11.487882", "rel_title": "Receptor binding domain of SARS-CoV-2 is a functional \u03b1v-integrin agonist", @@ -338068,6 +338822,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2022.04.06.22273526", + "rel_title": "Psychosocial predictors of COVID-19 vaccine uptake among pregnant women: a cross-sectional study in Greece", + "rel_date": "2022-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273526", + "rel_abs": "BackgroundUnvaccinated pregnant women with symptomatic COVID-19 have been found to have a higher risk of iatrogenic preterm births, intensive care unit admission, and invasive ventilation.\n\nObjectiveTo estimate the vaccination rate of pregnant women against the COVID-19 and to evaluate psychosocial factors associated with vaccine uptake among them.\n\nMethodsWe conducted an anonymous cross-sectional study with a convenience sample in Greece from December 2021 to March 2022. We measured socio-demographic data of pregnant women, COVID-19-related vaccination status, worry about the side effects of COVID-19 vaccines, trust in COVID-19 vaccines, and COVID-19-related stress.\n\nResultsThe study population included 812 pregnant women with a mean age of 31.6 years. Among the pregnant women, 58.6% had received a COVID-19 vaccine. The most important reasons that pregnant women were not vaccinated were doubts about the safety and effectiveness of COVID-19 vaccines (31.4%), fear that COVID-19 vaccines could be harmful to fetus (29.4%), and fear of adverse side effects of COVID-19 vaccines (29.4%). Increased danger and contamination fears, increased fears about economic consequences, and higher levels of trust in COVID-19 vaccines were related with COVID-19 vaccine uptake. On the other hand, increased compulsive checking and reassurance seeking and increased worry about the adverse side effects of COVID-19 vaccines reduced the likelihood of pregnant women being vaccinated against the COVID-19.\n\nConclusionsAn understanding of the psychosocial factors associated with COVID-19 vaccine uptake in pregnant women is paramount to persuade women to get vaccinated against the COVID-19. There is a need for targeted educational campaigns to increase knowledge about COVID-19 vaccines and reduce COVID-19 vaccine hesitancy in pregnancy.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Petros A Galanis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Irene Vraka", + "author_inst": "P & A Kyriakou Children's Hospital" + }, + { + "author_name": "Aglaia Katsiroumpa", + "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" + }, + { + "author_name": "Olympia Konstantakopoulou", + "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" + }, + { + "author_name": "Olga Siskou", + "author_inst": "University of Piraeus" + }, + { + "author_name": "Eleftheria Zogaki", + "author_inst": "Faculty of Midwifery" + }, + { + "author_name": "Daphne Kaitelidou", + "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2022.04.08.22273605", "rel_title": "Impact of SARS-CoV-2 vaccination on systemic immune responses in people living with HIV", @@ -339504,101 +340301,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.06.487394", - "rel_title": "Prime-pull immunization of mice with a BcfA-adjuvanted vaccine elicits mucosal immunity and prevents SARS CoV-2 infection and pathology", - "rel_date": "2022-04-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.06.487394", - "rel_abs": "Vaccines against SARS-CoV-2 that induce mucosal immunity capable of preventing infection and disease remain urgently needed. We show that intramuscular priming of mice with an alum and BcfA-adjuvanted Spike subunit vaccine, followed by a BcfA-adjuvanted mucosal booster, generated Th17 polarized tissue resident CD4+ T cells, and mucosal and serum antibodies. The serum antibodies efficiently neutralized SARS-CoV-2 and its Delta variant, suggesting cross-protection against a recent variant of concern (VOC). Immunization with this heterologous vaccine prevented weight loss following challenge with mouse-adapted SARS-CoV-2 and reduced viral replication in the nose and lungs. Histopathology showed a strong leukocyte and polymorphonuclear (PMN) cell infiltrate without epithelial damage in mice immunized with BcfA-containing vaccines. In contrast, viral load was not reduced in the upper respiratory tract of IL-17 knockout mice immunized with the same formulation, suggesting that the Th17 polarized T cell responses are critical for protection. We show that vaccines adjuvanted with alum and BcfA, delivered through a heterologous prime-pull regimen, protect against SARS-CoV-2 infection without causing enhanced respiratory disease.\n\nSIGNIFICANCEThere remains a need for SARS CoV-2 booster vaccines that generate mucosal immunity and prevent transmission. We show that systemic priming followed by a mucosal booster with a BcfA-adjuvanted subunit vaccine generates neutralizing antibodies and Th17 polarized systemic and tissue-resident immune responses that provide sterilizing immunity against wildtype SARS CoV-2, and a variant of concern. Importantly, in contrast to alum alone, the addition of BcfA prevents respiratory pathology. These results suggest that a BcfA-adjuvanted mucosal booster may elicit mucosal immunity in individuals previously immunized systemically with approved vaccines. This foundational study in mice sets the stage for testing our vaccine regimen in larger animal models as a booster vaccine.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Mohamed M. Shamseldin", - "author_inst": "Ohio State University" - }, - { - "author_name": "Ashley Zani", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Adam Kenney", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Jack Evans", - "author_inst": "Ohio State University" - }, - { - "author_name": "Cong Zeng", - "author_inst": "Ohio State University" - }, - { - "author_name": "Kaitlin A. Read", - "author_inst": "Ohio State University" - }, - { - "author_name": "Kyle Caution", - "author_inst": "Ohio State University" - }, - { - "author_name": "Jesse M. Hall", - "author_inst": "Ohio State University" - }, - { - "author_name": "Jessica M. Brown", - "author_inst": "Ohio State University" - }, - { - "author_name": "Gilian Gunsch", - "author_inst": "Ohio State University" - }, - { - "author_name": "Kara N. Corps", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Supranee Chaitwatponsakom", - "author_inst": "Ohio State University" - }, - { - "author_name": "Mahesh KC", - "author_inst": "Ohio State University" - }, - { - "author_name": "Mijia Lu", - "author_inst": "Ohio State University" - }, - { - "author_name": "Rajendar Deora", - "author_inst": "The Ohio State University College of Medicine" - }, - { - "author_name": "Jianrong Li", - "author_inst": "Ohio State University" - }, - { - "author_name": "Kenneth J. Oestreich", - "author_inst": "Ohio State University" - }, - { - "author_name": "Shan-Lu Liu", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Jacob S. Yount", - "author_inst": "Ohio State University" - }, - { - "author_name": "Purnima Dubey", - "author_inst": "The Ohio State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.04.07.487489", "rel_title": "Antibody Resistance of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2 and BA.3 Sub-lineages", @@ -339910,6 +340612,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.06.22273516", + "rel_title": "Impact of the COVID-19 epidemic on mortality in rural coastal Kenya", + "rel_date": "2022-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273516", + "rel_abs": "BackgroundThe impact of COVID-19 on all-cause mortality in sub-Saharan Africa remains unknown.\n\nMethodsWe monitored mortality among 306,000 residents of Kilifi Health and Demographic Surveillance System, Kenya, through four COVID-19 waves from April 2020-September 2021. We calculated expected deaths using negative binomial regression fitted to baseline mortality data (2010-2019) and calculated excess mortality as observed-minus-expected deaths. We excluded deaths in infancy because of under-ascertainment of births during lockdown. In February 2021, after two waves of wild-type COVID-19, adult seroprevalence of anti-SARS-CoV-2 was 25.1%. We predicted COVID-19-attributable deaths as the product of age-specific seroprevalence, population size and global infection fatality ratios (IFR). We examined changes in cause of death by Verbal Autopsy (VA).\n\nResultsBetween April 2020 and February 2021, we observed 1,000 deaths against 1,012 expected deaths (excess mortality -1.2%, 95% PI -6.6%, 5.8%). Based on SARS-CoV-2 seroprevalence, we predicted 306 COVID-19-attributable deaths (a predicted excess mortality of 30.6%) within this period. Monthly mortality analyses showed a significant excess among adults aged [≥]45 years in only two months, July-August 2021, coinciding with the fourth (Delta) wave of COVID-19. By September 2021, overall excess mortality was 3.2% (95% PI -0.6%, 8.1%) and cumulative excess mortality risk was 18.7/100,000. By VA, there was a transient reduction in deaths attributable to acute respiratory infections in 2020.\n\nConclusionsNormal mortality rates during extensive transmission of wild-type SARS-CoV-2 through February 2021 suggests that the IFR for this variant is lower in Kenya than elsewhere. We found excess mortality associated with the Delta variant but the cumulative excess mortality risk remains low in coastal Kenya compared to global estimates.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Mark Otiende Mr.", + "author_inst": "KEMRI-Wellcome Trust Research Programme" + }, + { + "author_name": "Amek Nyaguara", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Christian Bottomley", + "author_inst": "Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "David Walumbe", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "George Mochamah", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "David Amadi", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Christopher Nyundo", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Eunice Kagucia", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Anthony Etyang'", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Ifedayo Adetifa", + "author_inst": "Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "Eric Maitha", + "author_inst": "Department of Health, Kilifi County, Kenya" + }, + { + "author_name": "Elwyn Chondo", + "author_inst": "Department of Health, Kilifi County, Kenya" + }, + { + "author_name": "Eddy Nzomo", + "author_inst": "Kilifi County Hospital, Kilifi, Kenya" + }, + { + "author_name": "Rashid Aman", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "Mercy Mwangangi", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "Patrick Amoth", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "Kadondi Kasera", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "Wangari Ng'ang'a", + "author_inst": "Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "Edwine Barasa", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Benjamin Tsofa", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Joseph Mwangangi", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Philip Bejon", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Ambrose Agweyu", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Tom Williams", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + }, + { + "author_name": "Anthony Scott", + "author_inst": "KEMRI-Wellcome Research Trust Programme, Kilifi, Kenya" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.07.22273319", "rel_title": "Vaccine effectiveness of BNT162b2 against Omicron and Delta outcomes in adolescents", @@ -341238,109 +342055,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.06.487325", - "rel_title": "Delta-Omicron recombinant SARS-CoV-2 in a transplant patient treated with Sotrovimab", - "rel_date": "2022-04-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.06.487325", - "rel_abs": "BackgroundThe emergence of recombinant viruses is a threat to public health. Recombination of viral variants may combine variant-specific features that together catalyze viral escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown.\n\nMethodsMulti-method amplicon and metagenomic sequencing of a clinical swab and the in vitro grown virus allowed for high-confidence detection of a novel recombinant variant. Mutational, phylogeographic, and structural analyses determined features of the recombinant genome and spike protein. Neutralization assays using infectious as well as pseudotyped viruses and point mutants thereof defined the recombinants sensitivity to a panel of monoclonal antibodies and sera from vaccinated and/or convalescent individuals.\n\nResultsA novel Delta-Omicron SARS-CoV-2 recombinant was identified in an unvaccinated, immunosuppressed kidney transplant recipient treated with monoclonal antibody Sotrovimab. The recombination breakpoint is located in the spike N-terminal domain, adjacent to the Sotrovimab quaternary binding site, and results in a 5-Delta AY.45 and a 3-Omicron BA.1 mosaic spike protein. Delta and BA.1 are sensitive to Sotrovimab neutralization, whereas the Delta-Omicron recombinant is highly resistant to Sotrovimab, both with and without the RBD resistance mutation E340D.\n\nConclusionsRecombination between circulating SARS-CoV-2 variants can functionally contribute to immune escape. It is critical to validate phenotypes of mosaic viruses and monitor immunosuppressed COVID-19 patients treated with monoclonal antibodies for the selection of recombinant and immune escape variants. (Funded by NYU, the National Institutes of Health, and others)", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Ralf Duerr", - "author_inst": "New York University - School of Medicine" - }, - { - "author_name": "Hao Zhou", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" - }, - { - "author_name": "Takuya Tada", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" - }, - { - "author_name": "Dacia Dimartino", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Christian Marier", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Paul Zappile", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Guiqing Wang", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Jonathan Plitnick", - "author_inst": "NY State Department of Health" - }, - { - "author_name": "Sara Griesemer", - "author_inst": "NY State Department of Health" - }, - { - "author_name": "Roxie C. Girardin", - "author_inst": "University at Albany, SUNY" - }, - { - "author_name": "Jessica Machowski", - "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY" - }, - { - "author_name": "Sean Bialosuknia", - "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY" - }, - { - "author_name": "Erica Lasek-Nesselquist", - "author_inst": "NY State Department of Health, Wadsworth Center" - }, - { - "author_name": "Samuel L Hong", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Guy Baele", - "author_inst": "Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium" - }, - { - "author_name": "Meike Dittman", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Mila Brum Ortigoza", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Prithiv J. Prasad", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Kathleen McDonough", - "author_inst": "Wadsworth Center, NYSDOH" - }, - { - "author_name": "Nathaniel Landau", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine" - }, - { - "author_name": "Kirsten St. George", - "author_inst": "Wadsworth Center - NYSDOH" - }, - { - "author_name": "Adriana Heguy", - "author_inst": "New York University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.04.06.487306", "rel_title": "An Ultralong Bovine CDRH3 that Targets a Conserved, Cryptic Epitope on SARS-CoV and SARS-CoV-2", @@ -341648,6 +342362,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.29.22271489", + "rel_title": "Linking private health sector to public COVID-19 response in Kisumu, Kenya: Lessons Learnt", + "rel_date": "2022-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22271489", + "rel_abs": "BackgroundCOVID-19 is overwhelming health systems universally. Increased capacity to combat the epidemic is important, while continuing regular healthcare services. This paper describes an innovative Public Private Partnership (PPP) against COVID-19 that from the onset of the epidemic was established in Kisumu County, Western Kenya.\n\nMethodsAn explanatory research design was used. Qualitative in-depth interviews (n=49) were conducted with purposively selected participants including patients, health workers, and policy makers. Thematic analysis was undertaken on interview transcripts and triangulation was performed.\n\nResultsThe PPP hinged through the provision of central diagnostic COVID-19 services through a parastatal institute (KEMRI). Complementary tasks were divided between Kisumu Department of Health and public and private healthcare providers, supported by an NGO. Facilitators to this PPP included implementation of MoH Guidelines, digitalization of data, strengthening of counseling services and free access to COVID-19 testing services in private facilities. Barriers included, data accessibility, sub optimal financial management.\n\nConclusionCoordinated PPP can rapidly enhance capacity and quality of COVID-19 epidemic management in African settings. Our PPP model appears scalable, as proven by current developments. Lessons learnt from this initial PPP in Kisumu County will be beneficial to expanding epidemic preparedness to other Counties in Kenya and beyond.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Mevis Omollo", + "author_inst": "Kenya Medical Research Institute/Center for Global Health Research" + }, + { + "author_name": "Isdorah A Odero", + "author_inst": "Kenya Medical Research Institute/Center for Global Health Research" + }, + { + "author_name": "H C Barsosio", + "author_inst": "Kenya Medical Research Institute/Center for Global Health Research" + }, + { + "author_name": "Simon Karuki", + "author_inst": "Kenya Medical Research Institute/Center for Global Health Research" + }, + { + "author_name": "F Ter Kuile", + "author_inst": "Kenya Medical Research Institute/Center for Global Health Research" + }, + { + "author_name": "S O Okello", + "author_inst": "Kenya Medical Research Institute/Center for Global Health Research" + }, + { + "author_name": "K Oyoo", + "author_inst": "Kenya Medical Research Institute/Center for Global Health Research" + }, + { + "author_name": "A K K'Oloo", + "author_inst": "Kenya Medical Research Institute/Center for Global Health Research" + }, + { + "author_name": "K Otieno", + "author_inst": "Kenya Medical Research Institute/Center for Global Health Research" + }, + { + "author_name": "S V Duijn", + "author_inst": "Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands" + }, + { + "author_name": "N Houben", + "author_inst": "PharmAccess Foundation, Kisumu, Kenya" + }, + { + "author_name": "E Milimo", + "author_inst": "PharmAccess Foundation, Kisumu, Kenya" + }, + { + "author_name": "R Aroka", + "author_inst": "PharmAccess Foundation, Kisumu, Kenya" + }, + { + "author_name": "S N Onsongo", + "author_inst": "Kisumu County Department of Health, Kisumu, Kenya" + }, + { + "author_name": "T F Rinke de Wit", + "author_inst": "Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.04.486920", "rel_title": "Immunopharmacological evaluation of adjuvant efficacy of Monophosphoryl lipid-A and CpG ODN with SARS-CoV-2 RBD antigen", @@ -343004,73 +343793,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.30.22273194", - "rel_title": "Safety and Efficacy of Dupilumab for the Treatment of Hospitalized Patients with Moderate to Severe COVID 19: A Phase IIa Trial", - "rel_date": "2022-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273194", - "rel_abs": "BackgroundA profound need remains to develop further therapeutics for treatment of those hospitalized with COVID-19. Based on data implicating the type 2 cytokine interleukin (IL)-13 as a significant factor leading to critical COVID-19, this trial was designed to assess dupilumab, a monoclonal antibody that blocks IL-13 and IL-4 signaling, for treatment of inpatients with COVID-19.\n\nMethodsWe conducted a phase IIa randomized double-blind placebo-controlled trial to assess the safety and efficacy of dupilumab plus standard of care versus placebo plus standard of care in mitigating respiratory failure and death in those hospitalized with COVID-19. Subjects were followed prospectively for 60 days. The primary endpoint was the proportion of patients alive and free of invasive mechanical ventilation at 28 days.\n\nFindingsForty eligible subjects were enrolled from June to November of 2021. There was no difference in adverse events nor in ventilator free survival at day 28 between study arms. However, for the secondary endpoint of mortality at day 60, subjects randomized to dupilumab had a higher survival rate compared to the placebo group (89.5% vs 76.2%, adjusted HR 0.05, 95% CI: 0.0-0.72, p=0.03). There were fewer subjects admitted to the ICU in the dupilumab group compared to placebo (33.3% vs 66.7%; adjusted HR 0.44, 95% CI: 0.09-2.09, p=0.30). Lastly, we saw downstream evidence of IL-4 and IL-13 signaling blockade in the dupilumab group through analysis of immune biomarkers over time.\n\nInterpretationDupilumab was well tolerated and improved 60-day survival in patients hospitalized with moderate to severe COVID-19.\n\nTrial RegistrationThis trial is registered with ClinicalTrials.gov, NCT04920916.\n\nFundingVirginia Biosciences Health Research Corporation, PBM C19, Henske Family Foundation, National Institutes of Health, National Cancer Institute", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jennifer Sasson", - "author_inst": "University of Virginia" - }, - { - "author_name": "Alexandra N Donlan", - "author_inst": "University of Virginia" - }, - { - "author_name": "Jennie Z Ma", - "author_inst": "University of Virginia" - }, - { - "author_name": "Heather Haughey", - "author_inst": "University of Virginia" - }, - { - "author_name": "Rachael Coleman", - "author_inst": "University of Virginia" - }, - { - "author_name": "Uma Nayak", - "author_inst": "University of Virginia" - }, - { - "author_name": "Amy J. Mathers", - "author_inst": "University of Virginia" - }, - { - "author_name": "Sylvain Laverdure", - "author_inst": "Frederick National Laboratory" - }, - { - "author_name": "Robin Dewar", - "author_inst": "Frederick National Laboratory" - }, - { - "author_name": "Patrick E. H. Jackson", - "author_inst": "University of Virginia" - }, - { - "author_name": "Scott K. Heysell", - "author_inst": "University of Virginia" - }, - { - "author_name": "Jeffrey M. Sturek", - "author_inst": "University of Virginia" - }, - { - "author_name": "William Petri", - "author_inst": "University of Virginia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.03.22272610", "rel_title": "Cardiac impairment in Long Covid 1-year post-SARS-CoV-2 infection", @@ -343310,6 +344032,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.04.04.22273372", + "rel_title": "The trustworthiness and impact of trial preprints for COVID-19 decision-making: A methodological study", + "rel_date": "2022-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22273372", + "rel_abs": "PurposeTo assess the trustworthiness and impact of preprint trial reports during the COVID-19 pandemic.\n\nData sourcesWHO COVID-19 database and the L-OVE COVID-19 platform by the Epistemonikos Foundation (up to August 3rd, 2021)\n\nDesignWe compare the characteristics of COVID-19 trials with and without preprints, estimate time to publication of COVID-19 preprint reports, describe discrepancies in key methods and results between preprint and published trial reports, report the number of retracted preprints and publications, and assess whether including versus excluding preprint reports affects meta-analytic estimates and the certainty of evidence. For the effects of eight therapies on mortality and mechanical ventilation, we performed meta-analyses including preprints and excluding preprints at 1 month, 3 months, and 6 months after the first trial addressing the therapy became available either as a preprint or publication (120 meta-analyses in total).\n\nResultsWe included 356 trials, 101 of which are only available as preprints, 181 as journal publications, and 74 as preprints first and subsequently published in journals. Half of all preprints remain unpublished at six months and a third at one year. There were few important differences in key methods and results between trial preprints and their subsequent published reports. We identified four retracted trials, three of which were published in peer-reviewed journals. With two exceptions (2/60; 3.3%), point estimates were consistent between meta-analyses including versus excluding preprints as to whether they indicated benefit, no appreciable effect, or harm. There were nine comparisons (9/60; 15%) for which the rating of the certainty of evidence differed when preprints were included versus excluded, for four of these comparisons the certainty of evidence including preprints was higher and for five of these comparisons the certainty of evidence including preprints was lower.\n\nLimitationsThe generalizability of our results is limited to COVID-19. Preprints that are subsequently published in journals may be the most rigorous and may not represent all trial preprints.\n\nConclusionWe found no compelling evidence that preprints provide less trustworthy results than published papers. We show that preprints remain the only source of findings of many trials for several months, a length of time that is unacceptable in a health emergency. We show that including preprints may affect the results of meta-analyses and the certainty of evidence. We encourage evidence users to consider data from preprints in contexts in which decisions are being made rapidly and evidence is being produced faster than can be peer-reviewed.\n\nO_TEXTBOXSummary Box 1O_ST_ABSWhat is already known on this topicC_ST_ABSO_LIClinicians and decision-makers need rapidly available and credible data addressing the comparative effectiveness of treatments and prophylaxis for COVID-19.\nC_LIO_LIInvestigators have adopted preprint servers, which allow the rapid dissemination of research findings before publication in peer-reviewed journals.\nC_LI\n\nWhat this study addsO_LIWe found no compelling evidence that preprints provide less trustworthy results than published papers.\nC_LIO_LIWe show that including preprints may affect the results of meta-analyses and the certainty of evidence and we encourage evidence users to consider data from preprints in contexts in which decisions are being made rapidly and evidence is being produced faster than can be peer-reviewed.\nC_LI\n\nC_TEXTBOX", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Dena Zeraatkar", + "author_inst": "Harvard Medical School; McMaster University" + }, + { + "author_name": "Tyler Pitre", + "author_inst": "McMaster University" + }, + { + "author_name": "Gareth Leung", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Ellen Cusano", + "author_inst": "University of Calgary" + }, + { + "author_name": "Arnav Argawal", + "author_inst": "McMaster University" + }, + { + "author_name": "Faran Khalid", + "author_inst": "McMaster University" + }, + { + "author_name": "Zaira Escamilla", + "author_inst": "McMaster University" + }, + { + "author_name": "Matthew Cooper", + "author_inst": "University of Alberta" + }, + { + "author_name": "Maryam Ghadimi", + "author_inst": "McMaster University" + }, + { + "author_name": "Ying Wang", + "author_inst": "McMaster University" + }, + { + "author_name": "Francisca Verdugo", + "author_inst": "Epistemonikos Foundation" + }, + { + "author_name": "Gabriel Rada", + "author_inst": "Epistemonikos Foundation" + }, + { + "author_name": "Elena Kum", + "author_inst": "McMaster University" + }, + { + "author_name": "Anila Qasim", + "author_inst": "McMaster University" + }, + { + "author_name": "Jessica J Bartoszko", + "author_inst": "McMaster University" + }, + { + "author_name": "Reed Siemieniuk", + "author_inst": "McMaster University" + }, + { + "author_name": "Chirag J Patel", + "author_inst": "Harvard University" + }, + { + "author_name": "Gordon Guyatt", + "author_inst": "McMaster University" + }, + { + "author_name": "Romina Brignardello-Petersen", + "author_inst": "McMaster University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.28.22272848", "rel_title": "Biochemical, Biophysical, and Immunological Characterization of Respiratory Secretions in Severe SARS-CoV-2 (COVID-19) Infections", @@ -344966,57 +345779,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.30.22273203", - "rel_title": "COVID-19 vaccination coverage by company size and the effects of socioeconomic factors and workplace vaccination in Japan: a cohort study", - "rel_date": "2022-04-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273203", - "rel_abs": "BackgroundVaccination is considered the most effective control measure against COVID-19. Vaccine hesitancy and equitable vaccine allocation are important challenges to disseminating developed vaccines. To promote COVID-19 vaccination coverage, the government of Japan established the workplace vaccination program. However, while it appears that the program was effective in overcoming vaccine hesitancy, the program may have hindered the equitable allocation of vaccines because it mainly focused on employees of large companies. We investigated the relationship between company size and COVID-19 vaccination completion status of employees and the impact of the workplace vaccination program on this relationship.\n\nMethodsWe conducted an internet-based prospective cohort study from December 2020 (baseline) to December 2021. The data were collected using a self-administered questionnaire survey. Briefly, 27,036 workers completed the questionnaire at baseline and 18,560 at follow-up. After excluding ineligible respondents, we finally analyzed the data from 15,829 participants. At baseline, the participants were asked about the size of the company they worked for, and at follow-up they were asked about the month in which they received their second COVID-19 vaccine dose and the availability of a company-arranged vaccination opportunity.\n\nResultsIn each month throughout the observation period, the odds of having received a second COVID-19 vaccine dose were significantly lower for small-company employees than for large-company employees in the sex- and age-adjusted model. This difference decreased after adjusting for socioeconomic factors, and there was no significant difference after adjusting for the availability of a company-arranged vaccination opportunity.\n\nConclusionsThe workplace vaccination program implemented in Japan to control the COVID-19 pandemic may have been effective in overcoming vaccine hesitancy in workers; however, it may have caused an inequitable allocation of vaccines between companies of different sizes. Because people who worked for small companies were less likely to be vaccinated, it will be necessary to enhance support of vaccination for this population in the event of future infectious disease outbreaks.\n\nTrial registrationNot applicable.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Koji Mori", - "author_inst": "InstitUniversity of Occupational and Environmental Health, Japan," - }, - { - "author_name": "Takahiro Mori", - "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hajime Ando", - "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health" - }, - { - "author_name": "Ayako Hino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Keiji Muramatsu", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.27.22271628", "rel_title": "Spatial prediction of COVID-19 pandemic dynamics in the United States", @@ -345404,6 +346166,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.30.22273190", + "rel_title": "Lessons from a pandemic", + "rel_date": "2022-04-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273190", + "rel_abs": "ObjectivesSeveral interventions have been used around the world trying to contain the SARS-Cov-2 pandemic, such as quarantine, prohibition of mass demonstrations, isolation of sick people, tracing of virus carriers, semi-containment, promotion of barrier gestures, development of rapid auto-tests and vaccines among others. We propose a simple model to evaluate the potential impact of such interventions.\n\nMethodsA model for the reproduction number of an infectious disease including three main contexts of infection (indoor mass events, public indoor activities and household) and seven parameters is considered. We illustrate how these parameters could be obtained from the literature or from expert assumptions, and we apply the model to describe 20 scenarios that can typically occur during the different phases of a pandemic.\n\nResultsThis model provides a useful framework for better understanding and communicating the effects of different (combinations of) possible interventions, while encouraging constant updating of expert assumptions to better match reality.\n\nConclusionThis simple approach will bring more transparency and public support to help governments to think, decide, evaluate and adjust what to do during a pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yves Eggli", + "author_inst": "Unisant\u00e9 Center for Primary Care and Public Health - University of Lausanne" + }, + { + "author_name": "Valentin Rousson", + "author_inst": "Center for primary Care and public health (unisant\u00e9), University of Lausanne" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.25.22271678", "rel_title": "Androgen receptor polyQ alleles and COVID-19 severity in men: a replication study", @@ -346804,93 +347589,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.04.01.486695", - "rel_title": "Omicron breakthrough infection drives cross-variant neutralization and memory B cell formation", - "rel_date": "2022-04-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.01.486695", - "rel_abs": "Omicron is the evolutionarily most distinct SARS-CoV-2 variant (VOC) to date and displays multiple amino acid alterations located in neutralizing antibody sites of the spike (S) protein. We report here that Omicron breakthrough infection in BNT162b2 vaccinated individuals results in strong neutralizing activity not only against Omicron, but also broadly against previous SARS-CoV-2 VOCs and against SARS-CoV-1. We found that Omicron breakthrough infection mediates a robust B cell recall response, and primarily expands preformed memory B cells that recognize epitopes shared broadly by different variants, rather than inducing new B cells against strictly Omicron-specific epitopes. Our data suggest that, despite imprinting of the immune response by previous vaccination, the preformed B cell memory pool has sufficient plasticity for being refocused and quantitatively remodeled by exposure to heterologous S protein, thus allowing effective neutralization of variants that evade a previously established neutralizing antibody response.\n\nOne Sentence SummaryBreakthrough infection in individuals double- and triple-vaccinated with BNT162b2 drives cross-variant neutralization and memory B cell formation.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Jasmin Quandt", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Alexander Muik", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Nadine Salisch", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Bonny Gaby Lui", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Sebastian Lutz", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Kimberly Krueger", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ann-Kathrin Wallisch", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Petra Adams-Quack", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Maren Bacher", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Andrew Finlayson", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Orkun Ozhelvaci", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Isabel Vogler", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Katharina Grikscheit", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Sebastian Hoehl", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Udo Goetsch", - "author_inst": "Health Protection Authority, City of Frankfurt" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Goethe Universtiy Frankfurt" - }, - { - "author_name": "Oezlem Tuereci", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ugur Sahin", - "author_inst": "BioNTech SE" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.30.486345", "rel_title": "Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population", @@ -347142,6 +347840,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.30.486313", + "rel_title": "Identification of C270 as a novel site for allosteric modulators of SARS-CoV-2 papain-like protease", + "rel_date": "2022-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.30.486313", + "rel_abs": "The papain-like protease (PLpro) in coronavirus is one of key cysteine proteases responsible for the proteolytic processing of viral polyproteins, and plays an important role in dysregulation of host immune response. PLpro is a promising therapeutic target with a major challenge in inhibitor design due to the restricted S1/S2 sites for two consecutive glycine of substrates. Here we reported the discovery of two activators of the SARS-CoV-2 PLpro from a biochemical screening, and the identification of the unique residue, C270, as an allosteric and covalent regulation site for the activators. This site was also specifically modified by glutathione oxidized, resulting in the S-glutathionylation and activation of the protease. Furthermore, one compound was found to allosterically inhibit the protease by covalent binding to this crucial site. Together, these results elucidated an unrevealed molecular mechanism for allosteric modulation of the proteases activity, and provided a new strategy for discovery of allosteric inhibitors of the SARS-CoV-2 PLpro.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Hangchen Hu", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Qian Wang", + "author_inst": "School of Chinese Materia Medica, Nanjing University of Chinese Medicine" + }, + { + "author_name": "Haixia Su", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Qiang Shao", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Wenfeng Zhao", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Guofeng Chen", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Minjun Li", + "author_inst": "Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences" + }, + { + "author_name": "Yechun Xu", + "author_inst": "Shanghai Institute of Materia Medica Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.03.30.486373", "rel_title": "Prediction of infectivity of SARS-CoV2: Mathematical Model with Docking Simulation analysis between Spike Protein and ACE2", @@ -348910,29 +349655,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.30.22273165", - "rel_title": "Effect of COVID-19 vaccination on menstrual periods in a prospectively recruited cohort", - "rel_date": "2022-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273165", - "rel_abs": "COVID-19 vaccination protects against the potentially serious consequences of SARS-CoV2 infection, but some people have been hesitant to receive the vaccine because of reports that it could affect menstrual bleeding. To determine whether this occurs, we prospectively recruited a cohort of 79 individuals, each of whom recorded details of at least three consecutive menstrual cycles, during which time they each received at least one dose of COVID-19 vaccine. We find that either dose of the COVID-19 vaccine is associated with a delay to the subsequent period in spontaneously cycling participants (2.3 days after dose 1; 1.3 days after dose 2) but this change rapidly reverses. No change to timing was detected in those on hormonal contraception. We detected no change in menstrual flow associated with either dose of the vaccine, in either spontaneously cycling participants or those on hormonal contraception. We detected no association between menstrual changes and other commonly-reported side effects of vaccination, such as sore arm, fever and fatigue.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ee Von Woon", - "author_inst": "Imperial College London" - }, - { - "author_name": "Victoria Male", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "sexual and reproductive health" - }, { "rel_doi": "10.1101/2022.03.29.486331", "rel_title": "Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid", @@ -349252,6 +349974,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.30.22273175", + "rel_title": "SARS-CoV-2 Omicron neutralization and risk of infection among elderly after a booster dose of Pfizer vaccine", + "rel_date": "2022-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273175", + "rel_abs": "BackgroundThe protective immunity against Omicron following a BNT162b2 Pfizer booster dose among elderly is not well characterized.\n\nMethodsThirty-eight residents from three nursing homes were recruited for the study. Antibodies targeting the Spike protein of SARS-CoV-2 were measured with the S-Flow assay. Neutralizing activities in sera were measured as effective dilution 50% (ED50) with the S-Fuse assay using authentic isolates of Delta and Omicron.\n\nResultsAmong the 38 elderly included in the study, with median (inter-quartile range, IQR) age of 88 (81-92) years, 30 (78.9%) had been previously infected. The ED50 of neutralization were lower against Omicron than Delta, and higher among convalescent compared to naive residents. During an Omicron epidemic affecting two of the three nursing homes in December 2021-January 2022, 75% (6/8) of naive residents got infected, compared to 25% (6/24) of convalescents (P=0.03). Antibody levels to Spike and ED50 of neutralization against Omicron after the BNT162b2 booster dose were lower in those with breakthrough infection (n=12) compared to those without (n=20): median of 1256 vs 2523 BAU/mL (P=0.02) and median ED50 of 234 vs 1298 (P=0.0004), respectively.\n\nConclusionThis study confirmed the importance of receiving at least three antigenic exposures to the SARS-CoV-2 Spike protein for achieving satisfactory neutralizing antibody levels. In this population, protection against Omicron infection was increased in individuals who had been previously infected in addition to the three vaccine doses. Thus, a fourth antigenic exposure may be useful in the elderly population to prevent infection with Omicron, a variant known for its high escape immunity properties.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Timothee Bruel", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Laurie Pinaud", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Laura Tondeur", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Isabelle Staropoli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Francoise Porrot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Guivel-Benhassine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Mikael Attia", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Stephane Pelleau", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Tom Woundenberg", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cecile Duru", + "author_inst": "Hopital de Crepy-en-Valois" + }, + { + "author_name": "Aymar Davy Koffi", + "author_inst": "Hopital de Crepy-en-Valois" + }, + { + "author_name": "Sandrine Castelain", + "author_inst": "CHU Amiens" + }, + { + "author_name": "Sandrine Fernandes-Pellerin", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nathalie Jolly", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Louise Perrin de Facci", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Emmanuel Roux", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marie-Noelle Ungeheuer", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sylvie Van Der Werf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Michael White", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Arnaud Fontanet", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.29.22272716", "rel_title": "SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings.", @@ -351608,85 +352433,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.03.26.485903", - "rel_title": "The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response.", - "rel_date": "2022-03-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.26.485903", - "rel_abs": "Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense mechanisms triggered by the infected cell. The successful completion of the replicative viral cycle within a cell depends on the function of viral components versus the cellular defenses. Non-coding RNAs (ncRNAs) are important cellular modulators, either promoting or preventing the progression of viral infections. Among these ncRNAs, the long non-coding RNA (lncRNA) family is especially relevant due to their intrinsic functional properties and ubiquitous biological roles. Specific lncRNAs have been recently characterized as modulators of the cellular response during infection of human host cells by single stranded RNA viruses. However, the role of host lncRNAs in the infection by human RNA coronaviruses such as SARS-CoV-2 remains uncharacterized. In the present work, we have performed a transcriptomic study of a cohort of patients with different SARS-CoV-2 viral load. Our results revealed the existence of a SARS-CoV-2 infection-dependent pattern of transcriptional up-regulation in which specific lncRNAs are an integral component. To determine the role of these lncRNAs, we performed a functional correlation analysis complemented with the study of the validated interactions between lncRNAs and RNA-binding proteins (RBPs). This combination of in silico functional association studies and experimental evidence allowed us to identify a lncRNA signature composed of six elements - NRIR, BISPR, MIR155HG, FMR1-IT1, USP30-AS1, and U62317.2 - associated with the regulation of SARS-CoV-2 infection. We propose a competition mechanism between the viral RNA genome and the regulatory lncRNAs in the sequestering of specific RBPs that modulates the interferon response and the regulation of RNA surveillance by nonsense-mediated decay (NMD).\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC=\"FIGDIR/small/485903v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (46K):\norg.highwire.dtl.DTLVardef@4368c9org.highwire.dtl.DTLVardef@1948201org.highwire.dtl.DTLVardef@e31fd9org.highwire.dtl.DTLVardef@1400805_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractModel of interactions among lncRNA and cognate RNA-binding proteins in SARS-CoV-2 infection. According to our model, the viral genome can establish direct interactions with three core proteins (DDX3X, UPF1 and IGF2BP2) involved in mRNA metabolism and regulation of the interferon response, which are also components of a SARS-CoV-2 lncRNA-centered regulatory network. The competition between viral RNA and lncRNAs could act as a counteracting factor for the normal function of homeostatic lncRNA-centered regulatory networks, contributing to viral progression and replication. Black arrows depict physical interactions between network components; red arrows represent functional relationships.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Francisco J. Enguita", - "author_inst": "Instituto de Medicina Molecular Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal." - }, - { - "author_name": "Ana Lucia Leitao", - "author_inst": "MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Port" - }, - { - "author_name": "J Tyson McDonald", - "author_inst": "Department of Radiation Medicine, Georgetown University School of Medicine, Washington, DC 20007, USA." - }, - { - "author_name": "Viktorija Zaksas", - "author_inst": "Center for Translational Data Science, Biological Sciences Division, The University of Chicago, Chicago, IL 60615, USA." - }, - { - "author_name": "Saswati Das", - "author_inst": "Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr Ram Manohar Lohia Hospital, New Delhi-110001, India" - }, - { - "author_name": "Diego Galeano", - "author_inst": "Facultad de Ingenieria, Universidad Nacional de Asuncion, San Lorenzo, Central, Paraguay" - }, - { - "author_name": "Deanne Taylor", - "author_inst": "Department of Biomedical and Health Informatics, The Children Hospital of Philadelphia, Philadelphia, PA 19104, USA" - }, - { - "author_name": "Eve Syrkin Wurtele", - "author_inst": "Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology, Iowa State University, Ame" - }, - { - "author_name": "Amanda Saravia-Butler", - "author_inst": "Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA" - }, - { - "author_name": "Stephen B. Baylin", - "author_inst": "Johns Hopkins School of Medicine, Baltimore, MD 21287, USA" - }, - { - "author_name": "Robert Meller", - "author_inst": "Neuroscience Institute, Department of Neurobiology/ Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA 30310, USA." - }, - { - "author_name": "D. Marshall Porterfield", - "author_inst": "Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA" - }, - { - "author_name": "Douglas C. Wallace", - "author_inst": "Center for Mitochondrial and Epigenomic Medicine, Children Hospital of Philadelphia, Philadelphia, PA 19104, USA" - }, - { - "author_name": "Jonathan C. Schisler", - "author_inst": "McAllister Heart Institute, Department of Pharmacology, and Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, NC 27599," - }, - { - "author_name": "Christopher E. Mason", - "author_inst": "Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Afshin Beheshti", - "author_inst": "KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.03.25.485832", "rel_title": "A SARS-CoV-2 Spike Ferritin Nanoparticle Vaccine is Protective and Promotes a Strong Immunological Response in the Cynomolgus Macaque Coronavirus Disease 2019 (COVID-19) Model", @@ -352118,6 +352864,109 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.25.485875", + "rel_title": "Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models", + "rel_date": "2022-03-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.25.485875", + "rel_abs": "To combat future SARS-CoV-2 variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles presenting randomly-arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against conserved/relatively-occluded, rather than variable/immunodominant/exposed, epitopes. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD-nanoparticles in mice and macaques, observing stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants including Omicron and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest mosaic-8 RBD-nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Alexander A Cohen", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Neeltje A van Doremalen", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" + }, + { + "author_name": "Allison J. Greaney", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Hanne Andersen", + "author_inst": "Bioqual Inc." + }, + { + "author_name": "Ankur Sharma", + "author_inst": "Bioqual Inc." + }, + { + "author_name": "Tyler N Starr", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Jennifer R Keeffe", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Chengcheng Fan", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Jonathan E Schulz", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" + }, + { + "author_name": "Priyanthi N.P. Gnanapragasam", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Leesa M Kakutani", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Anthony P West Jr.", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Greg Saturday", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" + }, + { + "author_name": "Yu E. Lee", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Han Gao", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Claudia A Jette", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Mark G Lewis", + "author_inst": "Bioqual Inc" + }, + { + "author_name": "Tiong K Tan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alain R Townsend", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Vincent J Munster", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" + }, + { + "author_name": "Pamela J Bjorkman", + "author_inst": "California Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.21.22272700", "rel_title": "The Impact on Staff of Providing Non-Invasive Advanced Respiratory Support During the Covid-19 Pandemic A Qualitative Study in an Acute Hospital", @@ -353750,41 +354599,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.25.22272946", - "rel_title": "Understanding the role of mask-wearing during COVID-19 on the island of Ireland", - "rel_date": "2022-03-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.25.22272946", - "rel_abs": "BackgroundNon-pharmaceutical interventions (NPI) play a key role in managing epidemics, yet it is challenging to evaluate their impacts on disease spread and outcomes.\n\nMethodsTo estimate the effect of a mask-wearing intervention to mitigate the spread of SARS-CoV-2 on the island of Ireland, we focused on the potential for interindividual infectious contact over time as the outcome. This is difficult to measure directly; in a companion paper we estimated it using a multi-strain epidemiological model. We used data on mask-wearing and mobility in both Northern Ireland (NI) and the Republic of Ireland (ROI) to predict independently the estimated infectious contact over time. We made counterfactual predictions of infectious contact rates and hospitalisations under a hypothetical intervention where 90% of the population were wearing masks during early 2020, when in reality few people were wearing masks in public; this was mandated in both jurisdictions on 10th August 2020.\n\nResultsThere were 1601 hospitalisations with COVID-19 in NI between 12th March and 10th August 2020, and 1521 in ROI between 3rd April and 10th August 2020. Under the counterfactual mask-wearing scenario, we estimated 512 (95% CI 400, 730) hospitalisations in NI, and 344 (95% CI 266, 526) in ROI, during the same periods.\n\nConclusionsWe have estimated a large effect of population mask-wearing on COVID-19 hospitalisations. This could be partly due to other factors that were also changing over time.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Nicola Fitz-Simon", - "author_inst": "National University of Ireland Galway" - }, - { - "author_name": "John Ferguson", - "author_inst": "NUI Galway" - }, - { - "author_name": "Alberto Alvarez", - "author_inst": "NUI Galway" - }, - { - "author_name": "Mircea T. Sofonea", - "author_inst": "Univ. Montpellier" - }, - { - "author_name": "Tsukushi Kamiya", - "author_inst": "College de France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.24.22272854", "rel_title": "Vaccine effectiveness with BNT162b2 (Comirnaty, Pfizer-BioNTech) vaccine against reported SARS-CoV-2 Delta and Omicron infection among adolescents, Norway, August 2021 to January 2022", @@ -353992,6 +354806,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.25.22272942", + "rel_title": "Estimating time-dependent infectious contact: a multi-strain epidemiological model of SARS-CoV-2 on the island of Ireland", + "rel_date": "2022-03-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.25.22272942", + "rel_abs": "Mathematical modelling plays a key role in understanding and predicting the epidemiological dynamics of infectious diseases. We construct a flexible discrete-time model that incorporates multiple viral strains with different transmissibilities to estimate the changing infectious contact that generates new infections. Using a Bayesian approach, we fit the model to longitudinal data on hospitalisation with COVID-19 from the Republic of Ireland and Northern Ireland during the first year of the pandemic. We describe the estimated change in infectious contact in the context of governmentmandated non-pharmaceutical interventions in the two jurisdictions on the island of Ireland. We take advantage of the fitted model to conduct counterfactual analyses exploring the impact of lockdown timing and introducing a novel, more transmissible variant. We found substantial differences in infectious contact between the two jurisdictions during periods of varied restriction easing and December holidays. Our counterfactual analyses reveal that implementing lockdowns earlier would have decreased subsequent hospitalisation substantially in most, but not all cases, and that an introduction of a more transmissible variant - without necessarily being more severe - can cause a large impact on the health care burden.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Tsukushi Kamiya", + "author_inst": "College de France" + }, + { + "author_name": "Alberto Alvarez-Iglesias", + "author_inst": "NUI Galway" + }, + { + "author_name": "John Ferguson", + "author_inst": "NUI Galway" + }, + { + "author_name": "Shane Murphy", + "author_inst": "NUI Galway" + }, + { + "author_name": "Mircea T. Sofonea", + "author_inst": "Univ. Montpellier" + }, + { + "author_name": "Nicola Fitz-Simon", + "author_inst": "NUI Galway" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.24.22272899", "rel_title": "Tracking population mental health before and across stages of the COVID-19 pandemic in young adults", @@ -355264,77 +356117,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.21.22272480", - "rel_title": "Altered microRNA expression in severe COVID-19: potential prognostic and pathophysiological role", - "rel_date": "2022-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272480", - "rel_abs": "BackgroundThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is ongoing. The pathophysiology of SARS-CoV-2 infection is beginning to be elucidated but the role of microRNAs (miRNAs), small non-coding RNAs that regulate gene expression, remains incompletely understood. They play a role in the pathophysiology of viral infections with potential use as biomarkers. The objective of this study was to identify miRNAs as biomarkers of severe COVID-19 and to analyze their role in the pathophysiology of SARS-CoV-2 infection.\n\nMethodsmiRNA expression was measured in nasopharyngeal swabs from 20 patients with severe COVID-19, 21 patients with non-severe COVID-19 and 20 controls. Promising miRNAs to differentiate non-severe from severe COVID-19 patients were identified by differential expression analysis and sparse Partial Least Squares-Discriminant Analysis (sPLS-DA). ROC analysis, target prediction, GO enrichment and pathway analysis were used to analyze the role and the pertinence of these miRNAs in severe COVID-19.\n\nResultsThe number of expressed miRNAs was lower in severe COVID-19 patients compared to non-severe COVID-19 patients and controls. Among the differentially expressed miRNAs between severe COVID-19 and controls, 5 miRNAs were also differentially expressed between severe and non-severe COVID-19. sPLS-DA analysis highlighted 8 miRNAs, that allowed to discriminate the severe and non-severe COVID-19 cases. Target and functional analysis revealed enrichment for genes involved in viral infections and the cellular response to infection as well as one miRNA, hsa-miR-15b-5p, that targeted the SARS-CoV-2 RNA.\n\nThe comparison of results of differential expression analysis and discriminant analysis revealed three miRNAs, namely hsa-miR-125a-5p, hsa-miR-491-5p and hsa-miR-200b-3p. These discriminated severe from non-severe cases with areas under the curve ranging from 0.76 to 0.80.\n\nConclusionsOur analysis of miRNA expression in nasopharyngeal swabs revealed several miRNAs of interest to discriminate severe and non-severe COVID-19. These miRNAs represent promising biomarkers and possibly targets for antiviral or anti-inflammatory treatment strategies.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nathalie Garnier", - "author_inst": "Lille University" - }, - { - "author_name": "Kato Pollet", - "author_inst": "Lille University" - }, - { - "author_name": "Marie Fourcot", - "author_inst": "Lille University" - }, - { - "author_name": "Morgan Caplan", - "author_inst": "CHU Lille" - }, - { - "author_name": "Guillemette Marot", - "author_inst": "University Lille" - }, - { - "author_name": "Julien Goutay", - "author_inst": "CHU Lille" - }, - { - "author_name": "Julien Labreuche", - "author_inst": "CHU Lille" - }, - { - "author_name": "Fabrice Soncin", - "author_inst": "Inserm" - }, - { - "author_name": "Rabah Boukherroub", - "author_inst": "University Lille" - }, - { - "author_name": "Didier Hober", - "author_inst": "Lille University" - }, - { - "author_name": "- Lille COVID Research Network (LICORNE)", - "author_inst": "-" - }, - { - "author_name": "Sabine Szunerits", - "author_inst": "University of Lille" - }, - { - "author_name": "Julien Poissy", - "author_inst": "Lille University" - }, - { - "author_name": "Ilka Engelmann", - "author_inst": "CHU Lille" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.21.22272673", "rel_title": "Sequential appearance and isolation of a SARS-CoV-2 recombinant between two major SARS-CoV-2 variants in a chronically infected immunocompromised patient", @@ -355566,6 +356348,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.22.485230", + "rel_title": "A self-amplifying RNA vaccine against COVID-19 with long-term room-temperature stability", + "rel_date": "2022-03-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.22.485230", + "rel_abs": "mRNA vaccines were the first to be authorized for use against SARS-CoV-2 and have since demonstrated high efficacy against serious illness and death. However, limitations in these vaccines have been recognized due to their requirement for cold storage, short durability of protection, and lack of access in low-resource regions. We have developed an easily-manufactured, potent self-amplifying RNA (saRNA) vaccine against SARS-CoV-2 that is stable at room temperature. This saRNA vaccine is formulated with a nanostructured lipid carrier (NLC), providing enhanced stability, improved manufacturability, and protection against degradation. In preclinical studies, this saRNA/NLC vaccine induced strong humoral immunity, as demonstrated by high pseudovirus neutralization titers to the Alpha, Beta, and Delta variants of concern and induction of long-lived bone marrow-resident antibody secreting cells. Robust Th1-biased T-cell responses were also observed after prime or homologous prime-boost in mice. Notably, the saRNA/NLC platform demonstrated thermostability at room temperature for at least 6 months when lyophilized. Taken together, this saRNA delivered by NLC represents a potential improvement in RNA technology that could allow wider access to RNA vaccines for the current COVID-19 and future pandemics.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Emily A. Voigt", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Alana Gerhardt", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Derek Hanson", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Peter Battisti", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Sierra Reed", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Jasneet Singh", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Raodoh Mohamath", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Madeleine F. Jennewein", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Julie Bakken", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Samuel Beaver", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Christopher Press", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Patrick Soon-Shiong", + "author_inst": "ImmunityBio, Inc., Culver City, CA" + }, + { + "author_name": "Christopher J. Paddon", + "author_inst": "Amyris, Inc., Emeryville, CA" + }, + { + "author_name": "Christopher B. Fox", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + }, + { + "author_name": "Corey Casper", + "author_inst": "Access to Advanced Health Institute, Seattle, WA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.22.485373", "rel_title": "Cellulosic copper nanoparticles and a hydrogen peroxide-based disinfectant protect Vero E6 cells against infection by viral pseudotyped particles expressing SARS-CoV-2, SARS-CoV or MERS-CoV Spike protein.", @@ -357278,117 +358135,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.22.22272745", - "rel_title": "Effect of prior infection, vaccination, and hybrid immunity against symptomatic BA.1 and BA.2 Omicron infections and severe COVID-19 in Qatar", - "rel_date": "2022-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.22.22272745", - "rel_abs": "BACKGROUNDProtection offered by five different forms of immunity, combining natural and vaccine immunity, was investigated against SARS-CoV-2 Omicron symptomatic BA.1 infection, symptomatic BA.2 infection, BA.1 hospitalization and death, and BA.2 hospitalization and death, in Qatar, between December 23, 2021 and February 21, 2022.\n\nMETHODSSix national, matched, test-negative case-control studies were conducted to estimate effectiveness of BNT162b2 (Pfizer-BioNTech) vaccine, mRNA-1273 (Moderna) vaccine, natural immunity due to prior infection with pre-Omicron variants, and hybrid immunity from prior infection and vaccination.\n\nRESULTSEffectiveness of only prior infection against symptomatic BA.2 infection was 46.1% (95% CI: 39.5-51.9%). Effectiveness of only two-dose BNT162b2 vaccination was negligible at -1.1% (95% CI: -7.1-4.6), but nearly all individuals had received their second dose several months earlier. Effectiveness of only three-dose BNT162b2 vaccination was 52.2% (95% CI: 48.1-55.9%). Effectiveness of hybrid immunity of prior infection and two-dose BNT162b2 vaccination was 55.1% (95% CI: 50.9-58.9%). Effectiveness of hybrid immunity of prior infection and three-dose BNT162b2 vaccination was 77.3% (95% CI: 72.4-81.4%). Meanwhile, prior infection, BNT162b2 vaccination, and hybrid immunity all showed strong effectiveness >70% against any severe, critical, or fatal COVID-19 due to BA.2 infection. Similar levels and patterns of effectiveness were observed for BA.1 and for the mRNA-1273 vaccine.\n\nCONCLUSIONSThere are no discernable differences in the effects of prior infection, vaccination, and hybrid immunity against BA.1 versus BA.2. Hybrid immunity resulting from prior infection and recent booster vaccination confers the strongest protection against either subvariant. Vaccination enhances protection of those with a prior infection.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Heba N. Altarawneh", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Houssein Ayoub", - "author_inst": "Qatar University" - }, - { - "author_name": "Patrick Tang", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Mohammad R. Hasan", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "HADI M. YASSINE", - "author_inst": "Qatar University" - }, - { - "author_name": "Hebah A. Al-Khatib", - "author_inst": "Qatar University" - }, - { - "author_name": "Maria K. Smatti", - "author_inst": "Qatar University" - }, - { - "author_name": "Peter Coyle", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Zaina Al-Kanaani", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Einas Al-Kuwari", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Andrew Jeremijenko", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Anvar Hassan Kaleeckal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali Nizar Latif", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Riyazuddin Mohammad Shaik", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hanan F. Abdul-Rahim", - "author_inst": "Qatar University" - }, - { - "author_name": "Gheyath Nasrallah", - "author_inst": "Qatar University" - }, - { - "author_name": "Mohamed Ghaith Al-Kuwari", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Adeel A Butt", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hamad Eid Al-Romaihi", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Mohamed H. Al-Thani", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Abdullatif Al-Khal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Roberto Bertollini", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.21.22272722", "rel_title": "The dramatic surge of excess mortality in the United States between 2017 and 2021", @@ -357728,6 +358474,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.21.485184", + "rel_title": "Rapid genotyping of viral samples using Illumina short-read sequencing data", + "rel_date": "2022-03-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.21.485184", + "rel_abs": "The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numerous datasets and showed that the consensus genome of samples could be obtained reliably without further manual data curation. Our pipeline can be a valuable tool for fast identifying viral samples. The pipeline is publicly available on the projects github page (https://github.com/laczkol/QVG).", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alex Varadi", + "author_inst": "Department of Metagenomics, University of Debrecen, Debrecen, Hungary" + }, + { + "author_name": "Eszter Kaszab", + "author_inst": "Veterinary Medical Research Institute, Budapest, Hungary" + }, + { + "author_name": "Gabor Kardos", + "author_inst": "Department of Metagenomics, University of Debrecen, Debrecen, Hungary" + }, + { + "author_name": "Eszter Prepost", + "author_inst": "Department of Metagenomics, University of Debrecen, Debrecen, Hungary" + }, + { + "author_name": "Krisztina Szarka", + "author_inst": "Department of Metagenomics, University of Debrecen, Debrecen, Hungary" + }, + { + "author_name": "Levente Laczko", + "author_inst": "Department of Metagenomics, University of Debrecen, Debrecen, Hungary" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.03.22.485312", "rel_title": "Maximum likelihood pandemic-scale phylogenetics", @@ -359312,33 +360097,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.03.20.22272664", - "rel_title": "An umbrella review and meta-analysis of the use of renin-angiotensin system drugs and COVID-19 outcomes: what do we know so far?", - "rel_date": "2022-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.20.22272664", - "rel_abs": "BackgroundsEvidence from several meta-analyses are still controversial about the effects of angiotensin-converting enzyme inhibitors (ACEIs)/angiotensin-receptor blockers (ARBs) on COVID-19 outcomes.\n\nPurposeUmbrella review of systematic reviews/meta-analysis to provide comprehensive assessment of the effect of ACEIs/ARBs on COVID-19 related outcomes by summarising the currently available evidence.\n\nData SourceMedline (OVID), Embase, Scopus, Cochrane library and medRxiv from inception to 1st February 2021.\n\nStudy SelectionSystematic reviews with meta-analysis that evaluated the effect of ACEIs/ARBs on COVID-19 related clinical outcomes\n\nData ExtractionTwo reviewers independently extracted the data and assessed studies risk of bias using AMSTAR 2 Critical Appraisal Tool.\n\nData SynthesisPooled estimates were combined using the random-effects meta-analyses model including several sub-group analyses. Overall, 47 reviews were eligible for inclusion. Out of the nine COVID-19 outcomes evaluated, there was significant associations between ACEIs/ARBs use and each of death (OR=0.80, 95%CI=0.75-0.86; I2=51.9%), death/ICU admission as composite outcome (OR=0.86, 95%CI=0.80-0.92; I2=43.9%), severe COVID-19 (OR=0.86, 95%CI=0.78-0.95; I2=68%), and hospitalisation (OR=1.23, 95%CI=1.04-1.46; I2= 76.4%). The significant reduction in death/ICU admission, however, was higher among studies which presented adjusted measure of effects (OR=0.63, 95%CI=0.47-0.84) and were of moderate quality (OR=0.74, 95%CI=0.63-0.85).\n\nLimitationsThe effect of unmeasured confounding could not be ruled out. Only 21.3% (n=10) of the studies were of moderate quality.\n\nConclusionCollective evidence from observational studies indicate a good quality evidence on the significant association between ACEIs/ARBs use and reduction in death and death/ICU admission, but poor-quality evidence on both reducing severe COVID-19 and increasing hospitalisation. Our findings further support the current recommendations of not discontinuing ACEIs/ARBs therapy in patients with COVID-19.\n\nRegistrationThe study protocol was registered in PROSPERO (CRD42021233398).\n\nFunding SourceNone", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Amanj Kurdi", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Natalie Weir", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Tanja Mueller", - "author_inst": "University of Strathclyde" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.03.19.22272644", "rel_title": "More severe pneumonitis in children predicts the need for admission and elevation of some but not all markers of severe Covid-19.", @@ -359734,6 +360492,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.17.22272574", + "rel_title": "Maternal Antibody Response and Transplacental Transfer Following SARS-CoV-2 Infection or Vaccination in Pregnancy", + "rel_date": "2022-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272574", + "rel_abs": "BackgroundPregnant persons are at increased risk of severe COVID-19 and adverse obstetric outcomes. Understanding maternal antibody response and transplacental transfer after SARS-CoV-2 infection and COVID-19 vaccination is important to inform public health recommendations.\n\nMethodsThis prospective observational cohort study included 351 birthing individuals who had SARS-CoV-2 infection or COVID-19 vaccination during pregnancy. IgG and IgM to SARS-CoV-2 S1 receptor binding domain were measured in maternal and cord blood. Antibody levels and transplacental transfer ratios were compared across 1) disease severity for those with SARS-CoV-2 infection and 2) infection versus vaccination.\n\nFindingsThere were 252 individuals with SARS-CoV-2 infection and 99 who received COVID-19 vaccination during pregnancy. Birthing people with more severe SARS-CoV-2 infection category had higher maternal and cord blood IgG levels (p=0.0001, p=0.0001). Median IgG transfer ratio was 0.87-1.2. Maternal and cord blood IgG were higher after vaccination than infection (p=0.001, p=0.001). Transfer ratio was higher after 90 days in the vaccinated group (p<0.001). Modeling showed higher amplitude and half-life of maternal IgG following vaccination (p<0.0001). There were no significant differences by fetal sex.\n\nInterpretationCOVID-19 vaccination in pregnancy leads to higher and longer lasting maternal IgG levels, higher cord blood IgG, and higher transfer ratio after 90 days compared to SARS-CoV-2 infection. Greater infection severity leads to higher maternal and cord blood antibodies. Maternal IgG decreases over time following both vaccination and infection, reinforcing the importance of vaccination, even after infection, and vaccine boosters for pregnant patients.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sebastian Otero", + "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" + }, + { + "author_name": "Emily S Miller", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Ashwin Sunderraj", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Elisheva D Shanes", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Allison Sakowicz", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Jeffery A Goldstein", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Leena B Mithal", + "author_inst": "Northwestern University Feinberg School of Medicine; Ann & Robert H. Lurie Children's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.17.22272561", "rel_title": "SARS-CoV-2 infections in infants in Haiti 2020-2021; evidence from a serological cohort", @@ -361394,37 +362195,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.16.22272508", - "rel_title": "COVID-19 Disease Model with Reservoir of Infection : Cleaning Surfaces and Wearing Masks Strategies", - "rel_date": "2022-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22272508", - "rel_abs": "We propose an epidemic model in which all diseases are transmitted by direct transmission (infectives to susceptibles) and indirect transmission which occurs through shedding of virus by infectives and acquisition by susceptibles. The model takes into account the effect of latency period and time needed for a susceptible to become infective by indirect contact. Under the certain assumptions, the basic reproduction number of the model is identified from the direct and indirect basic reproduction numbers. The main goal is to analyse the asymptotic behaviours, global stability, bifurcation and to detecte the most sensitive parameters. Numerical simulations are carried out to illustrate the theoretical part.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Najm Fatiha", - "author_inst": "Ibn Tofail University" - }, - { - "author_name": "M. A. Aziz Alaoui", - "author_inst": "Le Havre University" - }, - { - "author_name": "Ahmed Aghriche", - "author_inst": "Ibn Tofail University" - }, - { - "author_name": "Yafia Radouane", - "author_inst": "Ibn Tofail University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.16.22271100", "rel_title": "Effectiveness of whole virus COVID-19 vaccine at protecting health care personnel against SARS-CoV-2 infections in Lima, Peru", @@ -361788,6 +362558,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.17.22272446", + "rel_title": "Founder effect contributes to the unique pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272446", + "rel_abs": "Alaska is the largest geographic state in the United States with the lowest population density and a mix of urban centers and isolated rural communities. The differences in population dynamics in Alaska from the contiguous United States may have contributed to a unique pattern of emergence and spread of SARS-CoV-2 variants observed in early 2021. Here we examined 2,323 virus genomes from Alaska and 278,635 virus genomes from the contiguous United States collected between the first week of December 2020 through the last week of June 2021. We focused on this timeframe because of the notable emergence and spread of the SARS-CoV-2 lineage B.1.1.519 observed in Alaska. We found that this variant was consistently detected in Alaska from the end of January through June of 2021 with a peak prevalence in April of 77.9% unlike the rest of the United States with a peak prevalence of 4.6%. In Alaska, the earlier emergence of B.1.1.519 coincided with a later peak of Alpha (B.1.1.7) when compared to the rest of the United States. We also observed differences in the composition of lineages and variants over time between the two most populated regions of Alaska. Although there was a modest increase in COVID-19 cases during the peak incidence of B.1.1.519, it is difficult to disentangle how social dynamics conflated changes in COVID-19 during this time. We suggest that the viral characteristics, such as amino acid substitutions in the spike protein, and a founder effect likely contributed to the unique spread of B.1.1.519 in Alaska.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Tracie J Haan", + "author_inst": "Institute of Arctic Biology, University of Alaska Fairbanks" + }, + { + "author_name": "Lisa K Smith", + "author_inst": "Alaska Division of Public Health" + }, + { + "author_name": "Stephanie DeRonde", + "author_inst": "Alaska Division of Public Health" + }, + { + "author_name": "Elva House", + "author_inst": "Alaska Division of Public Health" + }, + { + "author_name": "Jacob Zidek", + "author_inst": "Alaska Division of Public Health" + }, + { + "author_name": "Diana Puhak", + "author_inst": "Alaska Division of Public Health" + }, + { + "author_name": "Matthew Redlinger", + "author_inst": "Department of Biological Sciences, University of Alaska Anchorage" + }, + { + "author_name": "Jayme Parker", + "author_inst": "Alaska Division of Public Health" + }, + { + "author_name": "Brian M Barnes", + "author_inst": "Institute of Arctic Biology, University of Alaska Fairbanks" + }, + { + "author_name": "Jason L Burkhead", + "author_inst": "Department of Biological Sciences, University of Alaska Anchorage" + }, + { + "author_name": "Cindy Knall", + "author_inst": "WWAMI School of Medical Education, University of Alaska Anchorage" + }, + { + "author_name": "Eric Bortz", + "author_inst": "Department of Biological Sciences, WWAMI School of Medical Education, University of Alaska Anchorage," + }, + { + "author_name": "Jack Chen", + "author_inst": "Institute of Arctic Biology, Department of Biology and Wildlife, University of Alaska Fairbanks, Alaska Division of Public Health" + }, + { + "author_name": "Devin M Drown", + "author_inst": "Institute of Arctic Biology, Department of Biology and Wildlife, University of Alaska Fairbanks" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.16.22272519", "rel_title": "A log-odds system for waning and boosting of COVID-19 vaccine effectiveness", @@ -363176,53 +364017,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.15.22272438", - "rel_title": "COVID-19 Vaccine Hesitancy among Marginalized Populations in the U.S. and Canada: Protocol for a Scoping Review", - "rel_date": "2022-03-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.15.22272438", - "rel_abs": "IntroductionDespite the development of safe and highly efficacious COVID-19 vaccines, extensive barriers to vaccine deployment and uptake threaten the effectiveness of vaccines in controlling the pandemic. Notably, marginalization produces structural and social inequalities that render certain populations disproportionately vulnerable to COVID-19 incidence, morbidity, and mortality, and less likely to be vaccinated. The purpose of this scoping review is to provide a comprehensive overview of definitions/conceptualizations, elements, and determinants of COVID-19 vaccine hesitancy among marginalized populations in the U.S. and Canada.\n\nMaterials and MethodsThe proposed scoping review follows the framework outlined by Arksey and OMalley, and further developed by the Joanna Briggs Institute. It will comply with reporting guidelines from the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The overall research question is: What are the definitions/conceptualizations and factors associated with vaccine hesitancy in the context of COVID-19 vaccines among adults from marginalized populations in the U.S. and Canada. Search strategies will be developed using controlled vocabulary and selected keywords, and customized for relevant databases, in collaboration with a research librarian. The results will be analyzed and synthesized quantitatively (i.e., frequencies) and qualitatively (i.e., thematic analysis) in relation to the research questions, guided by a revised WHO Vaccine Hesitancy Matrix.\n\nDiscussionThis scoping review will contribute to honing and advancing the conceptualization of COVID-19 vaccine hesitancy and broader elements and determinants of underutilization of COVID-19 vaccination among marginalized populations, identify evidence gaps, and support recommendations for research and practice moving forward.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Peter A Newman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Luke Reid", - "author_inst": "University of Toronto" - }, - { - "author_name": "Suchon Tepjan", - "author_inst": "VOICES-Thailand Foundation" - }, - { - "author_name": "Sophia Fantus", - "author_inst": "The University of Texas Arlington School of Social Work" - }, - { - "author_name": "Kate Allan", - "author_inst": "University of Toronto" - }, - { - "author_name": "Thabani Nyoni", - "author_inst": "University of Toronto" - }, - { - "author_name": "Adrian Guta", - "author_inst": "University of Windsor" - }, - { - "author_name": "Charmaine C Williams", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.15.484467", "rel_title": "A conserved immune trajectory of recovery in hospitalized COVID-19 patients", @@ -363566,6 +364360,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.03.15.22272448", + "rel_title": "Impact of COVID-19 on Life Expectancy among Native Americans", + "rel_date": "2022-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.15.22272448", + "rel_abs": "BackgroundThere has been little systematic research on the mortality impact of COVID-19 in the Native American population.\n\nObjectiveWe provide estimates of loss of life expectancy in 2020 and 2021 for the Native American population.\n\nMethodsWe use data on age-specific all-cause mortality rates from CDC WONDER and the 2019 life table recently released by the National Vital Statistics System for Native Americans to calculate life tables for the Native American population in 2020 and 2021 and obtain estimates of life expectancy reductions during the COVID-19 pandemic.\n\nResultsThe pandemic has set Native Americans further behind other major racial/ethnic groups in terms of life expectancy: the estimated loss in life expectancy at birth for Native Americans is 4.5 years in 2020 and 6.4 years in 2021.\n\nConclusionsThese results underscore the disproportionate share of deaths experienced by Native Americans: a loss in life expectancy at birth in 2020 that is more than three years larger than that for Whites and about 1.5 years greater than the losses for the Black and Latino populations. Despite a successful vaccination campaign among Native Americans, the estimated loss in life expectancy at birth in 2021 unexpectedly exceeds that in 2020.\n\nContributionThe increased loss in life expectancy in 2021, despite higher vaccination rates than in other racial/ethnic groups, highlights the huge challenges faced by Native Americans in their efforts to control the deleterious consequences of the pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Noreen Goldman", + "author_inst": "Princeton University" + }, + { + "author_name": "Theresa Andrasfay", + "author_inst": "University of Southern California" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.03.15.484542", "rel_title": "Omicron BA.1 and BA.2 neutralizing activity elicited by a comprehensive panel of human vaccines", @@ -364986,77 +365803,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.10.22271304", - "rel_title": "ACE2 gene expression and inflammatory conditions in periodontal microenvironment of COVID-19 patients with and without diabetes evaluated by qPCR", - "rel_date": "2022-03-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22271304", - "rel_abs": "ObjectiveChronic periodontitis has been proposed to be linked to coronavirus disease (COVID-19) on the basis of its inflammation mechanism. We aimed to evaluate this association by investigating the expression of Angiotensin Converting Enzyme-2 (ACE2) in periodontal compartments, which contain dysbiosis-associated pathogenic bacteria, and how it can be directly or indirectly involved in exacerbating inflammation in periodontal tissue.\n\nMaterial and MethodsThis observational clinical study included 23 adult hospitalized patients admitted to Universitas Indonesia Hospital with PCR-confirmed COVID-19, while 6 non-COVID-19 participants come to periodontal clinic were included as control. Using real time-PCR (qPCR) and gingival crevicular fluids (GCF) samples from COVID-19 patients with and without diabetes and periodontitis, we assessed the mRNA expression of angiotensin-converting enzyme 2 (ACE2), IL-6, IL-8, complement C3, and LL-37 as well as the relative proportion of Porphyromonas gingivalis, Fusobacterium nucleatum, and Veillonella parvula to represent the dysbiosis condition in periodontal microenvironment. All analyses were performed to determine their relationship.\n\nResultsACE2 mRNA expression was detected in the GCF of periodontitis-COVID-19 patients with and without diabetes. However, only periodontitis-COVID-19 patients with diabetes showed a positive relationship between ACE2 expression and inflammatory conditions in the periodontal microenvironment. In addition, the interplay between pro-inflammatory cytokine (IL-6) and complement C3 could be used as a predictor of the severity of periodontal inflammation in COVID-19 patients with diabetes.\n\nConclusionThe study data show that the SARS-CoV-2 entry gene is expressed in the GCF of patients with COVID-19, and its expression correlates with inflammatory markers.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Boy M Bachtiar", - "author_inst": "Department of Oral Biology and Oral Science Research Center, Faculty of Dentistry Universitas Indonesia, Indonesia." - }, - { - "author_name": "EndangW W Bachtiar", - "author_inst": "Department of Oral Biology and Oral Science Research Center, Faculty of Dentistry Universitas Indonesia, Indonesia." - }, - { - "author_name": "Hari Sunarto", - "author_inst": "Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Yuniarti Soeroso", - "author_inst": "Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Benso Sulijaya", - "author_inst": "Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Citra F Theodorea", - "author_inst": "Department of Oral Biology and Oral Science Research Center, Faculty of Dentistry Universitas Indonesia, Indonesia." - }, - { - "author_name": "Irandi P Pratomo", - "author_inst": "Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Indonesia, Indonesia; Pulmonology and Respiratory Medicine Staff Group - CO" - }, - { - "author_name": "Yudhistira", - "author_inst": "Clinical Pathology Medicine Staff Group, Universitas Indonesia Hospital." - }, - { - "author_name": "Ardiana Kusumaningrum", - "author_inst": "Department of Microbiology, Faculty of Medicine, Universitas Indonesia;Clinical Microbiology Medicine Staff Group, Universitas Indonesia Hospital." - }, - { - "author_name": "Defi Efendi", - "author_inst": "Department of Pediatric Nursing, Faculty of Nursing Universitas Indonesia, and Neonatal Intensive Care Unit, Universitas Indonesia Hospital, Depok, Indonesia" - }, - { - "author_name": "Efa Apriyanti", - "author_inst": "Department of Pediatric Nursing, Faculty of Nursing Universitas Indonesia, and Paediatric Intensive Care Unit, Universitas Indonesia Hospital." - }, - { - "author_name": "Astri Deviana", - "author_inst": "Oral Biology Laboratory Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Nastiti R Utami", - "author_inst": "Oral Biology Laboratory Faculty of Dentistry, Universitas Indonesia, Indonesia." - }, - { - "author_name": "Anissa D Andriyani", - "author_inst": "Oral Biology Laboratory Faculty of Dentistry, Universitas Indonesia, Indonesia." - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2022.03.10.22272193", "rel_title": "Presence of Mediastinal Lymphadenopathy in Hospitalized Covid-19 Patients in a Tertiary Care Hospital in Pakistan - A cross-sectional study", @@ -365352,6 +366098,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.14.22272273", + "rel_title": "Understanding adherence to self-isolation in the first phase of COVID-19 response", + "rel_date": "2022-03-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272273", + "rel_abs": "ObjectiveTo gain a better understanding of decisions around adherence to self-isolation advice during the first phase of the COVID-19 response in England.\n\nDesignA mixed-methods cross sectional study.\n\nSetting: EnglandParticipants COVID-19 cases and contacts who were contacted by Public Health England (PHE) during the first phase of the response in England (January-March 2020).\n\nResultsOf 250 respondents who were advised to self-isolate, 63% reported not leaving home at all during their isolation period, 20% reported leaving only for lower risk activities (dog walking or exercise) and 16% reported leaving for potentially higher risk, reasons (shopping, medical appointments, childcare, meeting family or friends). Factors associated with adherence to never going out included: the belief that following isolation advice would save lives, experiencing COVID-19 symptoms, being advised to stay in their room (rather than just \"inside\"), having help from outside and having regular contact by text message from PHE. Factors associated with non-adherence included being angry about the advice to isolate, being unable to get groceries delivered and concerns about losing touch with friends and family. Interviews highlighted that a sense of duty motivated people to adhere to isolation guidance and where people did leave their homes, these decisions were based on rational calculations of the risk of transmission - people would only leave their homes when they thought they were unlikely to come into contact with others.\n\nConclusionsMeasures of adherence should be nuanced to allow for the adaptations people make to their behaviour during isolation. Understanding adherence to isolation and associated reasoning during the early stages of the pandemic is an essential part of pandemic preparedness for future emerging infectious diseases.\n\nStrengths and limitations of this studyO_LIOur participants were contacted directly by Public Health England during the first three months of the pandemic - the only cohort of cases and contacts who experienced self-isolation during this early phase of the pandemic.\nC_LIO_LIResults may not be directly generalisable to wider populations or later phases of pandemic response.\nC_LIO_LIWe classified reasons for leaving the home as higher or lower contact, as a proxy for potential risk of transmission, however further research published since we conducted our research as refined our understanding of transmission risk, highlighting the need for more in-depth research on adherence behaviour and transmission risk.\nC_LIO_LIThe mixed methods approach combined quantitative measures of adherence with an exploration of how and why these decisions were being made in the same people.\nC_LIO_LIOur study provides unique insights into self-isolation during the earliest stages of the pandemic, against a background of uncertainty and lack of information that will recur, inevitably, in the face of future pandemic and similar threats.\nC_LI", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Charlotte Robin", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Rosy Reynolds", + "author_inst": "University of Bristol" + }, + { + "author_name": "Helen Lambert", + "author_inst": "University of Bristol" + }, + { + "author_name": "Matthew Hickman", + "author_inst": "University of Bristol" + }, + { + "author_name": "James Rubin", + "author_inst": "King's College London" + }, + { + "author_name": "Louise E. Smith", + "author_inst": "King's College London" + }, + { + "author_name": "Lucy Yardley", + "author_inst": "University of Bristol" + }, + { + "author_name": "Shenghan Cai", + "author_inst": "University of Bristol" + }, + { + "author_name": "Tingting Zhang", + "author_inst": "University of Bristol" + }, + { + "author_name": "Piers Mook", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Oliver McManus", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Gemma Lasseter", + "author_inst": "University of Bristol" + }, + { + "author_name": "Polly Compston", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Sarah Denford", + "author_inst": "University of Bristol" + }, + { + "author_name": "Juan Zhang", + "author_inst": "University of Bristol" + }, + { + "author_name": "Richard Amlot", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Isabel Oliver", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.03.11.22272214", "rel_title": "C allele of rs479200 of the host EGLN1 gene - a risk factor for severe COVID-19 (pilot study)", @@ -366728,29 +367557,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.11.22272263", - "rel_title": "Surveillance of COVID-19 cases associated with dental settings using routine health data from the East of Scotland with a description of efforts to break chains of transmission from October 2020 to December 2021.", - "rel_date": "2022-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.11.22272263", - "rel_abs": "IntroductionDental settings have been considered high risk setting s for COVID-19. A Dental Public Health Team in South East Scotland have worked to risk assess the situation timeously to break chains of transmission.\n\nAimTo present routine data produced from a contact tracing service for COVID-19 cases in the dental setting with a focus on transmission.\n\nDesignObservational retrospective analysis of a routine data set of COVID-19 cases associated with a dental setting reported via the national contact tracing system for two health board areas in the east of Scotland.\n\nMethodsCOVID-19 cases were confirmed by PCR testing. Descriptive statistics are used to summarise the data collected over a 13-month period (Oct 2020-Dec 2021). A narrative presents themes identified during contact tracing that led to transmission within a dental setting and includes a case study.\n\nResultsA total of 811 incidents are included. No evidence of staff to patient transmission or vice versa was found in this study. Staff to staff transmission occurred in non-clinical areas contributing to 33% of total staff cases.\n\nConclusionTransmission of COVID-19 in a dental setting in the context of this study appears to be confined to non-clinical areas. Future pandemic plans should include tools to aid with implementation of guidance in non-clinical areas.\n\nIn brief pointsO_LIOutbreaks of COVID-19 in a dental setting appear to be confined to the non-clinical areas of dental practices.\nC_LIO_LIWe have found no evidence of staff to patient transmission or vice versa using our contact tracing methods.\nC_LIO_LIFuture pandemic preparedness would benefit from including current quality improvement tools to aid with implementation of new standard operating procedures and other regularly changing guidance.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Niall Mc Goldrick", - "author_inst": "NHS Fife" - }, - { - "author_name": "Emma O'Keefe", - "author_inst": "NHS Fife" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2022.03.11.22271912", "rel_title": "External validation of risk scores to predict in-hospital mortality in patients hospitalized due to coronavirus disease 2019.", @@ -367046,6 +367852,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.11.22272185", + "rel_title": "SEROLOGICAL TESTING OF BLOOD DONORS TO CHARACTERISE THE IMPACT OF COVID-19 IN MELBOURNE, AUSTRALIA, 2020", + "rel_date": "2022-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.11.22272185", + "rel_abs": "Rapidly identifying and isolating people with acute SARS-CoV-2 infection has been a core strategy to contain COVID-19 in Australia, but a proportion of infections go undetected. We estimated SARS-CoV-2 specific antibody prevalence (seroprevalence) among blood donors in metropolitan Melbourne following a COVID-19 outbreak in the city between June and September 2020. The aim was to determine the extent of infection spread and whether seroprevalence varied demographically in proportion to reported cases of infection. The design involved stratified sampling of residual specimens from blood donors (aged 20-69 years) in three postcode groups defined by low (<3 cases/1,000 population), medium (3-7 cases/1,000 population) and high (>7 cases/1,000 population) COVID-19 incidence based on case notification data. All specimens were tested using the Wantai SARS-CoV-2 total antibody assay. Seroprevalence was estimated with adjustment for test sensitivity and specificity for the Melbourne metropolitan blood donor and residential populations, using multilevel regression and poststratification. Overall, 4,799 specimens were collected between 23 November and 17 December 2020. Seroprevalence for blood donors was 0.87% (90% credible interval: 0.25-1.49%). The highest estimates, of 1.13% (0.25-2.15%) and 1.11% (0.28-1.95%), respectively, were observed among donors living in the lowest socioeconomic areas (Quintiles 1 and 2) and lowest at 0.69% (0.14-1.39%) among donors living in the highest socioeconomic areas (Quintile 5). When extrapolated to the Melbourne residential population, overall seroprevalence was 0.90% (0.26-1.51%), with estimates by demography groups similar to those for the blood donors. The results suggest a lack of extensive community transmission and good COVID-19 case ascertainment based on routine testing during Victorias second epidemic wave. Residual blood donor samples provide a practical epidemiological tool for estimating seroprevalence and information on population patterns of infection, against which the effectiveness of ongoing responses to the pandemic can be assessed.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Dorothy Machalek", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Kaitlyn M Vette", + "author_inst": "The Sydney Children's Hospitals Network" + }, + { + "author_name": "Marnie Downes", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "John B Carlin", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Suellen Nicholson", + "author_inst": "The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Rena Hirani", + "author_inst": "Australian Red Cross Lifeblood" + }, + { + "author_name": "David O Irving", + "author_inst": "Australian Red Cross Lifeblood" + }, + { + "author_name": "Iain B Gosbell", + "author_inst": "Australian Red Cross Lifeblood" + }, + { + "author_name": "Heather F Gidding", + "author_inst": "The Sydney Children's Hospitals Network" + }, + { + "author_name": "Hannah Shilling", + "author_inst": "The Royal Women's Hospital" + }, + { + "author_name": "Eithandee Aung", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Kristine Macartney", + "author_inst": "The Sydney Children's Hospitals Network" + }, + { + "author_name": "John M Kaldor", + "author_inst": "University of New South Wales" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.11.22272259", "rel_title": "Unsupervised clustering reveals phenotypes of AKI in ICU Covid19 patients", @@ -368698,53 +369571,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.03.09.22272160", - "rel_title": "Cross-sector Decision Landscape in Response to COVID-19: A Qualitative Analysis of North Carolina Decision-Makers", - "rel_date": "2022-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22272160", - "rel_abs": "ContextThe COVID-19 pandemic response has demonstrated the interconnectedness of individuals, organizations, and other entities jointly contributing to the production of community health. This response has involved stakeholders from numerous sectors who have been faced with new decisions, objectives, and constraints.\n\nObjectiveWe aimed to examine the cross-sector organizational decision landscape that formed in response to the COVID-19 pandemic.\n\nDesignWe applied a systems approach to the qualitative analysis of semi-structured interviews on the cross-sector, organizational response to the COVID-19 pandemic. We analyzed transcribed interviews using conventional content analysis to synthesize key themes.\n\nSettingSemi-structured interviews were conducted via secure, video-conferencing platform between October 2020 and January 2021.\n\nParticipantsForty-four state and local decision-makers representing organizations from nine sectors in North Carolina participated.\n\nMain Outcome MeasuresWe defined the decision landscape as including decision-maker roles, key decisions, and inter-relationships involved in producing community health.\n\nResultsDecision-maker roles were characterized by underlying tensions between balancing organizational mission with employee/community health and navigating organizational versus individual responsibility for reducing transmission. Key Decisions fell into several broad categories, including how to translate public health guidance into practice; when to institute, and subsequently loosen, public health restrictions; and how to address downstream social and economic impacts of public health restrictions. Lastly, given limited and changing information, as well as limited resources and expertise, the COVID-19 response required cross-sector collaboration, which was commonly coordinated by local health departments.\n\nConclusionsBy documenting the local, cross-sector decision landscape that formed in response to COVID-19, we illuminate the impacts different organizations may have on information/misinformation, prevention behaviors, and, ultimately, health. Public health researchers and practitioners must understand, and work within, this complex decision landscape when responding to COVID-19 and future community health challenges.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Caitlin B Biddell", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Karl Johnson", - "author_inst": "University of North Carolina Gillings School of Global Public Health" - }, - { - "author_name": "Mehul D Patel", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Raymond Smith", - "author_inst": "East Carolina University" - }, - { - "author_name": "Hillary K. Hecht", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Maria E. Mayorga", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Julie L Swann", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Kristen Hassmiller Lich", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.10.22272081", "rel_title": "Interstitial lung damage following COVID-19 hospitalisation: an interim analysis of the UKILD Post-COVID study.", @@ -369368,6 +370194,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.09.22272168", + "rel_title": "Long COVID and its associated factors among COVID survivors in the community from a middle-income country: an online cross-sectional study", + "rel_date": "2022-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22272168", + "rel_abs": "IntroductionPatients with COVID-19 usually recover and return to normal health, however some patients may have symptoms that last for weeks or even months after recovery. This persistent state of ill health is known as Long COVID if it continues for more than 12 weeks and are not explained by an alternative diagnosis. Long Covid has been overlooked in low and middle income countries. Therefore, we conducted an online survey among the COVID-19 survivors in the community to explore their Long COVID symptoms, factors associated with Long COVID and how Long COVID affected their work.\n\nMethodsThis was a cross sectional study conducted from July to September 2021, during the implementation of a nationwide movement control order (MCO). Data was collected using the REDCap electronic data capture tool. The questionnaire was distributed in social and news media. The questionnaire covers information such as socio-demographic characteristics, existing comorbidities, self-perception on health, information on the acute COVID-19 condition and treatment received, symptoms and duration of post-COVID condition and effects on occupation. Results: A total of 732 COVID-19 survivors responded. There were slightly more females (58.7%), younger and more highly educated respondents. More than half of them were overweight or obese and about two third were free of comorbidities. Among these respondents, about 56% were without or with mild symptoms during their acute COVID-19 conditions. A total of 21.1% of the respondents reported to experience Long COVID. The most commonly reported symptoms for Long COVID were fatigue, brain fog, depression, anxiety, insomnia, arthralgia or myalgia. Females had 58% higher odds (95% CI: 1.02, 2.45) of experiencing Long COVID. Patients with moderate and severe levels of acute COVID-19 symptoms had OR of 3.01 (95% CI: 1.21, 7.47) and 3.62 (95% CI: 1.31, 10.03) respectively for Long COVID.\n\nConclusionThis study provides additional insight on the symptoms and duration of post-COVID symptoms as well as the associated factors with Long COVID among COVID-19 survivors in Malaysia. Recognition of Long COVID and its associated factors is important in planning prevention, rehabilitation, clinical management to improve recovery and long-term COVID-19 outcomes.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Foong Ming Moy", + "author_inst": "University of Malaya Faculty of Medicine" + }, + { + "author_name": "Noran Naqiah Hairi", + "author_inst": "University of Malaya" + }, + { + "author_name": "Eugene Ri Jian Lim", + "author_inst": "International Medical University" + }, + { + "author_name": "Awang Bulgiba", + "author_inst": "University of Malaya" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.09.22272165", "rel_title": "Disentangling the effect of measures, variants and vaccines on SARS-CoV-2 Infections in England: A dynamic intensity model", @@ -371072,45 +371929,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.08.22272111", - "rel_title": "Risk Perceptions and Private Protective Behaviors: Evidence from COVID-19 Pandemic", - "rel_date": "2022-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.08.22272111", - "rel_abs": "We analyze data from a survey we administered during the COVID-19 pandemic to investigate the relationship between peoples subjective beliefs about risks and their private protective behaviors. On average, people substantially overestimate the absolute level of risk associated with economic activity, but have correct signals about their relative risk. Subjective risk beliefs are predictive of changes in economic activities independently of government policies. Government mandates restricting economic behavior, in turn, attenuate the relationship between subjective risk beliefs and protective behaviors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "M. Kate Bundorf", - "author_inst": "Duke University" - }, - { - "author_name": "Jill DeMatteis", - "author_inst": "Westat" - }, - { - "author_name": "Grant Miller", - "author_inst": "Stanford University" - }, - { - "author_name": "Maria Polyakova", - "author_inst": "Stanford University" - }, - { - "author_name": "Jialu Streeter", - "author_inst": "Stanford University" - }, - { - "author_name": "Jonathan Wivagg", - "author_inst": "Westat" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.03.09.22271788", "rel_title": "Comparison of influenza and COVID-19-associated hospitalizations among children < 18 years old in the United States - FluSurv-NET (October-April 2017-2021) and COVID-NET (October 2020-September 2021)", @@ -371578,6 +372396,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.09.483630", + "rel_title": "Differential Activity of Repurposed Drugs as Receptor Binding Domain Antagonists for Omicron and Native Strains of SarsCov2", + "rel_date": "2022-03-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.09.483630", + "rel_abs": "Omicron strain is the latest variant of concern of SarsCov2 virus. The mutations in this strain in the S protein Receptor Binding domain (RBD) enable it to be more transmissible as well as escape neutralizing activity by antibodies in response to vaccine. Thus, Omicron specific strategies are need to counter infection by this strain.\n\nWe investigated a collection of approved drugs shown to antagonize the binding of native strain RBD to human ACE2, for their ability to antagonize binding to Omicron strain RBD.\n\nWhile most of the drugs the drugs that antagonize binding to native RBD are also active for Omicron RBD but some were inactive, namely drugs that contain iodine are completely inactive against Omicron RBD. Our data strongly indicate that presence of a single iodine molecule in the drug renders it inactive against Omicron strain. Thus, there is molecular specificity of drugs for antagonizing Omicron strain RBD versus native strain RBD of this virus. Such information will pave way for specific drugs for Omicron. A pragmatic message from our data is that the often-used iodine containing mouth wash and rises may be ineffective in antagonizing receptor binding of Omicron strain.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Kranti Meher", + "author_inst": "Reagene Biosciences" + }, + { + "author_name": "Saranya K", + "author_inst": "Reagene Biosciences" + }, + { + "author_name": "Arpitha Reddy", + "author_inst": "Reagene Biosciences" + }, + { + "author_name": "Gopi Kadiyala", + "author_inst": "Kyntox Bio" + }, + { + "author_name": "Subramanian Iyer", + "author_inst": "Prodigy Biotech" + }, + { + "author_name": "Subhramanyam Vangala", + "author_inst": "Reagene Biosciences" + }, + { + "author_name": "Satish Chandran", + "author_inst": "Prodigy Biotech" + }, + { + "author_name": "Uday Saxena", + "author_inst": "Reagene Biosciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2022.03.07.22272032", "rel_title": "Changes in outpatient care patterns and subsequent outcomes during the COVID-19 pandemic: A retrospective cohort analysis from a single payer healthcare system", @@ -373006,37 +373871,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.05.22271959", - "rel_title": "13 cis retinoic acid improved the outcomes of COVID-19 patients. A randomized clinical trial", - "rel_date": "2022-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.05.22271959", - "rel_abs": "The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over 100 million people causing over 2.4 million deaths over the world, and it is still expanding. Given the urgency of the COVID-19 pandemic, the clinical investigation of approved drugs is a promising alternative to find a timely effective treatment. In this randomized trial, we investigated the activity of both oral and aerosolized 13 cis retinoic acid in the treatment of SARS-COV-2 added to standard of care treatment in patients with COVID-19 versus standard of care treatment alone. This was a randomized controlled trial conducted at Kafrelsheikh Universitys Quarantine Hospitals, Egypt. After obtaining informed consent, forty patients with a confirmed diagnosis of COVID-19 were enrolled in the study. They were randomly assigned to one of two groups: Group I; 20 patients received aerosolized and oral 13 cis retinoic acid plus standard of care treatment (13 cis RA group) and Group II; 20 patients received only standard care treatment as a control group. The two groups were age and gender matched. There was no statistically significant difference between them in any of the baseline characteristics or laboratory parameters. The results showed that there was a high significant difference between the two groups regarding intensive care unit (ICU) admission, mortality and improvement (P<0.05). Only 10.52 % of patients in the 13 cis retinoic acid group needed ICU admission compared to 28.57 % in the control arm. There was no mortality in the 13 cis retinoic acid group, whereas about 14.35% were died in the group II. All patients who received 13 cis retinoic acid noticed a high improvement (P<0.001), and the mean value for clinical improvement was 16.3{+/-}4.5 days. There was no significant difference regarding the laboratory parameters before and after 14 days of treatment in the group of patients received the standard of care treatment (P=0.66). Univariate logistic regression analysis showed overall mortality was significantly related to the patients age, serum ferritin, C-reactive protein, oxygen saturation, the presence of diabetes mellitus, obesity, and abdominal pain. We conclude that 13 cis retinoic acid is a promising drug in the treatment of patients with COVID-19 infection, when added to the standard of care treatment.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mahmoud R Elkazzaz", - "author_inst": "Kafr-elsheikh University College of Medicine" - }, - { - "author_name": "Yousry Esam-Eldin Abo-Amer", - "author_inst": "Hepatology,Gastroenterology and Infectious Diseases Department, Mahala Hepatology Teaching Hospital, Egypt" - }, - { - "author_name": "Amr Ahmed", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Tamer Hayadar", - "author_inst": "Internal Medicine Department, Faculty of Medicine , Kafrelshiekh University, Egypt" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.03.06.22271809", "rel_title": "Defining factors that influence vaccine-induced, cross-variant neutralizing antibodies for SARS-CoV-2 in Asians", @@ -373352,6 +374186,53 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.03.04.483019", + "rel_title": "Soluble P2X7 receptor is elevated in the plasma of COVID-19 patients and correlates with disease severity", + "rel_date": "2022-03-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.04.483019", + "rel_abs": "Inflammation is a tightly coordinated response against bacterial and viral infections, triggered by the production of pro-inflammatory cytokines. SARS-CoV-2 infection induces COVID-19 disease, characterized by an inflammatory response mediated through the activation of the NLRP3 inflammasome, which results in the production of IL-1{beta} and IL-18 along with pyroptotic cell death. The NLRP3 inflammasome could be also triggered by sterile danger signals such as extracellular ATP triggering the purinergic P2X7 receptor. Severe inflammation in the lungs of SARS-CoV-2 infected individuals is associated with pneumonia, hypoxia and acute respiratory distress syndrome, these being the causes of death associated with COVID-19. Both the P2X7 receptor and NLRP3 have been considered as potential pharmacological targets for treating inflammation in COVID-19. However, there is no experimental evidence of the involvement of the P2X7 receptor during COVID-19 disease. In the present study we determined the concentration of different cytokines and the P2X7 receptor in the plasma of COVID-19 patients and found that along with the increase in IL-6, IL-18 and the IL-1 receptor antagonist in the plasma of COVID-19 patients, there was also an increase in the purinergic P2X7 receptor. Increase in COVID-19 severity and C-reactive protein concentration positively correlated with increased concentration of the P2X7 receptor in the plasma, but not with IL-18 cytokine. The P2X7 receptor was found in the supernatant of human peripheral blood mononuclear cells after inflammasome activation. Therefore, our data suggest that determining levels of the P2X7 receptor in the plasma could be a novel biomarker of COVID-19 severity.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Julio Garcia-Villalba", + "author_inst": "Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital Virgen Arrixaca, 30120 Murcia, Spain" + }, + { + "author_name": "Laura Hurtado-Navarro", + "author_inst": "Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital Virgen Arrixaca, 30120 Murcia, Spain" + }, + { + "author_name": "Alejandro Pe\u00f1in-Franch", + "author_inst": "Biomedical Research Institute of Murcia IMIB-Arrixaca" + }, + { + "author_name": "Cristina Molina-Lopez", + "author_inst": "Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital Virgen Arrixaca, 30120 Murcia, Spain" + }, + { + "author_name": "Laura Martinez-Alarcon", + "author_inst": "Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital Virgen Arrixaca, 30120 Murcia, Spain" + }, + { + "author_name": "Diego Angosto-Bazarra", + "author_inst": "Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital Virgen Arrixaca, 30120 Murcia, Spain" + }, + { + "author_name": "Alberto Baroja-Mazo", + "author_inst": "Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital Virgen Arrixaca, 30120 Murcia, Spain" + }, + { + "author_name": "Pablo Pelegrin", + "author_inst": "Biomedical Research Institute of Murcia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.04.483032", "rel_title": "Chimeric mRNA based COVID-19 vaccine elicits potent neutralizing antibodies and protection against Omicron and Delta", @@ -374844,57 +375725,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.06.22271974", - "rel_title": "Competitive fitness of emerging SARS-CoV-2 variants is linked to their Distinctiveness relative to preceding lineages from that region", - "rel_date": "2022-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.06.22271974", - "rel_abs": "The COVID-19 pandemic has seen the persistent emergence of immune-evasive SARS-CoV-2 variants under the selection pressure of natural and vaccination-acquired immunity. However, it is currently challenging to quantify how immunologically distinct a new variant is compared to all the prior variants to which a population has been exposed. Here we define Distinctiveness of SARS-CoV-2 sequences based on a proteome-wide comparison with all prior sequences from the same geographical region. We observe a correlation between Distinctiveness relative to contemporary sequences and future change in prevalence of a newly circulating lineage (Pearson r = 0.75), suggesting that the Distinctiveness of emergent SARS-CoV-2 lineages is associated with their competitive fitness. We further show that the average Distinctiveness of sequences belonging to a lineage, relative to the Distinctiveness of other sequences that occur at the same place and time (n = 944 location/time data points), is predictive of future increases in prevalence (AUC = 0.88, 0.86-0.90 95% confidence interval). By assessing the Delta variant in India versus Brazil, we show that the same lineage can have different Distinctiveness-contributing positions in different geographical regions depending on the other variants that previously circulated in those regions. Finally, we find that positions that constitute epitopes contribute disproportionately (20-fold higher than the average position) to Distinctiveness. Overall, this study suggests that real-time assessment of new SARS-CoV-2 variants in the context of prior regional herd exposure via Distinctiveness can augment genomic surveillance efforts.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Michiel JM Niesen", - "author_inst": "nference" - }, - { - "author_name": "Karthik Murugadoss", - "author_inst": "nference" - }, - { - "author_name": "Patrick J Lenehan", - "author_inst": "nference" - }, - { - "author_name": "Aron Marchler-Bauer", - "author_inst": "National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH)" - }, - { - "author_name": "Jiyao Wang", - "author_inst": "National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH)" - }, - { - "author_name": "Ryan Connor", - "author_inst": "National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH)" - }, - { - "author_name": "J Rodney Brister", - "author_inst": "National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH)" - }, - { - "author_name": "AJ Venkatakrishnan", - "author_inst": "nference" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.04.22271706", "rel_title": "Remdesivir for the treatment of patients hospitalized with COVID-19 receiving supplemental oxygen: a targeted literature review and meta-analysis", @@ -375122,6 +375952,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.03.22271831", + "rel_title": "Zonal Model of Aerosol Persistence in ICUs: Utilization of Time and Space-resolved Sensor Network", + "rel_date": "2022-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.03.22271831", + "rel_abs": "The COVID-19 pandemic raised public awareness about airborne particulate matter (PM) due to the spread of infectious diseases via the respiratory route. The persistence of potentially infectious aerosols in public spaces and the spread of nosocomial infections in medical settings deserve careful investigation; however, a systematic approach characterizing the fate of aerosols in clinical environments has not been reported. This paper presents a methodology for mapping aerosol propagation using a low-cost PM sensor network in ICU and adjacent environments and the subsequent development of the data-driven zonal model. Mimicking aerosol generation by a patient, we generated trace NaCl aerosols and monitored their propagation in the environment. In positive (closed door) and neutral-pressure (open door) ICUs, up to 6% or 19%, respectively, of all PM escaped through the door gaps; however, the outside sensors did not register an aerosol spike in negative-pressure ICUs. The K-means clustering analysis of temporospatial aerosol concentration data suggests that ICU can be represented by three distinct zones: (1) near the aerosol source, (2) room periphery, and (3) outside the room. The data suggests two-phase plume behavior: dispersion of the original aerosol spike throughout the room, followed by an evacuation phase where \"well-mixed\" aerosol concentration decayed uniformly. Decay rates were calculated for positive, neutral, and negative pressure operations, with negative-pressure rooms clearing out nearly twice as fast. These decay trends closely followed the air exchange rates. This research demonstrates the methodology for aerosol monitoring in medical settings. This study is limited by a relatively small data set and is specific to single-occupancy ICU rooms. Future work needs to evaluate medical settings with high risks of infectious disease transmission.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kaitlyn Glenn", + "author_inst": "University of Washington" + }, + { + "author_name": "Jiayang He", + "author_inst": "University of Washington" + }, + { + "author_name": "Robert Rochlin", + "author_inst": "University of Washington" + }, + { + "author_name": "Selina Teng", + "author_inst": "University of Washington" + }, + { + "author_name": "James Hecker", + "author_inst": "University of Washington" + }, + { + "author_name": "Igor Novosselov", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.03.03.22270812", "rel_title": "SARS-CoV-2 Omicron Variant Infection of Individuals with High Titer Neutralizing Antibodies Post-3rd mRNA Vaccine Dose", @@ -376586,25 +377455,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.02.22271656", - "rel_title": "Analyzing county-wide trends in Tennessee Covid-19 rates, Median Household Income, and Presence of Hospital", - "rel_date": "2022-03-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271656", - "rel_abs": "The Covid-19 pandemic has caused millions of deaths and infections worldwide. Recent studies suggest that Covid-19 may be disproportionately affecting certain groups. The Tennessee Department of Health regularly publishes data on Covid infections and vaccinations. This data alongside data published from the 2010 census was used to analyze trends in Covid-19 rates for the State of Tennessee. The census data for the average household income of each county was cross-referenced with the covid data. A positive correlation between population of the county and the number of new cases reported on January 3rd, 2022, appeared when observing the data. A regression analysis (ANOVA) revealed that the data on population and covid rate was significant (P-value: 2.69E-10). The results from comparing the covid rates in a county with a hospital and a county without a hospital seemed to be the most significant. The data reported by the Sycamore institute on the Tennessee counties without a hospital was used to identify trends unique to these counties. The counties lacking a hospital were compared with counties with a similar population. 7 hospital-less counties were used for comparison, 6 counties (Fayette, Grainger, Haywood, Chester, Sequatchie, Clay) reported a greater number of cases than counties of a similar population. Of the 20 counties lacking a hospital, 16 fell within the bottom 50% of median household incomes, with 9 in the bottom 25% and 4 in the bottom 10%. Healthcare sites in rural areas may lack fundamental infrastructure. These areas may require unique interventions to address the healthcare concerns present.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Viraj Vipul Brahmbhatt", - "author_inst": "Union College" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.01.22271611", "rel_title": "Predicting missed health care visits during the COVID-19 pandemic using machine learning methods: Evidence from 55,500 individuals from 28 European Countries", @@ -376812,6 +377662,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.02.22271771", + "rel_title": "Effects of BA.1/BA.2 subvariant, vaccination, and prior infection on infectiousness of SARS-CoV-2 Omicron infections", + "rel_date": "2022-03-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271771", + "rel_abs": "BACKGROUNDQatar experienced a large SARS-CoV-2 Omicron (B.1.1.529) wave that started on December 19, 2021 and peaked in mid-January, 2022. We investigated effects of Omicron subvariant (BA.1 and BA.2), previous vaccination, and prior infection on infectiousness of Omicron infections, between December 23, 2021 and February 20, 2022.\n\nMETHODSUnivariable and multivariable regression analyses were conducted to estimate the association between the RT-qPCR cycle threshold (Ct) value of PCR tests (a proxy for SARS-CoV-2 infectiousness) and each of the Omicron subvariants, mRNA vaccination, prior infection, reason for RT-qPCR testing, calendar week of RT-qPCR testing (to account for phases of the rapidly evolving Omicron wave), and demographic factors.\n\nRESULTSCompared to BA.1, BA.2 was associated with 3.53 fewer cycles (95% CI: 3.46-3.60), signifying higher infectiousness. Ct value decreased with time since second and third vaccinations. Ct values were highest for those who received their boosters in the month preceding the RT-qPCR test--0.86 cycles (95% CI: 0.72-1.00) higher than for unvaccinated persons. Ct value was 1.30 (95% CI: 1.20-1.39) cycles higher for those with a prior infection compared to those without prior infection, signifying lower infectiousness. Ct value declined gradually with age. Ct value was lowest for those who were tested because of symptoms and was highest for those who were tested for travel-related purposes. Ct value was lowest during the exponential-growth phase of the Omicron wave and was highest after the wave peaked and was declining.\n\nCONCLUSIONSThe BA.2 subvariant appears substantially more infectious than the BA.1 subvariant. This may reflect higher viral load and/or longer duration of infection, thereby explaining the rapid expansion of this subvariant in Qatar.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Suelen H. Qassim", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Houssein Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "Sawsan AlMukdad", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Patrick Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Mohammad R. Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + }, + { + "author_name": "Hebah A. Al-Khatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Maria K. Smatti", + "author_inst": "Qatar University" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Gheyath Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed Ghaith Al-Kuwari", + "author_inst": "Primary Health Care Corporation" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al-Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.03.22271828", "rel_title": "Determinants of COVID-19 vaccine acceptability in Mozambique: the role of institutional trust", @@ -378588,41 +379549,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.01.22271685", - "rel_title": "Patients with CLL have similar high risk of death upon the omicron variant of COVID-19 as previously during the pandemic.", - "rel_date": "2022-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271685", - "rel_abs": "Previous studies have shown that patients with chronic lymphocytic leukemia (CLL) and coronavirus disease 2019 (COVID-19) have high mortality rates. The omicron variant has been reported to give milder disease in the general population, but outcomes of infections with the omicron variant among immunocompromised patients have not previously been reported. In a population-based cohort we assessed rates of hospitalizations, ICU-admissions, and 30-day all-cause mortality among all patients with CLL from Eastern Denmark testing positive for severe adult respiratory syndrome coronavirus 2 (SARS-CoV-2) in time periods before and after dominance of the omicron variant. Rates of hospitalizations and ICU-admissions declined significantly, whereas 30-day mortality remained as high as 23% in the period with dominance of the omicron sublineage BA.2 variant. Thus, patients with CLL in general and in particular those above 70 years of age with one or more comorbidities should be considered for closer monitoring and pre-emptive antiviral therapy upon a positive SARS-CoV-2 test.\n\nKey pointsO_LIThe omicron variant of COVID-19 leads to high fatality rates in CLL, despite milder disease in the background population\nC_LIO_LIPatients with CLL who test positive for SARS-CoV-2 in the era of the omicron variant should be considered for pre-emptive antiviral therapy\nC_LI\n\nExplanation of noveltyThe omicron variant has been reported to give milder disease in the general population, but outcomes of infections with the omicron variant among immunocompromised patients have not previously been reported. These population-based data on outcome for patients with CLL upon infection with the omicron variant of SARS-CoV-2 warrants closer monitoring and pre-emptive antiviral therapy upon a positive SARS-CoV-2 test for patients with CLL.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Carsten Utoft Niemann", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Caspar da Cunha-Bang", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Marie Helleberg", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Sisse Rye Ostrowski", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Christian Brieghel", - "author_inst": "Rigshospitalet" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2022.02.28.22271591", "rel_title": "Ammonium Sulfate Addition Reduces the Need for Guanidinium Isothiocyanate in the Denaturing Transport Medium Used for SARS-COV-2 RNA Detection", @@ -379086,6 +380012,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.01.22271202", + "rel_title": "Longitudinal monitoring of SARS-CoV-2 neutralizing antibody titers and its impact on employee personal wellness decisions", + "rel_date": "2022-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271202", + "rel_abs": "Virus neutralizing antibody (vnAb) titers are the strongest laboratory correlate of protection from SARS-CoV-2. Providing individuals with real-time measures of their vnAb titers is predicted to improve their ability to make personal wellness decisions. Yet, widespread commercial testing of SARS-CoV-2 vnAbs does not currently occur. Here, we examined whether knowing their vnAb titer impacted wellness decision-making among individuals. To this end, starting on January 1, 2021, we offered all employees from two companies free IMMUNO-COV testing and conducted a survey to assess their behaviors and decisions regarding booster vaccination. IMMUNO-COV is a clinically validated, surrogate virus assay that quantitates serum titers of SARS-CoV-2 vnAbs. To help participants gauge their level of protection based on their vnAb titer, we calibrated IMMUNO-COV titers to the World Health Organization (WHO) International Standard (IU/mL), making them comparable to published reports of correlates of protection, and we fit historical IMMUNO-COV vnAb titer values into predictive models of immune protection from COVID-19. As expected, data for the 56 program participants showed variability in vnAb titers post vaccination, rates vnAb decay, and fold-increases in vnAb titers after booster vaccination. Based on the participant survey, the majority (66%) of participants indicated that knowing their vnAb titer impacted their social behaviors and/or their decision on the timing of a booster vaccination. Several participants indicated that knowing their vnAb titer contributed to their peace of mind regarding their high level of protection from COVID-19. Together, these data demonstrate that regular determination of SARS-CoV-2 neutralizing antibody titers can significantly impact decisions regarding social interactions and timing of booster vaccinations.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Rianna Vandergaast", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Timothy Carey", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Lukkana Suksanpaisan", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Chase Lathrum", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Riya Narjari", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Michelle Haselton", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Luke Schnebeck", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Aroshi Wijesekara", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Andrew Duncan", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Luke Russell", + "author_inst": "Vyriad Inc." + }, + { + "author_name": "Shruthi Naik", + "author_inst": "Vyriad, Inc." + }, + { + "author_name": "Kah-Whye Peng", + "author_inst": "Imanis Life Sciences" + }, + { + "author_name": "Patrycja Lech", + "author_inst": "Vyriad, Inc." + }, + { + "author_name": "Stephen J Russell", + "author_inst": "Vyriad, Inc" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.01.22271708", "rel_title": "Racial/Ethnic Disparities in the Observed COVID-19 Case Fatality Rate Among the U.S. Population", @@ -380710,73 +381707,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.26.22271509", - "rel_title": "Effect of booster vaccination against Delta and Omicron variants in Iceland", - "rel_date": "2022-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.26.22271509", - "rel_abs": "By the end of July 2021, the majority of the Icelandic population had received vaccination against COVID-19. In mid-July a wave of SARS-CoV-2 infections, dominated by the delta variant, spread through the population, followed by an omicron wave in December. A booster vaccination campaign was initiated to curb the spread of the virus. We estimated the risk of infection for different vaccine combinations using vaccination data from 276,028 persons and 963,557 qPCR tests for 277,687 persons. We measured anti-Spike-RBD antibody levels and ACE2-Spike binding inhibitory activity in 371 persons who received one of four recommended vaccination schedules with or without an mRNA vaccine booster. Overall, we found different antibody levels and inhibitory activity between recommended vaccination schedules, which was reflected in the observed risk of SARS-CoV-2 infections. We observed an increased protection following mRNA boosters, against both omicron and delta variant infections, although BNT162b2 boosters provided greater protection against omicron than mRNA-1273 boosters.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Gudmundur L Norddahl", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Pall Melsted", - "author_inst": "deCODE genetics/Amgen; School of Engineering and Natural Sciences, University of Iceland" - }, - { - "author_name": "Kristbjorg Gunnarsdottir", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Gisli H Halldorsson", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Thorunn A Olafsdottir", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Arnaldur Gylfason", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Mar Kristjansson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Olafur T Magnusson", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Patrick Sulem", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Daniel F Gudbjartsson", - "author_inst": "deCODE genetics/Amgen, Inc; School of Engineering and Natural Sciences, University of Iceland" - }, - { - "author_name": "Unnur Thorsteinsdottir", - "author_inst": "deCODE genetics/Amgen, Inc; Faculty of Medicine, School of Health Sciences, University of Iceland" - }, - { - "author_name": "Ingileif Jonsdottir", - "author_inst": "deCODE genetics/Amgen, Inc" - }, - { - "author_name": "Kari Stefansson", - "author_inst": "deCODE genetics/Amgen, Inc; Faculty of Medicine, School of Health Sciences, University of Iceland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.27.22271579", "rel_title": "Vaccine hesitancy strongly correlates with COVID-19 deaths underreporting", @@ -380964,6 +381894,93 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2022.03.01.481391", + "rel_title": "Omicron-specific mRNA vaccine elicits potent immune responses in mice, hamsters, and nonhuman primates", + "rel_date": "2022-03-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.01.481391", + "rel_abs": "SARS-CoV-2 has infected more than 400 million people around the globe and caused millions of deaths. Since its identification in November 2021, Omicron, a highly transmissible variant, has become the dominant variant in most countries. Omicrons highly mutated spike protein, the main target of vaccine development, significantly compromises the immune protection from current vaccination. We develop an mRNA vaccine (SOmicron-6P) based on an Omicron-specific sequence. In mice, SOmicron-6P shows superior neutralizing antibodies inducing abilities to a clinically approved inactivated virus vaccine, a clinically approved protein subunit vaccine, and an mRNA vaccine (SWT-2P) with the same sequence of BNT162b2 RNA. Significantly, SOmicron-6P induces a 14.4[~]27.7-fold and a 28.3[~]50.3-fold increase of neutralizing activity against the pseudovirus of Omicron and authentic Omicron compared to SWT-2P, respectively. In addition, two doses SOmicron-6P significantly protects Syrian hamsters against challenge with SARS-CoV-2 Omicron variant and elicits high titers of nAbs in a dose-dependent manner in macaques. Our results suggest that SOmicron-6P offers advantages over current vaccines, and it will be helpful for those with weak immunity.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Yi Wu", + "author_inst": "Department of Radiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 23" + }, + { + "author_name": "Yanqiong Shen", + "author_inst": "School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China" + }, + { + "author_name": "Namei Wu", + "author_inst": "Department of Radiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 23" + }, + { + "author_name": "Xinghai Zhang", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430062, P. R. China" + }, + { + "author_name": "Shaohong Chen", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430062, P. R. China" + }, + { + "author_name": "Chang Yang", + "author_inst": "Department of Radiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 23" + }, + { + "author_name": "Junhui Zhou", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430062, P. R. China" + }, + { + "author_name": "Yan Wu", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430062, P. R. China" + }, + { + "author_name": "Da Chen", + "author_inst": "MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei," + }, + { + "author_name": "Li Wang", + "author_inst": "School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China" + }, + { + "author_name": "Yuye Wang", + "author_inst": "RNAlfa Biotech, Hefei, Anhui 230088, P. R. China" + }, + { + "author_name": "Jiejie Xu", + "author_inst": "RNAlfa Biotech, Hefei, Anhui 230088, P. R. China" + }, + { + "author_name": "Ke Liu", + "author_inst": "RNAlfa Biotech, Hefei, Anhui 230088, P. R. China" + }, + { + "author_name": "Chao Wang", + "author_inst": "MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei," + }, + { + "author_name": "Huajun Zhang", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430062, P. R. China" + }, + { + "author_name": "Ninuo Xia", + "author_inst": "School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China" + }, + { + "author_name": "Sandra Chiu", + "author_inst": "School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China" + }, + { + "author_name": "Yucai Wang", + "author_inst": "Department of Radiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 23" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.28.482305", "rel_title": "Time-Dependent Increase in Susceptibility and Severity of Secondary Bacterial Infection during SARS-CoV-2 Infection", @@ -382408,69 +383425,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.19.22271227", - "rel_title": "Assessment of indoor biological air quality at a mass gathering event in an unimproved exhibition facility during the COVID-19 pandemic using a novel air sampling technology.", - "rel_date": "2022-02-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.19.22271227", - "rel_abs": "The objective was to evaluate the determination of biomarkers of air quality during a mass gathering event at a convention center using a novel air sampling device, AirAnswers(R). This sampler has previously only been used in smaller locations. Here it was run at five crowded locations within the exhibit area for the four days duration of a trade show. The AirAnswers(R) device uses electro-kinetic flow to sample air at high rates and capture bio-aerosols on grounded electrodes in assayable form. Cartridges were removed from the devices and immediately conveyed to the Inspirotec facility in North Chicago, where assays were performed.\n\nBiomarkers determined were for allergens and molds previously described for this system. Testing for a new marker, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was also included. The method was validated by determination of capture efficiency with reference to an impinger sampler in a Class III controlled environment chamber. Average capture efficiency for triplicate runs was 14%. One SARS-CoV-2 positive sample as found at the registration area, which was physically separate from the main exhibit area.\n\nCat allergen Fel d 1was found in four of the locations, dog allergen Can f 1 at two. The airborne biomarker of mold proliferation, (1[->]3)-{beta}-D-Glucan, was above the assay range in all locations. The widespread presence of this mold marker could be accounted for by signs of water leakage. A generic 18S RNA marker for mold was developed and similarly showed the presence of mold in all locations, as was a genus marker for penicillium. A species marker for Cladosporium cladosporioides was in two locations. Species markers for Eurotium amstelodami and Trichoderma viride were each in a single location.\n\nThe main findings were of the widespread presence of mold markers, and the sporadic appearance of SARS-CoV-2. Masking was recommended but not enforced.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Julian Gordon", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Osama Abdullah", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Rachel Reboulet", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "kara Hanson", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Christine Sadowski", - "author_inst": "Formerly Inspirotec Inc" - }, - { - "author_name": "Hunter Rennels", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Steve Kuemmerle", - "author_inst": "Inspirotec Inc" - }, - { - "author_name": "Richard Tuttle", - "author_inst": "MRI-Global" - }, - { - "author_name": "Kristen Solocinski", - "author_inst": "MRI-Global" - }, - { - "author_name": "Brittany Knight", - "author_inst": "MRI-Global" - }, - { - "author_name": "Jacob Wilkinson", - "author_inst": "MRI-Global" - }, - { - "author_name": "Gavin Macgregor-Skinner", - "author_inst": "Global Biorisk Advisory Council" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.25.22271529", "rel_title": "Study on the usefulness of Direct Saliva sample Collection (DiSC) by polyester swab", @@ -382766,6 +383720,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.28.22271627", + "rel_title": "Oropharyngeal Microbiome Profiled at Admission is Predictive of the Need for Respiratory Support Among COVID-19 Patients", + "rel_date": "2022-02-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22271627", + "rel_abs": "The clinical course of infection due to respiratory viruses such as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2), the causative agent of Coronavirus Disease 2019 (COVID-19) is thought to be influenced by the community of organisms that colonizes the upper respiratory tract, the oropharyngeal microbiome. In this study, we examined the oropharyngeal microbiome of suspected COVID-19 patients presenting to the Emergency Department and an inpatient COVID-19 unit with symptoms of acute COVID-19. Of 115 enrolled patients, 74 were confirmed COVID-19+ and 50 had symptom duration of 14 days or less; 38 acute COVID-19+ patients (76%) went on to require respiratory support. Although no microbiome features were found to be significantly different between COVID-19+ and COVID-19-patients, when we conducted random forest classification modeling (RFC) to predict the need of respiratory support for the COVID-19+ patients our analysis identified a subset of organisms and metabolic pathways whose relative abundance, when combined with clinical factors (such as age and Body Mass Index), was highly predictive of the need for respiratory support (F1 score 0.857). Microbiome Multivariable Association with Linear Models (MaAsLin2) analysis was then applied to the features identified as predicative of the need for respiratory support by the RFC. This analysis revealed reduced abundance of Prevotella salivae and metabolic pathways associated with lipopolysaccharide and mycolic acid biosynthesis to be the strongest predictors of patients requiring respiratory support. These findings suggest that composition of the oropharyngeal microbiome in COVID-19 may play a role in determining who will suffer from severe disease manifestations.\n\nImportanceThe microbial community that colonizes the upper airway, the oropharyngeal microbiome, has the potential to affect how patients respond to respiratory viruses such as SARS-CoV2, the causative agent of COVID-19. In this study, we investigated the oropharyngeal microbiome of COVID-19 patients using high throughput DNA sequencing performed on oral swabs. We combined patient characteristics available at intake such as medical comorbidities and age, with measured abundance of bacterial species and metabolic pathways and then trained a machine learning model to determine what features are predicative of patients needing respiratory support in the form of supplemental oxygen or mechanical ventilation. We found that decreased abundance of some bacterial species and increased abundance of pathways associated bacterial products biosynthesis was highly predictive of needing respiratory support. This suggests that the oropharyngeal microbiome affects disease course in COVID-19 and could be targeted for diagnostic purposes to determine who may need oxygen, or therapeutic purposes such as probiotics to prevent severe COVID-19 disease manifestations.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Evan Stuart Bradley", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Abigail L Zeamer", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Vanni Bucci", + "author_inst": "UMass Medical School" + }, + { + "author_name": "Lindsey Cincotta", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Marie-Claire Salive", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Protiva Dutta", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Shafik Mutaawe", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Christopher Tocci", + "author_inst": "Worcester Polytechnic Institute" + }, + { + "author_name": "Ann Moorman", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Doyle V Ward", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Beth A McCormick", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "John P Haran", + "author_inst": "University of Massachusetts Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.28.22271604", "rel_title": "Medium-term impacts of the waves of the COVID-19 epidemic on treatments for non-COVID-19 patients in intensive care units: a retrospective cohort study in Japan", @@ -384070,37 +385087,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.25.481957", - "rel_title": "A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F", - "rel_date": "2022-02-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.25.481957", - "rel_abs": "The SARS-CoV-2 Omicron sub-variants BA.1 and BA.2 have become the dominant variants worldwide due to enhanced transmissibility and immune evasion. In response to the rise of BA.1 and BA.2, two recent studies by Liu et al. and Iketani et al. provide a detailed analysis of loss of therapeutic antibody potency through evaluation of escape by pseudotyped viruses harboring BA.1 and BA.2 receptor binding domain (RBD) point mutations. Surprisingly, Liu et al. and Iketani et al. observed a profoundly broad escape effect for the individual mutations S371L and S371F. This result cannot be explained by known escape mechanisms of the SARS-CoV-2 RBD, and conflicts with existing computational and experimental escape measurements for S371 mutations performed on monomeric RBD. Through an examination of these conflicting datasets and a structural analysis of the antibodies assayed by Liu et al. and Iketani et al., we propose a mechanism to explain S371L/F escape according to a perturbation of spike trimer conformational dynamics that has not yet been described for any SARS-CoV-2 escape mutation. The proposed mechanism is relevant to Omicron and future variant surveillance as well as therapeutic antibody design.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nathaniel L Miller", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Thomas Clark", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Rahul Raman", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ram Sasisekharan", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.25.481997", "rel_title": "Adenosine A2A Receptor (A2AR) agonists improve survival in K28-hACE2 mice following SARS CoV-2 infection", @@ -384336,6 +385322,89 @@ "type": "confirmatory results", "category": "genetics" }, + { + "rel_doi": "10.1101/2022.02.25.22271501", + "rel_title": "Impact of Omicron variant on the response to SARS-CoV-2 mRNA vaccination in multiple myeloma and monoclonal gammopathies", + "rel_date": "2022-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.25.22271501", + "rel_abs": "Multiple myeloma (MM) patients may have a reduced response to vaccination due to immunodeficiency. The humoral and cellular response to SARS-CoV-2 mRNA full vaccination and booster dose as well as the impact of spike variants, including the emerging Omicron one, are still unclear and have been investigated in this study in a cohort of MM patients and those with pre-malignant monoclonal gammopathies.\n\nFirstly, we have shown that MM patients with relapsed-refractory disease (MMR) had a reduced spike-specific antibody levels and neutralizing titers after SARS-CoV-2 mRNA full vaccination. Interestingly, all the analyzed variants, remarkably Omicron, had a significant negative impact on the neutralizing ability of the vaccine-induced antibodies in all patients with MM and in smoldering MM too. Moreover, lower spike-specific IL-2-producing CD4+ T cells and reduced cytotoxic spike-specific IFN-{gamma} and TNF--producing-CD8+ T cells were found in MM patients as compared to MGUS.\n\nFinally, we found that booster immunization improved SARS-CoV-2 spike humoral and cellular responses in newly diagnosed MM (MMD) patients and in most, but not all, MMR patients. After the booster dose, a significant increase of the neutralizing antibody titers against almost all the analyzed variants was achieved in MMD. On the other hand, in MMR patients, Omicron retain a negative impact on neutralizing ability, suggesting these patients need to be considered still at risk of Omicron SARS-CoV-2 infection with a clinically relevant disease.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Paola Storti", + "author_inst": "University of Parma" + }, + { + "author_name": "Valentina Marchica", + "author_inst": "University of Parma" + }, + { + "author_name": "Rosanna Vescovini", + "author_inst": "University of Parma" + }, + { + "author_name": "Valentina Franceschi", + "author_inst": "University of Parma" + }, + { + "author_name": "Luca Russo", + "author_inst": "University of Parma" + }, + { + "author_name": "Vincenzo Raimondi", + "author_inst": "University of Parma" + }, + { + "author_name": "Denise Toscani", + "author_inst": "University of Parma" + }, + { + "author_name": "Jessica Burroughs Garcia", + "author_inst": "University of Parma" + }, + { + "author_name": "Federica Costa", + "author_inst": "Universita del Piemonte Orientale" + }, + { + "author_name": "Benedetta Dalla Palma", + "author_inst": "Azienda Ospedaliero-Universitaria di Parma" + }, + { + "author_name": "Naomi Soressi", + "author_inst": "Azienda Ospedaliero-Universitaria di Parma" + }, + { + "author_name": "Mariateresa Giaimo", + "author_inst": "University of Parma" + }, + { + "author_name": "Nicolas Thomas Iannozzi", + "author_inst": "University of Parma" + }, + { + "author_name": "Laura Notarfranchi", + "author_inst": "University of Parma" + }, + { + "author_name": "Gabriella Sammarelli", + "author_inst": "Azienda Ospedaliero-Universitaria di Parma" + }, + { + "author_name": "Gaetano Donofrio", + "author_inst": "University of Parma" + }, + { + "author_name": "Nicola Giuliani", + "author_inst": "University of Parma" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.02.22.481100", "rel_title": "Mitoquinone mesylate targets SARS-CoV-2 and associated lung inflammation through host pathways", @@ -385876,41 +386945,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.21.22271309", - "rel_title": "Association of Workload and Practice of Respectful Maternity Care Among the Healthcare Providers, Before and During the COVID-19 Pandemic in South Western Nepal: A Cross-Sectional Study", - "rel_date": "2022-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271309", - "rel_abs": "IntroductionRespectful maternity care is an approach that involves respecting womens belief, choices, emotions, and dignity during the childbirth process. As the workload among maternity care workforce affects intrapartum quality care, respectful maternity care might have also been affected, particularly during the pandemic. Thus, this study was conducted to examine the association between workload among healthcare providers and their practice of respectful maternity care, before and during the pandemic.\n\nMethodsA cross-sectional study was conducted in South Western Nepal. A total of 267 healthcare providers from 78 birthing centers were included. Data collection was done through telephone interviews. The exposure variable was workload among the healthcare providers, and the outcome variable was respectful maternity care practice before and during the COVID-19 pandemic. Multilevel mixed-effect linear regression was used to examine the association.\n\nResultsThe median client-provider ratio before and during the pandemic was 21.7 and 13.0, respectively. The mean score of respectful maternity care practice was 44.5 (SD 3.8) before the pandemic, which was decreased to 43.6 (SD 4.5) during the pandemic. Client-provider ratio was negatively associated with respectful maternity care practice for both times; before (Coef. -5.16; 95% CI -8.41 to -1.91) and during (Coef. -7.47; 95% CI -12.72 to -2.23) the pandemic.\n\nConclusionsWhile a higher client-provider was associated with a lower respectful maternity care practice score both before and during the COVID-19 pandemic, the coefficient was larger during the pandemic. Therefore, workload among the healthcare providers should be considered before the implementation of respectful maternity care, and more attention should be given during the pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alpha Pokharel", - "author_inst": "Green Tara Nepal" - }, - { - "author_name": "Junko Kiriya", - "author_inst": "The University of Tokyo Graduate School of Medicine Faculty of Medicine: Tokyo Daigaku Daigakuin Igakukei Kenkyuka Igakubu" - }, - { - "author_name": "Akira Shibanuma", - "author_inst": "The University of Tokyo Graduate School of Medicine Faculty of Medicine: Tokyo Daigaku Daigakuin Igakukei Kenkyuka Igakubu" - }, - { - "author_name": "Ram Silwal", - "author_inst": "The University of Tokyo Graduate School of Medicine Faculty of Medicine: Tokyo Daigaku Daigakuin Igakukei Kenkyuka Igakubu" - }, - { - "author_name": "Masamine Jimba", - "author_inst": "The University of Tokyo Graduate School of Medicine Faculty of Medicine: Tokyo Daigaku Daigakuin Igakukei Kenkyuka Igakubu" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.02.22.22270091", "rel_title": "Abdominal Imaging Associates Body Composition with COVID-19 Severity", @@ -386206,6 +387240,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2022.02.22.22270838", + "rel_title": "Three-month follow-up of heterologous vs homologous third vaccination in kidney transplant recipients", + "rel_date": "2022-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.22.22270838", + "rel_abs": "ImportanceResponse to SARS-CoV-2 vaccines in kidney transplant recipients (KTR) is severely reduced. Heterologous 3rd vaccination combining mRNA and vector vaccines did not increase seroconversion at four weeks after vaccination but evolution of antibody levels beyond the first month remain unknown.\n\nObjectiveTo assess changes in antibody response following a 3rd vaccination with mRNA or vector vaccine in KTR from month one to month three after vaccination.\n\nDesign, Setting and ParticipantsThree-month follow-up (pre-specified secondary endpoint) of a single-center, single-blinded, 1:1 randomized, controlled trial on 3rd vaccination against SARS-CoV-2 in 201 KTR who did not develop SARS-CoV-2 spike protein antibodies following two doses of an mRNA vaccine.\n\nIntervention(s)mRNA (BNT162b2 or mRNA-1273) or vector (Ad26COVS1) as 3rd SARS-CoV-2 vaccine\n\nMain Outcomes and MeasuresMain outcome was seroconversion at the second follow-up between 60-120 days after the 3rd vaccination. Subsequently, higher cut-off levels associated with neutralizing capacity and protective immunity were applied (i.e. >15, >100, >141 and >264 BAU/mL). In addition, trajectories of antibody levels from month one to month three were analyzed. Finally, SARS-CoV-2 specific CD4 and CD8 T-cells at four weeks were compared among the 18 top responders in both groups.\n\nResultsA total of 169 patients were available for the three-month follow-up. Overall, seroconversion at three months was similar between both groups (45% versus 50% for mRNA and vector group, respectively; OR=1.24, 95%CI=[0.65, 2.37], p=0.539). However, when applying higher cut-off levels, a significantly larger number of individual in the vector group reached antibody levels > 141 and > 264 BAU/mL at the three-month follow-up (141 BAU/mL: 4% vs. 15% OR=4.96, 95%CI=[1.29, 28.21], p=0.009 and 264 BAU/mL: 1% vs. 10% OR=8.75, 95%CI=[1.13, 396.17], p=0.018 for mRNA vs. vector vaccine group, respectively). In line, antibody levels in seroconverted patients further increased from month one to month three in the vector group while remaining unchanged in the mRNA group (median increase: mRNA= 1.35 U/mL and vector = 27.6 U/mL, p = 0.004). Of particular note, there was no difference in the CD4 and CD8 T-cell response between the mRNA and vector vaccine group at month one.\n\nConclusions and RelevanceDespite a similar overall seroconversion rate at three months following 3rd vaccination in KTR, a heterologous 3rd booster vaccination with Ad26COVS1 resulted in significantly higher antibody levels in responders.\n\nTrial RegistrationEurdraCT: 2021-002927-39", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Andreas Heinzel", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Eva Schrezenmeier", + "author_inst": "Charite-Universitaetsmedizin, Berlin" + }, + { + "author_name": "Florina Regele", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Lukas Raab", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Michael Eder", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Christof Aigner", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Rhea Jabbour", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Constantin Aschauer", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Ana-Luisa Stefanski", + "author_inst": "Charite Berlin" + }, + { + "author_name": "Thomas Doerner", + "author_inst": "Charite" + }, + { + "author_name": "Klemens Budde", + "author_inst": "Charite" + }, + { + "author_name": "Roman Reindl-Schwaighofer", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Rainer Oberbauer", + "author_inst": "Medical University of Vienna" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2022.02.22.22271376", "rel_title": "Impact of key meteorological parameters on the spread of COVID-19 in Mumbai: Correlation and Regression Analysis", @@ -387430,57 +388531,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2022.02.22.22271342", - "rel_title": "Impact of BNT162b2 mRNA Vaccination on the Development of Short and Long-term Vaccine-Related Adverse Events in Inflammatory Bowel Disease: A Multi-Center Prospective Study", - "rel_date": "2022-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.22.22271342", - "rel_abs": "IntroductionSARS-CoV-2 vaccination has been effective in protecting against severe COVID-19 infections and related mortality. It is recommended for all individuals including patients with inflammatory bowel disease (IBD). However, safety data is lacking in this group of patients. Therefore, we aim to evaluate the short- and long-term vaccine related adverse events (AEs) in patients with IBD.\n\nMethodThis is a prospective, observational cohort study investigating short- and long-term AEs related to BNT162b2 vaccine in patients with IBD (study group) after first and second dose compared to healthy participants (study group). Patients were recruited at the time of attendance to clinic or infusion rooms. Short term (<3 weeks) localized and systemic AEs were assessed via questionnaire. Follow-up phone-based survey was made to collect data on long term (up to 24 weeks) AEs.\n\nResultsA total of 408 patients answered the questionnaires, 204 patients in each group, the study and control group. No serious adverse events were reported in either the study nor the control group after the first or the second dose. Participants in the control group reported more frequent pain at the injection site than those in the study group after the first dose (58 (57%) vs 38 (37%) respectively, P-value= 0.005). After the second dose, tiredness was reported more frequently in the control group [49 (48%)] compared to the study group [25 (24%), (P-value<0.001)]. At 20-24 weeks post vaccination, 386 out of 408 (94.6%) patients were willing to participate in the follow-up phone based questionnaire (196 (96.1%) in the study group vs 190 (93.1%) in the control group). In both groups, none of the patients reported local, systemic or severe adverse events (0 out of 386) at week 20-244 post second dose.\n\nConclusionThe BNT162b2 vaccine is safe in patients with IBD. No severe or long-term adverse events were reported in our study. The frequency of local and systemic adverse events after the second dose was generally higher among healthy participants compared to patients with IBD. Further studies including a larger cohort with longer follow-up duration are needed to assess for possible rare adverse events.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Mohammad Shehab", - "author_inst": "Mubarak Hospital" - }, - { - "author_name": "Fatema Alrashed", - "author_inst": "Kuwait University" - }, - { - "author_name": "Israa Abdullah", - "author_inst": "Kuwait Hospital" - }, - { - "author_name": "Ahmad Alfadhli", - "author_inst": "Mubarak Hospital" - }, - { - "author_name": "Hamad Ali", - "author_inst": "Kuwait University" - }, - { - "author_name": "Mohamed Abu-farha", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Arshad Channanath", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Jehad Abubaker", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Fahd Al-Mulla", - "author_inst": "Dasman Diabetes Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2022.02.21.22271127", "rel_title": "Favourable vaccine-induced SARS-CoV-2 specific T cell response profile in patients undergoing immune-modifying therapies", @@ -387764,6 +388814,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.21.481262", + "rel_title": "Serological screening in wild ruminants in Germany, 2021/22: No evidence of SARS-CoV-2, bluetongue virus or pestivirus spread but high seroprevalences against Schmallenberg virus", + "rel_date": "2022-02-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.21.481262", + "rel_abs": "Wildlife animals may be susceptible for multiple infectious agents of public health or veterinary relevance, thereby potentially forming a reservoir that bears the constant risk of re-introduction into the human or livestock population. Here, we serologically investigated 493 wild ruminant samples collected in the 2021/22 hunting season in Germany for the presence of antibodies against the severe acute respiratory coronavirus 2 (SARS-CoV-2) and four viruses pathogenic for domestic ruminants, namely the orthobunyavirus Schmallenberg virus (SBV), the reovirus bluetongue virus (BTV) and ruminant pestiviruses like bovine viral diarrhoea virus or border disease virus. The animal species comprised fallow deer, red deer, roe deer, mouflon and wisent. For coronavirus serology, additional 307 fallow, roe and red deer samples collected between 2017 and 2020 at three military training areas were included. While antibodies against SBV could be detected in about 13.6% of the samples collected in 2021/22, only one fallow deer of unknown age tested positive for anti-BTV antibodies and all samples reacted negative for antibodies against ruminant pestiviruses. In an ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2, 25 out of 493 (5.1%) samples collected in autumn and winter 2021/22 scored positive. This sero-reactivity could not be confirmed by the highly specific virus neutralization test, occurred also in 2017, 2018 and 2019, i.e. prior to the human SARS-CoV-2 pandemic, and was likewise observed against the RBD of the related SARS-CoV-1. Therefore, the SARS-CoV-2-seroreactivity was most likely induced by another, hitherto unknown deer virus belonging to the subgenus Sarbecovirus of betacoronaviruses.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kerstin Wernike", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Luisa Fischer", + "author_inst": "Institute of Wildlife Research" + }, + { + "author_name": "Mark Holsteg", + "author_inst": "Bovine Health Service, Chamber of Agriculture for North Rhine-Westphalia" + }, + { + "author_name": "Andrea Aebischer", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Anja Petrov", + "author_inst": "Central Institute of the Bundeswehr Medical Service Kiel" + }, + { + "author_name": "Katharina Marquart", + "author_inst": "Central Institute of the Bundeswehr Medical Service Kiel" + }, + { + "author_name": "Ulrich Schotte", + "author_inst": "Central Institute of the Bundeswehr Medical Service Kiel" + }, + { + "author_name": "Jakob Schoen", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Donata Hoffmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Silke Hechinger", + "author_inst": "Landesbetrieb Hessisches Landeslabor" + }, + { + "author_name": "Antonie Neubauer-Juric", + "author_inst": "Bavarian Health and Food Safety Authority" + }, + { + "author_name": "Julia Blicke", + "author_inst": "Ministry of Climate Protection, Environment, Energy and Mobility" + }, + { + "author_name": "Thomas C. Mettenleiter", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Martin Beer", + "author_inst": "Friedrich-Loeffler-Institut" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.21.481341", "rel_title": "Potent Neutralizing Activity of Polyclonal Equine Antibodies against Omicron SARS-CoV-2", @@ -389327,45 +390448,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2022.02.18.22271191", - "rel_title": "Childhood Trauma Exposure Increases Long COVID Risk", - "rel_date": "2022-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.18.22271191", - "rel_abs": "BackgroundA proportion of those who contract COVID-19 will develop long COVID (i.e., symptoms that persist for three months or more). Childhood trauma contributes to a pro-inflammatory state in adulthood evidenced by high morbidity and early mortality, but it has not yet been investigated as a risk factor for long COVID.\n\nMethodsParticipants (N=338) completed online measures of premorbid health, COVID-19 positivity, symptoms, recovery, depression, anxiety, and post-traumatic stress disorder (PTSD). Questionnaires about childhood and recent traumatic experiences were completed by half of the sample (N=162).\n\nResultsFifty-three percent of participants developed long COVID, of whom over 60% endorsed exercise intolerance and protracted myalgias, headaches, brain fog, and shortness of breath. Participants who experienced at least one childhood traumatic event were 3-fold more likely to develop the syndrome (OR=3.11, 95% CI, 1.49 to 6.48), while risk was nearly 6-fold increased for two or more events (OR=5.67, CI, 2.44 to 13.13). Regression models showed childhood trauma (OR=5.32, CI, 1.44 to 19.68), older age (OR=1.11, CI, 1.06 to 1.16), female sex (OR=4.02, CI, 1.34 to 12.12), along with chest pain (OR=8.77, CI, 2.80 to 27.43), brain fog (OR=3.33, CI, 1.16 to 9.57) and phantosmia (OR=5.90, CI, 1.40 to 24.86) during acute illness accurately classified long COVID status in 87% of participants.\n\nInterpretationsEarly adversity is a risk-factor for long COVID, likely due to altered immune response, central sensitization, and peripheral dysfunction. Childhood trauma, a crucial social determinant of health, should be routinely assessed in COVID-19 survivors and may aid in determining prognosis.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alicia W. Villanueva van den Hurk", - "author_inst": "University of Dayton" - }, - { - "author_name": "Cady Ujvari", - "author_inst": "University of Dayton" - }, - { - "author_name": "Noah Greenspan", - "author_inst": "Pulmonary Wellness Foundation; Pulmonary Wellness COVID Rehabilitation and Recovery Center" - }, - { - "author_name": "Dolores Malaspina", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Xavier F. Jimenez", - "author_inst": "Zucker School of Medicine at Hofstra University; Long Island Jewish Medical Center/Northwell Health" - }, - { - "author_name": "Julie Walsh-Messinger", - "author_inst": "University of Dayton" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.21.22271298", "rel_title": "Effectiveness of Covid-19 vaccines against symptomatic and asymptomatic SARS-CoV-2 infections in an urgent care setting", @@ -389817,6 +390899,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.21.22271289", + "rel_title": "Breakthrough SARS-CoV-2 infections in immune mediated disease patients undergoing B cell depleting therapy", + "rel_date": "2022-02-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271289", + "rel_abs": "ObjectivesImmunocompromised patients with immune mediated inflammatory diseases (IMIDs), undergoing therapy with B cell depleting agents are among the most vulnerable to experience severe COVID-19 disease as well as respond sub-optimally to SARS CoV-2 vaccines yet little is known about the frequency or severity of breakthrough infection in this population. We have analyzed a large cohort of vaccinated IMIDs patients undergoing B cell depleting therapy for the presence of breakthrough infection and assessed their outcomes.\n\nMethodsUtilizing specific ICD codes the pharmacy records and COVID-19 registry at the Cleveland clinic were used to identify all patients with IMIDS treated with B cell depleting monoclonal antibodies who were vaccinated against SARs CoV-2 and experienced breakthrough infections. Each EMR record was hand-reviewed to extract clinical data including vaccine history, demographics, comorbidities, other therapies, details of B cell depleting therapy, and outcomes. Univariate and multivariable logistic/proportional-odds regression models were used to examine the risk factors for severe outcomes.\n\nResultsOf 1696 IMIDS patients on B cell depleting therapies 74 developed breakthrough COVID-19. Outcomes were severe with 24 (35%) hospitalized, 11 (15%) patients requiring critical care and 6 (8 %) deaths. Monoclonal antibodies were used on an outpatient basis to treat 21 with only a single patient requiring hospitalization without oxygen support and no deaths.\n\nConclusionsIn IMIDS patients on B cell depleting therapies breakthrough infections are frequent and associated with severe outcomes. Outpatient use of monoclonal antibody therapy was associated with enhanced clinical outcomes.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Cassandra M Calabrese", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Elaine M Husni", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Brandon M Moss", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Anthony J Fernandez", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Yuxuan Jin", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Elizabeth Kirchner", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Leonard H Calabrese", + "author_inst": "Cleveland Clinic" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.18.22271195", "rel_title": "Early emergence phase of SARS-CoV-2 Delta variant in Florida", @@ -391469,85 +392594,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2022.02.17.22270679", - "rel_title": "Evolutionary Trajectories of SARS-CoV-2 Alpha and Delta Variants in White-Tailed Deer in Pennsylvania", - "rel_date": "2022-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22270679", - "rel_abs": "Introductory paragraphThe SARS-CoV-2 pandemic likely began by viral spillover from animals to humans1-3; today multiple animal species are known to be susceptible to infection4-8. White-tailed deer, Odocoileus virginianus are infected in North America at substantial levels9-11, and genomic data suggests that a variant in deer may have spilled back to humans12,13. Here we characterize SARS-CoV-2 in deer from Pennsylvania (PA) sampled during fall and winter 2021. Of 123 nasal swab samples analyzed by RT-qPCR, 20 (16.3%) were positive for SARS-CoV-2. Seven whole-genome sequences were obtained, together with six more partial spike sequences. These annotated as alpha and delta variants, the first reported observations of these lineages in deer, documenting multiple new jumps from humans to deer. The alpha lineage persisted in deer after its displacement by delta in humans, and deer-derived alpha variants diverged significantly from those in humans, consistent with a distinctive evolutionary trajectory in deer.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Andrew D Marques", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Scott Sherrill-Mix", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "John Everett", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Hriju Adhikari", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Shantan Reddy", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Julie C Ellis", - "author_inst": "Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - }, - { - "author_name": "Haley Zeliff", - "author_inst": "Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - }, - { - "author_name": "Sabrina S Greening", - "author_inst": "Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - }, - { - "author_name": "Carolyn C Cannuscio", - "author_inst": "Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Katherine M Strelau", - "author_inst": "Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Ronald G Collman", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Brendan J Kelly", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Kyle G Rodino", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104" - }, - { - "author_name": "Frederic D Bushman", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Roderick B Gagne", - "author_inst": "Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - }, - { - "author_name": "Eman Anis", - "author_inst": "Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, PA 19348" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.19.22271221", "rel_title": "Risk of SARS-CoV-2 reinfection 18 months after primary infection: population-level observational study.", @@ -391911,6 +392957,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.02.17.22271099", + "rel_title": "Timeliness of reporting of SARS-CoV-2 seroprevalence results and their utility for infectious disease surveillance", + "rel_date": "2022-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22271099", + "rel_abs": "Seroprevalence studies have been used throughout the COVID-19 pandemic to monitor infection and immunity. These studies are often reported in peer-reviewed journals, but the academic writing and publishing process can delay reporting and thereby public health action. Seroprevalence estimates have been reported faster in preprints and media, but with concerns about data quality. We aimed to (i) describe the timeliness of SARS-CoV-2 serosurveillance reporting by publication venue and study characteristics and (ii) identify relationships between timeliness, data validity, and representativeness to guide recommendations for serosurveillance efforts.\n\nWe included seroprevalence studies published between January 1, 2020 and December 31, 2021 from the ongoing SeroTracker living systematic review. For each study, we calculated timeliness as the time elapsed between the end of sampling and the first public report. We evaluated data validity based on serological test performance and correction for sampling error, and representativeness based on use of a representative sample frame and adequate sample coverages. We examined how timeliness varied with study characteristics, representativeness, and data validity using univariate and multivariate Cox regression.\n\nWe analyzed 1,844 studies. Median time to publication was 154 days (IQR 64-255), varying by publication venue (journal articles: 212 days, preprints: 101 days, institutional reports: 18 days, and media: 12 days). Multivariate analysis confirmed the relationship between timeliness and publication venue and showed that general population studies were published faster than special population or health care worker studies; there was no relationship between timeliness and study geographic scope, geographic region, representativeness, or serological test performance.\n\nSeroprevalence studies in peer-reviewed articles and preprints are published slowly, highlighting the limitations of using the academic literature to report seroprevalence during a health crisis. More timely reporting of seroprevalence estimates can improve their usefulness for surveillance, enabling more effective responses during health emergencies.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Claire Donnici", + "author_inst": "Cumming School of Medicine, University of Calgary, Calgary, AB, Canada" + }, + { + "author_name": "Natasha Ilincic", + "author_inst": "Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada" + }, + { + "author_name": "Christian Cao", + "author_inst": "Cumming School of Medicine, University of Calgary, Calgary, AB, Canada" + }, + { + "author_name": "Caseng Zhang", + "author_inst": "Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada" + }, + { + "author_name": "Gabriel Deveaux", + "author_inst": "Cumming School of Medicine, University of Calgary, Calgary, AB, Canada" + }, + { + "author_name": "David A Clifton", + "author_inst": "Institute of Biomedical Engineering, University of Oxford, UK" + }, + { + "author_name": "David Buckeridge", + "author_inst": "Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada" + }, + { + "author_name": "Niklas Bobrovitz", + "author_inst": "University of Toronto" + }, + { + "author_name": "Rahul K Arora", + "author_inst": "Institute of Biomedical Engineering, University of Oxford, UK; Cumming School of Medicine, University of Calgary, Calgary, AB, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.17.480904", "rel_title": "Low Density Lipoprotein Receptor-Related Protein 1 (LRP1) is a host factor for RNA viruses including SARS-CoV-2", @@ -393279,125 +394376,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.16.22270842", - "rel_title": "The SARS-CoV2 envelope is distinct from host membranes, exposes pro-coagulant lipids, and can be inactivated in vivo by surfactant-containing oral rinses.", - "rel_date": "2022-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22270842", - "rel_abs": "The lipid envelope of SARS-CoV2 is an essential component of the virus, however its molecular composition is unknown. Addressing this knowledge gap could support the design of anti-viral agents, and further understanding of viral interaction with extracellular host proteins, infectivity, pathogenicity, and innate immune system clearance. Lipidomics analysis of SARS-CoV2 particles generated from Vero or A549 cells revealed that the virus envelope comprised mainly of phospholipids (PL), primarily phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylinositol (PI), with very little cholesterol, sphingolipids or other lipids, indicating significant differences from host membranes. Unlike healthy cellular membranes, procoagulant aminoPL (aPL), specifically PE and phosphatidylserine (PS), were present on the external side at levels far exceeding those seen on activated platelets. As a result, purified virions directly promoted coagulation. To investigate whether these differences enabled the viral envelope to be selectively targeted at relevant sites in vivo, we tested whether non-toxic oral rinses containing lipid disrupting chemicals could reduce viral infectivity. Products containing PL-disrupting surfactant solutions (cetylpyridinium chloride (CPC) or ethyl lauroyl arginate) met EN14476 virucidal standards in vitro, however products containing essential oils, PVP-I, or Chlorhexidine did not, nor did rinses containing components that altered the critical micelle concentration of CPC. This result was recapitulated in vivo, where a 30-second oral rinse with CPC-mouthwash eliminated live virus in the oral cavity of COVID19 patients for at least 1hr, while PVP-Iodine and saline mouthwashes were ineffective. Thus, the SARS-CoV2 lipid envelope is distinct from the host plasma membrane which may enable design of selective anti-viral approaches, it exposes PE and PS which may influence thrombosis, pathogenicity, and inflammation, and can be selectively targeted in vivo by specific oral rinses.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Zack Saud", - "author_inst": "Cardiff University" - }, - { - "author_name": "Victoria J Tyrrell", - "author_inst": "Cardiff University" - }, - { - "author_name": "Andreas Zaragkoulias", - "author_inst": "Cardiff University" - }, - { - "author_name": "Majd B Protty", - "author_inst": "Cardiff University" - }, - { - "author_name": "Evelina Statkute", - "author_inst": "Cardiff University" - }, - { - "author_name": "Anzelika Rubina", - "author_inst": "Cardiff University" - }, - { - "author_name": "Kirsten Bentley", - "author_inst": "Cardiff University" - }, - { - "author_name": "Daniel A White", - "author_inst": "Cardiff University" - }, - { - "author_name": "Patricia Dos Santos Rodrigues", - "author_inst": "Cardiff University" - }, - { - "author_name": "Robert C Murphy", - "author_inst": "University of Colorado Denver" - }, - { - "author_name": "Harald Kofeler", - "author_inst": "Medical University of Graz" - }, - { - "author_name": "William J Griffiths", - "author_inst": "Swansea University" - }, - { - "author_name": "Jorge Alvarez-Jarreta", - "author_inst": "European Bioinformatics Institute" - }, - { - "author_name": "Richard William Brown", - "author_inst": "Cardiff and Vale University Health Board" - }, - { - "author_name": "Robert G Newcombe", - "author_inst": "Cardiff University" - }, - { - "author_name": "James Heyman", - "author_inst": "Cardiff and Vale University Health Board" - }, - { - "author_name": "Manon Pritchard", - "author_inst": "Cardiff University" - }, - { - "author_name": "Robert WJ Mcleod", - "author_inst": "Cardiff University" - }, - { - "author_name": "Arvind Arya", - "author_inst": "Betsi Cadwaladr University Health Board" - }, - { - "author_name": "Ceri-Ann Lynch", - "author_inst": "Cwm Taf University Health Board" - }, - { - "author_name": "David Owens", - "author_inst": "Cardiff and Vale University Health Board" - }, - { - "author_name": "Vince Jenkins", - "author_inst": "Cardiff and Vale University Health Board" - }, - { - "author_name": "Niklaas J Buurma", - "author_inst": "Cardiff University" - }, - { - "author_name": "Valerie B O'Donnell", - "author_inst": "Cardiff University" - }, - { - "author_name": "David W Thomas", - "author_inst": "Cardiff University" - }, - { - "author_name": "Richard J Stanton", - "author_inst": "Cardiff University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.15.22270954", "rel_title": "Validation of the RT-LAMP assay in a large cohort of nasopharyngeal swab samples shows that it is a useful screening method for detecting SARS-CoV-2 and its VOC variants", @@ -393713,6 +394691,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.16.480801", + "rel_title": "A natural broad-spectrum inhibitor of enveloped virus entry, effective against SARS-CoV-2 and Influenza A Virus in preclinical animal models.", + "rel_date": "2022-02-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.16.480801", + "rel_abs": "The COVID-19 pandemic has highlighted the need for novel antivirals for pandemic management and preparedness. Targeting host processes that are co-opted by viruses is an attractive strategy for developing antivirals with a high resistance barrier. Picolinic acid (PA) is a byproduct of tryptophan metabolism, endogenously produced in humans and other mammals. Here we report broad-spectrum antiviral effects of PA against enveloped viruses, including Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), Influenza A virus (IAV), Flaviviruses, Herpes Simplex Virus, and Human Parainfluenza Virus. We further demonstrate using animal models that PA is effective against SARS-CoV-2 and IAV, especially as an oral prophylactic. The mode of action studies revealed that PA inhibits viral entry of enveloped viruses, primarily by interfering with viral-cellular membrane fusion, inhibiting virus-mediated syncytia formation, and dysregulating cellular endocytosis. Overall, our data establish PA as a broad-spectrum antiviral agent, with promising preclinical efficacy against pandemic viruses SARS-CoV-2 and IAV.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Rohan Narayan", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Mansi Sharma", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Rajesh Thangavel Yadav", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Abhijith Biji", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Oyahida Khatun", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Raju S Rajmani", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Pallavi Raj Sharma", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Sharumathi Jeyashankar", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Priya Rani", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "C. Durga Rao", + "author_inst": "SRM University, Andhra Pradesh" + }, + { + "author_name": "Vijaya Satchidanandam", + "author_inst": "Indian Institute of Science, India" + }, + { + "author_name": "Saumitra Das", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Rachit Agarwal", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Shashank Tripathi", + "author_inst": "Indian Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.15.480527", "rel_title": "Non-productive exposure of PBMCs to SARS-CoV-2 induces cell-intrinsic innate immunity responses", @@ -395073,93 +396122,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2022.02.11.22270775", - "rel_title": "Favipiravir, lopinavir-ritonavir or combination therapy (FLARE): a randomised, double blind, 2x2 factorial placebo-controlled trial of early antiviral therapy in COVID-19", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270775", - "rel_abs": "BackgroundEarly antiviral treatment is effective for COVID-19 but currently available agents are expensive. Favipiravir is routinely used in many countries, but efficacy is unproven. Antiviral combinations have not been systematically studied. We aimed to evaluate the effect of favipiravir, lopinavir-ritonavir or the combination of both agents on SARS-CoV-2 viral load trajectory when administered early.\n\nMethodsWe conducted a Phase 2, proof of principle, randomised, placebo-controlled, 2x2 factorial, double-blind trial of outpatients with early COVID-19 (within 7 days of symptom onset) at two sites in the United Kingdom. Participants were randomised using a centralised online process to receive: favipiravir (1800mg twice daily on Day 1 followed by 400mg four times daily on Days 2-7) plus lopinavir-ritonavir (400mg/100mg twice daily on Day 1, followed by 200mg/50mg four times daily on Days 2-7); favipiravir plus lopinavir-ritonavir placebo; lopinavir-ritonavir plus favipiravir placebo; or both placebos. The primary outcome was SARS-CoV-2 viral load at Day 5, accounting for baseline viral load. ClinicalTrials{middle dot}gov: NCT04499677.\n\nFindingsBetween 6 October 2020 and 4 November 2021, we recruited 240 participants. For the favipiravir+lopinavir-ritonavir, favipiravir+placebo, lopinavir-ritonavir+placebo and placebo-only arms, we recruited 61, 59, 60 and 60 participants and analysed 55, 56, 55 and 58 participants respectively who provided viral load measures at Day 1 and Day 5. In the primary analysis, the mean viral load in the favipiravir+placebo arm had decreased by 0.57 log10 (95% CI -1.21 to 0.07, p=0.08) and in the lopinavir-ritonavir+placebo arm by 0.18 log10 (95% CI -0.82 to 0.46, p=0.58) more than in the placebo arm at Day 5. There was no significant interaction between favipiravir and lopinavir-ritonavir (interaction coefficient term: 0.59 log10, 95% CI -0.32 to 1.50, p=0.20). More participants had undetectable virus at Day 5 in the favipiravir+placebo arm compared to placebo only (46.3% vs 26.9%, odds ratio (OR): 2.47, 95% CI 1.08 to 5.65; p=0.03). Adverse events were observed more frequently with lopinavir-ritonavir, mainly gastrointestinal disturbance. Favipiravir drug levels were lower in the combination arm than the favipiravir monotherapy arm.\n\nInterpretationAt the current doses, no treatment significantly reduced viral load in the primary analysis. Favipiravir requires further evaluation with consideration of dose escalation. Lopinavir-ritonavir administration was associated with lower plasma favipiravir concentrations.\n\nFundingLifeArc, UK.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "David M Lowe", - "author_inst": "University College London" - }, - { - "author_name": "Li-An K Brown", - "author_inst": "University College London" - }, - { - "author_name": "Kashfia Chowdhury", - "author_inst": "University College London" - }, - { - "author_name": "Stephanie Davey", - "author_inst": "Royal Free London NHS Foundation Trust" - }, - { - "author_name": "Philip Yee", - "author_inst": "Royal Free London NHS Foundation Trust" - }, - { - "author_name": "Felicia Ikeji", - "author_inst": "University College London" - }, - { - "author_name": "Amalia Ndoutoumou", - "author_inst": "University College London" - }, - { - "author_name": "Divya Shah", - "author_inst": "Great Ormond Street Hospital NHS Foundation Trust" - }, - { - "author_name": "Alexander Lennon", - "author_inst": "Great Ormond Street Hospital NHS Foundation Trust" - }, - { - "author_name": "Abhulya Rai", - "author_inst": "Great Ormond Street Hospital NHS Foundation Trust" - }, - { - "author_name": "Akosua A Agyeman", - "author_inst": "University College London" - }, - { - "author_name": "Anna Checkley", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nicola Longley", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Hakim-Moulay Dehbi", - "author_inst": "University College London" - }, - { - "author_name": "Nick Freemantle", - "author_inst": "University College London" - }, - { - "author_name": "Judith Breuer", - "author_inst": "University College London" - }, - { - "author_name": "Joseph F Standing", - "author_inst": "University College London" - }, - { - "author_name": "- FLARE Investigators", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.13.22270755", "rel_title": "Co-infection with SARS-COV-2 Omicron and Delta Variants Revealed by Genomic Surveillance", @@ -395471,6 +396433,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.11.480131", + "rel_title": "Omicron-Based Vaccine Candidate Elicits Potent Neutralizing Antibodies in the Animal Model", + "rel_date": "2022-02-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.11.480131", + "rel_abs": "BackgroundOmicron variant (B. 1.1.529) is able to escape from naturally acquired and vaccine-induced immunity, which mandates updating the current COVID-19 vaccines. Here, we investigated and compared the neutralising antibody induction of the ancestral variant-based BIV1-CovIran vaccine, the Omicron variant-based BIV1-CovIran Plus vaccine, and the novel bivalent vaccine candidate, BBIV1-CovIran, against the Omicron and ancestral Wuhan variants on the rat model.\n\nMethodsViruses were isolated from a clinical specimen and virus characterisation performed. After inactivating the viral particles, the viruses were purified and formulated. Bivalent vaccines were a composition of 2.5 g (5 g total) or 5 g (10 g total) doses of each ansectral-based and Omicron-based monovalent vaccine. Subsequently, the potency of the monovalent and bivalent vaccines was investigated using the virus neutralisation test (VNT).\n\nResultsThe group that received three doses of the Omicron-specific vaccine demonstrated neutralisation activity against the Omicron variant with a geometric mean titer of 337.8. However, three doses of the Wuhan variant-specific vaccine could neutralise the Omicron variant at a maximum of 1/32 serum dilution. The neutralisation activity of the Omicron-specific vaccine, when administered as the booster dose after two doses of the Wuhan variant-specific vaccine, was 100% against the Omicron variant and the Wuhan variant at 1/64 and 1/128 serum dilution, respectively. Three doses of 5 g bivalent vaccine could effectively neutralise both variants at the minimum of 1/128 serum dilution. The 10 g bivalent vaccine at three doses showed even higher neutralisation titers: geometric mean titer of 338.0 against Omicron and 445.7 against Wuhan).\n\nConclusionIt is shown that the candidate bivalent vaccine could elicit a potent immune response against both Wuhan-Hu-1 and Omicron BA.1 variants. Therefore, we plan to evaluate the updated vaccine in the clinical trial setting.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Asghar Abdoli", + "author_inst": "Pasteur institute of Iran" + }, + { + "author_name": "Hamidreza Jamshidi", + "author_inst": "Department of Pharmacology, Faculty of Medicine, Shaheed Beheshti University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mehdi Lari Baghal", + "author_inst": "Research and Development Unit, Shifa Pharmed Co, Karaj, Iran" + }, + { + "author_name": "Mohammad Taqavian", + "author_inst": "Research and Development Unit, Biosunpharmed Co, Karaj, Iran" + }, + { + "author_name": "Hasan Jalili", + "author_inst": "Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.02.14.480394", "rel_title": "Increased Potency and Breadth of SARS-CoV-2 Neutralizing Antibodies After a Third mRNA Vaccine Dose", @@ -397323,85 +398320,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.14.22270965", - "rel_title": "Experiences of the physicians in the largest COVID-19 dedicated hospital of Bangladesh about COVID-19 and its aftermath", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270965", - "rel_abs": "BackgroundThe doctors and the other health care workers are the first-line fighters against COVID-19. This study aims to identify the prevalence, risk factors, clinical severity of COVID-19 infection among the doctors working in the COVID unit. We also analyzed the hospital data for admission and RT-PCR positivity among the physicians.\n\nMethodsIt was a cross-sectional survey and review of the hospital database. We surveyed from September 2021 to October 2021 and explored the hospital data from march 2020 to September 2021.We included 342 physicians for analysis in the survey. We reviewed hospital data of 1578 total admitted patients and 336 RT-PCR test positive physicians for analyzing the hospital admission rate, the positivity rate for COVID-19 among the physicians and the other patients in the different COVID-19 surges.\n\nFindingsIn this study, we demonstrated the physicians sufferings during the pandemic era. We have observed four surges in the hospital admission and RT-PCR for COVID-19 positivity rate among the physicians and the general population. The physicians experienced a similar surge in the hospital admission and positivity rate to the general population. The hospital admission was lower in the fourth surge among the physicians than the general population. The positivity rate was higher in the first, second and third surge among the physicians. In the survey, a total of 146(42%) respondents had COVID-19 infection, and among them, 50(34.2%) had re-detectable positive SARS-CoV-2 infection. Most of them experienced mild (77[52.7%]) to moderate (41[28.1%]) symptoms. Increasing age (OR, 95%CI, p-value; 1.15, 1.05-1.25, 0.002), male sex (OR, 95%CI, p-value; 5.8, 3.2-9.8, <0.001), and diabetes (OR, 95%CI, p-value; 25.6, 2-327.2, 0.01) were the risk factor of having COVID-19. Female sex and diabetes were the risk factors for re-detectable positive SARS-CoV-2 infection. (OR, 95%CI, p-value; 0.24, 0.09-0.67, 0.006; 44, 8.9-218.7, <0.001 respectively). Most respondents suffered for 7-14 days. Total 98(67%) suffered from post-COVID fatigue.\n\nConclusionsThe physicians observed four surges in hospital admission and COVID-19 positivity rate. A significant number of the COVID-warrior became positive for SARS-CoV-2, had re-detectable positive SARS-CoV-2 infection, and suffered in the post-COVID-19 state.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Reaz Mahmud", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Sultana Shahana Banu", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Nusrat Sultana", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Farhana Binte Monayem", - "author_inst": "Sarkari Karmachari Hospital" - }, - { - "author_name": "Ponkaj Kanti Datta", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Mohammad Mahfuzul Hoque", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "S.M. Habibur Rahman Habib", - "author_inst": "DNCC dedicated COVID-19 Hospital" - }, - { - "author_name": "Joynal Abedin", - "author_inst": "DNCC dedicated COVID-19 Hospital" - }, - { - "author_name": "Md. Fakhrul Islam", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Md. Arifuzzaman", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Md Khairul Islam", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Sudip Ranjan Deb", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Ahmed Hossain Chowdhury", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Kazi Gias Uddin Ahmed", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Md. Titu Miah", - "author_inst": "Dhaka Medical College and Hospital" - }, - { - "author_name": "Md. Mujibur Rahman", - "author_inst": "Bangabandhu Sheikh Mujib Medical University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.14.22270845", "rel_title": "Quantitative, multiplexed, targeted proteomics for ascertaining variant specific SARS-CoV-2 antibody response", @@ -397809,6 +398727,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.14.22270940", + "rel_title": "Ethnic differences in COVID-19 mortality in the second and third waves of the pandemic in England during the vaccine roll-out: a retrospective, population-based cohort study", + "rel_date": "2022-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270940", + "rel_abs": "ObjectivesTo assess whether ethnic differences in COVID-19 mortality in England have continued into the third wave and to what extent differences in vaccination rates contributed to excess COVID-19 mortality after accounting for other risk factors.\n\nDesignCohort study of 28.8 million adults using data from the Office for National Statistics Public Health Data Asset.\n\nSettingPeople living in private households or communal establishments in England.\n\nParticipants28,816,020 adults (47% male) aged 30-100 years in 2020 (mean age = 56), who were present at the 2011 Census and alive on 8 December 2020.\n\nMain outcome measuresDeath involving COVID-19 during the second (8 December 2020 to 12 June 2021) and third wave (13 June 2021 to 1 December 2021) of the pandemic. We calculated hazard ratios (HRs) separately for males to females to summarise the association between ethnic group and death involving COVID-19 in each wave, sequentially adjusting for age, residence type, geographical factors, sociodemographic characteristics, pre-pandemic health, and vaccination status.\n\nResultsAge-adjusted HRs of death involving COVID-19 were higher for most ethnic minority groups than the White British group during both waves, particularly for groups with lowest vaccination rates (Bangladeshi, Pakistani, Black African and Black Caribbean). In both waves, HRs were attenuated after adjusting for geographical factors, sociodemographic characteristics, and pre-pandemic health. Further adjusting for vaccination status substantially reduced residual HRs for Black African, Black Caribbean, and Pakistani groups in the third wave. The only groups where fully-adjusted HRs remained elevated were the Bangladeshi group (men: 2.19, 95% CI 1.72 to 2.78; women: 2.12, 95% CI 1.58 to 2.86) and men from the Pakistani group (1.24, 95% CI 1.06 to 1.46).\n\nConclusionPublic health strategies to increase vaccination uptake in ethnic minority groups could reduce disparities in COVID-19 mortality that cannot be accounted for by pre-existing risk factors.\n\nWhat is already known on this topicEthnic minority groups in England have been disproportionately affected by the COVID-19 pandemic during the first and second waves.\n\nCOVID-19 vaccination uptake is also lower among many ethnic minority groups, particularly Bangladeshi, Black African, Black Caribbean, and Pakistani groups.\n\nThere is a paucity of research into whether ethnic disparities in COVID-19 mortality have continued into the third wave and the extent to which differences in vaccination uptake contribute to differences in COVID-19 mortality.\n\nWhat this study addsUsing linked data on 28.8 million adults in England, we find that rates of COVID-19 mortality have remained higher than the White British group for most ethnic minority groups during the vaccine roll-out, notably for the Bangladeshi, Black African, Black Caribbean, and Pakistani groups.\n\nAfter adjustment for geographical factors, sociodemographic characteristics, pre-pandemic health status, and vaccination status, the only groups with elevated rates of COVID-19 mortality during the third wave were the Bangladeshi group and men from the Pakistani group, suggesting that increasing vaccination uptake in ethnic minority groups could reduce ethnic disparities in COVID-19 mortality.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Matthew L Bosworth", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Tamanna Ahmed", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Tim Larsen", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Luke Lorenzi", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Jasper Morgan", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Raghib Ali", + "author_inst": "MRC Epidemiology Unit, University of Cambridge, School of Clinical Medicine" + }, + { + "author_name": "Peter Goldblatt", + "author_inst": "UCL Institute of Health Equity, Department of Epidemiology & Public Health, University College London" + }, + { + "author_name": "Nazrul Islam", + "author_inst": "Nuffield Department of Population Health, University of Oxford" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "Diabetes Research Centre, University of Leicester" + }, + { + "author_name": "Veena Raleigh", + "author_inst": "The King's Fund" + }, + { + "author_name": "Daniel Ayoubkhani", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Neil Bannister", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Myer Glickman", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Vahe Nafilyan", + "author_inst": "Office for National Statistics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.14.22270941", "rel_title": "Bayesian Space-time SIR modeling of Covid-19 in two US states during the 2020-2021 pandemic.", @@ -399413,25 +400402,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.11.22270841", - "rel_title": "Underdispersion in the reported Covid-19 case and death numbers may suggest data manipulations", - "rel_date": "2022-02-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270841", - "rel_abs": "We suggest a statistical test for underdispersion in the reported Covid-19 case and death numbers, compared to the variance expected under the Poisson distribution. Screening all countries in the World Health Organization (WHO) dataset for evidence of underdispersion yields 21 country with statistically significant underdispersion. Most of the countries in this list are known, based on the excess mortality data, to strongly undercount Covid deaths. We argue that Poisson underdispersion provides a simple and useful test to detect reporting anomalies and highlight unreliable data.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Dmitry Kobak", - "author_inst": "Tuebingen University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.11.22270854", "rel_title": "Persistence of SARS-CoV-2 immunity, Omicron's footprints, and projections of epidemic resurgences in South African population cohorts.", @@ -399707,6 +400677,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.12.22270851", + "rel_title": "Empirical evidence of transmission over a school-household network for SARS-CoV-2; exploration of transmission pairs stratified by primary and secondary school.", + "rel_date": "2022-02-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.12.22270851", + "rel_abs": "BackgroundChildren play a key role in the transmission of many infectious diseases. They have many of their close social encounters at home or at school. We hypothesized that most of the transmission of respiratory infections among children occur in these two settings and that transmission patterns can be predicted by a bipartite network of schools and households.\n\nAim and methodsTo confirm transmission over a school-household network, SARS-CoV-2 transmission pairs in children aged 4-17 years were analyzed by study year and primary/secondary school. Cases with symptom onset between the 1st of March 2021 and the 4th of April 2021 identified by source and contact-tracing in the Netherlands were included. In this period, primary schools were open and secondary school students attended class at least once per week. Within pairs, spatial distance between the postcodes was calculated as the Euclidean distance.\n\nResultsA total of 4,059 transmission pairs were identified; 51.9% between primary schoolers; 19.6% between primary and secondary schoolers; 28.5% between secondary schoolers. Most (68.5%) of the transmission for children in the same study year occurred at school. In contrast, most of the transmission of children from different study years (64.3%) and most primary-secondary transmission (81.7%) occurred at home. The average spatial distance between infections was 1.2km (median 0.4) for primary school pairs, 1.6km (median 0) for primary-secondary school pairs and 4.1km (median 1.2) for secondary school pairs.\n\nConclusionThe results provide evidence of transmission on a bipartite school-household network. Schools play an important role in transmission within study years, and households play an important role in transmission between study years and between primary and secondary schools. Spatial distance between infections in a transmission pair reflects the smaller school catchment area of primary schools versus secondary schools. Many of these observed patterns likely hold for other respiratory pathogens.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Senna C.J.L. van Iersel", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Jantien A. Backer", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Rolina D. van Gaalen", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Stijn P. Andeweg", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "James D. Munday", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "- RIVM COVID-19 epidemiology and surveillance group", + "author_inst": "" + }, + { + "author_name": "Albert Jan van Hoek", + "author_inst": "National Institute for Public Health and the Environment" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.10.22270735", "rel_title": "COVID-19 in Japan: insights from the first three months of the epidemic", @@ -401006,61 +402023,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.02.09.479786", - "rel_title": "Predicting Epitope Candidates for SARS-CoV-2", - "rel_date": "2022-02-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.09.479786", - "rel_abs": "Epitopes are short amino acid sequences that define the antigen signature to which an antibody binds. In light of the current pandemic, epitope analysis and prediction is paramount to improving serological testing and developing vaccines. In this paper, we leverage known epitope sequences from SARS-CoV, SARS-CoV-2 and other Coronaviridae and use those known epitopes to identify additional antigen regions in 62k SARS-CoV-2 genomes. Additionally, we present epitope distribution across SARS-CoV-2 genomes, locate the most commonly found epitopes, discuss where epitopes are located on proteins, and how epitopes can be grouped into classes. We also discuss the mutation density of different regions on proteins using a big data approach. We find that there are many conserved epitopes between SARS-CoV-2 and SARS-CoV, with more diverse sequences found in Nucleoprotein and Spike Glycoprotein.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Akshay Agarwal", - "author_inst": "IBM Research" - }, - { - "author_name": "Kristen L. Beck", - "author_inst": "IBM Research" - }, - { - "author_name": "Sara Capponi", - "author_inst": "IBM Research" - }, - { - "author_name": "Mark Kunitomi", - "author_inst": "IBM Research" - }, - { - "author_name": "Gowri Nayar", - "author_inst": "IBM Research" - }, - { - "author_name": "Edward Seabolt", - "author_inst": "IBM Research" - }, - { - "author_name": "Gandhar Mahadeshwar", - "author_inst": "IBM Research" - }, - { - "author_name": "Simone Bianco", - "author_inst": "IBM Almaden Research Center" - }, - { - "author_name": "Vandana Mukherjee", - "author_inst": "IBM Research" - }, - { - "author_name": "James Kaufman", - "author_inst": "IBM Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.02.10.479867", "rel_title": "Lyophilized mRNA-lipid nanoparticles vaccine with long-term stability and high antigenicity against SARS-CoV-2", @@ -401516,6 +402478,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.02.09.479842", + "rel_title": "The rise and fall of SARS-CoV-2 variants and the emergence of competing Omicron lineages", + "rel_date": "2022-02-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.09.479842", + "rel_abs": "In late December of 2019, high throughput sequencing technologies enabled rapid identification of SARS-CoV-2 as the etiological agent of COVID-19, and global sequencing efforts are now a critical tool for monitoring the ongoing spread and evolution of this virus. Here, we analyze a subset (n=83,204) of all publicly available SARS-CoV-2 genomes (n=~5.6 million) that were randomly selected, but equally distributed over the course of the pandemic. We plot the emergence and extinction of new variants of concern (VOCs) over time and show how this corresponds to the ongoing accumulation of mutations in SARS-CoV-2 genomes and individual proteins. While the accumulation of mutations generally follows a linear regression, non-synonymous mutations are significantly greater in Omicron viruses than in previous variants-especially in the spike and nucleoproteins-and these differences are more pronounced in a recently identified sub-lineage (BA.2) of Omicron.\n\nImportanceOmicron is the fifth SARS-CoV-2 variant to be designated a Variant of Concern (VOC) by the World Health Organization (WHO). Here we provide a retrospective analysis of SARS-CoV-2 variants and explain how the Omicron variant is distinct. Our work shows that the spike and nucleoproteins have accumulated the most mutations in Omicron variants, but that the accessory proteins of SARS-CoV-2 sequences are changing most rapidly relative to their size. Collectively, this \"Observation\" provides a concise overview of SARS-CoV-2 evolution, reveals mutational differences between two Omicron lineages, and highlights changes in the SARS-CoV-2 proteome that have been under reported.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tanner Roy Wiegand", + "author_inst": "Montana State University" + }, + { + "author_name": "Aidan McVey", + "author_inst": "Montana State University" + }, + { + "author_name": "Anna Nemudraia", + "author_inst": "Montana State University" + }, + { + "author_name": "Artem Nemudryi", + "author_inst": "Montana State University" + }, + { + "author_name": "Blake Wiedenheft", + "author_inst": "Montana State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2022.02.09.479755", "rel_title": "Cell delivery peptides for small interfering RNAs targeting SARS-CoV-2 new variants through a bioinformatics and deep learning design", @@ -403036,49 +404033,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.02.08.479664", - "rel_title": "SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export", - "rel_date": "2022-02-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.08.479664", - "rel_abs": "SARS-CoV-2 is a betacoronavirus and the etiological agent of COVID-19, a devastating infectious disease. Due to its far-reaching effect on human health, there is an urgent and growing need to understand the viral molecular biology of SARS-CoV-2 and its interaction with the host cell. SARS-CoV-2 encodes 9 predicted accessory proteins, which are presumed to be dispensable for in vitro replication, most likely having a role in modulating the host cell environment to aid viral replication. Here we show that the ORF6 accessory protein interacts with cellular Rae1 to inhibit cellular protein production by blocking mRNA export. We utilised cell fractionation coupled with mRNAseq to explore which cellular mRNA species are affected by ORF6 expression and show that ORF6 can inhibit the export of many mRNA including those encoding antiviral factors such as IRF1 and RIG-I. We also show that export of these mRNA is blocked in the context of SARS-CoV-2 infection. Together, our studies identify a novel mechanism by which SARS-CoV-2 can manipulate the host cell environment to supress antiviral responses, providing further understanding to the replication strategies of a virus that has caused an unprecedented global health crisis.\n\nAuthor SummarySARS-CoV-2 is the virus responsible for the current COVID-19 pandemic. Coronaviruses, like SARS-CoV-2, replicate their genome in the cytoplasm of the host cell by hijacking the cellular machinery. In addition to structural proteins and viral enzymes, SARS-CoV-2 encodes 9 accessory proteins. Although these are not required for in vitro replication, they are thought to modulate the host cell environment to favour viral replication. In this work, we show that the ORF6 accessory protein can supress cellular protein production by blocking mRNA nuclear export through interacting with the cellular protein Rae1, a known mRNA export factor. We also investigated which cellular mRNAs were retained in the nucleus when ORF6 was overexpressed. Interestingly, we found that ORF6 inhibited the export of many different mRNAs, including those encoding antiviral factors, like IRF1 and RIG-I, even in the absence of stimulation by interferon. Importantly, we found that the export of these mRNAs was similarly affected in the context of SARS-CoV-2 infection. Therefore, we believe we have identified a novel mechanism that SARS-CoV-2 uses to suppress antiviral responses in order to make the cell more permissive to infection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ross Hall", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Anabel Gued\u00e1n", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Melvyn W. Yap", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "George R. Young", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ruth Harvey", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jonathan P. Stoye", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Kate N. Bishop", - "author_inst": "The Francis Crick Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.08.479661", "rel_title": "N-acylethanolamine acid amide hydrolase is a novel target for drugs against SARS-CoV-2 and Zika virus", @@ -403498,6 +404452,181 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.08.22270674", + "rel_title": "Trajectories of Neurological Recovery 12 Months after Hospitalization for COVID-19: A Prospective Longitudinal Study", + "rel_date": "2022-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.08.22270674", + "rel_abs": "Background/ObjectivesLittle is known about trajectories of recovery 12-months after hospitalization for severe COVID.\n\nMethodsWe conducted a prospective, longitudinal cohort study of patients with and without neurological complications during index hospitalization for COVID-19 from March 10, 2020-May 20, 2020. Phone follow-up batteries were performed at 6- and 12-months post-COVID symptom onset. The primary 12-month outcome was the modified Rankin Scale (mRS) comparing patients with or without neurological complications using multivariable ordinal analysis. Secondary outcomes included: activities of daily living (Barthel Index), telephone Montreal Cognitive Assessment (t-MoCA) and Neuro-QoL batteries for anxiety, depression, fatigue and sleep. Changes in outcome scores from 6 to 12-months were compared using non-parametric paired-samples sign test.\n\nResultsTwelve-month follow-up was completed in N=242 patients (median age 65, 64% male, 34% intubated during hospitalization) and N=174 completed both 6- and 12-month follow-up. At 12-months 197/227 (87%) had [≥]1 abnormal metric: mRS>0 (75%), Barthel<100 (64%), t-MoCA[≤]18 (50%), high anxiety (7%), depression (4%), fatigue (9%) and poor sleep (10%). 12-month mRS scores did not differ significantly among those with (N=113) or without (N=129) neurological complications during hospitalization after adjusting for age, sex, race, pre-COVID mRS and intubation status (adjusted OR 1.4, 95% CI0.8-2.5), though those with neurological complications had higher fatigue scores (T-score 47 vs 44, P=0.037). Significant improvements in outcome trajectories from 6- to 12-months were observed in t-MoCA scores (56% improved, median difference 1 point, P=0.002), and Neuro-QoL anxiety scores (45% improved, P=0.003). Non-significant improvements occurred in fatigue, sleep and depression scores in 48%, 48% and 38% of patients, respectively. Barthel and mRS scores remained unchanged between 6 and 12-months in >50% of patients.\n\nDiscussionAt 12-months post-hospitalization for severe COVID, 87% of patients had ongoing abnormalities in functional, cognitive or Neuro-QoL metrics and abnormal cognition persisted in 50% of patients without a prior history of dementia/cognitive abnormality. Only fatigue severity differed significantly between patients with or without neurological complications during index hospitalization. However, significant improvements in cognitive (t-MoCA) and anxiety (Neuro-QoL) scores occurred in 56% and 45% of patients, respectively, between 6- to 12-months. These results may not be generalizable to those with mild/moderate COVID.", + "rel_num_authors": 40, + "rel_authors": [ + { + "author_name": "Jennifer A. Frontera", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Dixon Yang", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Chaitanya medircherla", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "samuel baskharoun", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "kristie bauman", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Lena Bell", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "dhristie bhagat", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "steven bondi", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "alexander chervinsky", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "levi dygert", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "benjamin fuchs", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "daniel gratch", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "lisena hasanaj", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "jennifer horng", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "joshua huang", + "author_inst": "NYU Langone Hospital" + }, + { + "author_name": "ruben jauregui", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Yuan Ji", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Ethan Kahn", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "ethan koch", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Jessica Lin", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "susan liu", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "anlys olivera", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "jonathan rosenthal", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "thomas snyder", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "rebecca stainman", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "daniel. talmasov", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "betsy thomas", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "eduard valdes", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Ting Zhou", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "yingrong zhu", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "ariane lewis", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "aaron lord", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "kara melmed", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "sharon meropol", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "sujata thawani", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "andrea troxel", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "shadi yaghi", + "author_inst": "Brown School of Medicine" + }, + { + "author_name": "laura balcer", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "thomas wisniewski", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Steven Galetta", + "author_inst": "NYU Grossman School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.02.08.22270685", "rel_title": "Where is Omicron? Comparison of SARS-CoV-2 RT-PCR and Antigen Test Sensitivity at Commonly Sampled Anatomic Sites Over the Course of Disease", @@ -405086,125 +406215,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.07.22270020", - "rel_title": "Post-marketing active surveillance of myocarditis and pericarditis following vaccination with COVID-19 mRNA vaccines in persons aged 12-39 years in Italy: a multi-database, self-controlled case series study", - "rel_date": "2022-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270020", - "rel_abs": "ObjectivesTo investigate the association between SARS-CoV-2 mRNA vaccines, BNT162b2 and mRNA-1273, and myocarditis/pericarditis.\n\nDesignSelf-Controlled Case Series study (SCCS) using national data on COVID-19 vaccination and emergency care/hospital admissions.\n\nSettingItalian Regions (Lombardia, Friuli Venezia Giulia, Veneto, Lazio).\n\nParticipants2,861,809 individuals, aged 12-39 years, vaccinated with the first doses of mRNA vaccines (2,405,759 BNT162b2 and 456,050 mRNA-1273) between 27 December 2020 and 30 September 2021.\n\nMain outcome measuresFirst diagnosis of myocarditis/pericarditis within the study period. The incidence of events in the exposure risk periods (0-21 days from the vaccination day, subdivided in three equal intervals) for first and second dose was compared with baseline period. The SCCS model was fitted using conditional Poisson regression to estimate Relative Incidences (RI) and Excess of Cases (EC) per 100,000 vaccinated by dose, age, gender and brand.\n\nResultsDuring the study period, 441 participants aged 12-39 years developed myocarditis/pericarditis (346 BNT162b2 and 95 mRNA-1273). During the 21-day risk interval there were 114 cases of myocarditis/pericarditis (74 BNT162b2 and 40 mRNA-1273) corresponding to a RI of 1.27 (0.87-1.85) and 2.16 (1.50-3.10) after first and second dose, respectively.\n\nAn increased risk of myocarditis/pericarditis at [0-7) days was observed after first [RI=6.55; 95% Confidence Interval (2.73-15.72); EC per 100,000 vaccinated=2.0 (1.5-2.3)] and second dose [RI=7.59 (3.26-17.65); EC=5.5 (4.4-5.9)] of mRNA-1273 and after second dose of BNT162b2 [RI=3.39 (2.02-5.68); EC=0.8 (0.6-1.0)]. In males, an increased risk at [0-7) days was observed after first [RI=12.28, 4.09-36.83; EC=3.8 (3.1-4.0)] and second dose [RI=11.91 (3.88-36.53); EC=8.8 (7.2-9.4)] of mRNA-1273 and after second dose of BNT162b2 [RI=3.45 (1.78-6.68); EC=1.0 (0.6-1.2)]. In females, an increased risk at [0-7) days was observed after second dose of BNT162b2 [RI=3.38 (1.47-7.74); EC=0.7 (0.3-0.9)]. At [0-7) days an increased risk following second dose of BNT162b2 was observed in the 12-17 years old [RI=5.74, (1.52-21.72); EC=1.7 (0.7-1.9)] and in 18-29 years old [RI=4.02 (1.81-8.91); EC=1.1 (0.6-1.3)]. At [0-7) days an increased risk after first [RI=7.58 (2.62-21.94); EC=3.5 (2.4-3.8)] and second [RI=9.58 (3.32-27.58); EC=8.3 (6.7-9.2)] dose of mRNA-1273 was found in 18-29 years old and after first dose in 30-39 years old [RI=6.57 (1.32-32.63); EC=1.0 (0.3-1.1)].\n\nConclusionsThis population-based study indicates that mRNA vaccines were associated with myocarditis/pericarditis in the population younger than 40 years, whereas no association was observed in older subjects. The risk increased after the second dose and in the youngest for both vaccines, remained moderate following vaccination with BNT162b2, while was higher in males following vaccination with mRNA-1273. The public health implication of these findings should be weighed in the light of the overall efficacy and safety profile of both vaccines.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Marco Massari", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Stefania Spila-Alegiani", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Cristina Morciano", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Matteo Spuri", - "author_inst": "Department of Infectious Diseases, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Pasquale Marchione", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Patrizia Felicetti", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Valeria Belleudi", - "author_inst": "Department of Epidemiology ASL Roma, Lazio Regional Health Service, Rome, Italy" - }, - { - "author_name": "Francesca Romana Poggi", - "author_inst": "Department of Epidemiology ASL Roma, Lazio Regional Health Service, Rome, Italy" - }, - { - "author_name": "Marco Lazzeretti", - "author_inst": "Business Intelligence, Data Science e Data Analysis, ARIA SpA, Milan, Italy" - }, - { - "author_name": "Michele Ercolanoni", - "author_inst": "Business Intelligence, Data Science e Data Analysis, ARIA SpA, Milan, Italy" - }, - { - "author_name": "Elena Clagnan", - "author_inst": "ARCS Azienda Regionale di Coordinamento per la Salute, Udine, Italy" - }, - { - "author_name": "Emanuela Bovo", - "author_inst": "Veneto Tumour Registry, Azienda Zero, Padova, Italy" - }, - { - "author_name": "Gianluca Trifir\u00f2", - "author_inst": "Department of Diagnostics and Public Health, University of Verona, Verona, Italy" - }, - { - "author_name": "Ugo Moretti", - "author_inst": "Department of Diagnostics and Public Health, University of Verona, Verona, Italy" - }, - { - "author_name": "Giuseppe Monaco", - "author_inst": "Department of Health of Lombardy Region, Epidemiology Observatory, Milan, Italy" - }, - { - "author_name": "Olivia Leone", - "author_inst": "Department of Health of Lombardy Region, Epidemiology Observatory, Milan, Italy" - }, - { - "author_name": "Roberto Da Cas", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - }, - { - "author_name": "Fiorella Petronzelli", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Loriana Tartaglia", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Nadia Mores", - "author_inst": "Institute of Pharmacology, Pharmacovigilance, Policlinico Universitario A. Gemelli, Catholic University of Sacred Heart, Rome, Italy" - }, - { - "author_name": "Giovanna Zanoni", - "author_inst": "Immunology Unit, University Hospital, Verona, Italy" - }, - { - "author_name": "Paola Rossi", - "author_inst": "Direzione centrale salute, politiche sociali e disabilita, Friuli Venezia Giulia Region, Trieste, Italy" - }, - { - "author_name": "Sarah Samez", - "author_inst": "Centro Regionale di Farmacovigilanza, Friuli Venezia Giulia Region, Trieste, Italy" - }, - { - "author_name": "Cristina Zappetti", - "author_inst": "Direzione centrale salute, politiche sociali e disabilita, Friuli Venezia Giulia Region, Trieste, Italy" - }, - { - "author_name": "Anna Rosa Marra", - "author_inst": "Department of post-marketing surveillance, Agenzia Italiana del Farmaco (Italian Medicines Agency), Rome, Italy" - }, - { - "author_name": "Francesca Menniti-Ippolito", - "author_inst": "National Centre for Drug Research and Evaluation, Istituto Superiore di Sanit\u00e0 (National Institute of Health), Rome, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.07.22270596", "rel_title": "Role of Covid vaccine in determining ICU admission and death due to Covid -19 in Tamil Nadu", @@ -405484,6 +406494,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.07.479352", + "rel_title": "A highly attenuated SARS-CoV-2 related pangolin coronavirus variant has a 104nt deletion at the 3'-terminus untranslated region", + "rel_date": "2022-02-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.07.479352", + "rel_abs": "SARS-CoV-2 related coronaviruses (SARS-CoV-2r) from Guangdong and Guangxi pangolins have been implicated in the emergence of SARS-CoV-2 and future pandemics. We previously reported the culture of a SARS-CoV-2r GX_P2V from Guangxi pangolins. Here we report the GX_P2V isolate rapidly adapted to Vero cells by acquiring two genomic mutations: an alanine to valine substitution in the nucleoprotein and a 104-nucleotide deletion in the hypervariable region (HVR) of the 3-terminus untranslated region (3-UTR). We further report the characterization of the GX_P2V variant in in vitro and in vivo infection models. In cultured Vero and BGM cells, the GX_P2V variant produced minimal cell damage and small plaques. The GX_P2V variant infected golden hamsters and BALB/c mice but was highly attenuated. Golden hamsters infected intranasally had a short duration of productive infection. These productive infections induced neutralizing antibodies against pseudoviruses of GX_P2V and SARS-CoV-2. Collectively, our data show that the GX_P2V variant is highly attenuated in in vitro and in vivo infection models. Attenuation of the variant is likely due to the 104-nt deletion in the HVR in the 3-UTR. This study furthers our understanding of pangolin coronaviruses pathogenesis and provides novel insights for the design of live attenuated vaccines against SARS-CoV-2.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Shanshan Lu", + "author_inst": "Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, B" + }, + { + "author_name": "Shengdong Luo", + "author_inst": "Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China" + }, + { + "author_name": "Chang Liu", + "author_inst": "Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, B" + }, + { + "author_name": "Muli Li", + "author_inst": "National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Me" + }, + { + "author_name": "Xiaoping An", + "author_inst": "Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, B" + }, + { + "author_name": "Mengzhe Li", + "author_inst": "Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, B" + }, + { + "author_name": "Jun Hou", + "author_inst": "Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China" + }, + { + "author_name": "Huahao Fan", + "author_inst": "Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, B" + }, + { + "author_name": "Panyong Mao", + "author_inst": "Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China" + }, + { + "author_name": "Yi-Gang Tong", + "author_inst": "Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, B" + }, + { + "author_name": "Lihua Song", + "author_inst": "Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, B" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.07.22270274", "rel_title": "Clinical and Economic Impact of COVID-19 on Plantation Workers: Preliminary Results from the Guatemala Agricultural Workers and Respiratory Illness Impact (AGRI) Study", @@ -407196,41 +408265,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.02.05.22270416", - "rel_title": "Characteristics and preparedness for COVID-19 outbreaks of Australian residential aged care facilities: A cross-sectional survey", - "rel_date": "2022-02-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.05.22270416", - "rel_abs": "ObjectiveTo provide an overview of Australian residential aged care facilities (RACFs) COVID-19 outbreak preparedness and responses, 12 months after the pandemic began in early 2020.\n\nMethodsA cross-sectional survey of RACF managers was conducted as part of an overview of COVID-19 experience during 2020. Survey questions were based on findings of previous outbreak reviews.\n\nResultsComparison with available data from the Australian Institute for Health and Welfare suggested that survey respondents (n=331) were a representative sample. Almost all RACFs had outbreak management plans, including provision for a surge workforce. However, anticipated staff replacements fell short of those often required during outbreaks. Staff of most (83%) RACFs had completed online infection control training, and a smaller proportion (73%) face-to-face training, by the time of the survey. Exploratory analyses to identify RACF characteristics associated with increased outbreak risk found a strong association with location in Victoria (adjusted risk ratio [aRR] 12.8) where most community transmission occurred during 2020. The only other association was an increased risk in facilities where all staff had not completed face-to-face infection control training (aRR 2.1). Respondents ranked leadership and management; planning and preparation; and infection control as the top three of seven critical lines of defence against COVID-19.\n\nConclusionSurvey results suggest that, in early 2021, most Australian RACFs were better prepared for the ongoing risk of COVID-19 than in 2020. Continued implementation of the Aged Care Royal Commissions recommendations is needed to ensure the aged care sector is prepared for future infectious disease emergencies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Gwendolyn L Gilbert", - "author_inst": "Sydney Institute for Infectious Diseases, The University of Sydney" - }, - { - "author_name": "Jenna Smith", - "author_inst": "Sydney Health Literacy Lab, Sydney School of Public Health, The University of Sydney" - }, - { - "author_name": "Erin Cvejic", - "author_inst": "Sydney School of Public Health, The University of Sydney" - }, - { - "author_name": "Alan Lilly", - "author_inst": "Australian Catholic University" - }, - { - "author_name": "Kirsten McCaffery", - "author_inst": "Sydney Health Literacy Lab, Sydney School of Public Health, The University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.02.06.22270482", "rel_title": "Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City", @@ -407662,6 +408696,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.06.22270565", + "rel_title": "Cumulative seroprevalence among healthcare workers after the first wave of the COVID-19 pandemic in El Salvador, Central America.", + "rel_date": "2022-02-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.06.22270565", + "rel_abs": "BackgroundThe impact of novel coronavirus disease 2019 (COVID-19) on healthcare workers (HCWs) has been under-evaluated in Central America. We performed a seroepidemiological survey at a tertiary healthcare facility in El Salvador, where a large number of confirmed and far more suspected cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infected HCWs had been documented during the first wave of the pandemic.\n\nMethodsDuring January-February 2021, a total 973 HCWs were tested for SARS-CoV-2 antibodies. Participants completed a questionnaire asking of their demographic data. Occupational risk was assessed by statistically comparing the seropositivity rates among different occupational categories.\n\nResultsOverall seroprevalence in HCWs reached 52.6% (512 of 973). Of the seropositive individuals, 61.7% (316 of 512) had experienced a documented COVID-19 diagnosis, while the remaining 38.3% (196 of 512) were unrecognized seroconversions. Differences in seropositivity rates existed between occupational categories; nurses demonstrated the highest at 63.8% (222 of 348, risk ratio 1.44, p < 0.0001), followed by auxiliary HCWs assigned to patient-related work (55.9%, 52 of 93), and medical doctors (46.7%, 50 of 107). Several non-patient-related professions showed above-average seroprevalence, suggesting substantial SARS-CoV-2 contacts outside the workplace: 60.0% (6 of 10) and 68.0% (17 of 25) for nutritionists and pharmacists, respectively.\n\nConclusionsSARS-CoV-2 seroprevalence exceeded 50% among HCWs in El Salvador, with disparity among occupational categories with different workplace exposure risks. Importance of not only nosocomial infection prevention but also screening for transmissions having occurred outside the workplace were highlighted to efficiently control nosocomial spreads during a pandemic wave.\n\nKey pointsHealthcare workers in El Salvador were tested for SARS-CoV-2 antibodies. Seroprevalence reached 52.6%, with disparity among occupation; nurses ranked highest at 63.8% seropositivity. Alongside nosocomial transmissions, high seroprevalence associated with non-patient-related work suggested substantial SARS-CoV-2 contacts outside the workplace.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yu Nakagama", + "author_inst": "Osaka City University" + }, + { + "author_name": "Maria-Virginia Rodriguez-Funes", + "author_inst": "National Rosales Hospital" + }, + { + "author_name": "Rhina Dominguez", + "author_inst": "El Salvador National Institute of Health" + }, + { + "author_name": "Katherine-Sofia Candray-Medina", + "author_inst": "Osaka City University" + }, + { + "author_name": "Naoto Uemura", + "author_inst": "Oita University" + }, + { + "author_name": "Evariste Tshibangu-Kabamba", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yuko Nitahara", + "author_inst": "Osaka City University" + }, + { + "author_name": "Natsuko Kaku", + "author_inst": "Osaka City University" + }, + { + "author_name": "Akira Kaneko", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yasutoshi Kido", + "author_inst": "Osaka City University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.06.22270558", "rel_title": "Clinical Severity and mRNA Vaccine Effectiveness for Omicron, Delta, and Alpha SARS-CoV-2 Variants in the United States: A Prospective Observational Study", @@ -409494,89 +410583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.04.22270087", - "rel_title": "ARTIFICIAL INTELLIGENCE TOOLS FOR EFFECTIVE MONITORING OF POPULATION AT DISTANCE DURING COVID-19 PANDEMIC. RESULTS FROM AN ITALIAN PILOT FEASIBILITY STUDY (RICOVAI-19 STUDY).", - "rel_date": "2022-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.04.22270087", - "rel_abs": "In order to reduce the burden on healthcare systems and in particular to support an appropriate way to the Emergency Department (ED) access, home tele-monitoring patients was strongly recommended during the COVID-19 pandemic. Furthermore, paper from numerous groups has shown the potential of using data from wearable devices to characterize each individuals unique baseline, identify deviations from that baseline suggestive of a viral infection, and to aggregate that data to better inform population surveillance trends. However, no evidence about usage of Artificial Intelligence (AI) applicatives on digitally data collected from patients and doctors exists. With a growing global population of connected wearable users, this could potentially help to improve the earlier diagnosis and management of infectious individuals and improving timeliness and precision of tracking infectious disease outbreaks.\n\nDuring the study RICOVAI-19 (RICOVero ospedaliero con strumenti di Artificial Intelligence nei pazienti con COVid-19) performed in the Marche Region, Italy, we evaluated 129 subjects monitored at home in a six-months period between March 22, 2021 and October 22, 2021. During the monitoring, personal on demand health technologies were used to collect clinical and vital data in order to feed the database and the machine learning engine. The AI output resulted in a clinical stability index (CSI) which enables the system to deliver suggestions to the population and doctors about how intervene.\n\nResults showed the beneficial influence of CSI for predicting clinical classes of subjects and identifying who of them need to be admitted at ED. The same pattern of results was confirming the alert included in the decision support system in order to request further testing or clinical information in some cases.\n\nIn conclusion, our study does support a high impact of AI tools on COVID-19 outcomes to fight this pandemic by driving new approaches to public awareness.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Marco Mazzanti", - "author_inst": "Barts Heart Centre Foundation Trust, Cardiac Imaging Department, London, United Kngdom" - }, - { - "author_name": "Aldo Salvi", - "author_inst": "Dipartimento di Emergenza, Medicina Interna, di urgenza e subintensiva, SOD Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Stefania Giacomini", - "author_inst": "General Physician, Medicina Generale di territorio, Azienda sanitaria Unica Regionale (ASUR), Offagna (Ancona), Italy" - }, - { - "author_name": "Elisabetta Perazzini", - "author_inst": "General Physician, Medicina Generale di territorio, Azienda sanitaria Unica Regionale (ASUR), Offagna (Ancona), Italy" - }, - { - "author_name": "Cinzia Nitti", - "author_inst": "Medicina di urgenza e subintensiva, SOD Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Susanna Contucci", - "author_inst": "Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Massimo D'Angelo", - "author_inst": "AI for Health, Almawave S.p.A., Rome, Italy" - }, - { - "author_name": "Danilo Ballanti", - "author_inst": "AI for Health, Almawave S.p.A., Rome, Italy" - }, - { - "author_name": "Domenico Ursino", - "author_inst": "Computer Engineering, Rector's delegate for ICT services DII, Universita' Politecnica delle Marche, Ancona, Italy" - }, - { - "author_name": "Matteo Marcosignori", - "author_inst": "Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Raniero Romagnoli", - "author_inst": "AI for Health, Almawave S.p.A., Rome, Italy" - }, - { - "author_name": "Marcello Tavio", - "author_inst": "Divisione di Malattie Infettive, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Andrea Giacometti", - "author_inst": "Clinica di Malattie Infettive, Universita' Politecnica delle Marche, Ancona, Italy" - }, - { - "author_name": "Serena Tomassetti", - "author_inst": "Pronto Soccorso e OBI, Ospedali Riuniti, Ancona, Italy" - }, - { - "author_name": "Riccardo Bonazzi", - "author_inst": "Medical Division, Vivisol srl, Milan, Italy" - }, - { - "author_name": "Matteo Maccioni", - "author_inst": "Ehealth Engineering Lab, Aditech-Adilife srl, Ancona, Italy" - }, - { - "author_name": "Lina Zuccatosta", - "author_inst": "Divisione di Pneumologia, Ospedali Riuniti, Ancona, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.05.22269021", "rel_title": "Wastewater Surveillance of U.S. Coast Guard Installations and Seagoing Military Vessels to Mitigate the Risk of COVID-19 Outbreaks", @@ -409948,6 +410954,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.05.478644", + "rel_title": "A scalable pipeline for SARS-CoV-2 replicon construction based on de-novo synthesis", + "rel_date": "2022-02-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.05.478644", + "rel_abs": "Replicons are synthetic viral RNA molecules that recapitulate the self-replicating activities of the virus but are missing its infectivity potential. Here, we report on a scalable pipeline to generate a replicon of any SARS-CoV-2 strain using de-novo synthesis. Our pipeline relies only on publicly available sequencing data without requiring access to any material, simplifying logistical and bureaucratic issues of sample acquisition. In addition, our system retains the nucleotide sequence of most of the SARS-CoV-2 full genome and therefore better captures its underlying genomic and biological functions as compared to the popular pseudotypes or any replicon system published to-date. We utilized our system to synthesize a SARS-CoV-2 non-infectious version of the Beta strain. We then confirmed that the resulting RNA molecules are non-infectious and safe to handle in a BSL2/CL2 facility. Finally, we show that our replicon can be specifically inhibited by molnupiravir and RNAi treatments, demonstrating its utility for drug research and development.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ahmet Can Berkyurek", + "author_inst": "Eleven Therapeutics" + }, + { + "author_name": "Elian Lee", + "author_inst": "Twist Bioscience" + }, + { + "author_name": "Omer Weissbrod", + "author_inst": "Eleven Therapeutics" + }, + { + "author_name": "Roni Rasnic", + "author_inst": "Eleven Therapeutics" + }, + { + "author_name": "Ilaria Falciatori", + "author_inst": "Eleven Therapeutics" + }, + { + "author_name": "Siyuan Chen", + "author_inst": "Twist Bioscience" + }, + { + "author_name": "Yaniv Erlich", + "author_inst": "Eleven Therapeutics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "synthetic biology" + }, { "rel_doi": "10.1101/2022.02.03.22270182", "rel_title": "Humoral Antibody Kinetics with ChAdOx1-nCOV (CovishieldTM) and BBV-152 (CovaxinTM) Vaccine among Indian Healthcare workers: A 6-month Longitudinal Cross-sectional Coronavirus Vaccine-induced Antibody Titre (COVAT) Study", @@ -411588,41 +412637,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.03.22269712", - "rel_title": "Comparative evaluation of oral lesions: Tale - the Covid 19 Tells", - "rel_date": "2022-02-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22269712", - "rel_abs": "Introduction & ObjectivesThe COVID-19 pandemic has been raging across the globe since early January 2020. India has reported over 27 million cases and more than 3, 00,000 deaths. This study was planned to analyze the differences in demographic, clinical features and oral manifestations of COVID 19 patients hospitalized during COVID-19 pandemic.\n\nMethodsThis observational pilot study had total 36 participants, 12 each of mild, moderate and severe RT-PCR positive COVID cases hospitalized during COVID 19 pandemic. All demographic, clinical features, treatment details and oral manifestations were noted from first day of admission to hospital till treatment completion with follow up of minimum 7 days.\n\nResultsMean age of the patients was 39.44 {+/-}9.13 years with M: F ratio of 5:4. Most common clinical presentation was fever, shortness of breath and treatment involved was symptomatic with supplemental oxygen & mechanical ventilation. Most common oral site involved was tongue & oral lesions observed were herpes labialis, mucositis, burning sensation, dryness of oral cavity, angular chelitis, aphthous ulcers, geographic tongue, fissuring of tongue, candidiasis, coated tongue, sublingual varicosity, & scalloped tongue.\n\nInterpretation and ConclusionAll demographic, clinical and oral manifestations were significantly different in mild, moderate and severe cases of covid hospitalized patients. Though clinical symptoms were improved, oral lesions were worsened. Oral Lesions seen in covid patients were associated with multiple drug therapy for illness along with poor oral hygiene, but further etiology for lesions needs to be evaluated. Sublingual varicosity was observed in our hospitalised covid patients, but large sample observation is required for confirmation of findings and may be an early oral feature for covid detection. Prevention is always better than cure, so all patients positive for Covid should have a full mouth examination. Oral health should be priority during overall management of COVID patients and dentists should be a part of Covid management team.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rashmi P. Bhavasar", - "author_inst": "K.M.SHAH DENTAL COLLEGE AND HOSPITAL, SUMANDEEP VIDYAPEETH DEEMED TO BE UNIVERSITY, PIPARIA, VADODARA, GUJARAT." - }, - { - "author_name": "Namratha A Ajith", - "author_inst": "K M SHAH DENTAL COLLEGE AND HOSPITAL, SUMANDEEP DEEMED TO BE UNIVERSITY, VADODARA, GUJARAT, INDIA" - }, - { - "author_name": "Rahul Prakash Bhavasar", - "author_inst": "Dr. Ulhas Patil Medical College and Hospital, Jalgaon, Maharashtra, India" - }, - { - "author_name": "Arti Dhawal", - "author_inst": "SBSK&MIRC, Dhiraj Hospital, Sumandeep Vidyapeeth Deemed to be University, Vadodara, Gujarat" - }, - { - "author_name": "Vivek Vaswani", - "author_inst": "SBKS&MIRC, Dhiraj Hospital, Sumandeep Vidyapeeth Deemed to be University, Vadodara, Gujarat" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2022.02.02.22269952", "rel_title": "Serious hospital events following symptomatic infection with Sars-CoV-2 Omicron and Delta variants: an exposed-unexposed cohort study in December 2021 from the COVID-19 surveillance databases in France", @@ -411890,6 +412904,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.02.03.22270311", + "rel_title": "Psychological, endocrine and polygenic predictors of emotional well-being during the COVID-19 pandemic", + "rel_date": "2022-02-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270311", + "rel_abs": "The COVID-19 pandemic severely affected the lives of families, and the well-being of children and their parent. Prenatal stress, dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis, and genetic factors might influence individuals well-being in the presence of a major stressor such as the COVID-19 pandemic.\n\nThe present work is part of an ongoing birth cohort study and aims to investigate maternal perceived stress, early childhood HPA axis activity, and polygenic risk scores (PRSs) as predictors of emotional well-being during the COVID-19 pandemic. All participants are part of the ongoing birth cohort study POSEIDON. Emotional well-being of children (n=263) and mothers (n=241) was assessed during the COVID-19 pandemic using the CRISIS questionnaire in two waves between June 2020 and February 2021. Associations of well-being with previously assessed maternal perceived stress, childrens salivary and morning urine cortisol at 45 months, PRSs for depression, schizophrenia, loneliness were investigated.\n\nA positive association between the childrens and mothers emotional well-being was found. Lower emotional well-being was observed in both children and mothers during the pandemic compared to before. Childrens emotional well-being improved over the course of the pandemic. Prenatally assessed maternal perceived stress was associated with a decrease in childrens but not in the mothers well-being. Cortisol measures and PRSs were not significantly associated with emotional wellbeing.\n\nThe present study confirms that emotional well-being of children and mothers are linked, and were negatively affected by the COVID-19 pandemic, with differences in development over time.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Thao Nguyen", + "author_inst": "Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Lea Zillich", + "author_inst": "Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Ge" + }, + { + "author_name": "Metin Cetin", + "author_inst": "Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Ge" + }, + { + "author_name": "Alisha S.M. Hall", + "author_inst": "Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Ge" + }, + { + "author_name": "Jerome C. Foo", + "author_inst": "Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Ge" + }, + { + "author_name": "Lea Sirignano", + "author_inst": "Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Ge" + }, + { + "author_name": "Josef Frank", + "author_inst": "Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Ge" + }, + { + "author_name": "Tabea S. Send", + "author_inst": "Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Maria Gilles", + "author_inst": "Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Marcella Rietschel", + "author_inst": "Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Ge" + }, + { + "author_name": "Michael Deuschle", + "author_inst": "Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Germany" + }, + { + "author_name": "Fabian Streit", + "author_inst": "Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Ge" + }, + { + "author_name": "Stephanie H. Witt", + "author_inst": "Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, J5, 68159 Mannheim, Ge" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.02.02.22270287", "rel_title": "Risk factors for severe COVID-19 differ by age: a retrospective study of hospitalized adults", @@ -413502,65 +414583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.02.22270295", - "rel_title": "Real-life performance of a COVID-19 rapid antigen detection test targeting the SARS-CoV-2 nucleoprotein for diagnosis of COVID-19 due to the Omicron variant", - "rel_date": "2022-02-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270295", - "rel_abs": "ObjectivesIt has been suggested that rapid antigen detection assays (RADT) may perform suboptimally in terms of sensitivity for the diagnosis of SARS-CoV-2 Omicron variant infection. To address this issue, we conducted a prospective study in primary health centers to evaluate the clinical performance of the Panbio COVID-19 Ag Rapid Test Device in nasopharyngeal specimens (NP) carried out at the point of care.\n\nMethodsWe recruited 244 patients (median age, 40 years; range 2-96; 141 female) with clinical suspicion of COVID-19 (232 adults and 12 children). 228/244 patients had been fully vaccinated (two doses) with licensed COVID-19 vaccines prior to recruitment. Most patients (222/244) were SARS-CoV-2 naive prior to enrollment. Patients were tested by RT-PCR and RADT within 5 days since symptoms onset.\n\nResults126 patients (51.6%) tested positive by both RT-PCR and RADT, 90 patients (36.8%) returned negative results by both assays and 28 patients (11.4%) yielded discordant results (RT-PCR+/RADT-). No patients tested RT-PCR-/RADT+. Overall specificity and sensitivity of RADT was 100% (95% CI, 95.9-100%) and 81.8% (95% CI, 75-87.1%) respectively. The sensitivity of the assay increased from 79.6% (95% CI, 66.4-88.5) when considering specimens collected at days 0-1 after symptoms onset, to 86.4% (95% CI, 66.7-95.3) when grouping the specimens obtained on days 4-5.\n\nConclusionThe Panbio COVID-19 Ag Rapid Test Device perform well ([≥]80% sensitivity) as a point-of-care test for early diagnosis of COVID-19 due to the Omicron variant in primary healthcare centers.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Paul de Michelena", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Ignacio Torres", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Angela Ramos-Garcia", - "author_inst": "Health Care center Benimaclet, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Victoria Gosalbes", - "author_inst": "Health Care center Salvador Pau, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Nadia Ruiz", - "author_inst": "Health Care center Serreria, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Ana Sanmartin", - "author_inst": "Primary Health Directorate, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Pilar Botija", - "author_inst": "Primary Health Directorate, Health Department Clinico-Malvarrosa, Valencia, Spain." - }, - { - "author_name": "Sandrine Puojois", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Dixie Huntley", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Eliseo Albert", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "David Navarro", - "author_inst": "Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.01.22270285", "rel_title": "Association study of HLA with the kinetics of SARS-CoV-2 spike specific IgG antibody responses to BNT162b2 mRNA vaccine", @@ -413892,6 +414914,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.31.478564", + "rel_title": "ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data", + "rel_date": "2022-02-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.31.478564", + "rel_abs": "Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which, together with the joining genes (IGHJ), diversity genes (IGHD), constant genes (IGHC) and immunoglobulin light chains, code for antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype through the use of standard short read sequencing technologies. Here we introduce ImmunoTyper-SR, an algorithmic method for genotype and CNV analysis of the germline IGHV genes using Illumina whole genome sequencing (WGS) data. ImmunoTyper-SR is based on a novel combinatorial optimization formulation that aims to minimize the total edit distance between reads and their assigned IGHV alleles from a given database, with constraints on the number and distribution of reads across each called allele. We have validated ImmunoTyper-SR on 12 individuals with Illumina WGS data from the 1000 Genomes Project, whose IGHV allele composition have been studied extensively through the use of long read and targeted sequencing platforms, as well as nine individuals from the NIAID COVID Consortium who have been subjected to WGS twice. We have then applied ImmunoTyper-SR on 585 samples from the NIAID COVID Consortium to investigate associations between distinct IGHV alleles and anti-type I IFN autoantibodies which have been linked to COVID-19 severity.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Michael Ford", + "author_inst": "National Cancer Institute" + }, + { + "author_name": "Ananth Hari", + "author_inst": "University of Maryland" + }, + { + "author_name": "Oscar Rodriguez", + "author_inst": "University of Louisville" + }, + { + "author_name": "Junyan Xu", + "author_inst": "National Cancer Institute" + }, + { + "author_name": "Justin Lack", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Cihan Oguz", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Yu Zhang", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Sarah Weber", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Mary Magliocco", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Jason Barnett", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Sandhya Xirasagar", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Smilee Samuel", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Luisa Imberti", + "author_inst": "ASST Spedali Civili di Brescia" + }, + { + "author_name": "Paolo Bonfanti", + "author_inst": "University of Milano-Bicocca-Fondazione MBBM" + }, + { + "author_name": "Andrea Biondi", + "author_inst": "University of Milano-Bicocca-Fondazione MBBM" + }, + { + "author_name": "Clifton Dalgard", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Stephen Chanock", + "author_inst": "National Cancer Institute" + }, + { + "author_name": "Lindsey Rosen", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Steven Holland", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Helen Su", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Luigi Notarangelo", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Uzi Vishkin", + "author_inst": "University of Maryland" + }, + { + "author_name": "Corey Watson", + "author_inst": "University of Louisville" + }, + { + "author_name": "Cenk Sahinalp", + "author_inst": "NCI" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.01.31.478415", "rel_title": "Toward an atomistic model of SARS-CoV-2", @@ -415224,49 +416357,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.01.31.478460", - "rel_title": "A Genetically Encoded BRET-based SARS-CoV-2 Mpro Protease Activity Sensor", - "rel_date": "2022-02-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.31.478460", - "rel_abs": "The SARS-CoV-2 main protease, Mpro, is critical for its replication and is an appealing target for designing anti-SARS-CoV-2 agents. In this regard, a number of assays have been developed based on its cleavage sequence preferences to monitor its activity. These include the usage of Fluorescence Resonance Energy Transfer (FRET)-based substrates in vitro and a FlipGFP reporter, one which fluoresces after Mpro-mediated cleavage, in live cells. Here, we have engineered a pair of genetically encoded, Bioluminescence Resonance Energy Transfer (BRET)-based sensors for detecting SARS-CoV-2 Mpro proteolytic activity in living host cells as well as in vitro assays. The sensors were generated by sandwiching Mpro N-terminal autocleavage sites, either AVLQSGFR (short) or KTSAVLQSGFRKME (long), in between the mNeonGreen and nanoLuc proteins. Co-expression of the sensor with the Mpro in live cells resulted in its cleavage in a dose- and time-dependent manner while mutation of the critical C145 residue (C145A) in Mpro completely abrogated the sensor cleavage. Importantly, the BRET-based sensors displayed increased sensitivities and specificities as compared to the recently developed FlipGFP-based Mpro sensor. Additionally, the sensors recapitulated the inhibition of Mpro by the well-characterized pharmacological agent GC376. Further, in vitro assays with the BRET-based Mpro sensors revealed a molecular crowding-mediated increase in the rate of Mpro activity and a decrease in the inhibitory potential of GC376. The sensor developed here will find direct utility in studies related to drug discovery targeting the SARS-CoV-2 Mpro and functional genomics application to determine the effect of sequence variation in Mpro.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Anupriya M Geethakumari", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Wesam S Ahmed", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Saad H Rasool", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Asma H Fatima", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "S M Nasir Uddin", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Mustapha H Aouida", - "author_inst": "Hamad Bin Khalifa University" - }, - { - "author_name": "Kabir H Biswas", - "author_inst": "Hamad Bin Khalifa University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.01.30.478380", "rel_title": "Using Unassigned NMR Chemical Shifts to Model RNA Secondary Structure", @@ -415586,6 +416676,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.01.31.22270015", + "rel_title": "Emergency department utilization and hospitalizations for ambulatory care sensitive conditions among unattached people actively seeking a primary care provider during the COVID-19 pandemic: a retrospective cohort study", + "rel_date": "2022-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.31.22270015", + "rel_abs": "BackgroundPrimary care (PC) attachment improves healthcare access and prevention and management of chronic conditions. Yet, growing proportions of Canadians are unattached, signing-up on provincial waitlists. Understanding variations in healthcare utilization during COVID-19, and among potentially vulnerable unattached patients, is needed. This study compares emergency department (ED) utilization and hospitalization among those on and off a provincial PC waitlist, during the first two waves of COVID-19.\n\nMethodsWaitlist and administrative health data were linked to describe persons ever/never on the waitlist between January 1, 2017, and December 24, 2020. ED utilization and ambulatory care sensitive conditions (ACSC) hospitalization rates by current waitlist status were quantified from physician claims and hospitalization data. Relative differences during COVID-19 first and second waves were compared with the previous year.\n\nResultsDuring the study period, 100,867 Nova Scotians (10.1%) were on the waitlist. Those on the waitlist had higher ED utilization and ACSC hospitalizations. ED utilization was higher overall for individuals [≥]65 years and females; lowest during first two COVID-19 waves; and differed more by waitlist status for those <65 years. ED contacts and ACSC hospitalizations decreased during COVID-19 relative to the previous year, and for ED utilization this difference was more pronounced for those on the waitlist.\n\nInterpretationNova Scotians seeking PC attachment utilize hospital-based services more frequently than those not on the waitlist. Both groups had lower utilization during the COVID-19 pandemic than the year before. The degree to which forgone services produces downstream health burden remains to be seen.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Emily Gard Marshall", + "author_inst": "Department of Family Medicine Primary Care Research Unit, Dalhousie University, Halifax, NS; Nova Scotia Health, Halifax, NS; Department of Community Health and" + }, + { + "author_name": "David Stock", + "author_inst": "Department of Family Medicine Primary Care Research Unit, Dalhousie University, Halifax, NS; Department of Community Health and Epidemiology, Dalhousie Universi" + }, + { + "author_name": "Richard Buote", + "author_inst": "Department of Family Medicine Primary Care Research Unit, Dalhousie University, Halifax, NS" + }, + { + "author_name": "Melissa K. Andrew", + "author_inst": "Division of Geriatric Medicine, Department of Medicine, Dalhousie University, Halifax, NS; Maritime SPOR SUPPORT Unit, Halifax, NS" + }, + { + "author_name": "Mylaine Breton", + "author_inst": "Department of Community Health Sciences, Universit\u00e9 de Sherbrooke" + }, + { + "author_name": "Beno\u00eet Cossette", + "author_inst": "Department of Community Health Sciences, Universit\u00e9 de Sherbrooke" + }, + { + "author_name": "Michael E. Green", + "author_inst": "Departments of Family Medicine and Public Health Sciences, Queen's University, Kingston, ON; Institute for Clinical Evaluative Sciences, ON, Canada" + }, + { + "author_name": "Jennifer E. Isenor", + "author_inst": "College of Pharmacy, Dalhousie University, Halifax, NS" + }, + { + "author_name": "Maria Mathews", + "author_inst": "Department of Family Medicine, Schulich School of Medicine & Dentistry, Western University, London ON" + }, + { + "author_name": "Anders Lenskjold", + "author_inst": "Department of Family Medicine Primary Care Research Unit, Dalhousie University, Halifax, NS" + }, + { + "author_name": "Adrian MacKenzie", + "author_inst": "Nova Scotia Health, Halifax, NS; Department of Community Health and Epidemiology, Dalhousie University, Halifax, NS; Maritime SPOR SUPPORT Unit, Halifax, NS" + }, + { + "author_name": "Ruth Martin-Misener", + "author_inst": "School of Nursing, Dalhousie University, Halifax, NS" + }, + { + "author_name": "Beth McDougall", + "author_inst": "Nova Scotia Health, Halifax, NS; Department of Community Health and Epidemiology, Dalhousie University, Halifax, NS" + }, + { + "author_name": "Melanie Mooney", + "author_inst": "Nova Scotia Health, Halifax, NS" + }, + { + "author_name": "Lauren R. Moritz", + "author_inst": "Department of Family Medicine Primary Care Research Unit, Dalhousie University, Halifax, NS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2022.01.30.22270127", "rel_title": "Psychological distress and work and social adjustment in the COVID-19 pandemic: a cross-Country analysis", @@ -417210,29 +418375,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.01.30.22269992", - "rel_title": "\"Populist Attitude and Conspiracist beliefs contribution to the overconfidence about the risk of Covid-19: implications for Preventive Health Behaviors\"", - "rel_date": "2022-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.30.22269992", - "rel_abs": "Populism and Conspiracy beliefs seem to represent the zeitgeist of people depending on fast and simple information retrieved through social media. The Covid-19 emergency has simply catalyzed this process, not without consequences. Supported by literature review, we hypothesize that the higher the populist attitude the higher the tendency in believing in conspiracies, and that both higher populist attitudes and conspiracist beliefs may induce people in underestimating health related risks that may be reflected in a lowered tendency in adopting preventive health behaviors against Covid-19 spread. Data collected during the quarantine (December 2020, March 2021) mainly supported our hypotheses. Results are discussed in accord with the dramatic consequences it may have overconfidence in undermining the adoption of preventive health behaviors.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Agnese Giuliani", - "author_inst": "Sapienza University of Rome: Universita degli Studi di Roma La Sapienza" - }, - { - "author_name": "Fabio Presaghi", - "author_inst": "Sapienza University of Rome: Universita degli Studi di Roma La Sapienza" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.29.22269971", "rel_title": "Estimating COVID-19 Vaccination Effectiveness Using Electronic Health Records of an Academic Medical Center in Michigan", @@ -417428,6 +418570,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.01.30.478305", + "rel_title": "Combating the SARS-CoV-2 Omicron variant with non-Omicron neutralizing antibodies", + "rel_date": "2022-01-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.30.478305", + "rel_abs": "The highly mutated and transmissible Omicron variant has provoked serious concerns over its decreased sensitivity to the current coronavirus disease 2019 (COVID-19) vaccines and evasion from most anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibodies (NAbs). In this study, we explored the possibility of combatting the Omicron variant by constructing bispecific antibodies based on non-Omicron NAbs. We engineered ten IgG-like bispecific antibodies with non-Omicron NAbs named GW01, 16L9, 4L12, and REGN10987 by fusing the single-chain variable fragments (scFvs) of two antibodies through a linker and then connecting them to the Fc region of IgG1. Surprisingly, eight out of ten bispecific antibodies showed high binding affinity to the Omicron receptor-binding domain (RBD) and exhibited extreme breadth and potency against pseudotyped SARS-CoV-2 variants of concern (VOCs) including Omicron, as well as authentic Omicron(+R346K) variants. Six bispecific antibodies containing the cross-NAb GW01 neutralized Omicron variant and retained their abilities to neutralize other sarbecoviruses. Bispecific antibodies inhibited Omicron infection by binding to the ACE2 binding site. A cryo-electron microscopy (cryo-EM) structure study of the representative bispecific antibody FD01 in complex with the Omicron spike (S) revealed 5 distinct trimers and one unique bi-trimer conformation. The structure and mapping analyses of 34 Omicron S variant single mutants elucidated that two scFvs of the bispecific antibody synergistically induced the RBD-down conformation into 3-RBD-up conformation, enlarged the interface area, accommodated the S371L mutation, improved the affinity between a single IgG and the Omicron RBD, and hindered ACE2 binding by forming bi-trimer conformation. Our study offers an important foundation for anti-Omicron NAb design. Engineering bispecific antibodies based on non-Omicron NAbs may provide an efficient solution to combat the Omicron variant.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yingdan Wang", + "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University" + }, + { + "author_name": "Jiangyan Liu", + "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University" + }, + { + "author_name": "Yanqun Wang", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Mei Liu", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University" + }, + { + "author_name": "Qimin Wang", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University" + }, + { + "author_name": "Tong-Yu Zhu", + "author_inst": "Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shan" + }, + { + "author_name": "Yumei Wen", + "author_inst": "Fudan University" + }, + { + "author_name": "Zhenguo Chen", + "author_inst": "Fudan University" + }, + { + "author_name": "Jincun Zhao", + "author_inst": "GIRH" + }, + { + "author_name": "Fan Wu", + "author_inst": "Shanghai Public Health Clinical Center, Fudan University" + }, + { + "author_name": "Jinghe Huang", + "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Fudan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.27.478082", "rel_title": "Susceptibility of wild canids to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)", @@ -418908,77 +420109,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.28.22270005", - "rel_title": "Development and External Validation of a Mixed-Effects Deep Learning Model to Diagnose COVID-19 from CT Imaging", - "rel_date": "2022-01-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22270005", - "rel_abs": "ObjectivesTo develop and externally geographically validate a mixed-effects deep learning model to diagnose COVID-19 from computed tomography (CT) imaging following best practice guidelines and assess the strengths and weaknesses of deep learning COVID-19 diagnosis.\n\nDesignModel development and external validation with retrospectively collected data from two countries.\n\nSettingHospitals in Moscow, Russia, collected between March 1, 2020, and April 25, 2020. The China Consortium of Chest CT Image Investigation (CC-CCII) collected between January 25, 2020, and March 27, 2020.\n\nParticipants1,110 and 796 patients with either COVID-19 or healthy CT volumes from Moscow, Russia, and China, respectively.\n\nMain outcome measuresWe developed a deep learning model with a novel mixed-effects layer to model the relationship between slices in CT imaging. The model was trained on a dataset from hospitals in Moscow, Russia, and externally geographically validated on a dataset from a consortium of Chinese hospitals. Model performance was evaluated in discriminative performance using the area under the receiver operating characteristic (AUROC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). In addition, calibration performance was assessed using calibration curves, and clinical benefit was assessed using decision curve analysis. Finally, the models decisions were assessed visually using saliency maps.\n\nResultsExternal validation on the large Chinese dataset showed excellent performance with an AUROC of 0.936 (95%CI: 0.910, 0.961). Using a probability threshold of 0.5, the sensitivity, specificity, NPV, and PPV were 0.753 (0.647, 0.840), 0.909 (0.869, 0.940), 0.711 (0.606, 0.802), and 0.925 (0.888, 0.953), respectively.\n\nConclusionsDeep learning can reduce stress on healthcare systems by automatically screening CT imaging for COVID-19. However, deep learning models must be robustly assessed using various performance measures and externally validated in each setting. In addition, best practice guidelines for developing and reporting predictive models are vital for the safe adoption of such models.\n\nStatementsThe authors do not own any of the patient data, and ethics approval was not needed. The lead author affirms that this manuscript is an honest, accurate, and transparent account of the study being reported, that no important aspects of the study have been omitted, and that any discrepancies from the study as planned (and, if relevant, registered) have been explained. Patients and the public were not involved in the study.\n\nFundingThis study was funded by EPSRC studentship (No. 2110275), EPSRC Impact Acceleration Account (IAA) funding, and Amazon Web Services.\n\nSummaryO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIDeep learning can diagnose diseases from imaging data automatically\nC_LIO_LIMany studies using deep learning are of poor quality and fail to follow current best practice guidelines for the development and reporting of predictive models\nC_LIO_LICurrent methods do not adequately model the relationship between slices in CT volumetric data\nC_LI\n\nWhat this study addsO_LIA novel method to analyse volumetric imaging data composed of slices such as CT images using deep learning\nC_LIO_LIModel developed following current best-practice guidelines for the development and reporting of prediction models\nC_LI", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Joshua Bridge", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Yanda Meng", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Wenyue Zhu", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Thomas Fitzmaurice", - "author_inst": "Liverpool Heart and Chest Hospital NHS Foundation Trust" - }, - { - "author_name": "Caroline McCann", - "author_inst": "Liverpool Heart and Chest Hospital NHS Foundation Trust" - }, - { - "author_name": "Cliff Addison", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Manhui Wang", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Cristin Merritt", - "author_inst": "Alces Flight Limited" - }, - { - "author_name": "Stu Franks", - "author_inst": "Alces Software Limited" - }, - { - "author_name": "Maria Mackey", - "author_inst": "Amazon Web Services" - }, - { - "author_name": "Steve Messenger", - "author_inst": "Amazon Web Services" - }, - { - "author_name": "Renrong Sun", - "author_inst": "Hubei University of Chinese Medicine" - }, - { - "author_name": "Yitian Zhao", - "author_inst": "Ningbo Institute of Materials Technology and Engineering" - }, - { - "author_name": "Yalin Zheng", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.29.22270066", "rel_title": "Evaluation of the systemic and mucosal immune response induced by COVID-19 and the BNT162b2 mRNA vaccine for SARS-CoV-2", @@ -419222,6 +420352,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.01.29.22270064", + "rel_title": "The Correlation Between Brain Performance Capacity and COVID-19: A Cross-sectional Survey and Canonical Correlation Analysis", + "rel_date": "2022-01-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22270064", + "rel_abs": "ObjectiveTo generate a concept of brain performance capacity (BPC) with sleep, fatigue and mental workload as evaluation indicators and to analyze the correlation between BPC and the impact of COVID-19.\n\nMethodsA cluster sampling method was adopted to randomly select 259 civil air crew members. The measurements of sleep quality, fatigue and mental workload (MWL) were assessed using the Pittsburgh Sleep Quality Index (PSQI), Multidimensional Fatigue Inventory (MFI-20) and NASA Task Load Index. The impact of COVID-19 included 7 dimensions scored on a Likert scale. Canonical correlation analysis (CCA) was conducted to examine the relationship between BPC and COVID-19.\n\nResultsA total of 259 air crew members participated in the survey. Participants average PSQI score was 7.826 (SD = 3.796), with 49.8% reporting incidents of insomnia, mostly of a minor degree. Participants MFI was an average 56.112 (SD = 10.040), with 100% reporting some incidence of fatigue, mainly severe. The weighted mental workload (MWL) score was an average of 43.084 (SD = 17.543), with reports of mostly a mid-level degree. There was a significant relationship between BPC and COVID-19, with a canonical correlation coefficient of 0.507 (P=0.000), an eigenvalue of 0.364 and a contribution rate of 69.1%. All components of the BPC variable set: PSQI, MFI and MWL contributed greatly to BPC, with absolute canonical loadings of 0.790, 0.606 and 0.667, respectively; the same was true for the COVID-19 variable set, with absolute canonical loadings ranging from 0.608 to 0.951.\n\nConclusionMultiple indicators to measure BPC and the interrelationship of BPC and COVID-19 should be used in future research to gain a comprehensive understanding of anti-epidemic measures to ensure victory in the battle against the spread of the disease.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Yan Liu", + "author_inst": "Army Medical University" + }, + { + "author_name": "Xiao Chen", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ji Shu Xian", + "author_inst": "Army Medical University" + }, + { + "author_name": "Rui Wang", + "author_inst": "Army Medical University" + }, + { + "author_name": "Kang Ma", + "author_inst": "Army Medical University" + }, + { + "author_name": "Kai Xu", + "author_inst": "Army Medical University" + }, + { + "author_name": "Xue Yang", + "author_inst": "Army Medical University" + }, + { + "author_name": "Fei Long Wang", + "author_inst": "Army Medical University" + }, + { + "author_name": "Ning Mu", + "author_inst": "Army Medical University" + }, + { + "author_name": "Shi Wang", + "author_inst": "Army Medical University" + }, + { + "author_name": "Ying Lai", + "author_inst": "Army Medical University" + }, + { + "author_name": "Teng Li", + "author_inst": "Army Medical University" + }, + { + "author_name": "Chuan Yan Yang", + "author_inst": "Army Medical University" + }, + { + "author_name": "Yu Lian Quan", + "author_inst": "Army Medical University" + }, + { + "author_name": "Hua Feng", + "author_inst": "Army Medical University" + }, + { + "author_name": "Tunan Chen", + "author_inst": "Army Medical University" + }, + { + "author_name": "Lihua Wang", + "author_inst": "Army Medical University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.01.29.22270052", "rel_title": "Dynamics of antibody responses, cellular immunity, and breakthrough infections among Japanese healthcare workers during the 6 months after receiving two doses of BNT162b2 mRNA vaccine", @@ -420674,65 +421887,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.01.24.22269745", - "rel_title": "Cardiovascular, respiratory and functional effects of tele-supervised home-based exercise training in individuals recovering from COVID-19 hospitalization: A randomized clinical trial", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269745", - "rel_abs": "Our aim was to test the hypothesis that tele-supervised home-based exercise training (exercise) is an effective strategy for improving cardiovascular, respiratory, and functional capacity parameters in individuals that were hospitalized due to coronavirus disease 2019 (COVID-19). Thirty-two individuals (52 {+/-} 10 years; 17F) randomly assigned to exercise (N = 12) and control groups (N = 20), had their anthropometric (weight, body mass index), hemodynamic (brachial and central blood pressure), vascular (arterial stiffness), ventilatory (pulmonary function and respiratory muscle strength), and functional parameters (handgrip strength, five-time sit to stand [FTSTS], timed up and go test [TUG] and six-minute walking test [6MWT]) assessed at baseline (30 to 45 days of hospital discharged) and after 12 weeks of follow-up. Both groups similarly increased (P < 0.001) forced vital capacity (absolute and % of predicted), forced expiratory volume in the first second (absolute and % of predicted), and handgrip strength during follow-up. However, only exercise group reduced carotid-femoral pulse wave velocity (-2.0 {+/-} 0.6 m/s, P = 0.048), and increased (P < 0.05) resting oxygen saturation (1.9 {+/-} 0.6 %), mean inspiratory pressure (24.7 {+/-} 7.1 cmH2O), mean expiratory pressure (20.3 {+/-} 5.8 cmH2O) and % of predicted mean expiratory pressure (14 {+/-} 22 %) during follow-up. No significant changes were found in any other variable during follow-up. Present findings suggest that tele-supervised home-based exercise training can a potential adjunct therapeutic to rehabilitate individuals that were hospitalized due to COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Vanessa Teixeira do Amaral", - "author_inst": "Unesp" - }, - { - "author_name": "Ariane Aparecida Viana", - "author_inst": "Unesp" - }, - { - "author_name": "Alessandro Domingues Heubel", - "author_inst": "Ufscar" - }, - { - "author_name": "Stephanie Nogueira Linares", - "author_inst": "Ufscar" - }, - { - "author_name": "Bruno Martinelli", - "author_inst": "UNISAGRADO" - }, - { - "author_name": "Pedro Henrique Camprigher Witzler", - "author_inst": "Unesp" - }, - { - "author_name": "Gustavo Yudi Orikassa de Oliveira", - "author_inst": "Unesp" - }, - { - "author_name": "Gabriel de Souza Zanini", - "author_inst": "Unesp" - }, - { - "author_name": "Audrey Borghi Silva", - "author_inst": "Ufscar" - }, - { - "author_name": "Renata Goncalves Mendes", - "author_inst": "Ufscar" - }, - { - "author_name": "Emmanuel Gomes Ciolac", - "author_inst": "Unesp" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2022.01.27.22269909", "rel_title": "How dangerous is omicron and how effective are vaccinations?", @@ -421156,6 +422310,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.01.25.22269827", + "rel_title": "SARS-CoV-2 seroprevalence in children, parents and school personnel from June 2020 to April 2021: cohort study of 55 schools in Switzerland", + "rel_date": "2022-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269827", + "rel_abs": "We measured SARS-CoV-2 seroprevalence in cohorts of children, parents and school personnel in 55 randomly selected schools in the canton of Zurich, Switzerland. In June-September 2020, seroprevalence was low (4.4% to 5.8%) in all cohorts. In March-April 2021, seroprevalence in children and parents (18.1% and 20.9%) was slightly higher than in school personnel (16.9%). Childrens seroprevalence was slightly higher in classes with infected main teachers and families with one infected parent, and substantially higher in families with two infected parents.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Agne Ulyte", + "author_inst": "University of Zurich" + }, + { + "author_name": "Sarah R Haile", + "author_inst": "University of Zurich" + }, + { + "author_name": "Jacob Blankenberger", + "author_inst": "University of Zurich" + }, + { + "author_name": "Thomas Radtke", + "author_inst": "University of Zurich" + }, + { + "author_name": "Milo A. Puhan", + "author_inst": "University of Zurich" + }, + { + "author_name": "Susi Kriemler", + "author_inst": "University of Zurich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.25.22269762", "rel_title": "A longitudinal seroconversion panel shows anti-SARS-CoV-2 antibody levels up to 6.5 months after vaccination with mRNA-1273 (Moderna)", @@ -422848,49 +424041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2022.01.27.22269961", - "rel_title": "A Micronized Electrostatic Precipitator Respirator Effectively Removes Ambient SARS-CoV-2 Bioaerosols", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269961", - "rel_abs": "RationaleInhalation of ambient SARS-CoV-2-containing bioaerosols leads to infection and pandemic airborne transmission in susceptible populations. Filter-based respirators effectively reduce exposure but complicate normal respiration through breathing zone pressure differential and are therefore impractical for long-term use.\n\nObjectivesWe tested the comparative effectiveness of a prototyped micronized electrostatic precipitator (mEP) to a filter-based respirator (N95) in the removal of viral bioaerosols from a simulated inspired air stream.\n\nMethodsEach respirator was tested within a 16-liter environmental chamber housed within a Class III biological safety cabinet within biosafety level 3 containment. SARS-CoV-2 containing bioaerosols were generated into the chamber, drawn by vacuum through each respirator, and physical particle removal and viral genomic RNA were measured distal to the breathing zone of each device.\n\nMeasurement and Main ResultsThe mEP respirator removed particles (96.5{+/-}0.4%) approximating efficiencies of the N95 (96.9{+/-}0.6%). The mEP respirator similarly decreased SARS-CoV-2 viral RNA (99.792%) when compared to N95 removal (99.942%) as a function of particle removal from the airstream distal to the breathing zone of each respirator.\n\nConclusionsThe mEP respirator approximated performance of a filter-based N95 respirator for particle removal and viral RNA as a constituent of the SARS-CoV-2 bioaerosols generated for this evaluation. In practice, the mEP respirator would provide equivalent protection from ambient infectious bioaerosols as the N95 respirator without undue pressure drop to the wearer, thereby facilitating long-term use in an unobstructed breathing configuration.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rachel K Redmann", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Brandon J Beddingfield", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Skye Spencer", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Nicole R Chirichella", - "author_inst": "Tulane National Primate Research Center" - }, - { - "author_name": "Julian Henley", - "author_inst": "Henley Ion, Inc." - }, - { - "author_name": "Wes Hager", - "author_inst": "Phase Three Product Development" - }, - { - "author_name": "CHAD J ROY", - "author_inst": "Tulane University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.27.22269299", "rel_title": "Detection of SARS-CoV-2 Omicron, Delta, Alpha and Gamma variants using a rapid antigen test", @@ -423162,6 +424312,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.27.22269902", + "rel_title": "Anatomy of Covid outbreak of vaccinated: An observational case-control study of Covid breakthrough infections in medical college students at Rural Medical College, India", + "rel_date": "2022-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269902", + "rel_abs": "IntroductionBreakthrough infections about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported worldwide in both partially or completely vaccinated individuals irrespective of the type of vaccine. India, also emerged as the vaccine powerhouse producer, initiating the worlds one of the largest vaccination drives since January 16, 2021, with two vaccines named, BBV-152(COVAXIN) and AZD1222 (COVISHIELD). Breakthrough cases are reported from all over the globe for all kinds of vaccines. This is the investigation report into the outbreak of breakthrough COVID-19 infections at one of the medical colleges in Rural India unraveled in early October 2021. This report underscores the role of COVID-19 appropriate behavior along with vaccination and the role of IgG in evaluating immunity generated through vaccination.\n\nObjectiveThe study objective was to 1. Clinically characterize the recent breakthrough infection of COVID-19 (SARS-CoV-2) infection among (students) vaccinated in BKL Walawalkar Rural Medical College. 2. To evaluate COVID-19 appropriate behavior (CAB) in cases and controls. 3. To evaluate COVID-19 anti spike IgG in the cases in comparison with the control\n\nMethodsA total of 74 students studying at BKL Walawalkar Rural Medical College and vaccinated for COVID-19 were included in the study. RT-PCR diagnosis was done from 5 to 10 October 2021. The breakthrough infection in the cases was characterized using self-assessment questionnaires in comparison to the controls. The cases were assessed clinically and also using biochemical parameters. Both cases and controls were also assessed for their adherence to COVID-19 appropriate behavior using a separate semi-quantitative questionnaire and scoring system.\n\nResultsIn our study, out of the total subjects, 50% of Covaxin recipients had experienced vaccine breakthrough infection and 20% of Covishield recipients experienced breakthrough infection. Also, 6 out of the 35 cases were asymptomatic, and the rest were either having mild symptoms. None of them required any hospitalization or O2 therapy. The CAB score was lower in the cases when compared to controls. All the vaccine recipients show seroconversion. Anti-spike IgG antibodies titers are dynamic over time and across the clinically distinct groups. Irrespective of varying IgG titer, the vaccine protects against severity and possibly mortality.\n\nConclusionThe need for better awareness of COVID-19 appropriate methods as an alternative to and additive to vaccination is necessary to control the transmission of COVID-19 infection and decrease the disease severity. Vaccines are effective against preventing severe disease and possibly mortality. The use of serum anti-spike COVID-19 IgG is restricted to know the status of SARS-CoV-2 seroconversion.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Anup N Nillawar", + "author_inst": "BKL Walawalkar Rural Medical College, Sawarde, India" + }, + { + "author_name": "Monika N Chavan", + "author_inst": "BKL Walawalkar Rural Medical College, Sawarde, India" + }, + { + "author_name": "Sowmya Gayatri", + "author_inst": "ESIC Superspecialty Hospital, Hyderabad, India" + }, + { + "author_name": "Suvarna Patil", + "author_inst": "BKL Walawalkar Rural Medical College, Sawarde, India" + }, + { + "author_name": "Janhavi Deshpande", + "author_inst": "BKL Walawalkar Rural Medical College, Sawarde, India" + }, + { + "author_name": "Arvind Yadav", + "author_inst": "BKL Walawalkar Rural Medical College, Savarde, India" + }, + { + "author_name": "Prasanna Nakate", + "author_inst": "BKL Walawalkar Rural Medical College, Sawarde, India" + }, + { + "author_name": "Yogendra Shelke", + "author_inst": "BKL Walawalkar Rural Medical College, Maharashtra,India, 415606" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.24.22269379", "rel_title": "Humoral immune response of patients infected by earlier lineages of SARS-CoV-2 neutralizes wild types of the most prevalent variants in Brazil", @@ -424774,189 +425971,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.17.22269242", - "rel_title": "Efficacy and Safety of a Plant-Based Virus-Like Particle Vaccine for COVID-19 Adjuvanted with AS03", - "rel_date": "2022-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.17.22269242", - "rel_abs": "BackgroundSeveral COVID-19 vaccines are currently being deployed but supply constraints, concerns over durability of immune responses, solidifying vaccine hesitancy/resistance and vaccine efficacy in the face of emerging variants mean that new vaccines continue to be needed to fight the ongoing pandemic. The vaccine described here is an enveloped, coronavirus-like particle produced in plants (CoVLP) that displays the prefusion-stabilized spike (S) glycoprotein of SARS-CoV-2 (ancestral Wuhan strain) and is adjuvanted with AS03 (CoVLP+AS03).\n\nMethodsThis Phase 3 randomized, observer-blind, placebo-controlled trial was conducted at 85 centers in Argentina, Brazil, Canada, Mexico, the UK, and the USA. Adults [≥]18 years of age including those at high risk for COVID-19 complications were randomly assigned 1:1 to receive two intramuscular injections of CoVLP (3.75 g) adjuvanted with AS03 or placebo, 21 days apart. The primary efficacy endpoint was prevention of symptomatic ([≥] 1 symptom), PCR-confirmed SARS-CoV-2 infection with onset at least 7 days after the second injection and was triggered by the identification of [≥]160 virologically-confirmed cases. Tolerability and safety of CoVLP+AS03 were also determined.\n\nResultsA total of 24,141 volunteers were randomly assigned 1:1 to receive vaccine or placebo (N= 12,074 and 12,067, respectively: median age 29, range 18 to 86 years). Overall, 83% received both doses. 14.8% were SARS-CoV-2 seropositive at baseline. Symptomatic SARS-CoV-2 infection was confirmed in 165 study participants in the intention to treat (ITT) set and 157 in the per-protocol population (PP) set. Of the 157 in the PP set, 118 COVID-19 cases were in the placebo group and 39 COVID-19 cases were in the CoVLP+AS03 group for an overall vaccine efficacy (VE) of 71.0% (95% confidence interval (CI) 58.6, 80.0). Moderate-to-severe COVID-19 occurred in 8 and 32 participants in the CoVLP+AS03 and placebo groups, respectively: VE 78.1% (95% CI: 53.9, 90.5) in the PP set overall and 84.5% (95% CI: 62.0, 94.7) in those seronegative at recruitment.\n\nTo date, 100% of the sequenced strains (122/165 cases: 73.39%) were variants, dominated by Delta (45.9%) and Gamma (43.4%) strains. Vaccine efficacy by variant was 75.3% (95% CI 52.8, 87.9) against Delta and 88.6% (95% CI 74.6, 95.6) against Gamma. Cross-protection was also observed against Alpha, Lambda and Mu variants; although fewer cases were identified, all were in the placebo group. At diagnosis, viral loads in the CoVLP+AS03 breakthrough cases were >100-fold lower than in the placebo cases. Reactogenicity data for solicited adverse events (AEs) was analysed for a subset (N=4,136 in vaccine arm and N=3,683 for placebo) of participants. Reactogenicity was mostly mild to moderate, and transient, and occurred more frequently in the CoVLP+AS03 group. The safety analysis set used for unsolicited AE assessment comprised 24,076 participants who received at least one study injection: 12,036 received CoVLP+AS03 and 12,040 received placebo. All serious adverse events were assessed as unrelated, except two events reported in the same subject in the placebo group. No significant imbalance or safety concern was noted in medically attended AEs (MAAEs), adverse event of special interest (AESIs), AEs leading to withdrawal, deaths, or adverse events potentially associated with currently authorized vaccines.\n\nConclusionsThe CoVLP+AS03 vaccine candidate conferred an efficacy of 71.0% in preventing symptomatic SARS-CoV-2 infection caused by a spectrum of variants. Vaccine efficacy of 78.1% was observed against moderate and severe disease, while variant-specific efficacy ranged from 75.3% to 100%. Markedly lower viral loads in the CoVLP+AS03 group at the time of diagnosis suggests a significant virologic impact of vaccination even in the breakthrough cases. CoVLP+AS03 vaccine candidate was well tolerated, and no safety concerns were identified during the study. If approved by regulators, this more traditional protein+adjuvant vaccine produced using the novel plant-based platform may be able to make an important contribution to the global struggle against the increasingly complex family of SARS-CoV-2 viruses (Funded by Medicago with grants from the governments of Quebec and Canada; NCT04636697).", - "rel_num_authors": 42, - "rel_authors": [ - { - "author_name": "Karen Joyce Hager", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Gonzalo P\u00e9rez Marc", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr. Cosme Argerich, Buenos Aires, Argentina" - }, - { - "author_name": "Philipe Gobeil", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Ricardo Sobhie Diaz", - "author_inst": "Paulista School of Medicine, Federal University of Sao Paulo, Brazil, and Azidus Brasil Pesquisa e Desenvolvimento Ltda, Valinhos Sao Paulo, Brazil" - }, - { - "author_name": "Gretchen Heizer", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Conrado Llapur", - "author_inst": "Clinica Mayo de UMCB SRL, San Miguel de Tucuman Tucuman, Argentina" - }, - { - "author_name": "Alexander I. Makarkov", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Eduardo Vasconcellos", - "author_inst": "Instituto de Pesquisas Clinicas L2IP, Complexo Medico Hospitalar, DF, Brazil" - }, - { - "author_name": "Stephane Pillet", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Fernando Riera", - "author_inst": "Sanatorio Allende, Av. Hipolito Yrigoyen 384, Cordoba, Cordoba 5000, Argentina" - }, - { - "author_name": "Kapil Bhutada", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Priscila Geller Wolff", - "author_inst": "IBPClin Instituto Brasil de Pequisa Clinica, Gloria, Rio de Janeiro RJ, Brazil" - }, - { - "author_name": "Garry Wallace", - "author_inst": "Dawson Clinical Research Inc., Ontario, Canada" - }, - { - "author_name": "Hessam Aazami", - "author_inst": "Hope Clinical, California, United States" - }, - { - "author_name": "Christine E Jones", - "author_inst": "Clinical and Experimental Sciences, University of Southampton and NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospita" - }, - { - "author_name": "Fernando P. Polack", - "author_inst": "Fundacion INFANT, Buenos Aires, Argentina" - }, - { - "author_name": "Judith Atkins", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Iohann Boulay", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Jiwanjeet Dhaliwall", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Nathalie Charland", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Manon Couture", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Julia Jiang-Wright", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Nathalie Landry", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Sophie Lapointe", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Aur\u00e9lien Lorin", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Asif Mahmood", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Lawrence H Moulton", - "author_inst": "Department of International health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" - }, - { - "author_name": "Emmy Pahmer", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Julie Parent", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Pooja Saxena", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Annie Seguin", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Luan Tran", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Thomas Breuer", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Maria Angeles Ceregido", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Marguerite Koutsoukos", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Francois Roman", - "author_inst": "GlaxoSmithKline Vaccines, Wavre, Belgium" - }, - { - "author_name": "Junya Namba", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Marc-Andr\u00e9 D'Aoust", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Sonia Trepanier", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "Yosuke Kimura", - "author_inst": "Medicago Inc., Quebec, QC, Canada" - }, - { - "author_name": "- The CoVLP Study Team", - "author_inst": "-" - }, - { - "author_name": "Brian J Ward", - "author_inst": "Medicago Inc. and Research Institute of the McGill University Health Center, Montreal, QC, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.25.22269670", "rel_title": "TNF\u03b1-producing CD4+ T cells dominate the SARS-CoV-2-specific T cell response in COVID-19 outpatients and are associated with durable antibodies", @@ -425356,6 +426370,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2022.01.26.22269788", + "rel_title": "Adverse events following COVISHIELD (ChAdOx1nCoV-19) vaccination among health care workers in Sri Lanka; a multi-centre cross sectional survey", + "rel_date": "2022-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269788", + "rel_abs": "IntroductionA community vaccination programme is the best approach to combat the COVID-19 pandemic. Post-vaccine surveillance is important to identify adverse events (AE) following COVID -19 vaccination in the population.\n\nMethodsA multicentre cross-sectional survey was conducted in six provinces to estimate the prevalence of AE following the first dose of COVISHIELD (ChAdOx1nCoV-19) among all categories of health care workers (HCWs). A self-administered questionnaire was used to gather demographic data and AE.\n\nResultsOf 5140 participants 67.8% were females. The mean (SD) age was 40.69 ({+/-}9.85) years. At least one comorbidity was reported in 15.4%. At least one AE was reported in 86.6% and 49.3% had local AE. Fever (67.2%), headaches (57.3%), body aches (54.4%), chills (51.2%), fatigue (37.5%) and arthralgia (36%) were the most reported systemic AE. The majority of AE lasted less than 24 hours. Pain and redness at the site were the most reported local AE. Mean duration of onset of fever and pain at injection site from the time of the vaccination was 6.65 and 9.67 hours respectively.\n\nWhen participants were divided into two groups by mean age ([≤]40 and >40 years) and parameters were compared, most systemic (fever, nausea, fatigue, itching) and all local AE were significantly more prevalent in the [≤]40 age group.\n\nTwo percent had reactions within the first 20 minutes. Anaphylaxis developed in 12 participants. Past history of anaphylaxis, drug or food allergy were reported in 0.6%, 2.8% and 6.7% respectively. However, previous history of allergy was not significantly related to immediate reactions or anaphylaxis following vaccination. Despite having minor AE, 71.1% attended routine work while 0.2% required hospitalisation.\n\nConclusionsWhile 86.6% reported minor AE, only a few serious AE were reported. Overall, the first dose of the vaccine was well-tolerated by HCWs.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Suranga Ravinda Manilgama", + "author_inst": "Colombo North Teaching Hospital" + }, + { + "author_name": "Nirosha Madhuwanthi Hettiarachchi", + "author_inst": "Teaching Hospital Peradeniya" + }, + { + "author_name": "I Kumudini Jayasinghe", + "author_inst": "National Hospital Kandy" + }, + { + "author_name": "Shamila T De Silva", + "author_inst": "Faculty of Medicine, University of Kelaniya" + }, + { + "author_name": "Thilak Jayalath", + "author_inst": "Faculty of Medicine, University of Peradeniya" + }, + { + "author_name": "Thushari Wanigaratne", + "author_inst": "District General Hospital, Matale" + }, + { + "author_name": "Bandusiri P Rathnayake", + "author_inst": "Teaching Hospital Rathnapura" + }, + { + "author_name": "Navaneethakrishnan Suganthan", + "author_inst": "Faculty of Medicine, University of Jaffna" + }, + { + "author_name": "P Sudarshan", + "author_inst": "District General Hospital, Polonnaruwa" + }, + { + "author_name": "Manoji Pathirage", + "author_inst": "Faculty of Medicine, University of Peradeniya" + }, + { + "author_name": "Nalayini Rajaratnam", + "author_inst": "Teaching Hospital Jaffna" + }, + { + "author_name": "Ganaka Senaratne", + "author_inst": "Teaching Hospital Karapitiya" + }, + { + "author_name": "Vishaka Rajapaksha", + "author_inst": "National hospital Kandy" + }, + { + "author_name": "Asanga Wickramasinghe", + "author_inst": "Colombo North Teaching Hospital" + }, + { + "author_name": "S P A L Ranaweera", + "author_inst": "Colombo North Teaching Hospital" + }, + { + "author_name": "Arjuna H M Thilakarathna", + "author_inst": "Teaching Hospital Peradeniya" + }, + { + "author_name": "M Thilini D Kulaweera", + "author_inst": "High School Advanced Mathematics, Gampaha" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.24.477597", "rel_title": "Unadjuvanted intranasal spike vaccine booster elicits robust protective mucosal immunity against sarbecoviruses", @@ -426896,41 +427993,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2022.01.24.22269741", - "rel_title": "The Choice of Response Alternatives in COVID-19 Social Science Surveys", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269741", - "rel_abs": "Social science research is key for understanding and for predicting compliance with COVID-19 guidelines, and much of this research relies on survey data. While much focus is on the survey question stems, less is on the response alternatives presented that both constrain responses and convey information about the assumed expectations of the survey designers. The focus here is on the choice of response alternatives for the types of behavioral frequency questions used in many COVID-19 and other health surveys. We examine issues with two types of response alternatives. The first are vague quantifiers, like \"rarely\" and frequently.\" Using data from 30 countries from the Imperial COVID data hub, we show that the interpretation of these vague quantifiers (and their translations) depends on the norms in that country. If the mean amount of hand washing in your country is high, it is likely \"frequently\" corresponds to a higher numeric value for hand washing than if the mean in your country is low. The second type are precise numeric response alternatives and they can also be problematic. Using a US survey, respondents were randomly allocated to receive either response alternatives where most of the scale corresponds to low frequencies or where most of the scale corresponds to high frequencies. Those given the low frequency set provided lower estimates of the health behaviors. The choice of response alternatives for behavioral frequency questions can affect the estimates of health behaviors. How the response alternatives mold the responses should be taken into account for epidemiological modeling. We conclude with some recommendations for response alternatives for health behavioral frequency questions in surveys.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Daniel Wright", - "author_inst": "UNLV: University of Nevada Las Vegas" - }, - { - "author_name": "Sarah M Wolff", - "author_inst": "UNLV: University of Nevada Las Vegas" - }, - { - "author_name": "Rusi Jaspal", - "author_inst": "University of Brighton" - }, - { - "author_name": "Julie Barnett", - "author_inst": "University of Bath - Oakfield Campus: University of Bath" - }, - { - "author_name": "Glynis Breakwell", - "author_inst": "University of Bath - Oakfield Campus: University of Bath" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.24.477469", "rel_title": "Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants", @@ -427246,6 +428308,41 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.01.24.477502", + "rel_title": "Template-based design of peptides to inhibit SARS-CoV-2 RNA-dependent RNA polymerase complexation.", + "rel_date": "2022-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.24.477502", + "rel_abs": "The RNA-dependent RNA polymerase (RdRp) complex of SARS-CoV-2 lies at the core of its replication and transcription processes. The interfaces between the subunits of the RdRp complex are highly conserved, facilitating the design of inhibitors with high affinity for the interaction hotspots of the complex. Here, we report development and application of a structural bioinformatics protocol to design peptides that can inhibit RdRp complex formation by targeting the interface of its core subunit nonstructural protein (nsp) 12 with accesory factor nsp7. We adopt a top-down approach for protein design by using interaction hotspots of the nsp7-nsp12 complex obtained from a long molecular dynamics trajectory as template. A large library of peptide sequences constructed from multiple hotspot motifs of nsp12 is screened in silico to determine peptide sequences with highest shape and interaction complementarity for the nsp7-nsp12 interface. Two lead designed peptide are extensively characterized using orthogonal bioanalytical methods to determine their suitability for inhibition of RdRp complexation and anti-viral activity. Their binding affinity to nsp7 (target), as determined from surface plasmon resonance (SPR) assay, is found to be comparable to that of the nsp7-nsp12 complex. Further, one of the designed peptides gives 46 % inhibition of nsp7-nsp12 complex at 10:1 peptide:nsp7 molar concentration (from ELISA assay). Further optimization of cell penetrability and target affinity of these designed peptides is expected to provide lead candidates with high anti-viral activity against SARS-CoV-2.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Akshay Chenna", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Wajihul Hasan Khan", + "author_inst": "Indian Institute of Technology" + }, + { + "author_name": "Rozaleen Dash", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Anurag S Rathore", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Gaurav Goel", + "author_inst": "Indian Institute of Technology Delhi" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.01.24.477476", "rel_title": "The effect of COVID-19 mRNA vaccine on respiratory system: human lung carcinoma cells by means of Raman spectroscopy and imaging.", @@ -428706,61 +429803,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.18.22269433", - "rel_title": "Risk factors for developing symptomatic COVID-19 in older residents of nursing homes: A hypothesis-generating observational study", - "rel_date": "2022-01-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269433", - "rel_abs": "BackgroundCOVID-19 pandemic has had a major impact on society, including on residents of nursing homes (NH), who have a higher risk of complications and mortality due their physical and intellectual disabilities.\n\nAimTo identify which risk factors associated with developing COVID-19 infection with symptoms in institutionalized older people.\n\nMethodsA 1-year longitudinal multicenter study was conducted in 5 NH during the period December 2019 to March 2021. The inclusion criteria used were residents aged 65 years or over, living in the NH permanently, with a diagnostic test for COVID-19 confirmed by reverse transcription polymerase chain reaction and/or serological test. The main variable was symptomatic COVID-19, with at least one of the following symptoms (fever, respiratory difficulties, cough, diarrhea, sudden urinary incontinence and disorientation or delirium). Three assessments were performed: baseline, six and twelve months follow-up. Descriptive and bivariate analysis (calculating relative risk-RR) were performed, considering a 95% confidence level and a statistically significant p <0.05.\n\nResultsOf the total sample of 78 individuals who tested positive for COVID-19, mean age 84.6 years (SD={+/-}7.8), 62 (79.5%) were female; 40 (51.3%) participants presented with COVID-19 symptoms. Living in a private NH (RR=3.6, 95% CI [1.2-11.0], p=0.023) and having suffered a stroke (RR=4.1, 95% CI [1.1-14.7], p=0.033) were positively associated with developing COVID-19 infection with symptoms.\n\nConclusionsHaving suffered a stroke and living permanently in a private health care facility were positively associated with symptomatic COVID-19 in this sample of institutionalized older people.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Eduard Minobes-Molina", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Anna Escrib\u00e0-Salvans", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Sandra Rierola-Fochs", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Pau Farr\u00e9s-Godayol", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "M\u00edriam Molas-Tuneu", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Dyego Leandro Bezerra de Souza", - "author_inst": "Federal University of Rio Grande do Norte: Universidade Federal do Rio Grande do Norte" - }, - { - "author_name": "Dawn A Skelton", - "author_inst": "Glasgow Caledonian University" - }, - { - "author_name": "Ester Goutan-Roura", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Daniel Alonso-Masmitj\u00e0", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - }, - { - "author_name": "Javier Jerez-Roig", - "author_inst": "University of Vic - Central University of Catalonia: Universitat de Vic - Universitat Central de Catalunya" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" - }, { "rel_doi": "10.1101/2022.01.20.477164", "rel_title": "Severe acute respiratory disease in American mink (Neovison vison) experimentally infected with SARS-CoV-2", @@ -429072,6 +430114,25 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.21.477298", + "rel_title": "The N764K and N856K mutations in SARS-CoV-2 Omicron S protein generate potential cleavage sites for SKI-1/S1P protease", + "rel_date": "2022-01-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.21.477298", + "rel_abs": "Spike (S) protein is a key protein in coronaviruses life cycle. SARS-CoV-2 Omicron BA.1 variant of concern (VoC) presents an exceptionally high number of 30 substitutions, 6 deletions and 3 insertions in the S protein. Recent works revealed major changes in the SARS-CoV-2 Omicron biological properties compared to earlier variants of concern (VoCs). Here, these major changes could be explained, at least in part, by the mutations N764K and/or N856K in S2 subunit. These mutations were not previously detected in other VoCs. N764K and N856K generate two potential cleavage sites for SKI-1/S1P serine protease, known to cleave viral envelope glycoproteins. The new sites where SKI-1/S1P could cleave S protein might impede the exposition of the internal fusion peptide for membrane fusion and syncytia formation. Based on the human protein atlas, SKI-1/S1P protease is not found in lung tissues (alveolar cells type I/II and endothelial cells), but present in bronchus and nasopharynx. This may explain why Omicron has change of tissue tropism. Viruses have evolved to use several host proteases for cleavage/activation of envelope glycoproteins. Mutations that allow viruses to change of protease may have a strong impact in host range, cell and tissue tropism, and pathogenesis.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Halim Maaroufi", + "author_inst": "Universite Laval" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.01.21.477244", "rel_title": "Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment", @@ -430424,49 +431485,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.21.22269671", - "rel_title": "Impact of COVID-19 symptoms on social aspects of life of female long haulers: A qualitative study", - "rel_date": "2022-01-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.21.22269671", - "rel_abs": "IntroductionPersistent COVID-19 symptoms (long COVID) may bring numerous challenges to long haulers social lives. Women may have to endure more profound impacts given their social roles and existing structural inequality. This study aims to explore the impacts of long COVID on various aspects of social life among female long haulers.\n\nMethodsWe conducted 15 semi-structured interviews with female long haulers in the United States purposely recruited from Facebook groups, Slack groups, and organization websites. The interviews were audio recorded after appropriate consent and transcribed verbatim. Inductive approach was applied in thematic analysis, which consists of six stages: becoming familiar with data, developing initial codes, extracting themes, refining themes, labeling themes, and reporting. The MAXQDA software was used in data analysis.\n\nResultsPersistent COVID-19 symptoms negatively affected female long haulers social lives in many aspects including physical function, financial security, social relationship, conflict of social roles, and social stigma. Physical limitations changed their body image. Social isolation and work-family conflicts caused huge stress. They experienced internalization of stigma and job insecurities. Shifting to new methods of communication, especially social media may buffer the negative effects of social isolation because of long COVID.\n\nConclusionExisting policies and intervention programs need to be adapted to address the challenges and barriers that long haulers face in returning to normal social life, especially for females. Tailored social life-related recommendations and social support are needed for female long haulers.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Atefeh Aghaei", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Ran Zhang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Slone Taylor", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Cheuk Chi Tam", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Chih-Hsiang Yang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Xiaoming Li", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.18.22269467", "rel_title": "The Effects of Messaging on Expectations and Understanding of Long COVID: An Online Randomised Trial", @@ -430854,6 +431872,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.21.22269658", + "rel_title": "Modelling Quarantine Effects on SARS-CoV-2 Epidemiological Dynamics in Chilean Communes and their Relationship with the Social Priority Index", + "rel_date": "2022-01-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.21.22269658", + "rel_abs": "An epidemiological model [Susceptible, Un-quarantined infected, Quarantined infected, Confirmed infected (SUQC)] has previously been developed and applied to incorporate quarantine measures and calculate COVID-19 contagion dynamics and pandemic control in some Chinese regions. Here, we generalized this model to incorporate the disease recovery rate and applied our model to records of the total number of confirmed cases of people infected with the SARS-CoV-2 virus in some Chilean communes. In each commune, two consecutive stages were considered: a stage without quarantine and an immediately subsequent quarantine stage imposed by the Ministry of Health. To adjust the model, typical epidemiological parameters were determined, such as the confirmation rate and the quarantine rate. The latter allowed us to calculate the reproduction number. The mathematical model adequately reproduced the data, indicating a higher quarantine rate when quarantine was imposed by the health authority, with a corresponding decrease in the reproduction number of the virus down to values that prevent or decrease its exponential spread. In general, during this second stage, the communes with the lowest social priority indices had the highest quarantine rates, and therefore, the lowest effective viral reproduction numbers. This study provides useful evidence to address the health inequity of pandemics. The mathematical model applied here can be used in other regions or easily modified for other cases of infectious disease control by quarantine.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Dino G. Salinas", + "author_inst": "Facultad de Medicina, Universidad Diego Portales" + }, + { + "author_name": "Maria Leonor Bustamante", + "author_inst": "Faculty of Medicine, Universidad de Chile" + }, + { + "author_name": "Mauricio O. Gallardo", + "author_inst": "Facultad de Medicina, Universidad Diego Portales" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.22.22269682", "rel_title": "Social isolation during the COVID-19 pandemic in Spain: a population study", @@ -432518,33 +433563,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.19.22269572", - "rel_title": "Monitoring SARS-CoV-2 genome evolution in a localized population", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.19.22269572", - "rel_abs": "Despite seminal advances towards understanding its infection mechanism, SARS-CoV-2 continues to cause significant morbidity and mortality worldwide. Though mass immunization programs have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2 infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April, 2020 to October, 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this time period. We also highlight presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations (iSNVs) at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended time period within a geographically restricted area and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Asmita Gupta", - "author_inst": "Centre for DNA Fingerprinting and Diagnostics" - }, - { - "author_name": "Reelina Basu", - "author_inst": "Centre for DNA Fingerprinting and Diagnostics" - }, - { - "author_name": "Murali Dharan Bashyam", - "author_inst": "Centre for DNA Fingerprinting and Diagnostics (CDFD)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.19.22269510", "rel_title": "Microbial GWAS studies revealing combinations of Omicron RBD mutations existed and may contribute to antibody evasion and ACE2 binding", @@ -432848,6 +433866,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.01.21.22269322", + "rel_title": "Combination of Spironolactone and Sitagliptin Improves Clinical Outcomes of Outpatients with COVID-19: An Observational Study", + "rel_date": "2022-01-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.21.22269322", + "rel_abs": "RationaleCoronavirus disease 2019 (COVID-19) leads to hospitalization and death, especially in elderly and those with comorbidities. There are evidences showing that sitagliptin and spironolactone can potentially improve the clinical outcomes of COVID-19 cases.\n\nObjectiveIn this observational study on acutely symptomatic outpatient COVID-19 cases, we investigated the effects of spironolactone and sitagliptin on the outcomes of the disease.\n\nMethodsThis prospective cohort study was conducted at Shiraz University of Medical Sciences Clinics during the fifth wave of the COVID-19 pandemic between July 2021 and September 2021. We followed mild to moderate symptomatic COVID-19 patients, who were treated with either combination (spironolactone 100 mg daily and sitagliptin 100 mg daily) or standard (steroid, antiviral and/or supportive care) therapy up to 30 days. Our primary outcome was hospitalization rate. The secondary outcomes included ER visit, duration of disease, and complications, such as hypoglycemia, low blood pressure or altered mental status.\n\nResultsOf the 206 patients referred to clinics, 103 received standard therapy and 103 treated with combination therapy. There were no significant differences in baseline characteristics, except for slightly higher clinical score in control group (6.92 {+/-} 4.01 control, 4.87 {+/-} 2.92 combination; P <0.0001). Treatment with combination therapy was associated with lower admission rate (5.8% combination, 22.3% control; P = 0.0011), ER visits (7.8% combination, 23.3% control; P = 0.0021) and average duration of symptoms (6.67 {+/-} 2.30 days combination, 18.71 {+/-} 6.49 days control; P =<0.0001).\n\nConclusionIn this prospective cohort study of acutely ill outpatients with COVID-19, the combination of sitagliptin and spironolactone reduced duration of COVID infection and hospital visits better than standard therapeutic approaches. The effects of combination of sitagliptin and spironolactone in COVID-19 patients should be further verified in a double blind, randomized, placebo-controlled trial.\n\nIranian Registry of Clinical TrialsIRCT registration number: IRCT20201003048904N2, Registration date: December 10, 2020.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mohammad Ali Davarpanah", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Reuben Adatorwovor", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Yasaman Mansoori", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Fatemeh Sadat Rajaie Ramsheh", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Amir Parsa", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Mehdi Hajiani", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Hossein Faramarzi", + "author_inst": "Shiraz University of Medical Sciences" + }, + { + "author_name": "Ramakanth Kavuluru", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Kamyar Asadipooya", + "author_inst": "University of Kentucky" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.18.22269351", "rel_title": "mRNA-COVID19 vaccination can be considered safe and tolerable for frail patients", @@ -434236,93 +435305,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.18.22269200", - "rel_title": "Infection and transmission risks in schools and contribution to the COVID-19 pandemic in Germany - a retrospective observational study using nation-wide and regional health and education agency notification data", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269200", - "rel_abs": "IntroductionCurrently, information on infection and transmission risks of students and teachers in schools, the effect of infection control measures for schools as well as the contribution of schools to the overall population transmission of SARS-CoV-2 in Germany are limited to regional data sets restricted to short phases of the pandemic.\n\nMethodsWe used German federal state (NUTS-2) and county (NUTS-3) data from national and regional public health and education agencies to assess infection risk and secondary attack rates (SARs) from March 2020 to October 2021 in Germany. We used multiple regression analysis and infection dynamic modelling, accounting for urbanity, socioeconomic factors, local population infection dynamics and age-specific underdetection to investigate the effects of infection control measures.\n\nResultsWe included (1) nation-wide NUTS-2 level data from calendar weeks (W) 46-50/2020 and W08-40/2021 with 304676 infections in students and 32992 in teachers; (2) NUTS-3 level data from W09-25/2021 with 85788 student and 9427 teacher infections and (3) detailed data from 5 regions covering W09/2020 to W27/2021 with 12814 infections, 43238 contacts and 4165 secondary cases for students (for teachers 14801, 5893 and 472 respectively).\n\nIn counties with mandatory surgical mask wearing during class in all schools infection risk of students and teachers was reduced by 56/100.000 persons per 14 days and by 30% and 24% relative to the population respectively. Overall contribution to population infections of contacts in school settings was 2-13%. It was lowest during school closures and vacation and highest during normal presence class intervals. Infection risk for students increased with age and was similar to or lower than the population risk during second and third waves in Germany and higher in summer 2021. Infection risk of teachers was higher than the population during the second wave and similar or lower thereafter with stricter measures in place. SARs for students and staff were below 5% in schools throughout the study period. SARs in households more than doubled from 14% W21-39/2020 to 29-33% in W08-23/2021. Most contacts were reported for schools, yet most secondary cases originated in households. In schools, staff predominantly infected staff and students predominantly infected students.\n\nConclusionOpen schools under hygiene measures and testing strategies contribute up to 13% of nation-wide infections in Germany and as little as 2% during vacations/school closures. Tighter infection control measures stabilised school SARs whilst household SARs more than doubled as more transmissible variants became prevalent in Germany. Mandatory mask wearing during class in all school types effectively reduces secondary transmission in schools, as do reduced attendance class models.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Torben Heinsohn", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Berit Lange", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Patrizio Vanella", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Isti Rodiah", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Stephan Gl\u00f6ckner", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Alexander Joachim", - "author_inst": "University Hospital Cologne: Uniklinik Koln" - }, - { - "author_name": "Dennis Becker", - "author_inst": "Public Health Department Konstanz" - }, - { - "author_name": "Tobias Br\u00e4ndle", - "author_inst": "Agency for Schools and Vocational Training Hamburg" - }, - { - "author_name": "Stephan Dhein", - "author_inst": "Public Health Department Altenburger Land" - }, - { - "author_name": "Stephan Ehehalt", - "author_inst": "Public Health Department Stuttgart" - }, - { - "author_name": "Mira Fries", - "author_inst": "Public Health Department Cologne" - }, - { - "author_name": "Annette Galante-Gottschalk", - "author_inst": "Public Health Department Stuttgart" - }, - { - "author_name": "Stefanie Jehnichen", - "author_inst": "Public Health Department Konstanz" - }, - { - "author_name": "Sarah Kolkmann", - "author_inst": "Public Health Department Altenburger Land" - }, - { - "author_name": "Annelene Kossow", - "author_inst": "Public Health Department Cologne" - }, - { - "author_name": "Martin Hellmich", - "author_inst": "University of Cologne: Universitat zu Koln" - }, - { - "author_name": "J\u00f6rg D\u00f6tsch", - "author_inst": "University Hospital Cologne: Uniklinik Koln" - }, - { - "author_name": "G\u00e9rard Krause", - "author_inst": "Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.21.22269636", "rel_title": "Using Survey Data to Estimate the Impact of the Omicron Variant on Vaccine Efficacy against COVID-19 Infection", @@ -434606,6 +435588,97 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2022.01.19.476892", + "rel_title": "Molecular basis of broad neutralization against SARS-CoV-2 variants including Omicron by a human antibody", + "rel_date": "2022-01-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.19.476892", + "rel_abs": "Omicron, a newly emerging SARS-CoV-2 variant, carried a large number of mutations in the spike protein leading to an unprecedented evasion from many neutralizing antibodies (nAbs). Here, we performed a head-to-head comparison of Omicron with other existing highly evasive variants in terms of their reduced sensitivities to antibodies, and found that Omicron variant is significantly more evasive than Beta and Mu variants. Of note, some key mutations occur in the conserved epitopes identified previously, especially in the binding sites of Class 4 nAbs, contributing to the increased Ab evasion. We also reported a broadly nAb (bnAb), VacW-209, which effectively neutralized all tested SARS-CoV-2 variants and even SARS-CoV. Finally, we determined six cryo-electron microscopy structures of VacW-209 complexed with the spike ectodomains of wild-type, Delta, Mu, C.1.2, Omicron, and SARS-CoV, and revealed the molecular basis of the broadly neutralizing activities of VacW-209 against SARS-CoV-2 variants. Overall, Omicron has once again raised the alarm over virus variation with significantly compromised neutralization. BnAbs targeting more conserved epitopes among variants will continue to play a key role in pandemic control and prevention.\n\nOne sentence summaryStructural and functional analyses reveal that a human antibody named VacW-209 confers broad neutralization against SARS-CoV-2 variants including Omicron by recognizing a highly conserved epitope.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Zheng Zhang", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Bin Ju", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Qingbing Zheng", + "author_inst": "Xiamen University" + }, + { + "author_name": "Huimin Guo", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Qing Fan", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Tingting Li", + "author_inst": "Xiamen University" + }, + { + "author_name": "Shuo Song", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Hui Sun", + "author_inst": "Xiamen University" + }, + { + "author_name": "Senlin Shen", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Xinrong Zhou", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Lin Cheng", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Wenhui Xue", + "author_inst": "Xiamen University" + }, + { + "author_name": "Lingyan Cui", + "author_inst": "Xiamen University" + }, + { + "author_name": "Bing Zhou", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Xiangyang Ge", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Haiyan Wang", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Miao Wang", + "author_inst": "Shenzhen Third People s Hospital" + }, + { + "author_name": "Shaowei Li", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ningshao Xia", + "author_inst": "Xiamen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.01.18.476803", "rel_title": "Inflammation in the COVID-19 airway is due to inhibition of CFTR signaling by the SARS-CoV-2 Spike protein", @@ -436242,105 +437315,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2022.01.15.22269335", - "rel_title": "Retention of Neutralizing response against SARS-CoV-2 Omicron variant in Sputnik V vaccinated individuals", - "rel_date": "2022-01-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.15.22269335", - "rel_abs": "The new variant Omicron (B.1.1.529) of SARS-CoV-2, first identified in November 2021, is rapidly spreading all around the world. The Omicron becomes the dominant variant of SARS-CoV-2. There are many ongoing studies evaluating the effectiveness of existing vaccines. Studies on neutralizing activity of vaccinated sera against Omicron variant are currently being carried out in many laboratories.\n\nIn this study, we have shown the neutralizing activity of sera against SARS-CoV-2 Omicron (B.1.1.529) variant compared to the reference Wuhan D614G (B.1) variant in individuals vaccinated with 2 doses of Sputnik V or BNT162b2 in different time points up to 6 months after vaccination. We performed analysis on sample pools with comparable NtAb to Wuhan D614G variant. The decrease in neutralizing antibody (NtAb) to the Omicron variant was 8.1 folds for group of Sputnik V-vaccinated and 21.4 folds for group of BNT162b2-vaccinated. Analysis showed that 74.2% of Sputnik V- and 56.9% of BNT162b2-vaccinated sera had detectable NtAb to SARS-CoV-2 Omicron variant.\n\nThe decrease in NtAb to SARS-CoV-2 Omicron variant compared to Wuhan variant has been shown for many COVID-19 vaccines in use, with some showing no neutralization at all. Today the necessity of third booster vaccination is obvious. And the most effective approach, already shown in several studies, is the use of heterologous booster vaccination pioneered in COVID-19 vaccines by Sputnik V.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Daniele Lapa", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Daria Grousova", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Giulia Matusali", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Silvia Meschi", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Francesca Colavita", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Aurora Bettini", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Giulia Gramigna", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Massimo Francalancia", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Anna Rosa Garbuglia", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Enrico Girardi", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Vincenzo Puro", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Andrea Antinori", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Anna Kovyrshina", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Inna Dolzhikova", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Dmitry Shcheblyakov", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Amir Tukhvatulin", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Olga Zubkova", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Denis Logunov", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Boris Naroditsky", - "author_inst": "Gamaleya NRCEM" - }, - { - "author_name": "Francesco Vaia", - "author_inst": "INMI Lazzaro Spallanzani" - }, - { - "author_name": "Alexander Gintsburg", - "author_inst": "Gamaleya NRCEM" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.18.476863", "rel_title": "SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice", @@ -436712,6 +437686,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.01.15.476426", + "rel_title": "ASGR1 is a candidate receptor for SARS-CoV-2 that promotes infection of liver cells", + "rel_date": "2022-01-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.15.476426", + "rel_abs": "Backgroud & AimsCurrently, the COVID-19 pandemic, caused by SARS-CoV-2 infection, represents a serious public health problem worldwide. Although it has been shown that ACE2 serves as the main receptor for SARS-CoV-2 entry into host cells, studies have shown that ACE2 is expressed at extremely low levels in various tissues, especially in some organs where virus particles have been found, such as the heart and liver. Therefore, these organs potentially express additional SARS-CoV-2 receptors that have not yet been discovered.\n\nMethods & ResultsHere, by a genome-wide CRISPR-Cas9 activation library screening, we found that ASGR1 promoted SARS-CoV-2 infection of 293T cells. In Huh-7 and HepG2 cell lines, simultaneous knock out of ACE2 and ASGR1 prevented SARS-CoV-2 pseudovirus infection. In the immortalized THLE-2 hepatocyte cell line and primary liver parenchymal cells, both of which hardly express ACE2, SARS-CoV-2 could successfully establish an infection. After treatment with ASGR1 antibody, the infection rate significantly reduced. This suggests that SARS-CoV-2 infects liver cells mainly through an ASGR1-dependent mechanism. Finally, we also found that the soluble ASGR1 could not only prevent the SARS-CoV-2 pseudovirus, which binds to the ASGR1 receptors, from infecting host liver cells, but also had a protective effect on those expressing ACE2, indicating that administration of soluble ASGR1 protein may represent a new treatment approach.\n\nConclusionsColletively, these findings indicate that ASGR1 is a candidate receptor for SARS-CoV-2 that promotes infection of liver cells.\n\nLay SummaryWe show that ASGR1 is a candidate receptor for SARS-CoV-2 to infect liver cells.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Xinyi Yang", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Yuqi Zhu", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Xiaying Zhao", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Jun Liu", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Jingna Xun", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Songhua Yuan", + "author_inst": "Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China" + }, + { + "author_name": "Jun Chen", + "author_inst": "Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China" + }, + { + "author_name": "Hanyu Pan", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Jinlong Yang", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Jing Wang", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Zhimin Liang", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Xiaoting Shen", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Yue Liang", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Qinru Lin", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Huitong Liang", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Min Li", + "author_inst": "State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sci" + }, + { + "author_name": "Hongzhou Lu", + "author_inst": "Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China" + }, + { + "author_name": "Huanzhang Zhu", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.13.476267", "rel_title": "Evidence of increased Cathepsin B/L and decreased TMPRSS2 usage for cell entry by the SARS-CoV-2 Omicron variant", @@ -438127,85 +439188,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.16.22269146", - "rel_title": "Development and validation of the Symptom Burden Questionnaire\u2122 for Long COVID: a Rasch analysis", - "rel_date": "2022-01-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.16.22269146", - "rel_abs": "ObjectiveTo describe the development and initial validation of a novel patient-reported outcome measure of Long COVID symptom burden, the Symptom-Burden Questionnaire for Long COVID (SBQ-LC).\n\nMethod and FindingsThis multi-phase, prospective mixed-methods study took place between April and August 2021 in the United Kingdom (UK). A conceptual framework and initial item pool were developed from published systematic reviews. Further concept elicitation and content validation was undertaken with adults with lived experience (n = 13) and clinicians (n = 10), and face validity was confirmed by the Therapies for Long COVID Study Patient and Public Involvement group (n = 25). The draft SBQ-LC was field tested by adults with self-reported Long COVID recruited via social media and international Long COVID support groups (n = 274). Thematic analysis of interview and survey transcripts established content validity and informed construction of the draft questionnaire. Rasch analysis of field test data guided item and scale refinement and provided evidence of the final SBQ-LCs measurement properties. The Rasch-derived SBQ-LC is composed of 17 independent scales with promising psychometric properties. Respondents rate symptom burden during the past 7-days using a dichotomous response or 4-point rating scale. Each scale provides coverage of a different symptom domain and returns a summed raw score that may be converted to a linear (0 - 100) score. Higher scores represent higher symptom burden.\n\nConclusionsThe SBQ-LC is a comprehensive patient-reported assessment of Long COVID symptom burden developed using modern psychometric methods. It measures symptoms of Long COVID important to individuals with lived experience and may be used to evaluate the impact of interventions and inform best practice in clinical management.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Sarah E Hughes", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Shamil Haroon", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Anuradhaa Subramanian", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Christel McMullan", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Olalekan L Aiyegbusi", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Grace M Turner", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Louise Jackson", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Elin Haf Davies", - "author_inst": "Aparito Limited" - }, - { - "author_name": "Chris Frost", - "author_inst": "Aparito Limited" - }, - { - "author_name": "Gary McNamara", - "author_inst": "Aparito Limited" - }, - { - "author_name": "Gary Price", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Karen Matthews", - "author_inst": "Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham" - }, - { - "author_name": "Jennifer Camaradou", - "author_inst": "Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham" - }, - { - "author_name": "Jane Ormerod", - "author_inst": "Patient and Public Involvement, Therapies for Long COVID (TLC) study, University of Birmingham" - }, - { - "author_name": "Anita Walker", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Melanie J Calvert", - "author_inst": "University of BIrmingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.01.17.22269412", "rel_title": "EFCAB4B (CRACR2A) genetic variants associated with COVID-19 fatality", @@ -438473,6 +439455,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.15.22269231", + "rel_title": "A prospective, single-center study to evaluate the clinical performance of Meril ABFind in individuals vaccinated against COVID-19", + "rel_date": "2022-01-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.15.22269231", + "rel_abs": "BackgroundAccurate rapid antibody detection kits requiring minimum infrastructure are beneficial in detecting post-vaccination antibodies in large populations. ChAdOx1-nCOV (COVISHIELD) and BBV-152 (Covaxin) vaccines are primarily used in India.\n\nMethodsIn this single-centre prospective study, performance of Meril ABFind was investigated by comparing with Abbott SARS-CoV-2 IgG II Quant (Abbott Quant), GenScript cPass SARS-CoV-2 neutralization antibody detection kit (GenScript cPass), and COVID Kawach MERILISA (MERILISA) in 62 vaccinated health care workers (HCW) and 40 pre-pandemic samples.\n\nResultsIn the vaccinated subjects, Meril ABFind kit displayed high sensitivity of 93.3% (CI, 89.83%-96.77%), 94.92% (CI, 91.88%-97.96%), and 90.3% (CI, 86.20%-94.4%) in comparison to Abbott Quant, MERILISA, and GenScript cPass respectively. The results of the Meril ABFind in the COVISHIELD-vaccinated group were excellent with 100% sensitivity in comparison to the other three kits. In the Covaxin-vaccinated group, Meril ABFind displayed sensitivity ranging from 80% to 88.9%. In control samples, there were no false positives detected by Meril ABFind, while Abbott Quant, MERILISA, and GenScript cPass reported 2.5%, 10.0%, and 12.5% false positives, respectively. In the pre-pandemic controls, specificity of Meril ABFind was 100%, Abbott Quant 97.5%, MERILISA 90%, and GenScript cPass 87.5%.\n\nConclusionThe Meril ABFind kit demonstrated satisfactory performance when compared with the three commercially available kits and was the only kit without false positives in the pre-pandemic samples. This makes it a viable option for rapid diagnosis of post vaccination antibodies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jayanthi Shastri", + "author_inst": "Kasturba Hospital for Infectious Diseases" + }, + { + "author_name": "Sachee Agrawal", + "author_inst": "Kasturba Hospital for Infectious Diseases" + }, + { + "author_name": "Nirjhar Chatterjee", + "author_inst": "Kasturba Hospital for Infectious Diseases" + }, + { + "author_name": "Harsha Gupta", + "author_inst": "Kasturba Hospital for Infectious Diseases" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.16.22269361", "rel_title": "Resilient T cell responses to B.1.1.529 (Omicron) SARS-CoV-2 variant", @@ -439689,65 +440702,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2022.01.13.22269244", - "rel_title": "Prognostic Value of Serum/Plasma Neurofilament Light Chain for COVID-19 Associated Mortality", - "rel_date": "2022-01-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22269244", - "rel_abs": "Given the continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), early predictors of coronavirus disease 19 (COVID-19) mortality might improve patients outcomes. Increased levels of circulating neurofilament light chain (NfL), a biomarker of neuro-axonal injury, have been observed in patients with severe COVID-19. We investigated whether NfL provides non-redundant clinical value to previously identified predictors of COVID-19 mortality.\n\nWe measured serum or plasma NfL concentrations in a blinded fashion in 3 cohorts totaling 338 COVID-19 patients. In cohort 1, we found significantly elevated NfL levels only in critically ill COVID-19 patients compared to healthy controls. Longitudinal cohort 2 data showed that NfL is elevated late in the course of the disease, following two other prognostic markers of COVID-19: decrease in absolute lymphocyte count (ALC) and increase in lactate dehydrogenase (LDH). Significant correlations between LDH and ALC abnormalities and subsequent rise of NfL implicate multi-organ failure as a likely cause of neuronal injury at the later stages of COVID-19. Addition of NfL to age and gender in cohort 1 significantly improved the accuracy of mortality prediction and these improvements were validated in cohorts 2 and 3.\n\nIn conclusion, although substantial increase in serum/plasma NfL reproducibly enhances COVID-19 mortality prediction, NfL has clinically meaningful prognostic value only close to death, which may be too late to alter medical management. When combined with other prognostic biomarkers, rising longitudinal NfL measurements triggered by LDH and ALC abnormalities would identify patients at risk of COVID-19 associated mortality who might still benefit from escalated care.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Ruturaj Masvekar", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Peter Kosa", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Kimberly Jin", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Kerry Dobbs", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Michael A Stack", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Riccardo Castagnoli", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Virginia Quaresima", - "author_inst": "ASST Spedali Civili di Brescia, Brescia, Italy" - }, - { - "author_name": "Helen C Su", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Luisa Imberti", - "author_inst": "ASST Spedali Civili di Brescia, Brescia, Italy" - }, - { - "author_name": "Luigi Daniele Notarangelo", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - }, - { - "author_name": "Bibiana Bielekova", - "author_inst": "National Institute of Allergy and Infectious Diseases, NIH" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.01.13.21268270", "rel_title": "Health and Economic Consequences of Universal Paid Sick Leave Policies During the COVID-19 Pandemic", @@ -440151,6 +441105,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.13.22268861", + "rel_title": "SARS-CoV-2 Omicron Neutralization After Heterologous Vaccine Boosting", + "rel_date": "2022-01-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22268861", + "rel_abs": "As part of an ongoing study assessing homologous and heterologous booster vaccines, following primary EUA series, we assessed neutralization of D614G and Omicron variants prior to and 28 days after boost. Subset analysis was done in six combinations (N = 10/group): four homologous primary-booster combinations included mRNA-1273 two-dose priming followed by boosting with 100-g or 50-g mRNA-1273, Ad26.COV2.S single-dose priming followed by Ad26.COV2.S booster and BNT162b2 two-dose priming followed by BNT162b2 boosting; and two heterologous primary-booster combinations: BNT162b2 followed by Ad26.COV2.S and Ad26.COV2.S followed by BNT162b2. Neutralizing antibody (Nab) titers to D614G on the day of boost (baseline) were detected in 85-100% of participants, with geometric mean titers (GMT) of 71-343 in participants who received an mRNA vaccine series versus GMTs of 35-41 in participants primed with Ad26.OV2.S. Baseline NAb titers to Omicron were detected in 50-90% of participants who received an mRNA vaccine series (GMT range 12.8-24.5) versus 20-25% among participants primed with Ad26.COV2.S. The booster dose increased the neutralizing GMT in most combinations to above 1000 for D614G and above 250 for Omicron by Day 29. Homologous prime-boost Ad26.COV2.S had the lowest NAb on Day 29 (D614G GMT 128 and Omicron GMT 45). Results were similar between age groups. Most homologous and heterologous boost combinations examined will increase humoral immunity to the Omicron variant.", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Kirsten E Lyke", + "author_inst": "University of Maryland School of Medicine, Center for Vaccine Development and Global Health" + }, + { + "author_name": "Robert L Atmar", + "author_inst": "Baylor College of Medicine, Departments of Medicine and Molecular Virolgy & Microbiology" + }, + { + "author_name": "Clara P. Dominguez Islas", + "author_inst": "Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division" + }, + { + "author_name": "Christine M. Posavad", + "author_inst": "Fred Hutchinson Cancer Research Cneter, Department of Laboratory Medicine and Pathology, Vaccine and Infectious Diseases Division" + }, + { + "author_name": "Daniel Szydlo", + "author_inst": "Fred Hutchinson Cancer Research Center, Statistical Center for HIV/AIDS Research and Prevention (SCHARP)" + }, + { + "author_name": "Rahul PaulChourdhury", + "author_inst": "Fred Hutchinson Cancer Research Center, Statistical Center for HIV/AIDS Research and Prevention (SCHARP)" + }, + { + "author_name": "Meagan E. Deming", + "author_inst": "University of Maryland School of Medicine, Center for Vaccine Development and Global Health" + }, + { + "author_name": "Amanda Eaton", + "author_inst": "Duke University, Department of Surgery" + }, + { + "author_name": "Lisa A. Jackson", + "author_inst": "Kaiser Permanente Washington Health Research Institute" + }, + { + "author_name": "Angela R. Branche", + "author_inst": "University of Rochester, Department of Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Hana M. El Sahly", + "author_inst": "Baylor College of Medicine, Departments of Molecular Virology & Microbiology and Medicine" + }, + { + "author_name": "Christina A. Rostad", + "author_inst": "Emory University School of Medicine, Department of Pediatrics and Center for Childhood Infections and Vaccines" + }, + { + "author_name": "Judith M Martin", + "author_inst": "University of Pittsburgh, Department of Pediatrics" + }, + { + "author_name": "Christine Johnston", + "author_inst": "Fred Hutchinson Cancer Research Center and University of Washington, Departments of Medicine and Laboratory Medicine, Vaccine and Infectious Diseases Division" + }, + { + "author_name": "Richard E. Rupp", + "author_inst": "University of Texas Medical Branch, Sealy Institute for Vaccine Sciences" + }, + { + "author_name": "Mark J Mulligan", + "author_inst": "New York University Grossman School of Medicine, NYU Langone Vaccine Center and Division of Infectious Diseases and Immunology" + }, + { + "author_name": "Rebecca C. Brady", + "author_inst": "University of Cincinnati College of Medicine, Cincinnati Childrens Hospital Medical Center, Division of Infectious Diseases" + }, + { + "author_name": "Robert W. Frenck", + "author_inst": "University of Cincinnati College of Medicine, Cincinnati Childrens Hospital Medical Center, Division of Infectious Diseases" + }, + { + "author_name": "Mart\u00edn B\u00e4cker", + "author_inst": "NYU Langone Hospital, Long Island Vaccine Center Reserach Clinic and Division of Infectious Diseases, Department of Medicine" + }, + { + "author_name": "Angelica C. Kottkamp", + "author_inst": "NYU Grossman School of Medicine, NYU Langone Vaccine Center Bellevue Hospital Research Clinic and Division of Infectious Diseases and Immunology" + }, + { + "author_name": "Tara M. Babu", + "author_inst": "University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases" + }, + { + "author_name": "Kumaravel Rajakumar", + "author_inst": "University of Pittsburgh School of Medicine, Department of Pediatrics" + }, + { + "author_name": "Srilatha Edupuganti", + "author_inst": "Emory University School of Medicine, Division of Infectious Diseases, Hope Clinic of Emory Vaccine Center" + }, + { + "author_name": "David Dobrzynski", + "author_inst": "University of Rochester, Department of Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Rhea N. Coler", + "author_inst": "University of Washington School of Medicine, Seattle Children's Research Institute" + }, + { + "author_name": "Janet I. Archer", + "author_inst": "FHI360" + }, + { + "author_name": "Sonja Crandon", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Jillian A. Zemanek", + "author_inst": "Fred Hutchinson Cancer Research Center, Statistical Center for HIV/AIDS Research and Prevention (SCHARP)" + }, + { + "author_name": "Elizabeth R. Brown", + "author_inst": "Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division" + }, + { + "author_name": "Kathleen .M Neuzil", + "author_inst": "University of Maryland School of Medicine, Center for Vaccine Development and Global Heath" + }, + { + "author_name": "David S. Stephens", + "author_inst": "Emory University Department of Medicine" + }, + { + "author_name": "Diane J. Post", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Seema U. Nayak", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Paul C. Roberts", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "John Beigel", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "David Montefiori", + "author_inst": "Duke University, Duke Human Vaccine Institute and Department of Surgery" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.14.22269064", "rel_title": "Evaluation and modelling of the performance of an automated SARS-CoV-2 antigen assay according to sample type, target population and epidemic trends", @@ -441831,133 +442944,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2022.01.12.22269133", - "rel_title": "Humoral and T-cell immune response after three doses of mRNA SARS-CoV-2 vaccines in fragile patients: the Italian VAX4FRAIL study", - "rel_date": "2022-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269133", - "rel_abs": "BackgroundPatients with solid or hematological tumors, neurological and immune-inflammatory disorders represent potentially fragile subjects with increased risk to experience severe COVID-19 and inadequate response to SARS-CoV2 vaccination.\n\nMethodsWe designed a prospective Italian multicentric study to assess humoral and T-cell response to SARS-CoV2 vaccination in patients (n=378) with solid tumors (ST), hematological malignancies (HM), neurological (ND) and immuno-rheumatological diseases (ID). The immunogenicity of primary vaccination schedule and of the booster dose were analyzed.\n\nResultsOverall, patient seroconversion rate after two doses was 62.1%. A significant lower rate was observed in HM (52.4%) and ID (51.9%) patients compared to ST (95.6%) and ND (70.7%); a lower median level of antibodies was detected in HM and ID versus the others (p<0.0001). A similar rate of patients with a positive SARS-CoV2 T-cell response was observed in all disease groups, with a higher level observed in the ND group. The booster dose improved humoral responses in all disease groups, although with a lower response in HM patients, while the T-cell response increased similarly in all groups. In the multivariable logistic model, the independent predictors for seroconversion were disease subgroups, type of therapies and age. Notably, the ongoing treatment known to affect the immune system was associated with the worst humoral response to vaccination (p<0.0001), but had no effects on the T-cell responses.\n\nConclusionsImmunosuppressive treatment more than disease type per se is a risk factor for low humoral response after vaccination. The booster dose can improve both humoral and T-cell response.\n\nArticles main point- Lower rate of seroconversion was observed in fragile patients as compared to healthy controls\n- The booster dose improves humoral and T-cell response in all fragile patient groups\n- Immunosuppressive treatment was associated with the worst humoral response to vaccination, but had no effects on T-cell responses.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Paolo Corradini", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy; University of Milan, Italy" - }, - { - "author_name": "Chiara Agrati", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Giovanni Apolone", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy" - }, - { - "author_name": "Alberto Mantovani", - "author_inst": "Istituto Clinico Humanitas / Humanitas University" - }, - { - "author_name": "Diana Giannarelli", - "author_inst": "Istituto Nazionale Tumori Regina Elena IRCCS - IFO, Rome, Italy" - }, - { - "author_name": "Vincenzo Marasco", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy; University of Milan, Italy" - }, - { - "author_name": "Veronica Bordoni", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Alessandra Sacchi", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Giulia Matusali", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Carlo Salvarani", - "author_inst": "INMI L Spallanzani" - }, - { - "author_name": "Pier Luigi Zinzani", - "author_inst": "Azienda Ospedaliero Universitaria di Bologna IRCCS, Italy; University of Bologna, Italy" - }, - { - "author_name": "Renato Mantegazza", - "author_inst": "Fondazione IRCCS Isitituto Neurologico Carlo Besta, Milano, Italy" - }, - { - "author_name": "Fabrizio Tagliavini", - "author_inst": "Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy" - }, - { - "author_name": "Maria Teresa Lupo Stanghellini", - "author_inst": "IRCCS San Raffaele Scientific Institute, Milano, Italy" - }, - { - "author_name": "Fabio Ciceri", - "author_inst": "IRCSS San Raffaele Scientific Institute, Milano, Italy" - }, - { - "author_name": "Silvia Damian", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy" - }, - { - "author_name": "Antonio Uccelli", - "author_inst": "University of Genoa, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy" - }, - { - "author_name": "Daniela Fenoglio", - "author_inst": "IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy; University of Genoa, Italy" - }, - { - "author_name": "Nicola Silvestris", - "author_inst": "IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy; University of Bari Aldo Moro, Bari, Italy" - }, - { - "author_name": "Fausto Baldanti", - "author_inst": "Fondazione IRCCS Policlinico San Matteo; University of Pavia, Pavia, Italy" - }, - { - "author_name": "Giulia Piaggio", - "author_inst": "National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO), Rome, Italy" - }, - { - "author_name": "Gennaro Ciliberto", - "author_inst": "National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO), Rome, Italy" - }, - { - "author_name": "Aldo Morrone", - "author_inst": "San Gallicano Dermatological Institute IRCCS, Rome, Italy" - }, - { - "author_name": "Franco Locatelli", - "author_inst": "IRCCS Ospedale Pediatrico Bambino Gesu; University La Sapienza, Rome, Italy" - }, - { - "author_name": "Valentina Sinno", - "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy" - }, - { - "author_name": "Maria Rescigno", - "author_inst": "Humanitas University" - }, - { - "author_name": "Massimo Costantini", - "author_inst": "Azienda USL-IRCCS Reggio Emilia" - }, - { - "author_name": "- VAX4FRAIL Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.01.12.476120", "rel_title": "An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer", @@ -442369,6 +443355,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.01.11.21268036", + "rel_title": "Screening for SARS-CoV-2 persistence in Long COVID patients using sniffer dogs and scents from axillary sweats samples", + "rel_date": "2022-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.21268036", + "rel_abs": "ObjectivesDogs can be trained to identify several substances not detected by humans, corresponding to specific volatile organic compounds (VOCs). The presence of VOCs, triggered by SARS-CoV-2 infection, was tested in sweat from Long COVID patients.\n\nPatients and methodsAn axillary sweat sample of Long COVID patients and of COVID-19 negative, asymptomatic individuals was taken at home to avoid any hospital contact. Swabs were randomly placed in olfaction detection cones, and the material sniffed by at least 2 trained dogs.\n\nResultsForty-five Long COVID patients, mean age 45 (6-71), 73.3% female, with prolonged symptoms evolving for a mean of 15.2 months (5-22) were tested. Dogs discriminated in a positive way 23/45 (51.1%). Long COVID patients versus 0/188 (0%) control individuals (p<.0001).\n\nConclusionThis study suggests the persistence of a viral infection in some Long COVID patients and the possibility of providing a simple, highly sensitive, non-invasive test to detect viral presence, during acute and extended phases of COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Dominique GRANDJEAN", + "author_inst": "Ecole Nationale Veterinaire d'Alfort" + }, + { + "author_name": "Dorsaf SLAMA", + "author_inst": "Assistance Publique Hopitaux de Paris" + }, + { + "author_name": "Capucine GALLET", + "author_inst": "National Veterinary School of Alfort" + }, + { + "author_name": "Clothilde JULIEN", + "author_inst": "National Veterinary School of Alfort" + }, + { + "author_name": "Emilie SEYRAT", + "author_inst": "Long COVID patients, France" + }, + { + "author_name": "Marc BLONDOT", + "author_inst": "Long COVID patients, France" + }, + { + "author_name": "Maissa BENAZAZIEZ", + "author_inst": "Assistance Publique Hopitaux de Paris" + }, + { + "author_name": "Judith ELBAZ", + "author_inst": "Long COVID patient, France" + }, + { + "author_name": "Dominique SALMON", + "author_inst": "Assistance Publique Hopitaux de Paris" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.11.22269113", "rel_title": "Immunologic Response, Efficacy, and Safety of Vaccines Against COVID-19 in Children and Adolescents Aged 2 - 21 Years Old: A Systematic Review", @@ -443857,41 +444894,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.01.09.22268984", - "rel_title": "Household secondary attack rates of SARS-CoV-2 by variant and vaccination status: an updated systematic review and meta-analysis", - "rel_date": "2022-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.09.22268984", - "rel_abs": "We previously reported a household secondary attack rate (SAR) for SARS-CoV-2 of 18.9% through June 17, 2021. To examine how emerging variants and increased vaccination have affected transmission rates, we searched PubMed from June 18, 2021, through January 7, 2022. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95%CI, disaggregated by several covariates. SARs were used to estimate vaccine effectiveness based on the transmission probability for susceptibility (VES,p), infectiousness (VEI,p), and total vaccine effectiveness (VET,p). Household SAR for 27 studies with midpoints in 2021 was 35.8% (95%CI, 30.6%-41.3%), compared to 15.7% (95%CI, 13.3%-18.4%) for 62 studies with midpoints through April 2020. Household SARs were 38.0% (95%CI, 36.0%-40.0%), 30.8% (95%CI, 23.5%-39.3%), and 22.5% (95%CI, 18.6%-26.8%) for Alpha, Delta, and Beta, respectively. VEI,p, VES,p, and VET,p were 56.6% (95%CI, 28.7%-73.6%), 70.3% (95%CI, 59.3%-78.4%), and 86.8% (95%CI, 76.7%-92.5%) for full vaccination, and 27.5% (95%CI, -6.4%-50.7%), 43.9% (95%CI, 21.8%-59.7%), and 59.9% (95%CI, 34.4%-75.5%) for partial vaccination, respectively. Household contacts exposed to Alpha or Delta are at increased risk of infection compared to the original wild-type strain. Vaccination reduced susceptibility to infection and transmission to others.\n\nSummaryHousehold secondary attack rates (SARs) were higher for Alpha and Delta variants than previous estimates. SARs were higher to unvaccinated contacts than to partially or fully vaccinated contacts and were higher from unvaccinated index cases than from fully vaccinated index cases.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zachary J. Madewell", - "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" - }, - { - "author_name": "Yang Yang", - "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" - }, - { - "author_name": "Ira M. Longini Jr.", - "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" - }, - { - "author_name": "M. Elizabeth Halloran", - "author_inst": "Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Biostatistics, University of Washington, Seattle, WA" - }, - { - "author_name": "Natalie E. Dean", - "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.10.22269002", "rel_title": "Cardiopulmonary imaging utilization and findings among hospitalized COVID-19 patients in Latin America (From RIMAC: Registry IMAging Cardiopulmonary among hospitalized COVID-19 patients in LATAM)", @@ -444363,6 +445365,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.10.22269007", + "rel_title": "EFFECT OF FULL VACCINATION AND POST-COVID OLFACTORY DYSFUNCTION IN RECOVERED COVID-19 PATIENT. A RETROSPECTIVE LONGITUDINAL STUDY WITH PROPENSITY MATCHING.", + "rel_date": "2022-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.10.22269007", + "rel_abs": "BackgroundSymptoms after COVID-19 infection affect the quality of life of its survivor especially to the special senses including olfactory function. It is important to prevent the disability at an earlier stage. Vaccination as key prevention has been proven to be effective in reducing symptomatic disease and severity. However, the effects of vaccination on post COVID symptoms have not been evaluated. This study aimed to evaluate the possible protection of full vaccination and the occurrence of post-COVID olfactory dysfunction, specifically anosmia and hyposmia in patients who were diagnosed with COVID19.\n\nMethodA longitudinal analysis using the retrospective cohort of the Indonesian patient-based Post-COVID survey collected from July 2021 until December 2021, involving COVID-19 Patients confirmed by RT-PCR and/or Antigen test. Variables including demography, comorbidities, health behavior, type of vaccine, symptoms, and treatment were collected through an online questionnaire based on the American Academy of Otolaryngology-Head and Neck Surgery (AAO-HNS). Participants were matched (1:1) using propensity matching score into two exposure statuses, infected 1)>14 days of full vaccination and 2)<14 days or incomplete or unvaccinated. The olfactory dysfunction was assessed two weeks and four weeks after negative conversion with PCR using a self-measured olfactory questionnaire (MOQ). The Generalized Estimating Equation (GEE) was performed to assess the effect of full vaccination on post-COVID olfactory dysfunction. The Receiver Operating Characteristic determined the sensitivity and specificity of the cutoff value of the days from fully vaccinated to diagnosis and the olfactory dysfunction.\n\nResultsA total of 442 participants were extracted from the cohort and inoculated with the inactivated viral vaccine (99.5%). The prevalence of olfactory dysfunction in two weeks was 9.95% and 5.43% after four weeks. Adjusted by other variables, people who were infected >14 days after being fully vaccinated had a 69% (adjusted OR 0.31 95% CI 0.102-0.941) probability of developing olfactory dysfunction. Longer days of fully vaccinated to infection associated with increased risk (adjusted OR 1.012 95% CI 1.002-1.022 p-value 0.015). A cut-off of 88 days of full vaccination-to-diagnosis duration has Area Under Curve (AUC) of 0.693 (p=0.002), the sensitivity of 73.9%, and specificity of 63.3% in differentiating the olfactory dysfunction event in two weeks after COVID with a crude odds ratio of 4.852 (95% CI 1.831-12.855 p=0.001)\n\nConclusionAfter 14 days of full vaccination, the protective effect could reduce the chance of post-COVID olfactory dysfunction although a longer full vaccination-to-diagnosis duration increases the risk. It is important to consider a booster shot starting from 89 days after the last dose in those who received the inactivated viral regimen.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Bumi Herman", + "author_inst": "College of Public Health Sciences Chulalongkorn University Thailand" + }, + { + "author_name": "Pramon Viwattanakulvanid", + "author_inst": "College of Public Health Sciences Chulalongkorn University Thailand" + }, + { + "author_name": "Azhar Dzulhadj", + "author_inst": "School Of Biomedical Science, The University of Western Australia" + }, + { + "author_name": "Aye Chan Oo", + "author_inst": "College of Public Health Sciences Chulalongkorn University Thailand" + }, + { + "author_name": "Karina Patricia", + "author_inst": "Ciptomangunkusumo General Hospital Jakarta Indonesia" + }, + { + "author_name": "Sathirakorn Pongpanich", + "author_inst": "College of Public Health Science Chulalongkorn University Thailand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2022.01.10.21268250", "rel_title": "Cohort-specific serological recognition of SARS-CoV-2 variant RBD antigens", @@ -445827,37 +446868,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.08.22268920", - "rel_title": "Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England", - "rel_date": "2022-01-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.08.22268920", - "rel_abs": "BackgroundEarly estimates from South Africa indicated that the Omicron COVID-19 variant may be both more transmissible and have greater immune escape than the previously dominant Delta variant. The rapid turnover of the latest epidemic wave in South Africa as well as initial evidence from contact tracing and household infection studies has prompted speculation that the generation time of the Omicron variant may be shorter in comparable settings than the generation time of the Delta variant.\n\nMethodsWe estimated daily growth rates for the Omicron and Delta variants in each UKHSA region from the 23rd of November to the 23rd of December 2021 using surveillance case counts by date of specimen and S-gene target failure status with an autoregressive model that allowed for time-varying differences in the transmission advantage of the Delta variant where the evidence supported this. By assuming a gamma distributed generation distribution we then estimated the generation time distribution and transmission advantage of the Omicron variant that would be required to explain this time varying advantage. We repeated this estimation process using two different prior estimates for the generation time of the Delta variant first based on household transmission and then based on its intrinsic generation time.\n\nResultsVisualising our growth rate estimates provided initial evidence for a difference in generation time distributions. Assuming a generation time distribution for Delta with a mean of 2.5-4 days (90% credible interval) and a standard deviation of 1.9-3 days we estimated a shorter generation time distribution for Omicron with a mean of 1.5-3.2 days and a standard deviation of 1.3-4.6 days. This implied a transmission advantage for Omicron in this setting of 160%-210% compared to Delta. We found similar relative results using an estimate of the intrinsic generation time for Delta though all estimates increased in magnitude due to the longer assumed generation time.\n\nConclusionsWe found that a reduction in the generation time of Omicron compared to Delta was able to explain the observed variation over time in the transmission advantage of the Omicron variant. However, this analysis cannot rule out the role of other factors such as differences in the populations the variants were mixing in, differences in immune escape between variants or bias due to using the test to test distribution as a proxy for the generation time distribution.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sam Abbott", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Katharine Sherratt", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Moritz Gerstung", - "author_inst": "German Cancer Research Centre DKFZ" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.08.22268950", "rel_title": "Modelling COVID-19 Vaccine Breakthrough Infections in Highly Vaccinated Israel - the effects of waning immunity and third vaccination dose", @@ -446153,6 +447163,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.09.22268969", + "rel_title": "Omicron Impact in India: An Early Analysis of the Ongoing COVID-19 Third Wave", + "rel_date": "2022-01-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.09.22268969", + "rel_abs": "The Omicron variant of coronavirus has caused major disruptions world-wide with countries struggling to manage the overwhelming number of infections. Omicron is found to be significantly more transmissible compared to its predecessors and therefore almost every impacted country is exhibiting new infection peaks than seen earlier. In this work, we analyze the global statistics of Omicron-impacted countries including South Africa, the United Kingdom, the United States, France, and Italy to quantitatively estimate the intensity and severity of recent waves. Next, these statistics are used to estimate the impact of Omicron in India, which is experiencing an intense third wave of COVID-19 since 28 Dec., 2021. The rapid surge in the daily number of infections, comparable to the global trends, strongly suggests the dominance of the Omicron variant in infections in India. The logarithmic regression suggests the early growth rate of infections in this wave is nearly four times that in the second wave. Another notable difference in this wave is the relatively concurrent arrival of outbreaks all across the country; the effective reproduction number (Rt) although has significant variations among different regions. The test positivity rate (TPR) also displays a rapid growth in the last 10 days in several states. Preliminary estimates with the Susceptible-Infected-Removed (SIR) model suggest that the peak in India to occur in late January 2022 with a caseload exceeding that in the second wave. Although global Omicron trends, as analyzed in this work, suggest a decline in case fatality rate and hospitalizations compared to Delta, a sudden accumulation of active infections can potentially choke the already stressed healthcare infrastructure for the next few weeks.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Rajesh Ranjan", + "author_inst": "IIT Kanpur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.10.22268897", "rel_title": "Epidemiology of SARS-CoV-2 infection in Italy using real-world data: methodology and cohort description of the second phase of web-based EPICOVID19 study.", @@ -447752,65 +448781,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.07.22268869", - "rel_title": "BNT162b2 post-exposure-prophylaxis against COVID-19", - "rel_date": "2022-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268869", - "rel_abs": "BackgroundDuring the COVID-19 pandemic, post-exposure-prophylaxis is not a practice. Following exposure, only patient isolation is imposed. Moreover, no therapeutic prevention approach is applied. We asked whether evidence exists for reduced mortality rate following post-exposure-prophylaxis.\n\nMethodsTo estimate the effectiveness of post-exposure-prophylaxis, we obtained data from the Israeli Ministry of Health (MoH) registry. The study population consisted of Israeli residents aged 12 years and older, identified for the first time as PCR-positive for SARS-CoV-2, between December 20th, 2020 (the beginning of the vaccination campaign) and October 7th, 2021. We compared \"recently injected\" patients - that proved PCR-positive on the same day or on one of the five consecutive days after first vaccination (representing an unintended post-exposure-prophylaxis), to unvaccinated control group.\n\nResultsAmong Israeli residents identified PCR-positive for SARS-CoV-2, 11,690 were found positive on the day they received their first vaccine injection (BNT162b2) or on one of the 5 days thereafter. In patients over 65 years, 143 deaths occurred among 1413 recently injected (10.12%) compared to 280 deaths among the 1413 unvaccinated (19.82%), odd ratio (OR) 0.46 (95% confidence interval (CI), 0.36 to 0.57; P<0.001). The most significant reduction in the death toll was observed among the 55 to 64 age group, with 8 deaths occurring among the 1322 recently injected (0.61%) compared to 43 deaths among the 1322 unvaccinated control (3.25%), OR 0.18 (95% CI, 0.07 to 0.39; P<0.001).\n\nConclusionPost-exposure-prophylaxis is effective against death in COVID-19 infection.\n\nIsraeli MoH Registry NumberHMO-0372-20", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Zohar Shemuelian", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - }, - { - "author_name": "Yehuda Warszawer", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - }, - { - "author_name": "Omri Or", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - }, - { - "author_name": "Sagit Arbel-Alon", - "author_inst": "The Ministry of Welfare and Social Affairs, Chief Physician, Government of Israel, Jerusalem, Israel" - }, - { - "author_name": "Hilla Giladi", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - }, - { - "author_name": "Meytal Avgil Tsadok", - "author_inst": "TIMNA-Israel Ministry of Health's Big Data Platform, Ministry of Health, Jerusalem, Israel" - }, - { - "author_name": "Roy Cohen", - "author_inst": "TIMNA-Israel Ministry of Health's Big Data Platform, Ministry of Health, Jerusalem, Israel" - }, - { - "author_name": "Galit Shefer", - "author_inst": "TIMNA-Israel Ministry of Health's Big Data Platform, Ministry of Health, Jerusalem, Israel" - }, - { - "author_name": "Antonello Maruotti", - "author_inst": "Department Law, Economics, Politics and Modern Languages, Libera Universita' Maria SS Assunta, Rome, Italy" - }, - { - "author_name": "Giovanna Jona Lasinio", - "author_inst": "Depertment of Statistical Sciences, University of Rome La Sapienza" - }, - { - "author_name": "Eithan Galun", - "author_inst": "Goldyne Savad Institute of Gene and Cell Therapy, Hadassah Hebrew University Hospital, Jerusalem Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.05.22268777", "rel_title": "Persistence of immunity and impact of a third (booster) dose of an inactivated SARS-CoV-2 vaccine, BBV152; a phase 2, double-blind, randomised controlled trial", @@ -448278,6 +449248,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.07.475406", + "rel_title": "Comprehensive analysis of disease pathology in immunocompetent and immunocompromised hamster models of SARS-CoV-2 infection", + "rel_date": "2022-01-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.07.475406", + "rel_abs": "The pathogenesis of SARS-CoV-2 in the context of a specific immunological niche is not fully understood. Here, we used a golden Syrian hamster model to systematically evaluate the kinetics of host response to SARS-CoV-2 infection, following disease pathology, viral loads, antibody responses, and inflammatory cytokine expression in multiple organs. The kinetics of SARS-CoV-2 pathogenesis and genomewide lung transcriptome was also compared between immunocompetent and immunocompromised hamsters. We observed that the body weight loss was proportional to the SARS-CoV-2 infectious dose and lasted for a short time only in immunocompetent hamsters. Body weight loss was more prominent and prolonged in infected immunocompromised hamsters. While the kinetics of viral replication and peak live viral loads were not significantly different at low and high infectious doses (LD and HD), the HD-infected immunocompetent animals developed severe lung disease pathology. The immunocompetent animals cleared the live virus in all tested tissues by 12 days post-infection and generated a robust serum antibody response. In contrast, immunocompromised hamsters mounted an inadequate SARS-CoV-2 neutralizing antibody response, and the virus was detected in the pulmonary and multiple extrapulmonary organs until 16 days post-infection. These hamsters also had prolonged moderate inflammation with severe bronchiolar-alveolar hyperplasia/metaplasia. Consistent with the difference in disease presentation, distinct changes in the expression of inflammation and immune cell response pathways and network genes were seen in the lungs of infected immunocompetent and immunocompromised animals. This study highlights the interplay between the kinetics of viral replication and the dynamics of SARS-CoV-2 pathogenesis at organ-level niches and maps how COVID-19 symptoms vary in different immune contexts. Together, our data suggest that the histopathological manifestations caused by progressive SARS-CoV-2 infection may be a better predictor of COVID-19 severity than individual measures of viral load, antibody response, and cytokine storm at the systemic or local (lungs) levels in the immunocompetent and immunocompromised hosts.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Santhamani Ramasamy", + "author_inst": "Rutgers University" + }, + { + "author_name": "Afsal Kolloli", + "author_inst": "Rutgers University" + }, + { + "author_name": "Ranjeet Kumar", + "author_inst": "Rutgers University" + }, + { + "author_name": "Seema Hussain", + "author_inst": "Rutgers University" + }, + { + "author_name": "Patricia Soteropoulos", + "author_inst": "Rutgers University" + }, + { + "author_name": "Theresa Chang", + "author_inst": "Rutgers University" + }, + { + "author_name": "Selvakumar Subbian", + "author_inst": "Rutgers University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2022.01.04.21268536", "rel_title": "Prevalence, characteristics, and predictors of Long COVID among diagnosed cases of COVID-19", @@ -449618,33 +450631,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.03.22268663", - "rel_title": "The Governance of Pandemics in Primary Health Care: The Governance Strategies Adopted by Health Facility Governing Committees in Times of COVID Pandemic in Tanzania", - "rel_date": "2022-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.03.22268663", - "rel_abs": "The governance of COVID 19 in Lower and Middle-Income Countries (LMICs) is very critical for curbing its effects. However, it is unknown what governance strategies are adopted by Health Facility Governing Committees (HFGCs) s as a response to the pandemic. We employed an exploratory qualitative design to study the governance strategies adopted by HFGCs during the COVID19. Since COVID 19 is new, an inductive approach was used as it involves analyzing collected data with little or no predetermined theory for the study. A purposive sampling technique was employed in which multistage clustered sampling was used to select regions, councils, health facilities and respondents. In-depth interviews with HFGCs chairpersons and Focus Group Discussions with members of HFGCs were used to collect data. The data were analyzed based on the themes which emerged during data collection. We found five governance strategies that were found to be commonly adopted by many HFGCs which are financial allocation, re-planing, mobilization of resources, community sensitization and mobilization of stakeholders. however, these governance structures were not all adopted by all HFGCs. The HFGCs slowly adopted governance strategies in the times of COVID 19 pandemics because were unprepared. Despite being empowered by the Direct Health Facility Financing, still, the newest of the COVID 19 has been a challenge to many HFGCs. This calls for urgent capacity building for governance institutions on how to deal will pandemics in primary health facilities.\n\nKey Questions Box O_TEXTBOXKey Questions\n\nWhat is Already Known?[tpltrtarr] Governance of pandemics is very critical for minimizing its effects\n[tpltrtarr]Government in Lower and Middle-Income Countries (LMICs) reacted differently to bring the COVID 19 pandemic under control\n[tpltrtarr]Little is known on the governance strategies adopted by Health Facility Governing Committees (HFGCs) to control COVID 19 at the primary health care facilities in LMICs\n\n\nWhat are the new findings?[tpltrtarr] HFGCs response to the COVID 19 is mixed as some HFGCs were so active and others were so slowly in instituting governance strategies to combat the pandemic\n[tpltrtarr]The common governance strategies adopted were financial allocation, re-planning, embolization of resources, community sensitization and stakeholders mobilization\n[tpltrtarr]HFGCs in LMICs were not well prepared for the pandemic at the community level\n\n\nWhat do new findings imply?[tpltrtarr] Capacitated HFGCs in both soft and hard aspects cornerstone for effective governance of the pandemics in primary health care\n[tpltrtarr]Preparedness of pandemics in LMICs needs to go beyond upper-level governance structures\n\n\nC_TEXTBOX", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Anosisye Mwandulusya Kesale", - "author_inst": "Mzumbe University" - }, - { - "author_name": "Christopher Mahonge", - "author_inst": "Sokoine University of Agriculture" - }, - { - "author_name": "Mikidadi Muhanga", - "author_inst": "Sokoine University of Agriculture" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2022.01.05.22268808", "rel_title": "Adherence of SARS-CoV-2 delta variant to surgical mask and N95 respirators", @@ -449899,6 +450885,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.05.22268788", + "rel_title": "High Sensitivity and NPV for BinaxNOW Rapid Antigen Test in Children at a Mass Testing Site During Prevalent Delta Variant", + "rel_date": "2022-01-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268788", + "rel_abs": "SARS-CoV-2 continues to develop new, increasingly infectious variants including delta and omicron. We evaluated the efficacy of the Abbott BinaxNOW Rapid Antigen Test against Reverse Transcription Polymerase Chain Reaction (\"RT-PCR\") in 1054 pediatric participants presenting to a high-volume Coronavirus Disease 2019 (COVID-19) testing site while the delta variant was predominant. Participants were grouped by COVID-19 exposure and symptom status. RT-PCR demonstrated an overall prevalence of 5.2%. For all participants, sensitivity of the BinaxNOW was 92.7% (95% CI 82.4%-98.0%) and specificity was 98.0% (95% CI 97.0%-98.8%). For symptomatic participants, positive predictive value (PPV) was 72.7% (95% CI 54.5%-86.7%) and negative predictive value (NPV) was 99.2% (95% CI 98.2%-100%). Among asymptomatic participants, PPV was 71.4% (95% CI 53.7%-85.4%) and NPV was 99.7% (95% CI 99.0%-100%). Our reported sensitivity and NPV are higher than other pediatric studies, potentially because of higher viral load from the delta variant, but specificity and PPV are lower.\n\nImportanceThe BinaxNOW rapid antigen COVID-19 test had a sensitivity of nearly 92% in both symptomatic and asymptomatic children when performed at a high-throughput setting during the more transmissible delta variant dominant period. The test may play an invaluable role in asymptomatic screening and keeping children safe in school.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Kristie J Sun", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Mary Jane E Vaeth", + "author_inst": "Baltimore Convention Center Field Hospital" + }, + { + "author_name": "Matthew L Robinson", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Maryam Elhabashy", + "author_inst": "University of Maryland Baltimore County" + }, + { + "author_name": "Ishaan Gupta", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Sophia Purekal", + "author_inst": "Baltimore Convention Center Field Hospital" + }, + { + "author_name": "Elizabeth Adrianne Duque Hammershaimb", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Ria Peralta", + "author_inst": "Nova Southeastern University College of Osteopathic Medicine" + }, + { + "author_name": "Asia Mitchell", + "author_inst": "Baltimore Convention Center Field Hospital" + }, + { + "author_name": "Maisha Foyez", + "author_inst": "Baltimore Convention Center Field Hospital" + }, + { + "author_name": "J Kristie Johnson", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "James R Ficke", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Yukari C Manabe", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "James D Campbell", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Charles W Callahan", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Charles F Locke", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Melinda Kantsiper", + "author_inst": "Johns Hopkins Bayview Medical Center" + }, + { + "author_name": "- CONQUER COVID Consortium", + "author_inst": "" + }, + { + "author_name": "Jeffrey Fink", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Henry J Michtalik", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Shaker M Eid", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Lee-Ann Wagner", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Mark Phillips", + "author_inst": "Johns Hopkins Community Physicians" + }, + { + "author_name": "Zishan K Siddiqui", + "author_inst": "Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.06.22268745", "rel_title": "Older Adults Mount Less Durable Humoral Responses to a Two-dose COVID-19 mRNA Vaccine Regimen, but Strong Initial Responses to a Third Dose", @@ -451287,65 +452384,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.01.04.475015", - "rel_title": "SARS-CoV-2 Infection of Microglia Elicits Pro-inflammatory Activation and Apoptotic Cell Death", - "rel_date": "2022-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.04.475015", - "rel_abs": "Accumulating evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes various neurological symptoms in coronavirus disease 2019 (COVID-19) patients. The most dominant immune cells in the brain are microglia. Yet, the relationship between neurological manifestations, neuroinflammation, and host immune response of microglia to SARS-CoV-2 has not been well characterized. Here, we report that SARS-CoV-2 can directly infect human microglia, eliciting M1-like pro-inflammatory responses, followed by cytopathic effects. Specifically, SARS-CoV-2 infected human microglial clone 3 (HMC3), leading to inflammatory activation and cell death. RNA-seq analysis also revealed that ER stress and immune responses were induced in the early and apoptotic processes in the late phase of viral infection. SARS-CoV-2-infected HMC3 showed the M1 phenotype and produced pro-inflammatory cytokines such as interleukin (IL)-1{beta}, IL-6, and tumour necrosis factor (TNF-), but not the anti-inflammatory cytokine IL-10. After this pro-inflammatory activation, SARS-CoV-2 infection promoted both intrinsic and extrinsic death receptor-mediated apoptosis in HMC3. Using K18-hACE2 transgenic mice, murine microglia were also infected by intranasal inoculation of SARS-CoV-2. This infection induced the acute production of pro-inflammatory microglial IL-6 and TNF- and provoked a chronic loss of microglia. Our findings suggest that microglia are potential mediators of SARS-CoV-2-induced neurological problems and, consequently, can be targets of therapeutic strategies against neurological diseases in COVID-19 patients.\n\nIMPORTANCERecent studies reported neurological manifestations and complications in COVID-19 patients, which are associated with neuroinflammation. As microglia are the dominant immune cells in brains, it needs to be elucidate the relationship between neuroinflammation and host immune response of microglia to SARS-CoV-2. Here, we suggest that SARS-CoV-2 can directly infect human microglia with cytopathic effect (CPE) using human microglial clone 3 (HMC3). The infected microglia were promoted to pro-inflammatory activation following apoptotic cell death. This pro-inflammatory activation was accompanied by the high production of pro-inflammatory cytokines, and led to neurotoxic-M1 phenotype polarization. In vivo, murine microglia were infected and produced pro-inflammatory cytokines and provoked a chronic loss using K18-hACE2 mice. Thus, our data present that SARS-CoV-2-infected microglia are potential mediators of neurological problems in COVID-19 patients. In addition, HMC3 cells are susceptible to SARS-CoV-2 and exhibit the CPE, which can be further used to investigate cellular and molecular mechanisms of neuroinflammation reported in COVID-19 patients.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Gi Uk Jeong", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Jaemyun Lyu", - "author_inst": "Arontier Co., Ltd." - }, - { - "author_name": "Kyun-Do Kim", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Young Cheul Chung", - "author_inst": "Korea Institute of Toxicology" - }, - { - "author_name": "Gun Young Yoon", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Sumin Lee", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Insu Hwang", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Won-Ho Shin", - "author_inst": "Korea Institute of Toxicology" - }, - { - "author_name": "Junsu Ko", - "author_inst": "Arontier Co., Ltd." - }, - { - "author_name": "June-Yong Lee", - "author_inst": "Yonsei University" - }, - { - "author_name": "Young-Chan Kwon", - "author_inst": "Korea Research Institute of Chemical Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.04.474979", "rel_title": "SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein", @@ -451601,6 +452639,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2022.01.05.475095", + "rel_title": "Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2", + "rel_date": "2022-01-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.05.475095", + "rel_abs": "The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In the present work, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 {micro}M and 66 {micro}M. In addition, eight compounds inhibited PLpro with IC50 ranging from 1.7 {micro}M to 46 {micro}M. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Lucianna H. Santos", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Thales Kronenberger", + "author_inst": "University Hospital Tubingen" + }, + { + "author_name": "Renata G Almeida", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Elany Barbosa da Silva", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Rafael E O Rocha", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Joyce C Oliveira", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Luiza V Barreto", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Danielle Skinner", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Pavla Fajtova", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Miriam A Giardini", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Brendon Woodworth", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Conner Bardine", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Andre L Lourenco", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Charles S Craik", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Antti Poso", + "author_inst": "University of Eastern Finland" + }, + { + "author_name": "Larissa M Podust", + "author_inst": "University of California San Diego" + }, + { + "author_name": "James H McKerrow", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Jair L Siqueira-Neto", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Eufranio N da Silva Junior", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Rafaela Ferreira", + "author_inst": "Universidade Federal de Minas Gerais" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.01.05.475107", "rel_title": "Autophagy and evasion of immune system by SARS-CoV-2. Structural features of the Non-structural protein 6 from Wild Type and Omicron viral strains interacting with a model lipid bilayer.", @@ -453093,117 +454226,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.04.474908", - "rel_title": "Maternal cytokine response after SARS-CoV-2 infection during pregnancy", - "rel_date": "2022-01-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.04.474908", - "rel_abs": "ObjectiveDysregulation of the immune system during pregnancy is associated with adverse pregnancy outcomes. Recent studies report cytokine changes during the acute phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We examine whether there is a lasting association between SARS-CoV-2 infection during pregnancy and peripheral blood cytokine levels.\n\nStudy designWe conducted a case-control study at the Mount Sinai health system in NYC including 100 SARS-CoV-2 IgG antibody positive people matched to 100 SARS-CoV-2 IgG antibody negative people on age, race/ethnicity, parity, and insurance status. Blood samples were collected at a median gestational age of 34 weeks. Levels of 14 cytokines were measured.\n\nResultsIndividual cytokine levels and cytokine cluster Eigenvalues did not differ significantly between groups, indicating no persisting maternal cytokine changes after SARS-CoV-2 infection during pregnancy.\n\nConclusionOur findings suggest that the acute inflammatory response after SARS-CoV-2 infection may be restored to normal values during pregnancy.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Frederieke A.J. Gigase", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Nina M. Molenaar", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Roy D. Missall", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Anna-Sophie Rommel", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Whitney Lieb", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Erona Ibroci", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Sophie Ohrn", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Jezelle Lynch", - "author_inst": "Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Rachel Brody", - "author_inst": "Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Rebecca H. Jessel", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Rhoda S. Sperling", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Corina Lesseur", - "author_inst": "Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Francesco Callipari", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Romeo R. Galang", - "author_inst": "CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Margaret C. Snead", - "author_inst": "CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Teresa Janevic", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Joanne Stone", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Elizabeth A. Howell", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Jia Chen", - "author_inst": "Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Victor J.M. Pop", - "author_inst": "Department of Clinical and Medical Psychology, Tilburg University, Tilburg, The Netherlands" - }, - { - "author_name": "Siobhan M. Dolan", - "author_inst": "Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Veerle Bergink", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - }, - { - "author_name": "Lotje D. De Witte", - "author_inst": "Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.01.04.474803", "rel_title": "A synthetic bispecific antibody capable of neutralizing SARS-CoV-2 Delta and Omicron", @@ -453543,6 +454565,81 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.12.28.21268460", + "rel_title": "Comparison of infectious SARS-CoV-2 from the nasopharynx of vaccinated and unvaccinated individuals", + "rel_date": "2022-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.28.21268460", + "rel_abs": "The frequency of SARS-CoV-2 breakthrough infections in fully vaccinated individuals increased with the emergence of the Delta variant, particularly with longer time from vaccine completion. However, whether breakthrough infections lead to onward transmission remains unclear. Here, we conducted a study involving 125 patients comprised of 72 vaccinated and 53 unvaccinated individuals, to assess the levels of infectious virus in vaccinated and unvaccinated individuals. Quantitative plaque assays showed no significant differences in the titers of virus between these cohorts. However, the proportion of nasopharyngeal samples with culturable virus was lower in the vaccinated patients relative to unvaccinated patients (21% vs. 40%). Finally, time-to-event analysis with Kaplan-Myer curves revealed that protection from culturable infectious virus waned significantly starting at 5 months after completing a 2-dose regimen of mRNA vaccines. These results have important implications in timing of booster dose to prevent onward transmission from breakthrough cases.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Mario A. Pena-Hernandez", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Jon Klein", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Amyn Malik", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Andreas Coppi", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Chaney C Kalinich", + "author_inst": "Yale School of Public health" + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Julio Silva", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "- Yale SARS-CoV-2 Genomic Surveillance Initiative", + "author_inst": "" + }, + { + "author_name": "David R. Peaper", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Marie Landry", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Craig Wilen", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Wade L Schulz", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Saad B. Omer", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.02.473343", "rel_title": "RG203KR mutations in SARS-CoV-2 Nucleocapsid: Assessing the impact using Virus-like particle model system", @@ -455099,57 +456196,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.30.474610", - "rel_title": "Robust expansion of phylogeny for fast-growing genome sequence data", - "rel_date": "2022-01-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.30.474610", - "rel_abs": "Massive sequencing of SARS-CoV-2 genomes has led to a great demand for adding new samples to a reference phylogeny instead of building the tree from scratch. To address such challenge, we proposed an algorithm TIPars by integrating parsimony analysis with pre-computed ancestral sequences. Compared to four state-of-the-art methods on four benchmark datasets (SARS-CoV-2, Influenza virus, Newcastle disease virus and 16S rRNA genes), TIPars achieved the best performance in most tests. It took only 21 seconds to insert 100 SARS-CoV-2 genomes to a 100k-taxa reference tree using near 1.4 gigabytes of memory. Its efficient and accurate phylogenetic placements and incrementation for phylogenies with highly similar and divergent sequences suggest that it will be useful in a wide range of studies including pathogen molecular epidemiology, microbiome diversity and systematics.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Yongtao Ye", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited" - }, - { - "author_name": "Marcus Shum", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited" - }, - { - "author_name": "Joseph Tsui", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited" - }, - { - "author_name": "Guangchuang Yu", - "author_inst": "Southern Medical University" - }, - { - "author_name": "David Smith", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Huachen Zhu", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited, Joint Institute of Virology (Shantou University/The University of Hong Kong), EKIH" - }, - { - "author_name": "Joseph Wu", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited" - }, - { - "author_name": "Yi Guan", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited, Joint Institute of Virology (Shantou University/The University of Hong Kong), EKIH" - }, - { - "author_name": "Tommy Tsan-Yuk Lam", - "author_inst": "The University of Hong Kong, Laboratory of Data Discovery for Health Limited, Joint Institute of Virology (Shantou University/The University of Hong Kong), EKIH" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.30.474580", "rel_title": "SARS-CoV-2 entry sites are present in all structural elements of the human glossopharyngeal and vagal nerves: clinical implications", @@ -455477,6 +456523,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.01.22268615", + "rel_title": "Preserved recognition of Omicron Spike following COVID-19 mRNA vaccination in pregnancy", + "rel_date": "2022-01-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.01.22268615", + "rel_abs": "BackgroundSARS-CoV-2 infection is associated with enhanced disease severity in pregnant women. Despite the potential of COVID-19 vaccines to reduce severe disease, vaccine uptake remained relatively low among pregnant women. Just as coordinated messaging from the CDC and leading obstetrics organizations began to increase vaccine confidence in this vulnerable group, the evolution of SARS-CoV-2 variants of concerns (VOC) including the Omicron VOC raised new concerns about vaccine efficacy, given their ability to escape vaccine-induced neutralizing antibodies. Early data point to a milder disease course following omicron VOC infection in vaccinated individuals. Thus, these data suggest that alternate vaccine induced immunity, beyond neutralization, may continue to attenuate omicron disease, such as antibody-Fc-mediated activity. However, whether vaccine induced antibodies raised in pregnancy continue to bind and leverage Fc-receptors remains unclear.\n\nMethodsVOC including Omicron receptor binding domain (RBD) or full Spike specific antibody isotype binding titers and Fc{gamma}R binding were analyzed in pregnant women after the full dose regimen of either Pfizer/BioNtech BNT62b2 (n=10) or Moderna mRNA-1273 (n=10) vaccination using a multiplexing Luminex assay.\n\nFindingsComparable, albeit reduced, isotype recognition was observed to the Omicron Spike and receptor binding domain (RBD) following both vaccines. Yet, despite the near complete loss of Fc-receptor binding to the Omicron RBD, Fc-receptor binding was largely preserved to the Omicron Spike.\n\nInterpretationReduced binding titer to the Omicron RBD aligns with observed loss of neutralizing activity. Despite the loss of neutralization, preserved Omicron Spike recognition and Fc-receptor binding potentially continues to attenuate disease severity in pregnant women.\n\nFundingNIH and the Bill and Melinda Gates Foundation", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Yannic C Bartsch", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA" + }, + { + "author_name": "Caroline Atyeo", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA" + }, + { + "author_name": "Jaewon Kang", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA" + }, + { + "author_name": "Kathryn J Gray", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA" + }, + { + "author_name": "Andrea G. Edlow", + "author_inst": "Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Vincent Center for" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.01.22268603", "rel_title": "SARS-CoV-2 screening in patients in need of urgent inpatient treatment in the Emergency Department (ED) by digitally integrated point-of-care PCR: A clinical cohort study", @@ -457213,53 +458298,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.31.21268583", - "rel_title": "From Delta to Omicron: analysing the SARS-CoV-2 epidemic in France using variant-specific screening tests (September 1 to December 18, 2021)", - "rel_date": "2022-01-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.31.21268583", - "rel_abs": "We analysed 131,478 SARS-CoV-2 variant screening tests performed in France from September 1st to December 18, 2021. Tests consistent with the presence of the Omicron variant exhibit significantly higher cycle threshold Ct values, which could indicate lower amounts of virus genetic material. We estimate that the transmission advantage of the Omicron variant over the Delta variant is +105% (95% confidence interval: 96-114%). Based on these data, we use mechanistic mathematical modelling to explore scenarios for early 2022.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Mircea T. Sofonea", - "author_inst": "Univ. Montpellier" - }, - { - "author_name": "Benedicte Roquebert", - "author_inst": "Cerba Laboratory" - }, - { - "author_name": "Vincent Foulongne", - "author_inst": "CHU de Montpellier" - }, - { - "author_name": "Laura Verdurme", - "author_inst": "CERBA Laboratory" - }, - { - "author_name": "Sabine Trombert-Paolantoni", - "author_inst": "CERBA Laboratory" - }, - { - "author_name": "Mathilde Roussel", - "author_inst": "CERBA Laboratory" - }, - { - "author_name": "Stephanie Haim-Boukobza", - "author_inst": "CERBA Laboratory" - }, - { - "author_name": "Samuel Alizon", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.31.21268596", "rel_title": "Social isolation and psychological distress among southern US college students in the era of COVID-19", @@ -457559,6 +458597,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.28.21268481", + "rel_title": "Vaccination-infection interval determines cross-neutralization potency to SARS-CoV-2 Omicron after breakthrough infection by other variants", + "rel_date": "2022-01-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.28.21268481", + "rel_abs": "BackgroundThe immune profile against SARS-CoV-2 has dramatically diversified due to a complex combination of exposure to vaccines and infection by various lineages/variants, likely generating a heterogeneity in protective immunity in a given population. To further complicate this, the Omicron variant, with numerous spike mutations, has emerged. These circumstances have created the need to assess the potential of immune evasion by the Omicron in individuals with various immune histories.\n\nMethodsThe neutralization susceptibility of the variants including the Omicron and their ancestor was comparably assessed using a panel of plasma/serum derived from individuals with divergent immune histories. Blood samples were collected from either mRNA vaccinees or from those who suffered from breakthrough infections by the Alpha/Delta with multiple time intervals following vaccination.\n\nFindingsThe Omicron was highly resistant to neutralization in fully vaccinated individuals without a history of breakthrough infections. In contrast, robust cross-neutralization against the Omicron were induced in vaccinees that experienced breakthrough infections. The time interval between vaccination and infection, rather than the variant types of infection, was significantly correlated with the magnitude and potency of Omicron-neutralizing antibodies.\n\nConclusionsImmune histories with breakthrough infections can overcome the resistance to infection by the Omicron, with the vaccination-infection interval being the key determinant of the magnitude and breadth of neutralization. The diverse exposure history in each individual warrants a tailored and cautious approach to understanding population immunity against the Omicron and future variants.\n\nFundingThis study was supported by grants from the Japan Agency for Medical Research and Development (AMED).", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Sho Miyamoto", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Takeshi Arashiro", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yu Adachi", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Saya Moriyama", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Hitomi Kinoshita", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Takayuki Kanno", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Shinji Saito", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Harutaka Katano", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Shun Iida", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Akira Ainai", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Ryutaro Kotaki", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Souichi Yamada", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yudai Kuroda", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Tsukasa Yamamoto", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Keita Ishijima", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Eun-Sil Park", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yusuke Inoue", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yoshihiro Kaku", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Minoru Tobiume", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Naoko Iwata-Yoshikawa", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Nozomi Shiwa-Sudo", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Kenzo Tokunaga", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Seiya Ozono", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Takuya Hemmi", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Akira Ueno", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Noriko Kishida", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Shinji Watanabe", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Kiyoko Nojima", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yohei Seki", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Takuo Mizukami", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Hideki Hasegawa", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Hideki Ebihara", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Ken Maeda", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Shuetsu Fukushi", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yoshimasa Takahashi", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Tadaki Suzuki", + "author_inst": "National Institute of Infectious Diseases" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.26.21268408", "rel_title": "Severity of COVID-19 reinfection and associated risk factors: findings of a cross-sectional study in Bangladesh", @@ -459147,45 +460344,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.12.29.474469", - "rel_title": "Unsupervised genome-wide cluster analysis: nucleotide sequences of the omicron variant of SARS-CoV-2 are similar to sequences from early 2020", - "rel_date": "2021-12-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.29.474469", - "rel_abs": "The GISAID database contains more than 1,000,000 SARS-CoV-2 genomes, including sequences of the recently discovered SARS-CoV-2 omicron variant and of prior SARS-CoV-2 strains that have been collected from patients around the world since the beginning of the pandemic. We applied unsupervised cluster analysis to the SARS-CoV-2 genomes, assessing their similarity at a genome-wide level based on the Jaccard index and principal component analysis. Our analysis results show that the omicron variant sequences are most similar to sequences that have been submitted early in the pandemic around January 2020. Furthermore, the omicron variants in GISAID are spread across the entire range of the first principal component, suggesting that the strain has been in circulation for some time. This observation supports a long-term infection hypothesis as the omicron strain origin.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Georg Hahn", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Sanghun Lee", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Dmitry Prokopenko", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Surender Khurana", - "author_inst": "US Food and Drug Administration" - }, - { - "author_name": "Scott T. Weiss", - "author_inst": "Harvard Medical School, Harvard University, Boston, MA 02115, USA" - }, - { - "author_name": "Christoph Lange", - "author_inst": "Harvard School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.30.474453", "rel_title": "Preserved T cell reactivity to the SARS-CoV-2 Omicron variant indicates continued protection in vaccinated individuals.", @@ -459629,6 +460787,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2021.12.22.21268218", + "rel_title": "Soluble immune checkpoints are dysregulated in COVID-19 and heavy alcohol users with HIV infection", + "rel_date": "2021-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268218", + "rel_abs": "Immune checkpoints (ICPs) consist of paired receptor-ligand molecules that exert inhibitory or stimulatory effects on immune defense, surveillance, regulation, and self-tolerance. ICPs exist in both membrane and soluble forms in vivo and in vitro. Imbalances between inhibitory and stimulatory membrane-bound ICPs (mICPs) in malignant cells and immune cells in the tumor immune microenvironment (TIME) have been well documented. Blockades of inhibitory mICPs have emerged as an immense breakthrough in cancer therapeutics. However, the origin, structure, production regulation, and biological significance of soluble ICPs (sICPs) in health and disease largely remains elusive. Soluble ICPs can be generated through either alternative mRNA splicing and secretion or protease-mediated shedding from mICPs. Since sICPs are found in the bloodstream, they likely form a circulating immune regulatory system. In fact, there is increasing evidence that sICPs exhibit biological functions including (1) regulation of antibacterial immunity, (2) interaction with their mICP compartments to positively or negatively regulate immune responses, and (3) competition with their mICP compartments for binding to the ICP blocking antibodies, thereby reducing the efficacy of ICP blockade therapies. Here, we summarize current data of sICPs in cancer and infectious diseases. We particularly focus on sICPs in COVID-19 and HIV infection as they are the two ongoing global pandemics and have created the worlds most serious public health challenges. A \"storm\" of sICPs occurs in the peripheral circulation of COVID-19 patients and is associated with the severity of COVID-19. Similarly, sICPs are highly dysregulated in people living with HIV (PLHIV) and some sICPs remain dysregulated in PLHIV on antiretroviral therapy (ART), indicating these sICPs may serve as biomarkers of incomplete immune reconstitution in PLHIV on ART. We reveal that HIV infection in the setting of alcohol abuse exacerbates sICP dysregulation as PLHIV with heavy alcohol consumption have significantly elevated plasma levels of many sICPs. Thus, both stimulatory and inhibitory sICPs are present in the bloodstream of healthy people and their balance can be disrupted under pathophysiological conditions such as cancer, COVID-19, HIV infection, and alcohol abuse. There is an urgent need to study the role of sICPs in immune regulation in health and disease.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Wei Li", + "author_inst": "Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202" + }, + { + "author_name": "Fahim Syed", + "author_inst": "Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202" + }, + { + "author_name": "Richard X Yu", + "author_inst": "Department of Internal Medicine, School of Medicine, University of Nevada, Reno, NV 89502" + }, + { + "author_name": "Jing Yang", + "author_inst": "Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202" + }, + { + "author_name": "Ying Xia", + "author_inst": "Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202" + }, + { + "author_name": "Ryan F Relich", + "author_inst": "Indiana University School of Medicine" + }, + { + "author_name": "Shanxiang Zhang", + "author_inst": "Indiana University School of Medicine" + }, + { + "author_name": "Mandana Khalili", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Laurence Huang", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Melissa A Kacena", + "author_inst": "Indiana University School of Medicine" + }, + { + "author_name": "Xiaoqun Zheng", + "author_inst": "Wenzhou Medical University" + }, + { + "author_name": "Qigui Yu", + "author_inst": "Indiana University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.21.21268200", "rel_title": "Mathematical modelling of COVID-19 vaccination strategies in Kyrgyzstan", @@ -461253,53 +462474,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.27.21268462", - "rel_title": "Evolution of COVID-19 Health Disparities in Arizona", - "rel_date": "2021-12-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268462", - "rel_abs": "ObjectiveCOVID-19 burdens are disproportionally high in underserved and vulnerable groups in Arizona. As the pandemic progresses, it is unclear if the disparities have evolved. In this study, we aim to elicit the dynamic landscape of COVID-19 disparities at the community level and identify newly emerged vulnerable subpopulations.\n\nMaterials and MethodsWe compiled biweekly COVID-19 case counts of 274 zip code tabulation areas (ZCTAs) in Arizona from October 21, 2020, to November 25, 2021, during which the COVID-19 growth rate has changed significantly. Within each growth period, we detected health disparities by testing associations between the growth rate of COVID-19 cases in a ZCTA and the population composition of race/ethnicity, income, employment, and age. We then compared the associations between periods to discover temporal patterns of health disparities.\n\nResultsHigh percentage of Latinx or Black residents, high poverty rate, and young median age were risk factors of high cumulative COVID-19 case counts in a ZCTA. However, the impact of these factors on the growth rate of new COVID-19 cases varied. While high percentage of Black residents and young median age remained as risk factors of fast COVID-19 growth rate, high poverty rate became a protective factor. The association between the percentage of Latinx residents and the COVID-19 growth rate converted from positive to negative during summer 2021. The unemployment rate emerged as a new risk factor of fast COVID-19 growth rate after September 2021. Based on these findings, we identified 37 ZCTAs that are highly vulnerable to fast escalation of COVID-19 cases.\n\nDiscussion and ConclusionAs the pandemic progresses, disadvantaged communities continue suffering from escalated risk of COVID-19 infection. But the vulnerabilities have evolved. While the disparities related to Latinx ethnicity improved gradually, those related to Black ethnicity and young communities aggravated. The struggle of financially disadvantaged communities continued, although the burden had shifted from those living under the poverty line to those with a high unemployment rate. It is necessary to adjust current resource allocations and design and deploy new interventions to address emerging needs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Felix L Shen", - "author_inst": "Paradise Valley High School" - }, - { - "author_name": "Jingmin Shu", - "author_inst": "Arizona State University" - }, - { - "author_name": "Matthew Lee", - "author_inst": "Arizona State University" - }, - { - "author_name": "Hyunsung Oh", - "author_inst": "Arizona State University" - }, - { - "author_name": "Flavio Marsiglia", - "author_inst": "Arizona State University" - }, - { - "author_name": "Ming Li", - "author_inst": "University of Arizona" - }, - { - "author_name": "George Runger", - "author_inst": "Arizona State University" - }, - { - "author_name": "Li Liu", - "author_inst": "Arizona State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.28.21268472", "rel_title": "Neutralizing antibody responses to SARS-CoV-2: a population based seroepidemiological analysis in Delhi, India", @@ -461551,6 +462725,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.27.21268309", + "rel_title": "Replacement of the Gamma by the Delta variant in Brazil: impact of lineage displacement on the ongoing pandemic", + "rel_date": "2021-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268309", + "rel_abs": "The COVID-19 epidemic in Brazil was driven mainly by the spread of Gamma (P.1), a locally emerged Variant of Concern (VOC) that was first detected in early January 2021. This variant was estimated to be responsible for more than 96% of cases reported between January and June 2021, being associated with increased transmissibility and disease severity, a reduction in neutralization antibodies and effectiveness of treatments or vaccines, as well as diagnostic detection failure. Here we show that, following several importations predominantly from the USA, the Delta variant rapidly replaced Gamma after July 2021. However, in contrast to what was seen in other countries, the rapid spread of Delta did not lead to a large increase in the number of cases and deaths reported in Brazil. We suggest that this was likely due to the relatively successful early vaccination campaign coupled with natural immunity acquired following prior infection with Gamma. Our data reinforces reports of the increased transmissibility of the Delta variant and, considering the increasing concern due to the recently identified Omicron variant, argues for the necessity to strengthen genomic monitoring on a national level to quickly detect and curb the emergence and spread of other VOCs that might threaten global health.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Marta Giovanetti", + "author_inst": "Fundacao Oswaldo Cruz" + }, + { + "author_name": "Vagner Fonseca", + "author_inst": "Laboratorio de Genetica Celular e Molecular, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" + }, + { + "author_name": "Eduan Wilkinson", + "author_inst": "KwaZulu Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZuluNatal, Durban, South" + }, + { + "author_name": "Houriiyah Tegally", + "author_inst": "KwaZulu Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu Natal, Durban, Sout" + }, + { + "author_name": "Emmanuel James San", + "author_inst": "KwaZulu Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu Natal, Durban, Sout" + }, + { + "author_name": "Christian L. Althaus", + "author_inst": "University of Bern" + }, + { + "author_name": "Joilson Xavier", + "author_inst": "Laboratorio Central de Saude Publica do Estado de Minas Gerais, Fundacao Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil" + }, + { + "author_name": "Svetoslav Nanev Slavov", + "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto, SP, Brazil; Butantan Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Vincent Louis Viala", + "author_inst": "Butantan Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Alex Ranieri Jeronimo Lima", + "author_inst": "Butantan Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Gabriela Ribeiro", + "author_inst": "Butantan Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Jayme A. Souza-Neto", + "author_inst": "Sao Paulo State University (UNESP)" + }, + { + "author_name": "Heidge Fukumasu", + "author_inst": "Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil" + }, + { + "author_name": "Luiz Lehmann Coutinho", + "author_inst": "University of Sao Paulo, Centro de Genomica Funcional da ESALQ, Piracicaba, SP, Brazil" + }, + { + "author_name": "Rivaldo Venancio da Cunha", + "author_inst": "Fundacao Oswaldo Cruz, Bio Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil" + }, + { + "author_name": "Carla Freitas", + "author_inst": "Coordenacao Geral dos Laboratorios de Saude Publica Secretaria de Vigilancia em Saude, Ministerio da Saude, Brasilia, Distrito Federal, Brazil" + }, + { + "author_name": "Carlos F Campelo de A e Melo", + "author_inst": "Organizacao Pan-Americana da Sauude Organizacao Mundial da Sauude, Brasiilia, Distrito Federal, Brazil" + }, + { + "author_name": "Wildo Navegantes", + "author_inst": "Organizacao Pan Americana da Saude Organizacao Mundial da Saude, Brasilia, Distrito Federal, Brazil" + }, + { + "author_name": "Rodrigo Fabiano do Carmo Said", + "author_inst": "Organizacao Pan Americana da Saude Organizacao Mundial da Saude, Brasilia, Distrito Federal, Brazil" + }, + { + "author_name": "Maria Almiron", + "author_inst": "Organizacao Pan Americana da Saude Organizacao Mundial da Saude, Brasilia, Distrito Federal, Brazil" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Sandra Coccuzzo Sampaio", + "author_inst": "Instituto Butantan" + }, + { + "author_name": "Maria Carolina Elias", + "author_inst": "Instituto Butantan" + }, + { + "author_name": "Dimas Tadeu Covas", + "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto, SP, Brazil Butantan Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Edward C Holmes", + "author_inst": "University of Sydney" + }, + { + "author_name": "Jose Lourenco", + "author_inst": "University of Oxford" + }, + { + "author_name": "Simone Kashima", + "author_inst": "Hemocentro de Ribeirao Preto" + }, + { + "author_name": "Luiz Carlos Junior Alcantara", + "author_inst": "Oswaldo Cruz Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.26.21268421", "rel_title": "Relationship between temperature and relative humidity on the initial spread of COVID-19 cases and deaths in Brazil", @@ -463323,41 +464624,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.12.27.474315", - "rel_title": "Peptide-based epitope design on non-structural proteins of SARS-CoV-2", - "rel_date": "2021-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.27.474315", - "rel_abs": "The SARS-CoV-2 virus has caused the severe pandemic, COVID19 and since then its been critical to produce a potent vaccine to prevent the quick transmission and also to avoid alarming deaths. Among all type of vaccines peptide based epitope design tend to outshine with respect to low cost production and more efficacy. Therefore, we started with obtaining the necessary protein sequences from NCBI database of SARS-CoV-2 virus and filtered with respect to antigenicity, virulency, pathogenicity and non-homologous nature with human proteome using different available online tools and servers. The promising proteins was checked for containing common B and T-cell epitopes. The structure for these proteins were modeled from I-TASSER server followed by its refinement and validation. The predicted common epitopes were mapped on modeled structures of proteins by using Pepitope server. The surface exposed epitopes were docked with the most common allele DRB1*0101 using the GalaxyPepDock server. The epitopes, ELEGIQYGRS from Leader protein (NSP1), YGPFVDRQTA from 3c-like proteinase (nsp5), DLKWARFPKS from NSP9 and YQDVNCTEVP from Surface glycoprotein (spike protein) are the epitopes which has more hydrogen bonds. Hence these four epitopes could be considered as a more promising epitopes and these epitopes can be used for future studies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Swathika RS", - "author_inst": "SCBT, SASTRA University" - }, - { - "author_name": "Vimal S", - "author_inst": "SCBT, SASTRA University" - }, - { - "author_name": "Bhagya Shree E", - "author_inst": "SCBT, SASTRA University" - }, - { - "author_name": "Elakkiya Elumalai", - "author_inst": "Center for Bioinformatics, Pondicherry University" - }, - { - "author_name": "Krishna Kant Gupta", - "author_inst": "SCBT, SASTRA University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.27.474273", "rel_title": "Structures of the Omicron Spike trimer with ACE2 and an anti-Omicron antibody", @@ -463861,6 +465127,81 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.12.24.474095", + "rel_title": "Early Computational Detection of Potential High Risk SARS-CoV-2 Variants", + "rel_date": "2021-12-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.24.474095", + "rel_abs": "The ongoing COVID-19 pandemic is leading to the discovery of hundreds of novel SARS-CoV-2 variants on a daily basis. While most variants do not impact the course of the pandemic, some variants pose a significantly increased risk when the acquired mutations allow better evasion of antibody neutralisation in previously infected or vaccinated subjects or increased transmissibility. Early detection of such high risk variants (HRVs) is paramount for the proper management of the pandemic. However, experimental assays to determine immune evasion and transmissibility characteristics of new variants are resource-intensive and time-consuming, potentially leading to delays in appropriate responses by decision makers. Here we present a novel in silico approach combining spike (S) protein structure modelling and large protein transformer language models on S protein sequences to accurately rank SARS-CoV-2 variants for immune escape and fitness potential. These metrics can be combined into an automated Early Warning System (EWS) capable of evaluating new variants in minutes and risk-monitoring variant lineages in near real-time. The system accurately pinpoints the putatively dangerous variants by selecting on average less than 0.3% of the novel variants each week. With only the S protein nucleotide sequence as input, the EWS detects HRVs earlier and with better precision than baseline metrics such as the growth metric (which requires real-world observations) or random sampling. Notably, Omicron BA.1 was flagged by the EWS on the day its sequence was made available. Additionally, our immune escape and fitness metrics were experimentally validated using in vitro pseudovirus-based virus neutralisation test (pVNT) assays and binding assays. The EWS flagged as potentially dangerous all 16 variants (Alpha-Omicron BA.1/2/4/5) designated by the World Health Organisation (WHO) with an average lead time of more than one and a half months ahead of them being designated as such.\n\nOne-Sentence SummaryA COVID-19 Early Warning System combining structural modelling with machine learning to detect and monitor high risk SARS-CoV-2 variants, identifying all 16 WHO designated variants on average more than one and a half months in advance by selecting on average less than 0.3% of the weekly novel variants.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Karim Beguir", + "author_inst": "InstaDeep Ltd" + }, + { + "author_name": "Marcin J Skwark", + "author_inst": "InstaDeep Ltd" + }, + { + "author_name": "Yunguan Fu", + "author_inst": "InstaDeep Ltd" + }, + { + "author_name": "Thomas Pierrot", + "author_inst": "InstaDeep Ltd" + }, + { + "author_name": "Santiago Nicolas Lopez Carranza", + "author_inst": "InstaDeep Ltd" + }, + { + "author_name": "Alexandre Laterre", + "author_inst": "InstaDeep Ltd" + }, + { + "author_name": "Ibtissem Kadri", + "author_inst": "InstaDeep Ltd" + }, + { + "author_name": "Abir Korched", + "author_inst": "InstaDeep" + }, + { + "author_name": "Anna U Lowegard", + "author_inst": "InstaDeep" + }, + { + "author_name": "Bonny Gaby Lui", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Bianca Sanger", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Yunpeng Liu", + "author_inst": "BioNTech US" + }, + { + "author_name": "Asaf Poran", + "author_inst": "BioNTech US" + }, + { + "author_name": "Alexander Muik", + "author_inst": "BioNTech SE" + }, + { + "author_name": "Ugur Sahin", + "author_inst": "BioNTech SE" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.24.21268384", "rel_title": "Estimating the impact of implementation and timing of COVID-19 vaccination program in Brazil: a counterfactual analysis", @@ -465941,49 +467282,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.12.22.21268127", - "rel_title": "Humoral and cellular immune responses to SARS CoV-2 vaccination in Persons with Multiple Sclerosis and NMOSD patients receiving immunomodulatory treatments", - "rel_date": "2021-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268127", - "rel_abs": "BackgroundVaccination against SARS CoV-2 results in excellent personal protection against a severe course of COVID19. In persons with Multiple Sclerosis (PwMS) vaccination efficacy may be reduced by immunomodulatory medications.\n\nObjectiveTo assess the vaccination induced cellular and humoral immune response in PwMS receiving disease modifiying therapies.\n\nMethodsIn a monocentric observational study on PwMS and patients with Neuromyelitis optica we quantified the cellular and humoral immune responses to SARS CoV-2.\n\nResultsPwMS receiving Glatirameracetate, Interferon-{beta}, Dimethylfumarate, Cladribine or Natalalizumab had intact humoral and cellular immune responses following vaccination against SARS CoV-2. B-cell depleting therapies reduced B-cell responses but did not affect T cell responses. S1P inhibitors strongly reduced humoral and cellular immune responses.\n\nThere was a good agreement between the Interferon gamma release assay and the T-SPOT assay used to measure viral antigen induced T-cell responses.\n\nConclusionThis study demonstrates that S1P inhibitors impair the cellular and humoral immune response in SARS CoV-2 vaccination, whereas patients receiving B-cell depleting therapies mount an intact cellular immune response. These data can support clinicians in counselling their PwMS and NMOSD patients during the COVID 19 pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Henry Bock", - "author_inst": "Carl-Thiem Klinikum Cottbus" - }, - { - "author_name": "Thomas Juretzek", - "author_inst": "Carl-Thiem Klinkum Cottbus" - }, - { - "author_name": "Robert Handreka", - "author_inst": "Carl-Thiem Klinikum Cottbus" - }, - { - "author_name": "Johanna Ruhnau", - "author_inst": "Universitity Medicine Greifswald" - }, - { - "author_name": "Karl Reuner", - "author_inst": "Carl-Thiem Klinkum Cottbus" - }, - { - "author_name": "Heidrun Peltroche", - "author_inst": "Carl-Thiem Klinkum Cottbus" - }, - { - "author_name": "Alexander Dressel", - "author_inst": "Carl Thiem Klinikum" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.12.20.21268066", "rel_title": "Persisting Chemosensory Impairments in 366 Healthcare Workers Following COVID-19: An 11-Month Follow-up.", @@ -466199,6 +467497,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.21.21268203", + "rel_title": "Home Monitoring for Fever: An Inexpensive Screening Method to Prevent Household Spread of COVID-19", + "rel_date": "2021-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268203", + "rel_abs": "The COVID-19 pandemic surge has exceeded testing capacities in many parts of the world. We investigated the effectiveness of home temperature monitoring for early identification of COVID-19 patients.\n\nStudy DesignWe compared home temperature measurements from a convenience sample of 1180 individuals who reported being test positive for SARS-CoV-2 to an age, sex, and location matched control group of 1249 individuals who had not tested positive.\n\nMethodsAll individuals monitored their temperature at home using an electronic smartphone thermometer that relayed temperature measurements and symptoms to a centralized cloud based, de-identified data bank.\n\nResultsIndividuals varied in the number of times they monitored their temperature. When temperature was monitored for over 72 hours fever (> 37.6{degrees}C or 99.7{degrees}F or a change in temperature of > 1{degrees}C or 1.8{degrees}F) was detected in 73% of test positive individuals, a sensitivity comparable to rapid SARS-CoV-2 antigen tests. When compared our control group the specificity of fever for COVID-19 was 0.70. However, when fever was combined with complaints of loss of taste and smell, difficulty breathing, fatigue, chills, diarrhea, or stuffy nose the odds ratio of having COVID-19 was sufficiently high as to obviate the need to employ RTPCR or antigen testing to screen for and isolate coronavirus infected cases.\n\nConclusionsOur findings suggest that home temperature monitoring could serve as an inexpensive convenient screen for the onset of COVID-19, encourage earlier isolation of potentially infected individuals, and more effectively reduce the spread of infection in closed spaces.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Justin Kim", + "author_inst": "University of Florida College of Medicine" + }, + { + "author_name": "Marcus A Threadcraft", + "author_inst": "University of Florida College of Medicine" + }, + { + "author_name": "Wei Xue", + "author_inst": "University of Florida" + }, + { + "author_name": "Sijia Yue", + "author_inst": "University of Florida" + }, + { + "author_name": "Richard P Wenzel", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Frederick S Southwick", + "author_inst": "University of Florida College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.21.21268209", "rel_title": "Risk of Myopericarditis following COVID-19 mRNA vaccination in a Large Integrated Health System: A Comparison of Completeness and Timeliness of Two Methods", @@ -467779,49 +469116,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.24.21268370", - "rel_title": "A novel methodology for the synchronous collection and multimodal visualisation of continuous neurocardiovascular and neuromuscular physiological data in adults with long COVID", - "rel_date": "2021-12-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.24.21268370", - "rel_abs": "Reports suggest that adults with post-COVID-19 syndrome or long COVID may be affected by orthostatic intolerance syndromes, with autonomic nervous system dysfunction as a possible causal factor of neurocardiovascular instability (NCVI). Long COVID can also manifest as prolonged fatigue, which may be linked to neuromuscular function impairment (NMFI). The current clinical assessment for NCVI monitors neurocardiovascular performance upon the application of orthostatic stressors such as an active (i.e. self-induced) stand or a passive (tilt table) standing test. Lower limb muscle contractions may be important in orthostatic recovery via the skeletal muscle pump. In this study, adults with long COVID were assessed with a protocol that, in addition to the standard NCVI tests, incorporated simultaneous lower limb muscle monitoring for NMFI assessment. To accomplish such an investigation, a wide range of continuous non-invasive biomedical technologies were employed, including digital artery photoplethysmography for the extraction of cardiovascular signals, near-infrared spectroscopy for the extraction of regional tissue oxygenation in brain and muscle, and electromyography for assessment of timed muscle contractions in the lower limbs. With the novel technique described and exemplified in this paper, we were able to integrate signals from all instruments used in the assessment in a precisely synchronized fashion. We demonstrate that it is possible to visualize the interactions between all different physiological signals during the combined NCVI/NMFI assessment. Multiple counts of evidence were collected, which can capture the dynamics between skeletal muscle contractions and neurocardiovascular responses. The proposed multimodal data visualization can offer an overview of the functioning of the muscle pump during both supine rest and orthostatic recovery and can conduct comparison studies with signals from multiple participants at any given time in the assessment. This could help researchers and clinicians generate and test hypotheses based on the multimodal inspection of raw data, in long COVID and other clinical cohorts.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Feng Xue", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Ann Monaghan", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Glenn Jennings", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Lisa Byrne", - "author_inst": "St. James' Hospital, Dublin" - }, - { - "author_name": "Tim Foran", - "author_inst": "St. James' Hospital, Dublin" - }, - { - "author_name": "Eoin Duggan", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Roman Romero-Ortuno", - "author_inst": "Trinity College Dublin" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.12.23.21268276", "rel_title": "Risk of myocarditis following sequential COVID-19 vaccinations by age and sex", @@ -468017,6 +469311,145 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.12.23.473930", + "rel_title": "Human KIR+CD8+ T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19", + "rel_date": "2021-12-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.23.473930", + "rel_abs": "Previous reports show that Ly49+CD8+ T cells can suppress autoimmunity in mouse models of autoimmune diseases. Here we find a markedly increased frequency of CD8+ T cells expressing inhibitory Killer cell Immunoglobulin like Receptors (KIR), the human equivalent of the Ly49 family, in the blood and inflamed tissues of various autoimmune diseases. Moreover, KIR+CD8+ T cells can efficiently eliminate pathogenic gliadin-specific CD4+ T cells from Celiac disease (CeD) patients leukocytes in vitro. Furthermore, we observe elevated levels of KIR+CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 and influenza-infected patients, and this correlates with disease severity and vasculitis in COVID-19. Expanded KIR+CD8+ T cells from these different diseases display shared phenotypes and similar T cell receptor sequences. These results characterize a regulatory CD8+ T cell subset in humans, broadly active in both autoimmune and infectious diseases, which we hypothesize functions to control self-reactive or otherwise pathogenic T cells.\n\nOne-Sentence SummaryHere we identified KIR+CD8+ T cells as a regulatory CD8+ T cell subset in humans that suppresses self-reactive or otherwise pathogenic CD4+ T cells.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Jing Li", + "author_inst": "Stanford University" + }, + { + "author_name": "Maxim Elisha Zaslavsky", + "author_inst": "Stanford University" + }, + { + "author_name": "Yapeng Su", + "author_inst": "Institute for Systems Biology, Seattle" + }, + { + "author_name": "Michael Sikora", + "author_inst": "Stanford University" + }, + { + "author_name": "Vincent van Unen", + "author_inst": "Stanford University" + }, + { + "author_name": "Asbj\u00f8rn Christophersen", + "author_inst": "University of Oslo" + }, + { + "author_name": "Shin-Heng Chiou", + "author_inst": "Stanford University" + }, + { + "author_name": "Liang Chen", + "author_inst": "Stanford University" + }, + { + "author_name": "Jiefu Li", + "author_inst": "Stanford University" + }, + { + "author_name": "Xuhuai Ji", + "author_inst": "Stanford University" + }, + { + "author_name": "Julie Wilhelmy", + "author_inst": "Stanford University" + }, + { + "author_name": "Alana McSween", + "author_inst": "Stanford University" + }, + { + "author_name": "Vamsee Mallajosyula", + "author_inst": "Stanford University" + }, + { + "author_name": "Gopal Dhondalay", + "author_inst": "Stanford University" + }, + { + "author_name": "Kartik Bhamidipati", + "author_inst": "Stanford University" + }, + { + "author_name": "Joy Pai", + "author_inst": "Stanford University" + }, + { + "author_name": "Lucas Kipp", + "author_inst": "Stanford University" + }, + { + "author_name": "Jeffrey Dunn", + "author_inst": "Stanford University" + }, + { + "author_name": "Stephen Hauser", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jorge Oksenberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ansuman Satpathy", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "William Robinson", + "author_inst": "Stanford University" + }, + { + "author_name": "Lars Steinmetz", + "author_inst": "Stanford University" + }, + { + "author_name": "Chaitan Khosla", + "author_inst": "Stanford University" + }, + { + "author_name": "Paul Utz", + "author_inst": "Stanford University" + }, + { + "author_name": "Ludvig M. Sollid", + "author_inst": "University of Oslo" + }, + { + "author_name": "James Heath", + "author_inst": "Institute for Systems Biology, Seattle" + }, + { + "author_name": "Nielsen Fernandez-Becker", + "author_inst": "Stanford University" + }, + { + "author_name": "Kari Nadeau", + "author_inst": "Stanford University" + }, + { + "author_name": "Naresha Saligrama", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Mark Davis", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.23.473686", "rel_title": "IL4I1 binds to TMPRSS13 and competes with SARS-Cov2 Spike", @@ -469537,49 +470970,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.23.21268352", - "rel_title": "Early Treatment with fluvoxamine among patients with COVID-19: a cost-consequence model", - "rel_date": "2021-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268352", - "rel_abs": "BackgroundThree randomized trials have been conducted indicating a clinical benefit of early treatment with fluvoxamine versus placebo for adults with symptomatic COVID-19. We assessed the cost-consequences associated with the use of this early treatment in outpatient populations.\n\nMethodsUsing results from the three completed trials of fluvoxamine vs. placebo for the treatment of COVID-19, we performed a meta-analysis. We conducted a cost-consequence analysis using a decision-model to assess the health system benefits of the avoidance of progression to severe COVID-19. Outcomes of relevance to resource planning decisions in the US and elsewhere, including costs and days of hospitalization avoided, were reported. We constructed a decision-analytic model in the form of a decision tree to evaluate two treatment strategies for high-risk patients with confirmed, symptomatic COVID-19, from the perspective of a third-party payer:(1) treatment with a 10-day course of fluvoxamine (100mg twice daily); (2) current standard-of-care; (3) molnupiravir 5-day course. We used a time horizon of 28 days.\n\nResultsAdministration of fluvoxamine to symptomatic outpatients with COVID-19 at high-risk of developing progression to severe COVID-19 complications is substantially cost-saving in the US, in the amount of $232 per eligible patient, and saves an average of 0.15 hospital days per patient treated is likely to be similarly beneficial in other settings. Fluvoxamine is cost saving in locations where total hospital costs are >$738. Molnupiravir had an additional cost to the healthcare system of $404 per patient treated.\n\nConclusionsFluvoxamine is cost-saving for COVID-19 outpatient therapy.\n\nFundingFastGrants and Rainwater Charitable Foundation", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Fergal P Mills", - "author_inst": "InnomarConsulting" - }, - { - "author_name": "Gilmar Reis", - "author_inst": "CardResearch" - }, - { - "author_name": "Kristian Thorlund", - "author_inst": "McMaster University" - }, - { - "author_name": "Jamie I Forrest", - "author_inst": "Platform Life Sciences" - }, - { - "author_name": "Christina M Guo", - "author_inst": "Platform Life Sciences" - }, - { - "author_name": "David R Boulware", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Edward J Mills", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.12.22.21268045", "rel_title": "Essential Workers COVID-19 Vaccine Hesitancy, Misinformation and Informational Needs in the Republic of North Macedonia.", @@ -470003,6 +471393,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.22.473478", + "rel_title": "Accelerating manufacturing to start large-scale supply of a new adenovirus-vectored vaccine within 100 days", + "rel_date": "2021-12-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.22.473478", + "rel_abs": "The Coalition for Epidemic Preparedness Innovations 100-day moonshot aspires to launch a new vaccine within 100 days of pathogen identification. Here, we describe work to optimize adenovirus vector manufacturing for rapid response, by minimizing time to clinical trial and first large-scale supply, and maximizing the output from the available manufacturing footprint.\n\nWe describe a rapid viral seed expansion workflow that allows vaccine release to clinical trials within 60 days of antigen sequence identification, followed by vaccine release from globally distributed sites within a further 40 days. We also describe a new perfusion-based upstream production process, designed to maximize output while retaining simplicity and suitability for existing manufacturing facilities. This improves upstream volumetric productivity of ChAdOx1 nCoV-19 by around four-fold and remains compatible with the existing downstream process, yielding drug substance sufficient for 10000 doses from each liter of bioreactor capacity.\n\nTransition to a new production process across a large manufacturing network is a major task. In the short term, the rapid seed generation workflow could be used with the existing production process. We also use techno-economic modelling to show that, if linear scale-up were achieved, a single cleanroom containing two 2000 L bioreactors running our new perfusion-based process could supply bulk drug substance for around 120 million doses each month, costing <0.20 EUR/dose. We estimate that a manufacturing network with 32000 L of bioreactor capacity could release around 1 billion doses of a new vaccine within 130 days of genomic sequencing of a new pathogen, in a hypothetical surge campaign with suitable prior preparation and resources, including adequate fill-and-finish capacity.\n\nThis accelerated manufacturing process, along with other advantages such as thermal stability, supports the ongoing value of adenovirus-vectored vaccines as a rapidly adaptable and deployable platform for emergency response.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Carina CD Joe", + "author_inst": "Jenner Institute, University of Oxford" + }, + { + "author_name": "Rameswara R Segireddy", + "author_inst": "Jenner Institute, University of Oxford" + }, + { + "author_name": "Cathy Oliveira", + "author_inst": "Clinical Biomanufacturing Facility, University of Oxford" + }, + { + "author_name": "Adam Berg", + "author_inst": "Jenner Institute, University of Oxford" + }, + { + "author_name": "Yuanyuan Li", + "author_inst": "Jenner Institute, University of Oxford" + }, + { + "author_name": "Dimitrios Doultsinos", + "author_inst": "Jenner Institute, University of Oxford" + }, + { + "author_name": "Nitin Chopra", + "author_inst": "Sartorius Stedim Biotech GmbH" + }, + { + "author_name": "Steffi Scholze", + "author_inst": "Sartorius Stedim Biotech GmbH" + }, + { + "author_name": "Asma Ahmad", + "author_inst": "Repligen Corporation" + }, + { + "author_name": "Piergiuseppe Nestola", + "author_inst": "Sartorius Stedim Biotech GmbH" + }, + { + "author_name": "Julia Niemann", + "author_inst": "Sartorius Stedim Biotech GmbH" + }, + { + "author_name": "Alexander Douglas", + "author_inst": "Jenner Institute, University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.12.22.473934", "rel_title": "Waning immune responses against SARS-CoV-2 among vaccinees in Hong Kong", @@ -471538,117 +472991,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.21.473594", - "rel_title": "Construction of a potent pan-vaccine based on the evolutionary tendency of SARS-CoV-2 spike protein.", - "rel_date": "2021-12-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.21.473594", - "rel_abs": "SARS-CoV-2 continued to spread globally along with different variants. Here, we systemically analyzed viral infectivity and immune-resistance of SARS-CoV-2 variants to explore the underlying rationale of viral mutagenesis. We found that the Beta variant harbors both high infectivity and strong immune resistance, while the Delta variant is the most infectious with only a mild immune-escape ability. Remarkably, the Omicron variant is even more immune-resistant than the Beta variant, but its infectivity increases only in Vero E6 cells implying a probable preference for the endocytic pathway. A comprehensive analysis revealed that SARS-CoV-2 spike protein evolved into distinct evolutionary paths of either high infectivity plus low immune resistance or low infectivity plus high immune resistance, resulting in a narrow spectrum of the current single-strain vaccine. In light of these findings and the phylogenetic analysis of 2674 SARS-CoV-2 S-protein sequences, we generated a consensus antigen (S6) taking the most frequent mutations as a pan-vaccine against heterogeneous variants. As compared to the ancestry SWT vaccine with significantly declined neutralizations to emerging variants, the S6 vaccine elicits broadly neutralizing antibodies and full protections to a wide range of variants. Our work highlights the importance and feasibility of a universal vaccine strategy to fight against antigen drift of SARS-CoV-2.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Yongliang Zhao", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Wenjia Ni", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Simeng Liang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Lianghui Dong", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Min Xiang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Zeng Cai", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Danping Niu", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Qiuhan Zhang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Dehe Wang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Yucheng Zheng", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Zhen Zhang", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Dan Zhou", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Wenhua Guo", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University" - }, - { - "author_name": "Yongbing Pan", - "author_inst": "Wuhan Institute of Biological Products Co. Ltd." - }, - { - "author_name": "Xiaoli Wu", - "author_inst": "Wuhan Institute of Biological Products Co. Ltd." - }, - { - "author_name": "Yimin Yang", - "author_inst": "Wuhan Institute of Biological Products Co. Ltd." - }, - { - "author_name": "Zhaofei Jing", - "author_inst": "Wuhan Institute of Biological Products Co. Ltd." - }, - { - "author_name": "Yongzhong Jiang", - "author_inst": "Hubei Provincial Center for Diseases Control and Prevention" - }, - { - "author_name": "- SARS-CoV-2 Vaccine Task Force Group", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Yu Chen", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Huan Yan", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Yu Zhou", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Ke Xu", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - }, - { - "author_name": "Ke Lan", - "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University," - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.20.473471", "rel_title": "Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion", @@ -471932,6 +473274,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.23.21268314", + "rel_title": "Seroconversion rate after primary vaccination with two doses of BNT162b2 versus mRNA-1273 in solid organ transplant recipients: a systematic review and meta-analysis", + "rel_date": "2021-12-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268314", + "rel_abs": "In the general population, the seroconversion rate after primary vaccination with two doses of anti-SARS-CoV-2 mRNA vaccine reaches nearly 100%, with significantly higher antibody titers after mRNA-1273 vaccination compared to BNT162b2 vaccination. Here, we performed a systematic review and meta-analysis to compare the antibody response after two-dose mRNA-1273 versus BNT162b2 vaccination in solid organ transplant (SOT) recipients. A systematic literature research was performed in Pubmed, Web of Science, and the Cochrane library and original research papers were included for a meta-analysis to calculate vaccine-specific seroconversion rates for each of the mRNA vaccines. Next, the pooled relative seroconversion rate was estimated. Six studies that described the development of antibodies against receptor-binding domain (RBD) and/or S1 subunit of the spike protein were eligible for meta-analysis. Two of them also reported antibody titers. The meta-analysis revealed lower seroconversion rates in SOT recipients vaccinated with two doses of BNT162b2 (45.2%; 95% confidence interval (CI) 32.5%-58.3%) than patients vaccinated with two doses of mRNA-1273 (60.4%; 95% CI 47.4%-72.7%. The relative seroconversion rate amounted 0.79 (95% CI 0.71-0.88). This systematic review and meta-analysis indicates that, in SOT recipients, higher seroconversion rates were observed after vaccination with mRNA-1273 compared to BNT162b2.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Arno Verleye", + "author_inst": "Department of Nephrology and Hypertension, Antwerp University Hospital, Edegem, Belgium" + }, + { + "author_name": "Veerle Wijtvliet", + "author_inst": "Department of Nephrology and Hypertension, Antwerp University Hospital, Edegem, Belgium" + }, + { + "author_name": "Steven Abrams", + "author_inst": "Global Health Institute, Family Medicine and Population Health, University of Antwerp, Wilrijk, Belgium" + }, + { + "author_name": "Rachel Hellemans", + "author_inst": "Department of Nephrology and Hypertension, Antwerp University Hospital, Edegem, Belgium" + }, + { + "author_name": "Rania Bougrea", + "author_inst": "Department of Nephrology and Hypertension, Antwerp University Hospital, Edegem, Belgium" + }, + { + "author_name": "Annick Massart", + "author_inst": "Department of Nephrology and Hypertension, Antwerp University Hospital, Edegem, Belgium" + }, + { + "author_name": "Lissa Pipeleers", + "author_inst": "Department of Nephrology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium" + }, + { + "author_name": "Karl Martin Wissing", + "author_inst": "Department of Nephrology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium" + }, + { + "author_name": "Benedicte Y. De Winter", + "author_inst": "Laboratory of Experimental Medicine and Pediatrics and member of the Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Pierre Van Damme", + "author_inst": "Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Daniel Abramowicz", + "author_inst": "Department of Nephrology and Hypertension, Antwerp University Hospital, Edegem, Belgium" + }, + { + "author_name": "Kristien J. Ledeganck", + "author_inst": "Laboratory of Experimental Medicine and Pediatrics and member of the Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.12.23.21268285", "rel_title": "Dynamics of immune recall following SARS-CoV-2 vaccination or breakthrough infection", @@ -474140,49 +475545,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.16.473063", - "rel_title": "Passage of SARS-CoV-2 in cells expressing human and mouse ACE2 selects for mouse-adapted and ACE2-independent viruses", - "rel_date": "2021-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.473063", - "rel_abs": "Human ACE2 (hACE2) is the key cell attachment and entry receptor for SARS-CoV-2, with the original SARS-CoV-2 isolates unable to use mouse ACE2 (mACE2). Herein we describe a new system for generating mouse-adapted SARS-CoV-2 in vitro by serial passaging virus in co-cultures of cell lines expressing hACE2 and mACE2. Mouse-adapted viruses emerged with up to five amino acid changes in the spike protein, all of which have been seen in human isolates. Mouse-adapted viruses replicated to high titers in C57BL/6J mouse lungs and nasal turbinates, and caused severe lung histopathology. One mouse-adapted virus was also able to replicate efficiently in ACE2-negative cell lines, with ACE2-independent entry by SARS-CoV-2 representing a new biology for SARS-CoV-2 that has potential widespread implications for disease and intervention development.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kexin Yan", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Troy Dumenil", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Bing Tang", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Thuy T Le", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Cameron Bishop", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Andreas Suhrbier", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Daniel J Rawle", - "author_inst": "QIMR Berghofer Medical Research Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.19.21268042", "rel_title": "Government messaging about COVID-19 vaccination in Canada and Australia: a Narrative Policy Framework study", @@ -474430,6 +475792,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.20.21268048", + "rel_title": "Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268048", + "rel_abs": "The Omicron SARS-CoV-2 virus contains extensive sequence changes relative to the earlier arising B.1, B.1.1 and Delta SARS-CoV-2 variants that have unknown effects on viral infectivity and response to existing vaccines. Using SARS-CoV-2 virus-like particles (SC2-VLPs), we examined mutations in all four structural proteins and found that Omicron showed 3-fold higher capsid assembly and cell entry relative to Delta, a property conferred by S and N protein mutations. Thirty-eight antisera samples from individuals vaccinated with Pfizer/BioNTech, Moderna, Johnson & Johnson vaccines and convalescent sera from unvaccinated COVID-19 survivors had 15-fold lower efficacy to prevent cell transduction by VLPs containing the Omicron mutations relative to the ancestral B.1 spike protein. A third dose of Pfizer vaccine elicited substantially higher neutralization titers against Omicron, resulting in detectable neutralizing antibodies in 8 out of 8 subjects compared to 1 out of 8 pre-boost. Furthermore, the monoclonal antibody therapeutics Casirivimab and Imdevimab had robust neutralization activity against B.1, B.1.1 or Delta VLPs but no detectable neutralization of Omicron VLPs. Our results suggest that Omicron is more efficient at assembly and cell entry compared to Delta, and the antibody response triggered by existing vaccines or previous infection, at least prior to boost, will have limited ability to neutralize Omicron. In addition, some currently available monoclonal antibodies will not be useful in treating Omicron-infected patients.\n\nOne-Sentence SummaryOmicron SARS-CoV-2 virus-like particles have enhanced infectivity that is only weakly neutralized by vaccination without boost or prior infection, or antibody therapeutics.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Abdullah Muhammad Syed", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Alison Ciling", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" + }, + { + "author_name": "Mir M. Khalid", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA" + }, + { + "author_name": "Bharath Sreekumar", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA" + }, + { + "author_name": "Pei-Yi Chen", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA" + }, + { + "author_name": "G. Renuka Kumar", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA" + }, + { + "author_name": "Ines Silva", + "author_inst": "Curative Inc., 430 S Cataract Ave San Dimas, CA, 91773-2902, USA" + }, + { + "author_name": "Bilal Milbes", + "author_inst": "Curative Inc., 430 S Cataract Ave San Dimas, CA, 91773-2902, USA" + }, + { + "author_name": "Noah Kojima", + "author_inst": "Curative Inc., 430 S Cataract Ave San Dimas, CA, 91773-2902, USA" + }, + { + "author_name": "Victoria Hess", + "author_inst": "Curative Inc., 430 S Cataract Ave San Dimas, CA, 91773-2902, USA" + }, + { + "author_name": "Maria Shacreaw", + "author_inst": "Curative Inc., 430 S Cataract Ave San Dimas, CA, 91773-2902, USA" + }, + { + "author_name": "Lauren Lopez", + "author_inst": "Curative Inc., 430 S Cataract Ave San Dimas, CA, 91773-2902, USA" + }, + { + "author_name": "Matthew Brobeck", + "author_inst": "Curative Inc., 430 S Cataract Ave San Dimas, CA, 91773-2902, USA" + }, + { + "author_name": "Fred Turner", + "author_inst": "Curative Inc., 430 S Cataract Ave San Dimas, CA, 91773-2902, USA" + }, + { + "author_name": "Lee Spraggon", + "author_inst": "Curative Inc., 430 S Cataract Ave San Dimas, CA, 91773-2902, USA" + }, + { + "author_name": "Taha Y. Taha", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA" + }, + { + "author_name": "Takako Tabata", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA" + }, + { + "author_name": "Irene P. Chen", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA" + }, + { + "author_name": "Melanie Ott", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA" + }, + { + "author_name": "Jennifer A. Doudna", + "author_inst": "Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.21.21268116", "rel_title": "Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa", @@ -476257,57 +477714,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.17.21267362", - "rel_title": "The role of airborne transmission in a large single source outbreak of SARS-CoV-2 in a Belgian nursing home in 2020", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267362", - "rel_abs": "ObjectivesTo better understand the conditions which have led to one of the largest COVID-19 outbreaks in Belgian nursing homes in 2020.\n\nSettingA nursing home in Flanders, Belgium, which experienced a massive outbreak of COVID-19 after a cultural event. An external volunteer who dressed as a legendary figure visited consecutively the 4 living units and tested positive for SARS-CoV-2 the next day. Within days, residents started to display symptoms and the outbreak spread rapidly within the nursing home.\n\nMethodsWe interviewed key informants and collected standardized data from all residents retrospectively. A batch of 115 positive samples with a Ct value of <37 by qRT-PCR were analysed using whole-genome sequencing. Six months after the outbreak, ventilation assessment of gathering rooms in the nursing home was done using a tracer gas test with calibrated CO2 sensors.\n\nResultsTimeline of diagnoses and symptom onsets clearly pointed to the cultural event as the start of the outbreak, with the volunteer as index case. The genotyping of positive samples depicted the presence of one large cluster, suggesting a single source outbreak.\n\nThe global attack rate among residents was 77% with a significant association between infection and presence at the event. Known risk factors such as short distance to or physical contact with the volunteer, and wearing of a mask during the event were not associated with early infection. The ventilation assessment showed a high background average CO2 level in four main rooms varying from 657 ppm to 846 ppm.\n\nConclusionsOur investigation shows a rapid and widespread single source outbreak of SARS-CoV-2 in a nursing home, in which airborne transmission was the most plausible explanation for the massive intra-facility spread. Our results underscore the importance of ventilation and air quality for the prevention of future outbreaks in closed facilities.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Bea Vuylsteke", - "author_inst": "Institute of Tropical Medicine" - }, - { - "author_name": "Lize Cuypers", - "author_inst": "Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, 3000 Leuven, Belgium" - }, - { - "author_name": "Guy Baele", - "author_inst": "Department of Microbiology and Immunology, Rega Institute, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium" - }, - { - "author_name": "Marianne Stranger", - "author_inst": "Air Quality Measurements, Health Unit, VITO NV, 2400 Mol, Belgium" - }, - { - "author_name": "Sarah Lima Paralovo", - "author_inst": "Air Quality Measurements, Health Unit, VITO NV, 2400 Mol, Belgium" - }, - { - "author_name": "Emmanuel Andre", - "author_inst": "Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, 3000 Leuven, Belgium" - }, - { - "author_name": "Joke Dirks", - "author_inst": "Artsenpraktijk Mol, 2400 Mol" - }, - { - "author_name": "Piet Maes", - "author_inst": "Department of Microbiology and Immunology, Rega Institute, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium" - }, - { - "author_name": "Marie Laga", - "author_inst": "Department of Public Health, Institute of Tropical Medicine, 2000 Antwerp, Belgium" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.18.21267628", "rel_title": "RESISTANCE CONFERRING MUTATIONS IN SARS-CoV-2 DELTA FOLLOWING SOTROVIMAB INFUSION", @@ -476579,6 +477985,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.20.21268095", + "rel_title": "Worldwide clustering and infection cycles as universal features of multiscale stochastic processes in the SARS-CoV-2 pandemic", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268095", + "rel_abs": "Predicting the evolution of the current epidemic depends significantly on understanding the nature of the underlying stochastic processes. To unravel the global features of these processes, we analyse the world data of SARS-CoV-2 infection events, scrutinising two eight-month periods associated with the epidemics outbreak and initial immunisation phase. Based on the correlation-network mapping, K-means clustering, and multifractal time series analysis, our results reveal universal patterns, suggesting potential predominant drivers of the pandemic. More precisely, the Laplacian eigenvectors localisation has revealed robust communities of different countries and regions that then cluster according to similar shapes of infection fluctuations. Apart from quantitative measures, the immunisation phase differs significantly from the epidemic outbreak by the countries and regions constituting each cluster. While the similarity grouping possesses some regional components, the appearance of large clusters spanning different geographic locations is persevering. Furthermore, cyclic trends are characteristic of the identified clusters, dominating large temporal fluctuations of infection evolution, which are prominent in the immunisation phase. Meanwhile, persistent fluctuations around the local trend occur in intervals smaller than 14 days. These results provide a basis for further research into the interplay between biological and social factors as the primary cause of infection cycles and a better understanding of the impact of socio-economical and environmental factors at different phases of the pandemic.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Marija Mitrovic Dankulov", + "author_inst": "Institute of Physics Belgrade Serbia" + }, + { + "author_name": "Bosiljka Tadic", + "author_inst": "Jozef Stefan Institute Slovenia" + }, + { + "author_name": "Roderick Melnik", + "author_inst": "Wiflid Laurier University Waterloo, ON Canada" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.20.21267829", "rel_title": "KNOWLEDGE, ATTITUDES AND PRACTICE AMONG HEALTHCARE WORKERS TOWARDS COVID 19 PREVENTIVE MEASURES AT WOMEN AND NEW BORN HOSPITAL OF THE UNIVERSITY TEACHING HOSPITALS IN LUSAKA ZAMBIA", @@ -478163,33 +479596,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.16.473030", - "rel_title": "Modeling the dynamics of within-host viral infection and evolution predicts quasispecies distributions and phase boundaries separating distinct classes of infections", - "rel_date": "2021-12-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.473030", - "rel_abs": "We use computational modeling to study within-host viral infection and evolution. In our model, viruses exhibit variable binding to cells, with better infection and replication countered by a stronger immune response and a high rate of mutation. By varying host conditions (permissivity to viral entry T and immune clearance intensity A) for large numbers of cells and viruses, we study the dynamics of how viral populations evolve from initial infection to steady state and obtain a phase diagram of the range of cell and viral responses. We find three distinct replicative strategies corresponding to three physiological classes of viral infections: acute, chronic, and opportunistic. We show similarities between our findings and the behavior of real viral infections such as common flu, hepatitis, and SARS-CoV-2019. The phases associated with the three strategies are separated by a phase transition of primarily first order, in addition to a crossover region. Our simulations also reveal a wide range of physical phenomena, including metastable states, periodicity, and glassy dynamics. Lastly, our results suggest that the resolution of acute viral disease in patients whose immunity cannot be boosted can only be achieved by significant inhibition of viral infection and replication.\n\nAuthor summaryVirus, in particular RNA viruses, often produce offspring with slightly altered genetic composition. This process occurs both across host populations and within a single host over time. Here, we study the interactions of viruses with cells inside a host over time. In our model, the viruses encounter host cell defenses characterized by two parameters: permissivity to viral entry T and immune response A). The viruses then mutate upon reproduction, eventually resulting in a distribution of related viral types termed a quasi-species distribution. Across varying host conditions (T, A), three distinct viral quasi-species types emerge over time, corresponding to three classes of viral infections: acute, chronic and opportunistic. We interpret these results in terms of real viral types such as common flu, hepatitis, and also SARS-CoV-2019. Analysis of viral of viral mutant populations over a wide range of permissivity and immunity, for large numbers of cells and viruses, reveals phase transitions that separate the three classes of viruses, both in the infection-cycle dynamics and at steady state. We believe that such a multiscale approach for the study of within-host viral infections, spanning individual proteins to collections of cells, can provide insight into developing more effective therapies for viral disease.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Greyson R Lewis", - "author_inst": "UCSF Biophysics Graduate Group" - }, - { - "author_name": "Wallace F Marshall", - "author_inst": "UCSF, Center for Cellular Construction, Chan Zuckerberg Biohub" - }, - { - "author_name": "Barbara A Jones", - "author_inst": "IBM Research - Almaden" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.12.17.473179", "rel_title": "Disrupted Peyer's patch microanatomy in COVID-19 including germinal centre atrophy independent of local virus", @@ -478565,6 +479971,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.12.17.472912", + "rel_title": "Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.", + "rel_date": "2021-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.17.472912", + "rel_abs": "SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evo-lution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC=\"FIGDIR/small/472912v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@d9d710org.highwire.dtl.DTLVardef@1b66a3corg.highwire.dtl.DTLVardef@f89a6eorg.highwire.dtl.DTLVardef@162d443_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ezequiel G. Mogro", + "author_inst": "IBBM - Instituto de Biotecnologia y Biologia Molecular" + }, + { + "author_name": "Daniela Bottero", + "author_inst": "IBBM - Instituto de Biotecnologia y Biologia Molecular" + }, + { + "author_name": "Mauricio J. Lozano", + "author_inst": "IBBM - Instituto de Biotecnologia y Biologia Molecular" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.17.473113", "rel_title": "Pre-clinical evaluation of antiviral activity of nitazoxanide against Sars-CoV-2", @@ -479889,53 +481322,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.17.21267996", - "rel_title": "Antibody Responses to 3rd Dose mRNA Vaccines in Nursing Home and Assisted Living Residents", - "rel_date": "2021-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267996", - "rel_abs": "A comparison of SARS-CoV-2 wild-type and the beta variant virus neutralization capacity between 2 and 3 mRNA vaccine series in nursing home residents, and between nursing home and assisted living residents strongly supports 3rd dose vaccine recommendations, and equivalent polices for nursing homes and assisted living settings. Findings suggest that residents mount a robust humoral response to a 3rd mRNA vaccination, and have greater neuralization capacity compared to a 2 dose series.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ali Zhang", - "author_inst": "Michael G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Jessica A Breznik", - "author_inst": "McMaster Immunology Research Centre, McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Rumi Clare", - "author_inst": "Department of Medicine, Michael G. DeGroote School of Medicine McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Ishac Nazy", - "author_inst": "Department of Medicine, Michael G. DeGroote School of Medicine McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Matthew S Miller", - "author_inst": "Michael G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Dawn M.E. Bowdish", - "author_inst": "McMaster Immunology Research Centre, McMaster University Hamilton, ON, Canada" - }, - { - "author_name": "Andrew P Costa", - "author_inst": "Department of Health Research Methods Evidence, and Impact, McMaster University Hamilton, Canada" - }, - { - "author_name": "- COVID-in-LTC Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.15.472838", "rel_title": "A third vaccination with a single T cell epitope protects against SARS-CoV-2 infection in the absence of neutralizing antibodies", @@ -480311,6 +481697,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.16.21267912", + "rel_title": "Prolonged Detection of SARS CoV2 RNA in Extracellular Vesicles in Nasal Swab RT-PCR Negative Patients", + "rel_date": "2021-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267912", + "rel_abs": "BackgroundThere is a prolonged RT-PCR positivity seen in COVID-19 infected patients up to 2-3 months. We aim to investigate the presence of viral particles inside Extracellular vesicles (EV) and its role in underlying liver disease patients.\n\nMethodsSARS CoV2 nasal RT-PCR positive n=78 {n=24(66.6%) chronic liver disease (CLD); n=52 (81.3%) non-liver disease} were studied. SARS CoV2 patients were also followed up for day (d) 7, 14 and 28. Extracellular vesicles were isolated using differential ultracentrifugation. SARS CoV2 RNA was measured using qRT-PCR by Altona Real Star kit.\n\nResultsIn baseline RT-PCR positive patients, SARS-CoV2 RNA inside the EV was present in 64/74 (82%) patients with comparable viral load between VTM and EV (mean 1CT - 0.033{+/-}0.005 vs. 1CT - 0.029{+/-}0.014, p=ns). On follow-up at day 7, of the 24 patients negative for COVID19, 10 (41%) had persistence of virus in the EV (1CT - 0.028{+/-}0.004) and on day 14, 14 of 40 (35%) negative RT-PCR had EVs with SARS CoV2 RNA (1CT - 0.028{+/-}0.06). The mean viral load decreased at day7 and day14 in nasal swab from baseline (p=0.001) but not in EV. SARS-CoV2 RNA otherwise undetectable in plasma, was found to be positive in EV in 12.5% of COVID19 positive patients. Interestingly, significantly prolonged and high viral load was found in EV at day 14 in CLD-COVID19 patients compared to COVID19 alone (p=0.002). The high cellular injury was seen in CLD-COVID19 infected patients with significant high levels of EV associated with endothelial cells and hepatocytes than COVID19 alone (p=0.004; 0.001).\n\nConclusionIdentification of SARS-CoV2 RNA in EV, in RT-PCR negative patients indicates persistence of infection for and likely recurrence of the infection. EV associated RNA may determine the clinical course of subjects with undetectable SARS-CoV2 virus and this may also have relevance in management of chronic liver disease patients.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "P Debishree Subudhi", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi India" + }, + { + "author_name": "Sheetalnath Rooge", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi India" + }, + { + "author_name": "Swati Thangriyal", + "author_inst": "Institute of Liver and Biliary Sciences, New Delhi, India" + }, + { + "author_name": "Sivang Goswami", + "author_inst": "Institute of Liver and Biliary Sciences" + }, + { + "author_name": "Reshu Aggarwal", + "author_inst": "Institute of Liver and Biliary Sciences" + }, + { + "author_name": "Ekta Gupta", + "author_inst": "Institute of Liver and Biliary Sciences" + }, + { + "author_name": "Sukriti Baweja", + "author_inst": "Institute of Liver and Biliary Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.17.21267926", "rel_title": "Persistence of immune response in health care workers after two doses BNT162b2 in a longitudinal observational study", @@ -482051,57 +483480,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.17.21267655", - "rel_title": "Presentation, characteristics, treatments and outcomes of mechanically ventilated patients with COVID-19 in Bulgaria", - "rel_date": "2021-12-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267655", - "rel_abs": "BackgroundThe first surge of coronavirus disease 2019 (COVID-19) cases in Bulgaria occurred in the fall of 2020. Here we describe the clinical presentation, patient characteristics, treatments and outcomes of mechanically ventilated COVID-19 patients in a newly formed COVID-19 ICU at a tertiary cardiac center in Sofia, Bulgaria.\n\nMethodsThis is a retrospective observational study of mechanically ventilated COVID-19 patients admitted to Sveta Ekaterina University Hospital in Sofia, Bulgaria, between November 4th, 2020 and January 6th, 2021. Data were collected from electronic and written patient records and charts.\n\nResultsWe identified 38 critical care patients admitted with respiratory failure and treated with mechanical ventilation at our COVID-19 ICU during this period. The median age was 66 (IQR 57-76, range 27-89) and 74% were male. Most patients, 36 (95%), had at least one comorbidity. The most common comorbidities were hypertension, valvular heart disease, ischemic heart disease and diabetes mellitus. Overall, 27 (71%) patients had a concomitant cardiac disease other than hypertension and 24% were recent cardiac surgical patients. Inotropic support was required in 29 (76%) patients, renal replacement therapy in 12 (32%) patients and prone positioning and ECMO were used in 5 (13%) and 2 (5%) patients respectively. The median duration of mechanical ventilation was 7.5 (IQR 5-14) days overall and 9 (IQR 6-13) days for survivors. At 30-days 28 (74%) of patients had died. Overall, 32 (84%) patients died in hospital and only 6 (16%) patients were discharged home.\n\nConclusionsDuring the first major surge of COVID-19 cases in Bulgaria, despite the wave arriving later than in other countries, the healthcare system was largely unprepared. In our setting, mortality in mechanically ventilated patients was very high at 84%. Several factors might have contributed to these results, namely the predominance of cardiovascular comorbidities in our patient population, the strained ICU capacity and the lack of medical personnel.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Neda Bakalova", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Ivats Natsev", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Hristo Damov", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Irina Yatsenko", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Stefanija Jovinska", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Rostislav Enev", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Mikhail Cholakov", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Filip Abedinov", - "author_inst": "Sveta Ekaterina University Hospital" - }, - { - "author_name": "Denitza Kalendjieva", - "author_inst": "Sveta Ekaterina University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.12.16.472920", "rel_title": "Amyloidogenesis of SARS-CoV-2 Spike Protein", @@ -482325,6 +483703,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, + { + "rel_doi": "10.1101/2021.12.14.21267806", + "rel_title": "REACT-1 round 15 final report: Increased breakthrough SARS-CoV-2 infections among adults who had received two doses of vaccine, but booster doses and first doses in children are providing important protection", + "rel_date": "2021-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267806", + "rel_abs": "BackgroundIt has been nearly a year since the first vaccinations against SARS-CoV-2 were delivered in England. The third wave of COVID-19 in England began in May 2021 as the Delta variant began to outcompete and largely replace other strains. The REal-time Assessment of Community Transmission-1 (REACT-1) series of community surveys for SARS-CoV-2 infection has provided insights into transmission dynamics since May 2020. Round 15 of the REACT-1 study was carried out from 19 October to 5 November 2021.\n\nMethodsWe estimated prevalence of SARS-CoV2 infection and used multiple logistic regression to analyse associations between SARS-CoV-2 infection in England and demographic and other risk factors, based on RT-PCR results from self-administered throat and nose swabs in over 100,000 participants. We estimated (single-dose) vaccine effectiveness among children aged 12 to 17 years, and among adults compared swab-positivity in people who had received a third (booster) dose with those who had received two vaccine doses. We used splines to analyse time trends in swab-positivity.\n\nResultsDuring mid-October to early-November 2021, weighted prevalence was 1.57% (1.48%, 1.66%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). Weighted prevalence increased between rounds 14 and 15 across most age groups (including older ages, 65 years and over) and regions, with average reproduction number across rounds of R=1.09 (1.08, 1.11). During round 15, there was a fall in prevalence from a maximum around 20-21 October, with an R of 0.76 (0.70, 0.83), reflecting falls in prevalence at ages 17 years and below and 18 to 54 years. School-aged children had the highest weighted prevalence of infection: 4.95% (4.39%, 5.58%) in those aged 5 to 12 years and 5.21% (4.61%, 5.87%) in those aged 13 to 17 years. In multiple logistic regression, age, sex, key worker status and presence of one or more children in the home were associated with swab positivity. There was evidence of heterogeneity between rounds in swab positivity rates among vaccinated individuals at ages 18 to 64 years, and differences in key demographic and other variables between vaccinated and unvaccinated adults at these ages. Vaccine effectiveness against infection in children was estimated to be 56.2% (41.3%, 67.4%) in rounds 13, 14 and 15 combined, adjusted for demographic factors, with a similar estimate obtained for round 15 only. Among adults we found that those who received a third dose of vaccine were less likely to test positive compared to those who received only two vaccine doses, with adjusted odds ratio (OR) =0.38 (0.26, 0.55).\n\nDiscussionSwab-positivity was very high at the start of round 15, reaching a maximum around 20 to 21 October 2021, and then falling through late October with an uncertain trend in the last few days of data collection. The observational nature of survey data and the relatively small proportion of unvaccinated adults call into question the comparability of vaccinated and unvaccinated groups at this relatively late stage in the vaccination programme. However, third vaccine doses for eligible adults and the vaccination of children aged 12 years and over are associated with lower infection risk and, thus, remain a high priority (with possible extension to children aged 5-12 years). These should help reduce SARS-CoV-2 transmission during the winter period when healthcare demands typically rise.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Marc Chadeau-Hyam", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Oliver Eales", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "Barbara Bodinier", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Haowei Wang", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "David Haw", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "Matthew Whitaker", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Caroline E. Walters", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "Jakob Jonnerby", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "Christina Atchinson", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Peter J. Diggle", + "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" + }, + { + "author_name": "Andrew J. Page", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Graham Taylor", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical" + }, + { + "author_name": "Helen Ward", + "author_inst": "School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at " + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "Paul Elliott", + "author_inst": "School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.15.21267605", "rel_title": "The effect of anti-SARS-CoV-2 monoclonal antibody, bamlanivimab, on endogenous immune response to COVID-19 vaccination", @@ -483685,33 +485154,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.12.14.21267742", - "rel_title": "Impact of Population Mixing Between a Vaccinated Majority and Unvaccinated Minority on Disease Dynamics. Implications for SARS-CoV-2", - "rel_date": "2021-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267742", - "rel_abs": "BackgroundThe speed of vaccine development has been a singular achievement during the SARS-CoV-2 pandemic, though uptake has not been universal. Vaccine opponents often frame their opposition in terms of the rights of the unvaccinated. Our objective was to explore the impact of mixing of vaccinated and unvaccinated populations on risk among vaccinated individuals.\n\nMethodsWe constructed a simple Susceptible-Infectious-Recovered (SIR) compartmental model of a respiratory infectious disease with two connected sub-populations: vaccinated individuals and unvaccinated individuals. We simulated a spectrum of patterns of mixing between vaccinated and unvaccinated groups that ranged from random mixing to like-with-like mixing (complete assortativity), where individuals preferentially have contact with others with the same vaccination status. We evaluated the dynamics of an epidemic within each subgroup, and in the population as a whole.\n\nResultsThe relative risk of infection was markedly higher among unvaccinated individuals than among vaccinated individuals. However, the contact-adjusted contribution of unvaccinated individuals to infection risk during the epidemic was disproportionate, with unvaccinated individuals contributing to infections among the vaccinated at a rate higher than would have been expected based on contact numbers alone. As assortativity increased, attack rates among the vaccinated decreased, but the contact-adjusted contribution to risk among vaccinated individuals derived from contact with unvaccinated individuals increased.\n\nInterpretationWhile risk associated with avoiding vaccination during a virulent pandemic accrues chiefly to the unvaccinated, the choices of unvaccinated individuals impact the health and safety of vaccinated individuals in a manner disproportionate to the fraction of unvaccinated individuals in the population.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto" - }, - { - "author_name": "Afia Amoako", - "author_inst": "University of Toronto" - }, - { - "author_name": "David Fisman", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.14.21267199", "rel_title": "The COVID-19 pandemic amplified long-standing racial disparities in the United States criminal justice system", @@ -484419,6 +485861,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.14.472513", + "rel_title": "Metalloproteinase-dependent and TMPRSS2-independnt cell surface entry pathway of SARS-CoV-2 requires the furin-cleavage site and the S2 domain of spike protein", + "rel_date": "2021-12-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.14.472513", + "rel_abs": "The ongoing global vaccination program to prevent SARS-CoV-2 infection, the causative agent of COVID-19, has had significant success. However, recently virus variants have emerged that can evade the immunity in a host achieved through vaccination. Consequently, new therapeutic agents that can efficiently prevent infection from these new variants, and hence COVID-19 spread are urgently required. To achieve this, extensive characterization of virus-host cell interactions to identify effective therapeutic targets is warranted. Here, we report a cell surface entry pathway of SARS-CoV-2 that exists in a cell type-dependent manner is TMPRSS2-independent but sensitive to various broad-spectrum metalloproteinase inhibitors such as marimastat and prinomastat. Experiments with selective metalloproteinase inhibitors and gene-specific siRNAs revealed that a disintegrin and metalloproteinase 10 (ADAM10) is partially involved in the metalloproteinase pathway. Consistent with our finding that the pathway is unique to SARS-CoV-2 among highly pathogenic human coronaviruses, both the furin cleavage motif in the S1/S2 boundary and the S2 domain of SARS-CoV-2 spike protein are essential for metalloproteinase-dependent entry. In contrast, the two elements of SARS-CoV-2 independently contributed to TMPRSS2-dependent S2 priming. The metalloproteinase pathway is involved in SARS-CoV-2-induced syncytia formation and cytopathicity, leading us to theorize that it is also involved in the rapid spread of SARS-CoV-2 and the pathogenesis of COVID-19. Thus, targeting the metalloproteinase pathway in addition to the TMPRSS2 and endosome pathways could be an effective strategy by which to cure COVID-19 in the future.\n\nAuthor SummaryTo develop effective therapeutics against COVID-19, it is necessary to elucidate in detail the infection mechanism of the causative agent, SARS-CoV-2, including recently emerging variants. SARS-CoV-2 binds to the cell surface receptor ACE2 via the Spike protein, and then the Spike protein is cleaved by host proteases to enable entry. Selection of target cells by expression of these tissue-specific proteases contributes to pathogenesis. Here, we found that the metalloproteinase-mediated pathway is important for SARS-CoV-2 infection, variants included. This pathway requires both the prior cleavage of Spike into two domains and a specific sequence in the second domain S2, conditions met by SARS-CoV-2 but lacking in the related human coronavirus SARS-CoV. The contribution of several proteases, including metalloproteinases, to SARS-CoV-2 infection was cell type dependent, especially in cells derived from kidney, ovary, and endometrium, in which SARS-CoV-2 infection was metalloproteinase-dependent. In these cells, inhibition of metalloproteinases by treatment with marimastat or prinomastat, whose safety was previously confirmed in clinical trials, was important in preventing cell death. Our study provides new insights into the complex pathogenesis unique to COVID-19 and relevant to the development of effective therapies.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mizuki Yamamoto", + "author_inst": "Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Jin Gohda", + "author_inst": "Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Ayako Kobayashi", + "author_inst": "Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Keiko Tomita", + "author_inst": "Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Youko Hirayama", + "author_inst": "Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Naohiko Koshikawa", + "author_inst": "Department of Life Science and Technology, Tokyo Institute of Technology" + }, + { + "author_name": "Motoharu Seiki", + "author_inst": "Division of Cancer Cell Research, The Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Kentaro Semba", + "author_inst": "Department of Life Science and Medical Bio-Science, Waseda University" + }, + { + "author_name": "Tetsu Akiyama", + "author_inst": "Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo" + }, + { + "author_name": "Yasushi Kawaguchi", + "author_inst": "Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Division of Molecular Virology, Department of Microbio" + }, + { + "author_name": "Jun-ichiro Inoue", + "author_inst": "Research Platform Office, The Institute of Medical Science, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.15.472779", "rel_title": "Genomic determinants of Furin cleavage in diverse European SARS-related bat coronaviruses", @@ -486030,121 +487531,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.12.15.21267834", - "rel_title": "Comparison of the Immunogenicity of five COVID-19 vaccines in Sri Lanka", - "rel_date": "2021-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.15.21267834", - "rel_abs": "We assessed antibody responses 3 months post-vaccination in those who received mRNA-1273 (n=225), Sputnik V (n=128) or the first dose of Gam-COVID-Vac (n=184) and compared the results with previously reported data of Sinopharm and AZD1222 vaccinees. 99.5% of Moderna >94% of AZD1222 or Sputnik V, 72% to 76% of Gam-COVID-Vac (first dose) and 38.1% to 68.3% of Sinopharm vaccinees had ACE2 blocking antibodies above the positive threshold. The ACE2 blocking antibody levels were highest to lowest was Moderna > Sputnik V/ AZD1222 (had equal levels)> first dose of Gam-COVID-Vac > Sinopharm. All Moderna recipients had antibodies above the positive threshold to the ancestral (WT), B.1.1.7, B.1.351.1 and 80% positivity rate for B.1.617.2. Positivity rates of Sputnik V vaccinees for WT and variants, were higher than AZD1222 vaccinees, while Sinopharm vaccinees had the lowest positivity rates (<16.7%). These findings highlight the need for further studies to understand the effects on clinical outcomes.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Chandima Jeewandara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Inoka Aberathna", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Saubhagya Danasekara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Laksiri Gomes", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Suranga Fernando", - "author_inst": "Ministry of Health, Sri Lanka" - }, - { - "author_name": "Dinuka Guruge", - "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka." - }, - { - "author_name": "Thushali Ranasinghe", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Banuri Gunasekara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Achala Kamaladasa", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Heshan Kuruppu", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Gayasha Somathilaka", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Jeewantha Jayamali", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Deshni Jayathilaka", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Helanka Wijayathilake", - "author_inst": "Ministry of Health, Sri Lanka" - }, - { - "author_name": "Pradeep Pushpakumara", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Michael Harvie", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Thashmi Nimasha", - "author_inst": "University of Sri Jayewardenepura" - }, - { - "author_name": "Shiromi de Silva", - "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka" - }, - { - "author_name": "Ruwan Wijayamuni", - "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka." - }, - { - "author_name": "Lisa Schimanski", - "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.\"" - }, - { - "author_name": "Pramila Rijal", - "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK." - }, - { - "author_name": "Jack Tan", - "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK." - }, - { - "author_name": "Alain Townsend", - "author_inst": "University of Oxford" - }, - { - "author_name": "Graham Ogg", - "author_inst": "MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK." - }, - { - "author_name": "Gathsaurie Neelika Malavige", - "author_inst": "University of Sri Jayewardenepura" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.12.14.21267460", "rel_title": "Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales", @@ -486460,6 +487846,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.12.14.21267713", + "rel_title": "Transmission of SARS-CoV-2 by children and young people in households and schools: a meta-analysis of population-based and contact-tracing studies", + "rel_date": "2021-12-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267713", + "rel_abs": "BackgroundThe role of children and young people (CYP) in transmission of SARS-CoV-2 in household and educational settings remains unclear. We undertook a systematic review and meta-analysis of contact-tracing and population-based studies at low risk of bias.\n\nMethodsWe searched 4 electronic databases on 28 July 2021 for contact-tracing studies and population-based studies informative about transmission of SARS-CoV-2 from 0-19 year olds in household or educational settings. We excluded studies at high risk of bias, including from under-ascertainment of asymptomatic infections. We undertook multilevel random effects meta-analyses of secondary attack rates (SAR: contact-tracing studies) and school infection prevalence, and used meta-regression to examine the impact of community SARS-CoV-2 incidence on school infection prevalence.\n\nFindings4529 abstracts were reviewed, resulting in 37 included studies (16 contact-tracing; 19 population studies; 2 mixed studies). The pooled relative transmissibility of CYP compared with adults was 0.92 (0.68, 1.26) in adjusted household studies. The pooled SAR from CYP was lower (p=0.002) in school studies 0.7% (0.2, 2.7) than household studies (7.6% (3.6, 15.9). There was no difference in SAR from CYP to child or adult contacts. School population studies showed some evidence of clustering in classes within schools. School infection prevalence was associated with contemporary community 14-day incidence (OR 1.003 (1.001, 1.004), p<0.001).\n\nInterpretationWe found no difference in transmission of SARS-CoV-2 from CYP compared with adults within household settings. SAR were markedly lower in school compared with household settings, suggesting that household transmission is more important than school transmission in this pandemic. School infection prevalence was associated with community infection incidence, supporting hypotheses that school infections broadly reflect community infections. These findings are important for guiding policy decisions on shielding, vaccination school and operations during the pandemic.\n\nFundingNo funding obtained.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Russell M Viner", + "author_inst": "UCL Great Ormond St. Institute of Child Health" + }, + { + "author_name": "Claire Waddington", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Oliver Mytton", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Robert Booy", + "author_inst": "University of Sydney" + }, + { + "author_name": "Joana Cruz", + "author_inst": "UCL Great Ormond St. Institute of Child Health" + }, + { + "author_name": "Joseph Ward", + "author_inst": "UCL Great Ormond St. Institute of Child Health" + }, + { + "author_name": "Shamez Ladhani", + "author_inst": "Public Health England" + }, + { + "author_name": "Jasmina Panovska-Griffiths", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chris Bonell", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "G.J. Melendez-Torres", + "author_inst": "University of Exeter" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.14.21267804", "rel_title": "Emerging from the COVID-19 pandemic: impacts of variants, vaccines, and duration of immunity", @@ -488264,49 +489705,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.13.21267657", - "rel_title": "Simple decision rules to predict local surges in COVID-19 hospitalizations during the winter and spring of 2022", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267657", - "rel_abs": "Low rates of vaccination, emergence of novel variants of SARS-CoV-2, and increasing transmission relating to seasonal changes leave many U.S. communities at risk for surges of COVID-19 during the winter and spring of 2022 that might strain hospital capacity, as in previous waves. The trajectories of COVID-19 hospitalizations during this period are expected to differ across communities depending on their age distributions, vaccination coverage, cumulative incidence, and adoption of risk mitigating behaviors. Yet, existing predictive models of COVID-19 hospitalizations are almost exclusively focused on national- and state-level predictions. This leaves local policymakers in urgent need of tools that can provide early warnings about the possibility that COVID-19 hospitalizations may rise to levels that exceed local capacity. In this work, we develop simple decision rules to predict whether COVID-19 hospitalization will exceed the local hospitalization capacity within a 4- or 8-week period if no additional mitigating strategies are implemented during this time. These decision rules use real-time data related to hospital occupancy and new hospitalizations associated with COVID-19, and when available, genomic surveillance of SARS-CoV-2. We showed that these decision rules present reasonable accuracy, sensitivity, and specificity (all [≥]80%) in predicting local surges in hospitalizations under numerous simulated scenarios, which capture substantial uncertainties over the future trajectories of COVID-19 during the winter and spring of 2022. Our proposed decision rules are simple, visual, and straightforward to use in practice by local decision makers without the need to perform numerical computations.\n\nSignificance StatementIn many U.S. communities, the risk of exceeding local healthcare capacity during the winter and spring of 2022 remains substantial since COVID-19 hospitalizations may rise due to seasonal changes, low vaccination coverage, and the emergence of new variants of SARS-CoV-2, such as the omicron variant. Here, we provide simple and easy-to-communicate decision rules to predict whether local hospital occupancy is expected to exceed capacity within a 4- or 8-week period if no additional mitigating measures are implemented. These decision rules can serve as an alert system for local policymakers to respond proactively to mitigate future surges in the COVID-19 hospitalization and minimize risk of overwhelming local healthcare capacity.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Reza Yaesoubi", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Shiying You", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Qin Xi", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Nicolas A Menzies", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto Dalla Lana School of Public Health" - }, - { - "author_name": "Yonatan Grad", - "author_inst": "Harvard T. H. Chan School of Public Health" - }, - { - "author_name": "Joshua A Salomon", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.12.21267681", "rel_title": "COVID-19 in French Nursing Homes during the Second Pandemic Wave: A Mixed-Methods Cross-Sectional Study", @@ -488526,6 +489924,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.13.21267670", + "rel_title": "Third BNT162b2 vaccination neutralization of SARS-CoV-2 Omicron infection", + "rel_date": "2021-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267670", + "rel_abs": "Using isolates of SARS-CoV-2 WT, Beta, Delta and most importantly Omicron we studied the capability of the BNT162b2 vaccine given in two or three doses to neutralize major SARS-CoV-2 variants of concern (VOC).\n\nWe demonstrate low neutralization efficiency against delta and wild-type for vaccines with more than 5 months following the second BNT162b2 dose, with no neutralization efficiency against Omicron. We demonstrate the importance of a third dose, by showing a 100-fold increase in neutralization efficiency of Omicron following a third dose, with a 4-fold reduced neutralization compared to that against the Delta VOC. The durability of the effect of the third dose is yet to be determined.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Ital Nemet", + "author_inst": "Ministry of Health, Tel Hashomer, Israel" + }, + { + "author_name": "Limor Kliker", + "author_inst": "Ministry of Health, Tel Hashomer, Israel" + }, + { + "author_name": "Yaniv Lustig", + "author_inst": "Ministry of Health, Tel Hashomer, Israel" + }, + { + "author_name": "Neta S Zuckerman", + "author_inst": "Ministry of Health, Tel Hashomer, Israel" + }, + { + "author_name": "Carmit Cohen", + "author_inst": "Sheba Medical Center, Tel Hashomer, Israel" + }, + { + "author_name": "Yitshak Kreiss", + "author_inst": "Sheba Medical Center, Tel Hashomer, Israel" + }, + { + "author_name": "Sharo Alroy-Preis", + "author_inst": "Ministry of Health, Jerusalem, Israel" + }, + { + "author_name": "Gili Regev-Yochay", + "author_inst": "Sheba Medical Center, Tel Hashomer, Israel" + }, + { + "author_name": "Ella Mendelson", + "author_inst": "Ministry of Health, Tel Hashomer, Israel" + }, + { + "author_name": "Michal Mandelboim", + "author_inst": "Ministry of Health, Tel Hashomer, Israel" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.13.21267620", "rel_title": "Durability of mRNA-1273 against COVID-19 in the time of Delta: Interim results from an observational cohort study", @@ -490130,65 +491583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.10.21267613", - "rel_title": "The impact of remote home monitoring of people with COVID-19 using pulse oximetry: a national population and observational study.", - "rel_date": "2021-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267613", - "rel_abs": "BackgroundRemote home monitoring of people testing positive for COVID-19 using pulse oximetry was implemented across England during the Winter of 2020/21 to identify falling blood oxygen saturation levels at an early stage. This was hypothesised to enable earlier hospital admission, reduce the need for intensive care and improve survival. This study is an evaluation of the clinical effectiveness of the pre-hospital monitoring programme, COVID oximetry @home (CO@h).\n\nMethodsWe analysed relationships at a geographical area level between the extent to which people aged 65 or over were enrolled onto the programme and outcomes over the period between November 2020 to February 2021\n\nFindingsFor every 10% increase in coverage of the programme, mortality was reduced by 2% (95% confidence interval: -4% to 1%), admissions increased by 3% (-1% to 7%), in-hospital mortality fell by 3% (-8% to 3%) and lengths of stay increased by 1{middle dot}8% (-1{middle dot}2% to 4{middle dot}9%). None of these results are statistically significant.\n\nInterpretationThere are several possible explanations for our findings. One is that the CO@h did not have the hypothesised impact. Another is that the low rates of enrolment and incomplete data in many areas reduced the chances of detecting any impact that may have existed. Also, CO@h has been implemented in many different ways across the country and these may have had varying levels of effect.\n\nFundingThis is independent research funded by the National Institute for Health Research, Health Services & Delivery Research programme (RSET Project no. 16/138/17; BRACE Project no. 16/138/31) and NHSEI. NJF is an NIHR Senior Investigator. The views expressed in this publication are those of the authors and not necessarily those of the National Institute for Health Research or the Department of Health and Social Care.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSExisting evidence before this study and the search strategy used to obtain this evidence has been published previously by the authors in a systematic review. Previous quantitative studies have assessed remote oximetry monitoring services for COVID-19 patients mostly at individual sites and focussed on their safety. However, their effectiveness has been little studied. This may reflect the challenges of identifying reliable counterfactuals during a rapidly evolving pandemic.\n\nAdded value of this studyThis study is part of a wider mixed methods evaluation that followed the rapid implementation of remote monitoring across the English NHS during the Winter of 2020/21. It adds to the evidence of the effectiveness of such programmes at a national level.\n\nImplications of the available evidenceThere is some existing evidence that remote monitoring of COVID-19 patients can be locally effective although we have not been able to replicate such findings at a wider level. Missing data and lower coverage of the service than expected may have influenced our results, and the effectiveness of some local programmes could have been lost among the analysis of national data. Future implementation requires better data collection strategies which could be focussed within fewer local areas, and effective learning from areas that have achieved better population coverage.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christopher Sherlaw-Johnson", - "author_inst": "Nuffield Trust" - }, - { - "author_name": "Theo Georghiou", - "author_inst": "Nuffield Trust" - }, - { - "author_name": "Steve Morris", - "author_inst": "Cambridge University" - }, - { - "author_name": "Nadia Crellin", - "author_inst": "Nuffield Trust" - }, - { - "author_name": "Ian Litchfield", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Efthalia Massou", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Manbinder Sidhu", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Sonila Tomini", - "author_inst": "University College London" - }, - { - "author_name": "Cecilia Vindrola-Padros", - "author_inst": "University College London" - }, - { - "author_name": "Holly Walton", - "author_inst": "University College London" - }, - { - "author_name": "Naomi Fulop", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.11.21267259", "rel_title": "Time-Varying Mortality Risk Suggests Increased Impact of Thrombosis in Hospitalized Covid-19 Patients", @@ -490516,6 +491910,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.12.12.21267518", + "rel_title": "Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2", + "rel_date": "2021-12-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.12.21267518", + "rel_abs": "The ongoing COVID-19 pandemic calls for more effective diagnostic tools, and T cell response assessment can serve as an independent indicator of prior COVID-19 exposure while also contributing to a more comprehensive characterization of SARS-CoV-2 immunity. In this study, we systematically assessed the immunogenicity of 118 epitopes with immune cells collected from multiple cohorts of vaccinated, convalescent, and healthy unexposed and SARS-CoV-2 exposed donors. We identified seventy-five immunogenic epitopes, 24 of which were immunodominant. We further confirmed HLA restriction for 49 epitopes, and described association with more than one HLA allele for 14 of these. After excluding two cross-reactive epitopes that generated a response in pre-pandemic samples, we were left with a 73-epitope set that offers excellent diagnostic specificity without losing sensitivity compared to full-length antigens, which evoked a robust cross-reactive response. We subsequently incorporated this set of epitopes into an in vitro diagnostic Corona-T-test which achieved a diagnostic accuracy of 95% in a clinical trial. When applied to a cohort of asymptomatic seronegative individuals with a history of prolonged SARS-CoV-2 exposure, this test revealed a lack of specific T cell response combined with strong cross-reactivity to full-length antigens, indicating that abortive infection had occurred in these individuals.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Aleksei Titov", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + }, + { + "author_name": "Regina Shaykhutdinova", + "author_inst": "National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia" + }, + { + "author_name": "Olga V. Shcherbakova", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + }, + { + "author_name": "Yana V. Serdyuk", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + }, + { + "author_name": "Savely A. Sheetikov", + "author_inst": "National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia" + }, + { + "author_name": "Ksenia V. Zornikova", + "author_inst": "National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia" + }, + { + "author_name": "Alexandra V. Maleeva", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + }, + { + "author_name": "Alexandra Khmelevskaya", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + }, + { + "author_name": "Dmitry V. Dianov", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + }, + { + "author_name": "Naina T. Shakirova", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + }, + { + "author_name": "Dmitry B. Malko", + "author_inst": "Faculty of Computer Science, HSE University, Moscow, Russia" + }, + { + "author_name": "Maxim Shkurnikov", + "author_inst": "Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow" + }, + { + "author_name": "Stepan Nersisyan", + "author_inst": "Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow" + }, + { + "author_name": "Alexander Tonevitsky", + "author_inst": "Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow" + }, + { + "author_name": "Ekaterina G. Khamaganova", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + }, + { + "author_name": "Anton V. Ershov", + "author_inst": "LLC \"DNKOM\", Moscow, Russia; I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia (Sechenov University), Moscow, Russia" + }, + { + "author_name": "Elena Y. Osipova", + "author_inst": "Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russia" + }, + { + "author_name": "Ruslan V. Nikolaev", + "author_inst": "Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russia" + }, + { + "author_name": "Dmitry E. Pershin", + "author_inst": "Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russia" + }, + { + "author_name": "Viktoria A. Vedmedskia", + "author_inst": "Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russia" + }, + { + "author_name": "Mikhail Maschan", + "author_inst": "Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russia" + }, + { + "author_name": "Victoria R. Ginanova", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + }, + { + "author_name": "Grigory A. Efimov", + "author_inst": "National Research Center for Hematology, Moscow, Russia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.10.21267618", "rel_title": "Measuring the impact of COVID-19 vaccination and immunity waning: a modelling study for Portugal", @@ -491952,93 +493453,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.08.21267452", - "rel_title": "Accuracy and usability of saliva and nasal rapid antigen self-testing for detection of SARS-CoV-2 infection in the general population: a head-to-head comparison", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267452", - "rel_abs": "BackgroundSARS-CoV-2 self-tests may lower the threshold of testing and produce a result quickly. This could support the early detection of infectious cases and reduce further community transmission. However, the diagnostic accuracy of (unsupervised) self-testing with rapid antigen diagnostic tests (Ag-RDTs) is mostly unknown. We therefore conducted a large-scale head-to-head comparison of the diagnostic accuracy of a self-performed SARS-CoV-2 saliva and nasal Ag-RDT, each compared to a molecular reference test, in the general population in the Netherlands.\n\nMethodsIn this cross-sectional study we consecutively included individuals aged 16 years and older presenting for SARS-CoV-2 testing at three Dutch public health service test sites irrespective of their indication for testing, vaccination status, and symptomatology. Participants were sampled for molecular testing at the test site and received two self-tests (the Hangzhou AllTest saliva self-test and the SD Biosensor nasal self-test by Roche Diagnostics) to perform at home within a few hours without knowledge of their molecular test result. Information on presence and type of symptoms, user experiences, and results of both self-tests were collected via an online questionnaire. For each self-test, sensitivity, specificity, positive and negative predictive values were determined with molecular testing as reference standard.\n\nFindingsThe SARS-CoV-2 molecular reference test positivity rate was 6.5% in the 2,819 participants. Overall sensitivities with 95% confidence intervals were 46.7% (85/182; 39.3%-54.2%) for the saliva Ag-RDT, and 68.9% (124/180; 61.6%-75.6%) for the nasal Ag-RDT. With a viral load cut-off ([≥]5.2 log10 SARS-CoV-2 E-gene copies/mL) as a proxy of infectiousness, sensitivities increased to 54.9% (78/142; 46.4%-63.3%) for the saliva Ag-RDT and 83.9% (120/143; 76.9%-89.5%) for the nasal Ag-RDT.\n\nFor the nasal Ag-RDT, sensitivities were 78.5% [71.1%-84.8%] and 22.6% [9.6%-41.1%] in those with and without symptoms at the time of sampling, which increased to 90.4% (113/125; 83.8%-94.9%) and 38.9% (7/18; 17.3%-64.3%) after applying the viral load cut-off. In those with and without prior confirmed SARS-CoV-2, sensitivities were 36.8% [19/372; 16.3%-61.6%] and 72.7% [161/2437; 65.1%-79.4%] for the nasal Ag-RDT, which increased to 100% (7/7; 59.0%-100%) and 83.1% (113/126; 75.7%-89.0%) after applying the viral load cut-off.\n\nThe diagnostic accuracy of the nasal Ag-RDT did not differ by COVID-19 vaccination status, sex, and age. Specificities were >99%, positive predictive values >70% and negative predictive values >95%, for the saliva Ag-RDT, and >99%, >90%, and >95% for the nasal Ag-RDT, respectively, in most analyses.\n\nInterpreting the results was considered (very) easy for both self-tests.\n\nInterpretationThe Hangzhou AllTest self-performed saliva Ag-RDT is not reliable for SARS-CoV-2 infection detection overall nor in the studied subgroups. The SD Biosensor self-performed nasal Ag-RDT had high sensitivity in individuals with symptoms and in those without a prior SARS-CoV-2 infection. The overall accuracy in individuals with symptoms was comparable to that found in previous studies with professional sampling for this Ag-RDT. The extremely low sensitivity of the nasal Ag-RDT in asymptomatic individuals and in individuals who had had a prior SARS-CoV-2 infection is an important finding and warrants further investigation.\n\nFundingDutch Ministry of Health, Welfare, and Sport.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Ewoud Schuit", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Roderick P Venekamp", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Irene K Veldhuijzen", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Wouter van den Bijllaardt", - "author_inst": "Amphia Hospital" - }, - { - "author_name": "Suzan D Pas", - "author_inst": "Bravis Hospital" - }, - { - "author_name": "Joep J.J.J.M. Stohr", - "author_inst": "Amphia Hospital" - }, - { - "author_name": "Esther B Lodder", - "author_inst": "Public Health Service West-Brabant" - }, - { - "author_name": "Marloes Hellwich", - "author_inst": "Public Health Service Hart voor Brabant" - }, - { - "author_name": "Richard Molenkamp", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Zsofia Igloi", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Constantijn Wijers", - "author_inst": "Public Health Service Rotterdam-Rijnmond" - }, - { - "author_name": "Irene H Vroom", - "author_inst": "Public Health Service Rotterdam-Rijnmond" - }, - { - "author_name": "Carla R S Nagel-Imming", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Wanda G H Han", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Jan A J Kluytmans", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Susan van den Hof", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Janneke H H M Van de Wijgert", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Karel G M Moons", - "author_inst": "University Medical Center Utrecht" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.09.21267539", "rel_title": "Food for thought: Eating before saliva collection and interference with SARS-CoV-2 detection", @@ -492406,6 +493820,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.09.21267571", + "rel_title": "Coronavirus (COVID-19) Spike in Georgia: An Epidemiologic Study of Data, Modelling, and Policy Implications to Understand the Gender-and Race-Specific Variations", + "rel_date": "2021-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267571", + "rel_abs": "ObjectiveThe purpose of this study was to investigate the gender-and race-specific predictive variations in COVID-19 cases and deaths in Georgia, USA.\n\nMethodsThe data were extracted from the Georgia Department of Public Health (GDPH). Statistical methods, such as descriptive statistics, Artificial neural networks (ANN), and Bayesian approach, were utilized to analyze the data.\n\nResultsMore Whites died from COVID-19 than African-Americans/Blacks in Cobb, Hall, Gwinnett, and non-Georgia residents; however, more Blacks died in Dekalb and Fulton counties. The highest posterior mean for female deaths was obtained in Gwinnett County (77.17; 95% CI, 74.23-80.07) and for male deaths in Fulton County (73.48; 95% CI, 72.18-74.49). For overall race/ethnicity, Whites had the highest posterior mean for deaths (183.18; 95% CI, 128.29-238.27) compared with Blacks (162.48; 95% CI, 127.15- 197.42). Assessing the classification of the chronic medical conditions using ANN, Cobb and Hall Counties showed the highest mean AUC-ROC of the models (78% and 79%, respectively).\n\nConclusionsThe predictive models of COVID-19 transmission will help public health practitioners and researchers to better understand the course of the COVID-19 pandemic. The study findings are generalizable to populations with geographic and racial/ethnic similarities and may be used to determine gender/race-specific future virus models for effective interventions or policy modifications.\n\nHuman SubjectsNo personal identifiable information was obtained.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Fahad Mostafa", + "author_inst": "Texas Tech University" + }, + { + "author_name": "Riya Ganji", + "author_inst": "Texas Tech University Health Sciences Center" + }, + { + "author_name": "Julie St. John", + "author_inst": "Texas Tech University Health Sciences Center" + }, + { + "author_name": "Hafiz Khan", + "author_inst": "Texas Tech University Health Sciences Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.10.21267594", "rel_title": "Estimates of reduced vaccine effectiveness against hospitalization, infection, transmission and symptomatic disease of a new SARS-CoV-2 variant, Omicron (B.1.1.529), using neutralizing antibody titers", @@ -494078,61 +495523,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.12.09.21267203", - "rel_title": "Reduced Odds of SARS-CoV-2 Reinfection after Vaccination among New York City Adults, June-August 2021", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267203", - "rel_abs": "BackgroundBelief in immunity from prior infection and concern that vaccines might not protect against new variants are contributors to vaccine hesitancy. We assessed effectiveness of full and partial COVID-19 vaccination against reinfection when Delta was the predominant variant in New York City.\n\nMethodsWe conducted a case-control study in which case-patients with reinfection during June 15- August 31, 2021 and control subjects with no reinfection were matched (1:3) on age, sex, timing of initial positive test in 2020, and neighborhood poverty level. Conditional logistic regression was used to calculate matched odds ratios (mOR) and 95% confidence intervals (CI).\n\nResultsOf 349,598 adult residents who tested positive for SARS-CoV-2 infection in 2020, did not test positive again >90 days after initial positive test through June 15, 2021, and did not die before June 15, 2021, 1,067 were reinfected during June 15-August 31, 2021. Of 1,048 with complete matching criteria data, 499 (47.6%) were known to be symptomatic for COVID-19-like-illness, and 75 (7.2%) were hospitalized. Unvaccinated individuals, compared with fully vaccinated individuals, had elevated odds of reinfection (mOR, 2.23; 95% CI, 1.90, 2.61), of symptomatic reinfection (mOR, 2.17; 95% CI, 1.72, 2.74), and of reinfection with hospitalization (mOR, 2.59; 95% CI, 1.43, 4.69). Partially versus fully vaccinated individuals had 1.58 (95% CI: 1.22, 2.06) times the odds of reinfection. All three vaccines authorized or approved for use in the U.S. were similarly effective.\n\nConclusionAmong adults with previous SARS-CoV-2 infection, vaccination reduced odds of reinfections when the Delta variant predominated.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alison Levin-Rector", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Lauren Firestein", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Emily McGibbon", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Jessica Sell", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Sungwoo Lim", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Ellen H. Lee", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Don Weiss", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Anita Geevarughese", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Jane R. Zucker", - "author_inst": "New York City Department of Health and Mental Hygiene; Centers for Disease Control and Protection" - }, - { - "author_name": "Sharon K. Greene", - "author_inst": "New York City Department of Health and Mental Hygiene" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.09.21267355", "rel_title": "Estimating Active Cases of COVID-19", @@ -494516,6 +495906,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.06.21262384", + "rel_title": "A descriptive analysis of 2020 California Occupational Safety and Health Administration COVID-19-related complaints", + "rel_date": "2021-12-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21262384", + "rel_abs": "COVID-19 mortality disproportionately affected specific occupations and industries. The Occupational Safety and Health Administration (OSHA) protects the health and safety of workers by setting and enforcing standards for working conditions. Workers may file OSHA complaints about unsafe conditions. Complaints may indicate poor workplace safety during the pandemic. We evaluated COVID-19-related complaints filed with California (Cal)/OSHA between January 1, 2020 and December 14, 2020 across seven industries. To assess whether workers in occupations with high COVID-19-related mortality were also most likely to file Cal/OSHA complaints, we compared industry-specific per-capita COVID-19 confirmed deaths from the California Department of Public Health with COVID-19-related complaints. Although 7,820 COVID-19-related complaints were deemed valid by Cal/OSHA, only 627 onsite inspections occurred and 32 citations were issued. Agricultural workers had the highest per-capita COVID-19 death rates (402 per 100,000 workers) but were least represented among workplace complaints (44 per 100,000 workers). Health Care workers had the highest complaint rates (81 per 100,000 workers) but the second lowest COVID-19 death rate (81 per 100,000 workers). Industries with the highest inspection rates also had high COVID-19 mortality. Our findings suggest complaints are not proportional to COVID-19 risk. Instead, higher complaint rates may reflect worker groups with greater empowerment, resources, or capacity to advocate for better protections. This capacity to advocate for safe workplaces may account for relatively low mortality rates in potentially high-risk occupations. Future research should examine factors determining worker complaints and complaint systems to promote participation of those with the greatest need of protection.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Marilyn D Thomas", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Ellicott C Matthay", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kate A Duchowny", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Alicia R Riley", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Harmon Khela", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Yea-Hung C Chen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kirsten Bibbins-Domingo", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "M. Maria Glymour", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.12.06.471446", "rel_title": "Minimal cross-over between mutations associated with Omicron variant of SARS-CoV-2 and CD8+ T cell epitopes identified in COVID-19 convalescent individuals", @@ -495976,29 +497413,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.12.08.21267167", - "rel_title": "Access to healthcare as an important moderating variable for understanding geography of immunity levels for COVID-19 - preliminary insights from Poland", - "rel_date": "2021-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267167", - "rel_abs": "BackgroundBiases in COVID-19 burden and uncertainty in estimation of the corresponding epidemiologic indexes is a known and common phenomenon in infectious diseases. We investigated to what extent healthcare access (HCA) related supply/demand interfered with registered data on COVID-19 in Poland.\n\nMaterial and methodsWe run a multiple linear regression model with interactions to explain geographic variation in seroprevalence, hospitalizations (on voivodeship - NUTS-2 level) and current (beginning of the 4th wave - 15.09-21.11.2021) case notifications/crude mortality (on poviat - old NUTS-4 level). We took vaccination coverage and cumulative case notifications up to the so called 3rd wave as predictor variables and supply/demand (HCA) as moderating variables.\n\nResultsHCA with interacting terms (mainly demand) explained to the great extent the variance of current incidence and most variance of current mortality. HCA (mainly supply) is significantly moderating cumulative case notifications till the 3rd wave explaining the variance in seroprevalence and hospitalization.\n\nConclusionsSeeking causal relations between vaccination-or infection-gained immunity level and current infection dynamics could be misleading without understanding socio-epidemiologic context such as the moderating role of HCA (sensu lato). After quantification, HCA could be incorporated into epidemiologic models for improved prediction of real disease burden.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Andrzej Jarynowski", - "author_inst": "Institute for Interdisciplinary Research" - }, - { - "author_name": "Vitaly Belik", - "author_inst": "FU Berlin" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.09.21267516", "rel_title": "Changes in the trajectory of Long Covid symptoms following COVID-19 vaccination: community-based cohort study", @@ -496194,6 +497608,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.08.21267494", + "rel_title": "Omicron strain spreads with the doubling time of 3.2-3.6 days in South Africa province of Gauteng that achieved herd immunity to Delta variant", + "rel_date": "2021-12-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267494", + "rel_abs": "Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529), was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been detected on all continents. We analyzed the exponential growth of Omicron over the four-week periods in two most populated South Africas provinces, Gauteng and KwaZulu-Natal, arriving at the doubling time estimates of respectively 3.3 days [95% CI: 3.2-3.4 days] and 2.7 days [95% CI: 2.3-3.3 days]. Similar or even shorter doubling times were observed in other locations: Australia (3.0 days), New York State (2.5 days), UK (2.4 days), and Denmark (2.0 days). Log- linear regression suggests that the spread began in Gauteng around October 11, 2021, however, due to presumable stochasticity in the initial spread, this estimate can be inaccurate. Phylogenetics-based analysis indicates that the Omicron strain started to diverge in between October 6 and October 29, 2021. We estimated that the weekly growth of the ratio of Omicron to Delta is in the range 7.2-10.2, considerably higher than the growth of the ratio of Delta to Alpha (estimated to be in in the range 2.5-4.2), and Alpha to pre-existing strains (estimated to be in the range of 1.8-2.7). High relative growth does not necessarily imply higher Omicron infectivity. A two-strain SEIR model suggests that the growth advantage of Omicron may stem from immune evasion, which permits this VOC to infect both the recovered and the fully vaccinated individuals. As we demonstrated within the model, immune evasion is more concerning than increased transmissibility, because it can facilitate larger epidemic outbreaks.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Frederic Grabowski", + "author_inst": "Institute of Fundamental Technological Research, Polish Academy of Sciences" + }, + { + "author_name": "Marek Kocha\u0144czyk", + "author_inst": "Institute of Fundamental Technological Research, Polish Academy of Sciences" + }, + { + "author_name": "Tomasz Lipniacki", + "author_inst": "Institute of Fundamental Technological Research, Polish Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.08.21267483", "rel_title": "Risk of hospitalization and mortality after breakthrough SARS-CoV-2 infection by vaccine type and previous SARS-CoV-2 infection utilizing medical claims data", @@ -497490,53 +498931,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2021.12.08.21267459", - "rel_title": "Genetic overlap between idiopathic pulmonary fibrosis and COVID-19", - "rel_date": "2021-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267459", - "rel_abs": "Genome-wide association studies (GWAS) of coronavirus disease 2019 (COVID-19) and idiopathic pulmonary fibrosis (IPF) have identified genetic loci associated with both traits, suggesting possible shared biological mechanisms. Using updated GWAS of COVID-19 and IPF, we evaluated the genetic overlap between these two diseases and identified four genetic loci (including one novel) with likely shared causal variants between severe COVID-19 and IPF. Although there was a positive genetic correlation between COVID-19 and IPF, two of these four shared genetic loci had an opposite direction of effect. IPF-associated genetic variants related to telomere dysfunction and spindle assembly showed no association with COVID-19 phenotypes. Together, these results suggest there are both shared and distinct biological processes driving IPF and severe COVID-19 phenotypes.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Richard J Allen", - "author_inst": "University of Leicester" - }, - { - "author_name": "Beatriz Guillen-Guio", - "author_inst": "University of Leicester" - }, - { - "author_name": "Emma Croot", - "author_inst": "University of Leicester" - }, - { - "author_name": "Luke M Kraven", - "author_inst": "University of Leicester" - }, - { - "author_name": "Samuel Moss", - "author_inst": "Imperial College London" - }, - { - "author_name": "Iain Stewart", - "author_inst": "Imperial College London" - }, - { - "author_name": "R Gisli Jenkins", - "author_inst": "Imperial College London" - }, - { - "author_name": "Louise V Wain", - "author_inst": "University of Leicester" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.12.08.21266760", "rel_title": "Humoral and cellular responses to SARS-CoV-2 vaccination in patients with lymphoid malignancies", @@ -497992,6 +499386,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.07.21267204", + "rel_title": "Outbreak of COVID-19 among vaccinated and unvaccinated homeless shelter residents- Sonoma County, California, July 2021", + "rel_date": "2021-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267204", + "rel_abs": "In July 2021, the Sonoma County Health Department was alerted to three cases of COVID-19 among residents of a homeless shelter in Santa Rosa, California. Among 153 shelter residents, 83 (54%) were fully vaccinated; 71 (86%) vaccinated residents had received the Janssen COVID-19 vaccine and 12 (14%) received an mRNA (Pfizer BioNTech or Moderna) COVID-19 vaccine. Within 1 month, 116 shelter residents (76%) received positive SARS-CoV-2 test results, including 66 fully vaccinated residents and 50 not fully vaccinated. 9 fully vaccinated and 1 unvaccinated were hospitalized for COVID-19. All hospitalized cases had at least one underlying medical condition. Two deaths occurred, one in a vaccinated resident and one in a non-vaccinated resident. Specimens from 52 residents underwent whole genome sequencing; all were identified as SARS-CoV-2, Delta Variant AY.13 lineage. Additional mitigation measures are needed in medically vulnerable congregate setting where limited resources make individual quarantine and isolation not feasible.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Aleksandr Bukatko", + "author_inst": "Sonoma County Health Department, California" + }, + { + "author_name": "Mark Lobato", + "author_inst": "Sonoma County Health Department, California" + }, + { + "author_name": "Emily Mosites", + "author_inst": "Centers for Disease Control and Prevention COVID-19 Response" + }, + { + "author_name": "Cameron Stainken", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Katheryn Reihl", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Mojgan Deldari", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "John Bell", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "MaryKate Morris", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Debra Wadford", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Kathleen Harriman", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Sundari Mase", + "author_inst": "Sonoma County Health Department, California" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.07.21267425", "rel_title": "Rapid assessment of COVID-19 mortality risk with GASS classifiers", @@ -499624,73 +501077,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.07.21267293", - "rel_title": "SPECIFIC DETECTION OF SARS-COV-2 B.1.1.529 (OMICRON) VARIANT BY FOUR RT-qPCR DIFFERENTIAL ASSAYS", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267293", - "rel_abs": "In this report, we describe four RT-qPCR assays that enable rapid identification of the newly emerging SARS-COV-2 Omicron (B.1.1.529) variant of concern. The assays target Omicron characteristic mutations in the nsp6 (Orf1a), spike and nucleocapsid genes. We demonstrate that the assays are straightforward to assemble and perform, are amendable for multiplexing, and may be used as a reliable first-line tool to identify B.1.1.529 suspected samples. Importantly, this is a preliminary development report. Further validation and optimization of the assays described herein will be published hereafter.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "ORAN ERSTER", - "author_inst": "Israel Central Virology laboratory" - }, - { - "author_name": "Adi Beth Din", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Hadar Asraf", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Virginia Levy", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Areej Kabat", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Batya Mannasse", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Roberto Azar", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Ohad Shifman", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "shirley Lazar", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Michal Mandelboim", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel, School of Public Health, Sackler Faculty" - }, - { - "author_name": "Shay Fleishon", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel, School of Public Health, Sackler Faculty" - }, - { - "author_name": "Neta S Zuckerman", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.04.471153", "rel_title": "Elucidating design principles for engineering cell-derived vesicles to inhibit SARS-CoV-2 infection", @@ -499878,6 +501264,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.07.21267073", + "rel_title": "A Scaling Law for PCR Positivity in the COVID Second Wave", + "rel_date": "2021-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267073", + "rel_abs": "In this preliminary report, PCR positivity data in the second wave of the COVID pandemic (September-January 2020) are shown to obey a scaling law given by: O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD where % P0 and {Sigma}0 are the y- and x-intercepts of a plot of positivity, %P, against the number of tests, {Sigma}. The law holds across international, regional and local boundaries, as demonstrated for Great Britain, Austria, Germany and Sweden, the nine English regions, London - Yorkshire & Humber, and various Local Health Authorities in England. One possible explanation for scaling might be Dorfman pooling.\n\nThe scaling law can be used to remove a systematic or false positive (FP) component from the daily number of positive tests, or cases, to yield the real number of cases. The results correlate strongly with the ZOE survey for London (R2=0.787) and Excess Deaths for England (R2=0.833). The cumulative total of FPs can be estimated as 1.4M by the beginning of 2021, in line with other estimates.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Keith Johnson", + "author_inst": "IP Consultant" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.06.21267238", "rel_title": "Parental perspectives on the grief and support needs of children and young people bereaved during the Covid-19 pandemic: Qualitative findings from a national survey", @@ -501526,57 +502931,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2021.12.06.21267339", - "rel_title": "Systematic review of cardiac adverse effects in children and young people un-der 18 years of age after SARS-CoV-2 vaccination", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267339", - "rel_abs": "BackgroundReports of myocarditis and pericarditis following vaccination with mRNA vaccines for SARS-CoV-2 have occurred after countries began vaccinating adolescents. We undertook a systematic review of cardiac adverse effects associated with SARS-CoV-2 vaccine in children and young people (CYP)< 18 years.\n\nMethodsSystematic review with protocol prospectively registered with PROSPERO (CRD42021275380).\n\nSix electronic databases were searched from 1 December 2019 to 14 September 2021. Eligible studies were those reporting on CYP with reported or proven myocarditis, pericarditis and/or myopericarditis associated with vaccination against SARS-CoV-2. We summarized findings across all clinical cases reported in case report / case series studies. As a number of studies reported data from two publicly available vaccine surveillance systems, we updated estimates of reporting rates for cardiac adverse events up to 31 October for the US Vaccine Adverse Event Reporting System (VAERS) and 13 November for EudraVigilance covering European Union and European Economic Area (EUEA) countries.\n\nResultsTwenty-one studies were included from 338 identified records. Seventeen were case reports/series describing a total of 127 CYP. Three studies described reporting rates from passive surveillance databases (VAERS, EudraVigilance, and the WHO VigiBase) and one described 22 cases from the US Vaccine Safety Datalink (VSD).\n\nClinical series reported that 99.2% presented with chest pain, 100% had raised troponin and 73.8% had an abnormal ECG. Cardiovascular magnetic resonance (CMR) in 91 cases identified myocardial injury in 61.5%, with 90.1% showing late gadolinium enhancement. NSAIDs were the most common treatment (76.0%).\n\nOne US dataset (VSD) estimated a significant excess of 29.6 events per million vaccine doses across both sexes and doses. There were 1129 reports of myocarditis and 358 reports of pericarditis from across the USA and EU/EEA. The VAERS reporting rate per million for myocarditis was 12.4 for boys and 1.4 for girls after the first dose, and 49.6 for boys and 6.1 for girls after the second dose. There was a marked trend for VAERS reporting to be highest soon after initiation of the vaccine schedule, suggesting reporting bias.\n\nConclusionsCardiac adverse effects are very rare after mRNA vaccination for COVID-19 in CYP <18 years. The great majority of cases are mild and self-limiting without significant treatment. No data are yet available on children under 12 years. Larger detailed longitudinal studies are urgently needed from active surveillance sources.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Joana Cruz", - "author_inst": "University College of London" - }, - { - "author_name": "Amedine Duret", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Rachel Harwood", - "author_inst": "Alder Hey in the Park" - }, - { - "author_name": "Lorna K. Fraser", - "author_inst": "Martin House Research Centre, University of York" - }, - { - "author_name": "Caroline B. Jones", - "author_inst": "Alder Hey Childrens Hospital Liverpool" - }, - { - "author_name": "Joseph Ward", - "author_inst": "UCL Great Ormond St. Institute of Child Health" - }, - { - "author_name": "Elizabeth Whittaker", - "author_inst": "Faculty of Medicine, Imperial College London" - }, - { - "author_name": "Simon E Kenny", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Russell M Vinner", - "author_inst": "UCL Great Ormond St. Institute of Child Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.12.06.21267391", "rel_title": "The Impact of Mass Exodus on the Resurgence of COVID19 Cases: Study Case of Regions in Indonesia", @@ -501756,6 +503110,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.12.02.21267182", + "rel_title": "COVID-19 infections post-vaccination by HIV status in the United States", + "rel_date": "2021-12-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267182", + "rel_abs": "ImportanceRecommendations for additional doses of COVID vaccine are restricted to people with HIV who have advanced disease or unsuppressed HIV viral load. Understanding SARS-CoV-2 infection risk post-vaccination among PWH is essential for informing vaccination guidelines.\n\nObjectiveEstimate the risk of breakthrough infections among fully vaccinated people with (PWH) and without (PWoH) HIV in the US.\n\nDesign, setting, and participantsThe Corona-Infectious-Virus Epidemiology Team (CIVET)-II cohort collaboration consists of 4 longitudinal cohorts from integrated health systems and academic health centers. Each cohort identified individuals [≥]18 years old, in-care, and fully vaccinated for COVID-19 through 30 June 2021. PWH were matched to PWoH on date fully vaccinated, age group, race/ethnicity, and sex at birth. Incidence rates per 1,000 person-years and cumulative incidence of breakthrough infections with 95% confidence intervals ([,]) were estimated by HIV status. Cox proportional hazards models estimated adjusted hazard ratios (aHR) of breakthrough infections by HIV status adjusting for demographic factors, prior COVID-19 illness, vaccine type (BNT162b2, [Pfizer], mRNA-1273 [Moderna], Jansen Ad26.COV2.S [J&J]), calendar time, and cohort. Risk factors for breakthroughs among PWH, were also investigated.\n\nExposureHIV infection\n\nOutcomeCOVID-19 breakthrough infections, defined as laboratory evidence of SARS-CoV-2 infection or COVID-19 diagnosis after an individual was fully vaccinated.\n\nResultsAmong 109,599 individuals (31,840 PWH and 77,759 PWoH), the rate of breakthrough infections was higher in PWH versus PWoH: 44 [41, 48] vs. 31 [29, 33] per 1,000 person-years. Cumulative incidence at 210 days after date fully vaccinated was low, albeit higher in PWH versus PWoH overall (2.8% versus 2.1%, log-rank p<0.001, risk difference=0.7% [0.4%, 1.0%]) and within each vaccine type. Breakthrough infection risk was 41% higher in PWH versus PWoH (aHR=1.41 [1.28, 1.56]). Among PWH, younger age (18-24 versus 45-54), history of COVID-19 prior to fully vaccinated date, and J&J vaccination (versus Pfizer) were associated with increased risk of breakthroughs. There was no association of breakthrough with HIV viral load suppression or CD4 count among PWH.\n\nConclusions and RelevanceCOVID-19 vaccination is effective against infection with SARS-CoV-2 strains circulating through 30 Sept 2021. PWH have an increased risk of breakthrough infections compared to PWoH. Recommendations for additional vaccine doses should be expanded to all PWH.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Sally B Coburn", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Elizabeth Humes", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Raynell Lang", + "author_inst": "Johns Hopkins Bloomberg School of Public Health, University of Calgary" + }, + { + "author_name": "Cameron Stewart", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Brenna C Hogan", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Kelly A Gebo", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Sonia Napravnik", + "author_inst": "University of North Carolina at Chapel HIll" + }, + { + "author_name": "Jessie K Edwards", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Lindsay E Browne", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Lesley S Park", + "author_inst": "Standford Center for Population Health Sciences" + }, + { + "author_name": "Amy C Justice", + "author_inst": "Yale Schools of Public Health and MEdicine, VA Connecticut Healthcare System" + }, + { + "author_name": "Kirsha Gordon", + "author_inst": "Yale School of Medicine, VA Connecticut Healthcare System" + }, + { + "author_name": "Michael A Horberg", + "author_inst": "Kaiser Permanente Mid-Atlantic Permanente Research Institute" + }, + { + "author_name": "Julia M Certa", + "author_inst": "Kaiser Permanente Mid-Atlantic Permanente Research Institute" + }, + { + "author_name": "Eric Watson", + "author_inst": "Kaiser Permanente Mid-Atlantic Permanente Research Institute" + }, + { + "author_name": "Celeena R Jefferson", + "author_inst": "Kaiser Permanente Mid-Atlantic Permanente Research Institute" + }, + { + "author_name": "Michael J Silverberg", + "author_inst": "Kaiser Permanente Northern California" + }, + { + "author_name": "Jacek Skarbinski", + "author_inst": "Kaiser Permanente Northern California" + }, + { + "author_name": "Wendy A Leyden", + "author_inst": "Kaiser Permanente Northern California" + }, + { + "author_name": "Carolyn F Williams", + "author_inst": "Division of AIDS at National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Keri N Althoff", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2021.11.03.467161", "rel_title": "Critical Negatively Charged Residues Are Important for the Activity of SARS-CoV-1 and SARS-CoV-2 Fusion Peptides", @@ -503148,61 +504601,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.02.21267191", - "rel_title": "Prevalence of SARS-CoV-2 infection among COVID-19 RT-PCR laboratory workers in Bangladesh", - "rel_date": "2021-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267191", - "rel_abs": "BackgroundHealth care workers (HCWs) at the frontline are confronting a substantial risk of infection during the coronavirus disease 2019 (COVID-19) pandemic. This emerging virus created specific hazards to researchers and laboratory staff in a clinical setting, underlined by rapid and extensive worldwide transmission. This study aimed to investigate the prevalence of SARS-CoV-2 infection among COVID-19 RT-PCR laboratory health workers in Bangladesh.\n\nMaterials & MethodsThis retrospective study was conducted between October 2 to December 2, 2020. A total of 508 participants, including doctors, scientific officers, medical technologists, and cleaners working in several COVID-19 RT-PCR laboratories, were included in this study. Data were collected from each participant using a semi-structured questionnaire prepared in the format of an anonymous Google form. All participants provided informed consent. The Ethical clearance was obtained from the Institutional Ethics Review Committee of Shaheed Suhrawardy Medical College, Dhaka, Bangladesh. All statistical analyses were performed using SPSS (Statistical Package for the Social Sciences) version 25.0 software (SPSS, Inc).\n\nResultsOut of the 508 participants, 295 tested positive for SARS CoV-2 RT-PCR. Among the positive cases, 202 were men, 93 were women, with the median age of 30 years. The most positive cases were medical technologists (53.22%) followed by doctors (28.8%). Out of the 271 symptomatic positive cases, the most typical symptoms were fever (78.5%), fatigue (70%), loss of smell and taste (65%), cough (64%), and others. Hypertension, obesity, and diabetes were found in 8.8%, 8.8%, and 7.1% positive cases. A + blood group was present in 37% of the positive cases, followed by the B+ blood group (27%) and O+ blood group (25%). Inadequate supply of personal protection equipment (PPE), absence of negative pressure ventilation, laboratory contamination, and no training on molecular test methods were found in 13.8%, 67.8%, 44.7%, and 40.6% of positive cases, respectively.\n\nConclusionEvaluating the infection status of laboratory health workers is crucial for drawing attention from the public, providing practical suggestions for government agencies, and increasing protective measures for laboratory health workers.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mohammad Jahidur Rahman Khan", - "author_inst": "Shaheed Suhrawardy Medical College" - }, - { - "author_name": "Samshad Jahan shumu", - "author_inst": "Shaheed Suhrawardy Medical College" - }, - { - "author_name": "Ruksana Raihan", - "author_inst": "US-Bangla Medical College" - }, - { - "author_name": "Nusrat Mannan", - "author_inst": "US-Bangla Medical College" - }, - { - "author_name": "Md Selim Reza", - "author_inst": "RT-PCR LAB, Bangabandhu Sheikh Mujib Medical College" - }, - { - "author_name": "Nazia Hasan Khan", - "author_inst": "United Hospital Limited" - }, - { - "author_name": "Amirul Huda Bhuiyan", - "author_inst": "Dhaka Medical College" - }, - { - "author_name": "Paroma Deb", - "author_inst": "Dhaka Medical College" - }, - { - "author_name": "Farzana Mim", - "author_inst": "Jahangirnagar University" - }, - { - "author_name": "Arifa Akram", - "author_inst": "National Institute of Laboratory Medicine and Referral Centre" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.02.21267164", "rel_title": "Estimation of heterogeneous instantaneous reproduction numbers with application to characterize SARS-CoV-2 transmission in Massachusetts counties", @@ -503594,6 +504992,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.02.21267168", + "rel_title": "The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267168", + "rel_abs": "BackgroundDelta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to emergence of multiple sublineages, many of which are well-mixed between countries.\n\nAimHere, we aim to study the emergence and spread of the Delta lineage in Russia.\n\nMethodsWe use a phylogeographic approach to infer imports of Delta sublineages into Russia, and phylodynamic models to assess the rate of their spread.\n\nResultsWe show that nearly the entire Delta epidemic in Russia has probably descended from a single import event despite genetic evidence of multiple Delta imports. Indeed, over 90% of Delta samples in Russia are characterized by the nsp2:K81N+ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. The AY.122 lineage was frequent in Russia among Delta samples from the start, and has not increased in frequency in other countries where it has been observed, suggesting that its high prevalence in Russia has probably resulted from a random founder effect.\n\nConclusionThe apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Galya V. Klink", + "author_inst": "IITP RAS" + }, + { + "author_name": "Ksenia R Safina", + "author_inst": "Skolkovo Institute of Science and Technology" + }, + { + "author_name": "Elena Nabieva", + "author_inst": "Skolkovo Institute of Science and Technology (Skoltech)" + }, + { + "author_name": "Nikita Shvyrev", + "author_inst": "National Research University Higher School of Economics" + }, + { + "author_name": "Sofya Garushyants", + "author_inst": "IITP RAS" + }, + { + "author_name": "Evgeniia Iskanderovna Alekseeva", + "author_inst": "Skolkovo Institute of Science and Technology" + }, + { + "author_name": "Andrey B. Komissarov", + "author_inst": "Smorodintsev Istitute of Influenza" + }, + { + "author_name": "Daria M. Danilenko", + "author_inst": "Smorodintsev Istitute of Influenza" + }, + { + "author_name": "Andrey A. Pochtovyy", + "author_inst": "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" + }, + { + "author_name": "Elizaveta V. Divisenko", + "author_inst": "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" + }, + { + "author_name": "Lyudmila A. Vasilchenko", + "author_inst": "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" + }, + { + "author_name": "Elena V. Shidlovskaya", + "author_inst": "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" + }, + { + "author_name": "Nadezhda A. Kuznetsova", + "author_inst": "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" + }, + { + "author_name": "- The Coronavirus Russian Genetics Initiative (CoRGI) Consortium", + "author_inst": "" + }, + { + "author_name": "Andrei E Samoilov", + "author_inst": "Central Research Institute of Epidemiology" + }, + { + "author_name": "Alexey Neverov", + "author_inst": "Central Research Institute for Epidemiology" + }, + { + "author_name": "Anfisa Popova", + "author_inst": "Central Research Institute for Epidemiology" + }, + { + "author_name": "Gennady Fedonin", + "author_inst": "Central research institute for epidemiology" + }, + { + "author_name": "- The CRIE Consortium", + "author_inst": "" + }, + { + "author_name": "Vasiliy G. Akimkin", + "author_inst": "Central Research Institute for Epidemiology" + }, + { + "author_name": "Dmitry Lioznov", + "author_inst": "Smorodintsev Istitute of Influenza" + }, + { + "author_name": "Vladimir Gushchin", + "author_inst": "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" + }, + { + "author_name": "Vladimir Shchur", + "author_inst": "HSE University" + }, + { + "author_name": "Georgii A Bazykin", + "author_inst": "Skoltech" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.03.21267225", "rel_title": "Persistent Symptoms Among Frontline Health Workers Post-acute COVID-19 Infection", @@ -504838,153 +506347,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.01.470767", - "rel_title": "A public antibody class recognizes a novel S2 epitope exposed on open conformations of SARS-CoV-2 spike", - "rel_date": "2021-12-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.01.470767", - "rel_abs": "Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigated the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We found that [~]82% of SARS-CoV-2 S-reactive B cells show a naive phenotype, which represents an unusually high fraction of total human naive B cells ([~]0.1%). Approximately 10% of these naive S-reactive B cells shared an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. A proportion of memory B cells, comprising switched ([~]0.05%) and unswitched B cells ([~]0.04%), was also reactive with S and some of these cells were reactive with ADAMTS13, which is associated with thrombotic thrombocytopenia. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Mathieu Claireaux", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Tom G Caniels", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Marlon de Gast", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Julianna Han", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Denise Guerra", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Gius Kerster", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Barbera DC van Schaik", - "author_inst": "Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, " - }, - { - "author_name": "Aldo Jongejan", - "author_inst": "Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, " - }, - { - "author_name": "Angela I Schriek", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Marloes Grobben", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Philip JM Brouwer", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Karlijn van der Straten", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Yoann Aldon", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Joan Capella-Pujol", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Jonne L Snitselaar", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Wouter Olijhoek", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Aafke Aartse", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Mitch Brinkkemper", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Ilja Bontjer", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Judith A Burger", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Meliawati Poniman", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Tom PL Bijl", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Jonathan L Torres", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Jeffrey Copps", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Isabel Cuella Martin", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Steven W de Taeye", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Godelieve J de Bree", - "author_inst": "Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Infection and I" - }, - { - "author_name": "Andrew B Ward", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Kwinten Sliepen", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Antoine HC van Kampen", - "author_inst": "Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, " - }, - { - "author_name": "Perry D Moerland", - "author_inst": "Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, " - }, - { - "author_name": "Rogier W Sanders", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - }, - { - "author_name": "Marit J van Gils", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.01.470697", "rel_title": "Macaque-human differences in SARS-CoV-2 Spike antibody response elicited by vaccination or infection", @@ -505296,6 +506658,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.02.471028", + "rel_title": "Systems immune profiling of variant-specific vaccination against SARS-CoV-2", + "rel_date": "2021-12-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.02.471028", + "rel_abs": "Lipid-nanoparticle(LNP)-mRNA vaccines offer protection against COVID-19. However, multiple variant lineages caused widespread breakthrough infections. There is no report on variant-specific vaccines to date. Here, we generated LNP-mRNAs specifically encoding wildtype, B.1.351 and B.1.617 SARS-CoV-2 spikes, and systematically studied their immune responses in animal models. All three LNP-mRNAs induced potent antibody responses in mice. However, WT-LNP-mRNA vaccination showed reduced neutralization against B.1.351 and B.1.617; and B.1.617-specific vaccination showed differential neutralization. All three vaccine candidates elicited antigen-specific CD8 and CD4 T cell responses. Single cell transcriptomics of B.1.351-LNP-mRNA and B.1.617-LNP-mRNA vaccinated animals revealed a systematic landscape of immune cell populations and global gene expression. Variant-specific vaccination induced a systemic increase in reactive CD8 T cell population, with a strong signature of transcriptional and translational machineries in lymphocytes. BCR-seq and TCR-seq unveiled repertoire diversity and clonal expansions in vaccinated animals. These data provide direct systems immune profiling of variant-specific LNP-mRNA vaccination in vivo.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Lei Peng", + "author_inst": "Yale University" + }, + { + "author_name": "Jonathan Park", + "author_inst": "Yale University" + }, + { + "author_name": "Zhenhao Fang", + "author_inst": "Yale University" + }, + { + "author_name": "Xiaoyu Zhou", + "author_inst": "Yale University" + }, + { + "author_name": "Matthew Dong", + "author_inst": "Yale University" + }, + { + "author_name": "Qiancheng Xiong", + "author_inst": "Yale University" + }, + { + "author_name": "Chenxiang Lin", + "author_inst": "Yale University" + }, + { + "author_name": "Sidi Chen", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.03.471057", "rel_title": "Unconventional secretion of unglycosylated ORF8 is critical for the cytokine storm during SARS-CoV-2 infection", @@ -506544,29 +507953,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.30.21267029", - "rel_title": "Assessment of correlations between risk factors and symptom presentation among defined at-risk groups following a confirmed COVID-19 diagnosis", - "rel_date": "2021-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21267029", - "rel_abs": "This study analyzes the specific linkages between symptoms within individual COVID patients belonging to at-risk groups. The goal was to determine how strongly linked patient symptoms are within these at-risk groups to find any associations between factors such as comorbidities and COVID symptoms. In this study, de-identified patient data from the N3C database was utilized in order to link representative immunocompromised states with specific symptoms, and non-immunocompromised state with the same, to determine if the strength of the correlation changes for these at-risk groups. Multiple autoimmune disorders resulting in immunocompromised state were analyzed, to determine if severity of immune response and inflammatory action plays a role in any potential differences. An exploratory approach using statistical methods and visualization techniques appropriate to multidimensional data sets was taken. The identified correlations may allow pattern analysis in disease presentation specific to a given population, potentially informing pattern recognition, symptom presentation, and treatment approaches in patients with immune comorbidities.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dylan Aidlen", - "author_inst": "Northeastern University" - }, - { - "author_name": "Jamie Henzy", - "author_inst": "Northeastern University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.12.01.21267147", "rel_title": "Comparison of Saliva and Mid-Turbinate Swabs for Detection of COVID-19", @@ -506758,6 +508144,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.11.30.470642", + "rel_title": "Variance in Variants: Propagating Genome Sequence Uncertainty into Phylogenetic Lineage Assignment", + "rel_date": "2021-12-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.30.470642", + "rel_abs": "Genetic sequencing is subject to many different types of errors, but most analyses treat the resultant sequences as if they are known without error. Next generation sequencing methods rely on significantly larger numbers of reads than previous sequencing methods in exchange for a loss of accuracy in each individual read. Still, the coverage of such machines is imperfect and leaves uncertainty in many of the base calls. On top of this machine-level uncertainty, there is uncertainty induced by human error, such as errors in data entry or incorrect parameter settings. In this work, we demonstrate that the uncertainty in sequencing techniques will affect downstream analysis and propose a straightforward method to propagate the uncertainty.\n\nOur method uses a probabilistic matrix representation of individual sequences which incorporates base quality scores as a measure of uncertainty that naturally lead to resampling and replication as a framework for uncertainty propagation. With the matrix representation, resampling possible base calls according to quality scores provides a bootstrap- or prior distribution-like first step towards genetic analysis. Analyses based on these re-sampled sequences will include a more complete evaluation of the error involved in such analyses.\n\nWe demonstrate our resampling method on SARS-CoV-2 data. The resampling procedures adds a linear computational cost to the analyses, but the large impact on the variance in downstream estimates makes it clear that ignoring this uncertainty may lead to overly confident conclusions. We show that SARS-CoV-2 lineage designations via Pangolin are much less certain than the bootstrap support reported by Pangolin would imply and the clock rate estimates for SARS-CoV-2 are much more variable than reported.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "David Champredon", + "author_inst": "Public Health Agency of Canada - National Microbiology Laboratory" + }, + { + "author_name": "Devan G Becker", + "author_inst": "The University of Western Ontario" + }, + { + "author_name": "Connor Chato", + "author_inst": "The University of Western Ontario" + }, + { + "author_name": "Gopi Gugan", + "author_inst": "The University of Western Ontario" + }, + { + "author_name": "Art G Poon", + "author_inst": "The University of Western Ontario" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.11.30.21266716", "rel_title": "Third COVID-19 Vaccine Dose Boosts Neutralising Antibodies in Poor Responders", @@ -508558,237 +509979,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.11.24.469906", - "rel_title": "Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines", - "rel_date": "2021-11-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.24.469906", - "rel_abs": "IntroductoryThe evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the emergence of many new variant lineages that have exacerbated the COVID-19 pandemic. Some of those variants were designated as variants of concern/interest (VOC/VOI) by national or international authorities based on many factors including their potential impact on vaccines. To ascertain and rank the risk of VOCs and VOIs, we analyzed their ability to escape from vaccine-induced antibodies. The variants showed differential reductions in neutralization and replication titers by post-vaccination sera. Although the Omicron variant showed the most escape from neutralization, sera collected after a third dose of vaccine (booster sera) retained moderate neutralizing activity against that variant. Therefore, vaccination remains the most effective strategy to combat the COVID-19 pandemic.", - "rel_num_authors": 54, - "rel_authors": [ - { - "author_name": "Li Wang", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Markus H Kainulainen", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Nannan Jiang", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Han Di", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Gaston Bonenfant", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Lisa Mills", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Michael Currier", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Punya Shrivastava-Ranjan", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Brenda M Calderon", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Mili Sheth", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Brian R Mann", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Jaber Hossain", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Xudong Lin", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Sandra Lester", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Elizabeth Pusch", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Joyce Jones", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Dan Cui", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Payel Chatterjee", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Harley M Jenks", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Esther Morantz", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Gloria Larson", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Masato Hatta", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Jennifer Harcourt", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Azaibi Tamin", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Yan Lin", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Ying Tao", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Kun Zhao", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Kristine Lacek", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Ashely Burroughs", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Terianne Wong", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Suxiang Tong", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "John R Barnes", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Mark W Tenforde", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Wesley H Self", - "author_inst": "Vanderbilt University, Nashville, Tennessee, USA" - }, - { - "author_name": "Nathan I Shapiro", - "author_inst": "Harvard University, Cambridge, Massachusetts, USA" - }, - { - "author_name": "Matthew C Exline", - "author_inst": "Ohio State University, Columbus, Ohio, USA" - }, - { - "author_name": "D. Clark Files", - "author_inst": "Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA" - }, - { - "author_name": "Kevin W Gibbs", - "author_inst": "Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA" - }, - { - "author_name": "David N Hager", - "author_inst": "Johns Hopkins University, Baltimore, Maryland, USA" - }, - { - "author_name": "Manish Patel", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Alison S Laufer Halpin", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Laura K McMullan", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Justin S Lee", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Hongjie Xia", - "author_inst": "The University of Texas Medical Branch at Galveston, Texas" - }, - { - "author_name": "Xuping Xie", - "author_inst": "The University of Texas Medical Branch at Galveston, Texas" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "The University of Texas Medical Branch at Galveston, Texas" - }, - { - "author_name": "C. Todd Davis", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Christina F Spiropoulou", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Natalie J. Thornburg", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "M. Steven Oberste", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Vivien Dugan", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "- SSEV Bioinformatics Working Group", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "David E Wentworth", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Bin Zhou", - "author_inst": "COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.11.28.468932", "rel_title": "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography", @@ -509052,6 +510242,29 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.11.29.470346", + "rel_title": "In silico study on the effects of disulfide bonds in ORF8 of SARS-CoV-2", + "rel_date": "2021-11-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.29.470346", + "rel_abs": "The COVID-19 epidemic, caused by virus SARS-CoV-2, has been a pandemic and threatening everyones health in the past two years. In SARS-CoV-2, the accessory protein ORF8 plays an important role in immune modulation. Here we present an in silico study on the effects of the disulfide bonds in ORF8, including the effects on the structures, the binding sites and free energy when ORF8 binds to the human leukocyte antigen (HLA-A). Using the explicit solvent Molecular Dynamics (MD) simulations, we collect the conformational ensembles on ORF8 with different disulfide bonds reduction schemes. With a new visualization technique on the local geometry, we analyze the effects of the disulfide bonds on the structure of ORF8. We find that the disulfide bonds have large influences on the loop regions of the surface. Moreover, by performing docking between HLA-A and the conformational ensembles of ORF8, we predict the preferred binding sites and find that most of them are little affected by the disulfide bonds.Further, we estimate the binding free energy between HLA-A and ORF8 with different disulfide bonds reductions. In the end, from the comparison with the available experimental results on the epitopes of ORF8, we validated our binding sites prediction. All the above observations may provide inspirations on inhibitor/drug design against ORF8 based on the binding pathway with HLA-A.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yadi Cheng", + "author_inst": "Beijing Institute of Technology" + }, + { + "author_name": "Xubiao Peng", + "author_inst": "Beijing Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.11.29.470362", "rel_title": "Peptide-antibody Fusions Engineered by Phage Display Exhibit Ultrapotent and Broad Neutralization of SARS-CoV-2 Variants", @@ -510496,33 +511709,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.11.29.21266623", - "rel_title": "Transient adverse events after REGN-CoV2 administration for mild COVID-19 patients and their potential predictive factors: a single center analysis", - "rel_date": "2021-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21266623", - "rel_abs": "BackgroundREGN-COV2, a monoclonal antibody cocktail drug against the SARS-COV-2 virus, has proven to be effective in preventing the development of severe COVID-19 and is increasingly being administered in outpatient and home settings. Adverse events such as fever and decreased oxygen saturation may occur after administration of REGN-COV2, and although these symptoms are generally mild and transient, predicting the occurrence of these adverse events is useful in developing a monitoring plan for patients.\n\nMethodsWe performed a retrospective analysis of 76 patients who received REGN-CoV2 between August and September 2021. We collected information on fever, decreased oxygen saturation requiring oxygen supplementation, and other adverse events from medical records. Patients were divided into two subgroups: those who presented with fever or oxygen desaturation and those who did not, and underlying medical conditions and laboratory data were compared between each group. The parameters that exhibited significant differences were further tested using Fishers exact test to evaluate whether appropriate thresholds could be set to distinguish the incidence group from the non-incidence group.\n\nFindingsOf the 76 patients, 47 had fever of 38.5{degrees}C or higher within 24 hours after administration, and 27 of these patients had a body temperature of 37.5{degrees}C or lower before administration. Oxygen was required in 17 cases, 7 of which required oxygen more than 24 hours after administration of REGN-COV2, and additional treatment such as dexamethasone was given as the disease progressed to moderate. Among the parameters analyzed, lymphocyte count and IFN{lambda}3 showed significant differences between the fever and non-fever groups. This was also the case in the comparison excluding patients who had fever before administration. There was also a significant difference in ferritin and CRP between the oxygen required and non-required groups. In addition to IFN{lambda}3, ferritin, and CRP, there was a significant difference in LDH between the group that required additional treatment and the group that did not. When lymphocytes count <950/{micro}L was used to predict fever, the sensitivity and specificity were 55% and 79%, respectively, with odds ratio 4.746 (95% CI: 1.666 to 14.12, p=0.004) in contingency table analysis. Similarly, when IFN{lambda}3 >5.0 was used as the cutoff, sensitivity 72%, specificity 76%, odds ratio 8.220 (2.857 to 22.22; p<0.0001).\n\nInterpretationsTransient fever and decreased oxygen saturation are common adverse events after REGN-CoV2 administration, and their occurrence correlated with the severity factor of COVID-19 itself. Evaluation of these items at the time of administration is useful not only for predicting the severity of COVID-19 but also for the development of adverse events in patients receiving REGN-CoV2.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Gen Kano", - "author_inst": "Kyoto Yamashiro General Medical Center" - }, - { - "author_name": "Kyoko Taniguchi", - "author_inst": "Kyoto Yamashiro General Medical Center" - }, - { - "author_name": "Yukiko Oue", - "author_inst": "Kyoto Yamashiro General Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.25.470044", "rel_title": "Anticipating future SARS-CoV-2 variants of concern through ab initio quantum mechanical modeling", @@ -510766,6 +511952,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.11.27.21266930", + "rel_title": "Dosing interval strategies for two-dose COVID-19 vaccination in 13 low- and middle-income countries of Europe: health impact modelling and benefit-risk analysis", + "rel_date": "2021-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.27.21266930", + "rel_abs": "BackgroundIn settings where the COVID-19 vaccine supply is constrained, extending the intervals between the first and second doses of the COVID-19 vaccine could let more people receive their first doses earlier. Our aim is to estimate the health impact of COVID-19 vaccination alongside benefit-risk assessment of different dosing intervals for low- and middle-income countries of Europe.\n\nMethodsWe fitted a dynamic transmission model to country-level daily reported COVID-19 mortality in 13 low- and middle-income countries in the World Health Organization European Region (Albania, Armenia, Azerbaijan, Belarus, Bosnia and Herzegovina, Bulgaria, Georgia, Republic of Moldova, Russian Federation, Serbia, North Macedonia, Turkey, and Ukraine). A vaccine product with characteristics similar to the Oxford/AstraZeneca COVID-19 (AZD1222) vaccine was used in the base case scenario and was complemented by sensitivity analyses around efficacies related to other COVID-19 vaccines. Both fixed dosing intervals at 4, 8, 12, 16, and 20 weeks and dose-specific intervals that prioritise specific doses for certain age groups were tested. Optimal intervals minimise COVID-19 mortality between March 2021 and December 2022. We incorporated the emergence of variants of concern into the model, and also conducted a benefit-risk assessment to quantify the trade-off between health benefits versus adverse events following immunisation.\n\nFindingsIn 12 of the 13 countries, optimal strategies are those that prioritise the first doses among older adults (60+ years) or adults (20-59 years). These strategies lead to dosing intervals longer than six months. In comparison, a four-week fixed dosing interval may incur 10.2% [range: 4.0% - 22.5%; n = 13 (countries)] more deaths. There is generally a negative association between dosing interval and COVID-19 mortality within the range we investigated. Assuming a shorter first dose waning duration of 120 days, as opposed to 360 days in the base case, led to shorter optimal dosing intervals of 8-12 weeks. Benefit-risk ratios were the highest for fixed dosing intervals of 8-12 weeks.\n\nInterpretationWe infer that longer dosing intervals of over six months, which are substantially longer than the current label recommendation for most vaccine products, could reduce COVID-19 mortality in low- and middle-income countries of WHO/Europe. Certain vaccine features, such as fast waning of first doses, significantly shorten the optimal dosing intervals.\n\nFundingWorld Health Organization", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yang Liu", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Carl AB Pearson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Frank G Sandmann", + "author_inst": "Public Health England" + }, + { + "author_name": "Rosanna C Barnard", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Jong-Hoon Kim", + "author_inst": "International Vaccine Institute" + }, + { + "author_name": "- CMMID COVID-19 Working Group", + "author_inst": "" + }, + { + "author_name": "Stefan Flasche", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Mark Jit", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Kaja Abbas", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.26.21266899", "rel_title": "A generic method and software to estimate the transmission advantage of pathogen variants in real-time : SARS-CoV-2 as a case-study", @@ -512378,101 +513615,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.24.21266809", - "rel_title": "Pandemic inequity in a megacity: a multilevel analysis of individual, community, and health care vulnerability risks for COVID-19 mortality in Jakarta, Indonesia", - "rel_date": "2021-11-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266809", - "rel_abs": "BackgroundThe 33 recognized megacities comprise approximately 7% of the global population, yet account for 20% COVID-19 deaths. The specific inequities and other factors within megacities that affect vulnerability to COVID-19 mortality remain poorly defined. We assessed individual, community-level and health care factors associated with COVID-19-related mortality in a megacity of Jakarta, Indonesia, during two epidemic waves spanning March 2, 2020, to August 31, 2021.\n\nMethodsThis retrospective cohort included all residents of Jakarta, Indonesia, with PCR-confirmed COVID-19. We extracted demographic, clinical, outcome (recovered or died), vaccine coverage data, and disease prevalence from Jakarta Health Office surveillance records, and collected sub-district level socio-demographics data from various official sources. We used multi-level logistic regression to examine individual, community and sub-district-level health care factors and their associations with COVID-19-mortality.\n\nFindingsOf 705,503 cases with a definitive outcome by August 31, 2021, 694,706 (98{middle dot}5%) recovered and 10,797 (1{middle dot}5%) died. The median age was 36 years (IQR 24-50), 13{middle dot}2% (93,459) were <18 years, and 51{middle dot}6% were female. The sub-district level accounted for 1{middle dot}5% of variance in mortality (p<0.0001). Individual-level factors associated with death were older age, male sex, comorbidities, and, during the first wave, age <5 years (adjusted odds ratio (aOR) 1{middle dot}56, 95%CI 1{middle dot}04-2{middle dot}35; reference: age 20-29 years). Community-level factors associated with death were poverty (aOR for the poorer quarter 1{middle dot}35, 95%CI 1{middle dot}17-1{middle dot}55; reference: wealthiest quarter), high population density (aOR for the highest density 1{middle dot}34, 95%CI 1{middle dot}14-2{middle dot}58; reference: the lowest), low vaccine coverage (aOR for the lowest coverage 1{middle dot}25, 95%CI 1{middle dot}13-1{middle dot}38; reference: the highest).\n\nInterpretationIn addition to individual risk factors, living in areas with high poverty and density, and low health care performance further increase the vulnerability of communities to COVID-19-associated death in urban low-resource settings.\n\nFundingWellcome (UK) Africa Asia Programme Vietnam (106680/Z/14/Z).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed on November 22, 2021, for articles that assessed individual, community, and healthcare vulnerability factors associated with coronavirus disease 2019 (COVID-19) mortality, using the search terms (\"novel coronavirus\" OR \"SARS-CoV-2\" OR \"COVID-19\") AND (\"death\" OR \"mortality\" OR \"deceased\") AND (\"community\" OR \"social\") AND (\"healthcare\" OR \"health system\"). The 33 recognized megacities comprise approximately 7% of the global population, yet account for 20% COVID-19 deaths. The specific inequities and other factors within megacities that affect vulnerability to COVID-19 mortality remain poorly defined. At individual-level, studies have shown COVID-19-related mortality to be associated with older age and common underlying chronic co-morbidities including hypertension, diabetes, obesity, cardiac disease, chronic kidney disease and liver disease. Only few studies from North America, and South America have reported the association between lower community-level socio-economic status and healthcare performance with increased risk of COVID-19-related death. We found no studies have been done to assess individual, community, and healthcare vulnerability factors associated with COVID-19 mortality risk, especially in lower-and middle-income countries (LMIC) where accessing quality health care services is often challenging for substantial proportions of population, due to under-resourced and fragile health systems. In Southeast Asia, by November 22, 2021, COVID-19 case fatality rate had been reported at 2{middle dot}2% (23,951/1,104,835) in Vietnam, 1{middle dot}7% (47,288/2,826,853) in Philippines, 1{middle dot}0% (20,434/2,071,009) in Thailand, 1{middle dot}2% (30,063/2,591,486) in Malaysia, 2{middle dot}4% (2,905/119,904) in Cambodia, and 0{middle dot}3% in Singapore (667/253,649). Indonesia has the highest number of COVID-19 cases and deaths in the region, reporting 3{middle dot}4% case fatality rate (143,744 /4,253,598), with the highest number of cases in the capital city of Jakarta. A preliminary analysis of the first five months of surveillance in Jakarta found that 497 of 4265 (12%) hospitalised patients had died, associated with older age, male sex; pre-existing hypertension, diabetes, or chronic kidney disease; clinical diagnosis of pneumonia; multiple (>3) symptoms; immediate intensive care unit admission, or intubation.\n\nAdded value of this studyThis retrospective population-based study of the complete epidemiological surveillance data of Jakarta during the first eighteen months of the epidemic is the largest studies in LMIC to date, that comprehensively analysed the individual, community, and healthcare vulnerability associated with COVID-19-related mortality among individuals diagnosed with PCR-confirmed COVID-19. The overall case fatality rate among general population in Jakarta was 1{middle dot}5% (10,797/705,503). Individual factors associated with risk of death were older age, male sex, comorbidities, and, during the first wave, age <5 years (adjusted odds ratio (aOR) 1{middle dot}56, 95%CI 1{middle dot}04-2{middle dot}35; reference: age 20-29 years). The risk of death was further increased for people living in sub-districts with high rates of poverty (aOR for the poorer quarter 1{middle dot}35, 95%CI 1{middle dot}17-1{middle dot}55; reference: wealthiest quarter), high population density (aOR for the highest density 1{middle dot}34, 95%CI 1{middle dot}14-2{middle dot}58), and low COVID-19 vaccination coverage (aOR for the lowest coverage 1{middle dot}25, 95%CI 1{middle dot}13-1{middle dot}38; reference: the highest).\n\nImplications of all available evidenceDifferences in socio-demographics and access to quality health services, among other factors, greatly influence COVID-19 mortality in low-resource settings. This study affirmed that in addition to well-known individual risk factors, community-level socio-demographics and healthcare factors further increase the vulnerability of communities to die from COVID-19 in urban low-resource settings. These results highlight the need for accelerated vaccine rollout and additional preventive interventions to protect the urban poor who are most vulnerable to dying from COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Henry Surendra", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Ngabila Salama", - "author_inst": "DKI Jakarta Health Office" - }, - { - "author_name": "Karina D Lestari", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Verry Adrian", - "author_inst": "DKI Jakarta Health Office" - }, - { - "author_name": "Widyastuti Widyastuti", - "author_inst": "DKI Jakarta Health Office" - }, - { - "author_name": "Dwi Oktavia", - "author_inst": "DKI Jakarta Health Office" - }, - { - "author_name": "Rosa N Lina", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Bimandra A Djaafara", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Ihsan Fadilah", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Rahmat Sagara", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Lenny L Ekawati", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Ahmad Nurhasim", - "author_inst": "The Conversation Indonesia" - }, - { - "author_name": "Riris Andono A Ahmad", - "author_inst": "Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada" - }, - { - "author_name": "Aria Kekalih", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Ari F Syam", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Anuraj H Shankar", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Guy Thwaites", - "author_inst": "Oxford University Clinical Research Unit" - }, - { - "author_name": "J Kevin Baird", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Raph L Hamers", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - }, - { - "author_name": "Iqbal RF Elyazar", - "author_inst": "Eijkman-Oxford Clinical Research Unit" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.24.21266837", "rel_title": "Changes in antidepressant use in Australia: A nationwide analysis prior to and during the COVID-19 pandemic (2015-2021)", @@ -512700,6 +513842,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.22.21266522", + "rel_title": "A comparison of health care use after severe COVID-19, respiratory syncytial virus, and influenza in children", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266522", + "rel_abs": "AimTo explore whether children in specialist care with COVID-19 have increased post-discharge health care use when compared to children in specialist care with 1) respiratory syncytial virus (RSV) infection, and 2) other respiratory tract infections (RTIs).\n\nMethodsIn 34,214 children aged 1 month to 5 years who were registered with one or more hospital visit (outpatient or inpatient) with a diagnosis of COVID-19 (N=128), RSV infection (N=4,009), or other RTIs (N=34,458) from 2017-2021, we used a difference-in-differences study design to investigate the individual all-cause primary and specialist health care use from 12 weeks prior to 12 weeks after the hospital visit, stratified on infants (1-12 months) and children (1-5 years).\n\nResultsWe found a slight increase in primary health care use in the first four weeks after the hospital visit for infants with COVID-19 when compared to infants with RSV infection (6 [95%CI=2 to 13] per 10,000, 0.52% relative increase). For infants diagnosed with COVID-19, we found a similar post-visit increase in inpatients when compared to infants with RSV infection, which lasted for 12 weeks.\n\nConclusionsOur findings imply slightly increased health care use among infants after hospital visit for COVID-19 than among infants with other respiratory tract infections, for which potential etiological mechanisms deserve future clinical research. Severe COVID-19 in young children will not represent any markedly increased burden on the health services.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Vilde Bergstad Larsen", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Ketil St\u00f8rdal", + "author_inst": "University of Oslo" + }, + { + "author_name": "Kjetil Telle", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Fredrik Methi", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Karin Magnusson", + "author_inst": "Norwegian Institute of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.11.23.21266759", "rel_title": "Social Class, Race/Ethnicity, and COVID-19 Mortality Among Working Age Adults in the United States", @@ -514084,73 +515261,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.22.21266565", - "rel_title": "Impacts of vaccination and asymptomatic testing on SARS-CoV-2 transmission dynamics in a university setting", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266565", - "rel_abs": "We investigate the impact of vaccination and asymptomatic testing uptake on SARS-CoV-2 transmission in a university student population using a stochastic compartmental model. We find that the magnitude and timing of outbreaks is highly variable depending on the transmissibility of the most dominant strain of SARS CoV-2 and under different vaccine uptake levels and efficacies. When delta is the dominant strain, low level interventions (no asymptomatic testing, 30% vaccinated with a vaccine that is 80% effective at reducing infection) lead to 53-71% of students become infected during the first term. Asymptomatic testing is most useful when vaccine uptake is low: when 30% of students are vaccinated, 90% uptake of asymptomatic testing leads to almost half the case numbers. With high interventions (90% using asymptomatic testing, 90% vaccinated) cumulative incidence is 7-9%, with around 80% of these cases estimated to be asymptomatic. However, under emergence of a new variant that is at least twice as transmissible as delta and with the vaccine efficacy against infection reduced to 55%, large outbreaks are likely in universities, even with very high (90%) uptake of vaccination and 100% uptake of asymptomatic testing. If vaccine efficacy against infection against this new variant is higher (70%), then outbreaks can be mitigated if there is least 50% uptake of asymptomatic testing additional to 90% uptake of vaccination. Our findings suggest that effective vaccination is critical for controlling SARS-CoV-2 transmission in university settings with asymptomatic testing ranging from additionally useful to critical, depending on effectiveness and uptake of vaccination. Other measures may be necessary to control outbreaks under the emergence of a more transmissible variant with vaccine escape.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Emily J Nixon", - "author_inst": "University of Bristol" - }, - { - "author_name": "Amy C Thomas", - "author_inst": "University of Bristol" - }, - { - "author_name": "Daniel A Stocks", - "author_inst": "University of Bristol" - }, - { - "author_name": "Antoine M. G. Barreaux", - "author_inst": "University of Bristol" - }, - { - "author_name": "Gibran Hemani", - "author_inst": "University of Bristol" - }, - { - "author_name": "Adam Trickey", - "author_inst": "University of Bristol" - }, - { - "author_name": "Rachel Kwiatkowska", - "author_inst": "University of Bristol" - }, - { - "author_name": "Josephine G Walker", - "author_inst": "University of Bristol" - }, - { - "author_name": "David Ellis", - "author_inst": "University of Bristol" - }, - { - "author_name": "Leon Danon", - "author_inst": "Department of Engineering Mathematics, University of Bristol, UK." - }, - { - "author_name": "Caroline Relton", - "author_inst": "University of Bristol" - }, - { - "author_name": "Hannah Christensen", - "author_inst": "University of Bristol" - }, - { - "author_name": "Ellen Brooks Pollock", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.23.21266734", "rel_title": "Establishing and characterising large COVID-19 cohorts after mapping the Information System for Research in Primary Care in Catalonia to the OMOP Common Data Model", @@ -514506,6 +515616,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.11.24.469842", + "rel_title": "Single-domain antibodies efficiently neutralize SARS-CoV-2 variants of concern", + "rel_date": "2021-11-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.24.469842", + "rel_abs": "Virus-neutralizing antibodies are one of the few treatment options for COVID-19. The evolution of SARS-CoV-2 virus has led to the emergence of virus variants with reduced sensitivity to some antibody-based therapies. The development of potent antibodies with a broad spectrum of neutralizing activity is urgently needed. Here we isolated a panel of single-domain antibodies that specifically bind to the receptor-binding domain of SARS-CoV-2 S glycoprotein. Three of the selected antibodies exhibiting most robust neutralization potency were used to generate dimeric molecules. We observed that these modifications resulted in up to a 200-fold increase in neutralizing activity. The most potent heterodimeric molecule efficiently neutralized each of SARS-CoV-2 variant of concern, including Alpha, Beta, Gamma, Delta and Omicron variants. This heterodimeric molecule could be a promising drug candidate for a treatment for COVID-19 caused by virus variants of concern.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Irina A Favorskaya", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Dmitry V Shcheblyakov", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Ilias B Esmagambetov", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Inna V Dolzhikova", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Irina A Alekseeva", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Anastasia I Korobkova", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Daria V Voronina", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Ekaterina I Ryabova", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Artem A Derkaev", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Anna V Kovyrshina", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Anna A Iliukhina", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Andrey G Botikov", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Olga L Voronina", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Daria A Egorova", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Olga V Zubkova", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Natalia N Ryzhova", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Ekaterina I Aksenova", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Marina S Kunda", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Denis Y Logunov", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Boris S Naroditsky", + "author_inst": "N. F. Gamaleya National Research Center" + }, + { + "author_name": "Alexandr L Gintsburg", + "author_inst": "N. F. Gamaleya National Research Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.11.22.469642", "rel_title": "Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single cell RNA sequencing", @@ -515786,29 +516995,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.11.17.21266461", - "rel_title": "Space-time Classification Index for Assessing COVID-19 Hotspots", - "rel_date": "2021-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266461", - "rel_abs": "ObjectivesTo develop new methods to address problems associated with use of traditional measures of disease surveillance, including prevalence and positivity rates.\n\nMethodsWe use data from the public New York Times Github repository to develop a space-time classification index of COVID-19 hotspots. The Local Indicator of Spatial Association (LISA) statistic is applied to identify daily clusters of COVID-19 cases, from July 4th to July 19th.\n\nResultsThe classification index is a spatial and temporal assessment tool that seeks to incorporate temporal trends of the clusters that are \"high-high\" and \"high-low\". Two classifications support the index: severity and temporal duration. We define severity as the number of times a county is statistically significant and temporal duration captures the number of consecutive days a county is a hotspot.\n\nConclusionsThe space-time classification index provides a statistically robust measure of the spatial patterns of COVID-19 hotspots. Spatial information is not captured through measures like the positivity rate, which merely divides the number of cases by tests conducted. The index proposed in this paper can guide intervention efforts by classifying counties with six-levels of importance.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "David Haynes II", - "author_inst": "Institute for Health Informatics, University of Minnesota" - }, - { - "author_name": "Chetan Tiwari", - "author_inst": "Departments of Geosciences & Computer Science, Georgia State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.17.21266441", "rel_title": "Pausing methotrexate improves immunogenicity of COVID-19 vaccination in patients with rheumatic diseases", @@ -516192,6 +517378,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.11.21.469423", + "rel_title": "Conserved recombination patterns across coronavirus subgenera", + "rel_date": "2021-11-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.21.469423", + "rel_abs": "Recombination contributes to the genetic diversity found in coronaviruses and is known to be a prominent mechanism whereby they evolve. It is apparent, both from controlled experiments and in genome sequences sampled from nature, that patterns of recombination in coronaviruses are non-random and that this is likely attributable to a combination of sequence features that favour the occurrence of recombination breakpoints at specific genomic sites, and selection disfavouring the survival of recombinants within which favourable intra-genome interactions have been disrupted. Here we leverage available whole-genome sequence data for six coronavirus subgenera to identify specific patterns of recombination that are conserved between multiple subgenera and then identify the likely factors that underlie these conserved patterns. Specifically, we confirm the non-randomness of recombination breakpoints across all six tested coronavirus subgenera, locate conserved recombination hot- and cold-spots, and determine that the locations of transcriptional regulatory sequences are likely major determinants of conserved recombination breakpoint hot-spot locations. We find that while the locations of recombination breakpoints are not uniformly associated with degrees of nucleotide sequence conservation, they display significant tendencies in multiple coronavirus subgenera to occur in low guanine-cytosine content genome regions, in non-coding regions, at the edges of genes, and at sites within the Spike gene that are predicted to be minimally disruptive of Spike protein folding. While it is apparent that sequence features such as transcriptional regulatory sequences are likely major determinants of where the template-switching events that yield recombination breakpoints most commonly occur, it is evident that selection against misfolded recombinant proteins also strongly impacts observable recombination breakpoint distributions in coronavirus genomes sampled from nature.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Arne de Klerk", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Phillip Ivan Swanepoel", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rentia Francis Lourens", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Mpumelelo Zondo", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Isaac Abodunran", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Spyros Lytras", + "author_inst": "MRC - University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Oscar MacLean", + "author_inst": "University of Glasgow" + }, + { + "author_name": "David L Robertson", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Sergei L Kosakovsky Pond", + "author_inst": "Temple University Institute for Genomics and Evolutionary Medicine" + }, + { + "author_name": "Jordan D Zehr", + "author_inst": "Temple University" + }, + { + "author_name": "Venkatesh Kumar", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Michael J Stanhope", + "author_inst": "Cornell University" + }, + { + "author_name": "Gordon Harkins", + "author_inst": "University of the Western Cape" + }, + { + "author_name": "Ben Murrell", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Darren Martin", + "author_inst": "University of Cape Town" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.11.23.21266709", "rel_title": "COVID-19 vaccination and menstrual cycle changes: A United Kingdom (UK) retrospective case-control study", @@ -517776,73 +519037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.17.21266499", - "rel_title": "Comprehensive genomic, immunological and clinical analysis of COVID-19 vaccine breakthrough infections: a prospective, comparative cohort study", - "rel_date": "2021-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266499", - "rel_abs": "ObjectivesAs the COVID-19 pandemic is still ongoing and SARS-CoV-2 variants are circulating worldwide, an increasing number of breakthrough infections have been detected despite the good efficacy of COVID-19 vaccines.\n\nMethodsA prospective, comparative cohort study was conducted in Beijing Ditan Hospital to evaluate the clinical, immunological and genomic characteristics of COVID-19 breakthrough infections. Data on 88 COVID-19 breakthrough cases (vaccinated group) and 41 unvaccinated cases (unvaccinated group) from June 1 to August 20, 2021 were extracted from a cloud database. Among these 129 COVID-19 cases, we successfully sequenced 33 whole genomes, including 16 from the vaccinated group and 17 from the unvaccinated group.\n\nResultsAsymptomatic and mild cases predominated in both groups, but 2 patients developed severe disease in the unvaccinated group. Between the two groups, the median time of viral shedding in the vaccinated group were significantly lower than those in the unvaccinated group (p = 0.003). A comparison of dynamic IgG titres of cases in the two groups indicated that IgG titres in the vaccinated group showed a significantly increasing trend (P =0.028). The CD4+T lymphocyte count was lower in the unvaccinated group, and there was a significant difference between the two groups (p=0.018). In the vaccinated group, the number of moderate cases who received Sinopharm BBIBP (42 cases) was significantly higher than those who received Sinovac Coronavac (p=0.020). Whole-genome sequencing revealed 23 cases of delta variants, including 15 patients from the vaccinated group. However, no significant difference was observed in either the RT-qPCR results or viral shedding time.\n\nConclusionsCOVID-19 vaccine breakthrough infections were mainly asymptomatic and mild, the IgG titres were significantly higher and increased rapidly, and the viral shedding was short. Delta variants may be more likely to cause breakthrough infections, and vaccination may not reduce the viral loads and shedding time.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Di Tian", - "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, China" - }, - { - "author_name": "Yang Song", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China." - }, - { - "author_name": "Man Zhang", - "author_inst": "Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control (CDC), Beijing, China; Research Centre for Preve" - }, - { - "author_name": "Yang Pan", - "author_inst": "Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control (CDC), Beijing, China; Research Centre for Preve" - }, - { - "author_name": "Ziruo Ge", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Yao Zhang", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Xingxiang Ren", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Jing Wen", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Yanli Xu", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Hong Guo", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China." - }, - { - "author_name": "Peng Yang", - "author_inst": "Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control (CDC), Beijing, China; Research Centre for Preve" - }, - { - "author_name": "Zhihai Chen", - "author_inst": "Emergency Department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China." - }, - { - "author_name": "Wenbo Xu", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.20.21266644", "rel_title": "Immunogenicity of heterologous prime/boost inactivated and mRNA COVID-19 vaccine", @@ -518026,6 +519220,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.11.19.21266537", + "rel_title": "Effectiveness of Vaccination Against Reported SARS-CoV-2 Infection in United States Coast Guard Personnel Between May and August 2021: A Time-Series Analysis", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266537", + "rel_abs": "BackgroundThe United States Coast Guard (CG) began voluntary use of SARS-CoV-2 vaccines under an Emergency Use Authorization on December 16, 2020. Vaccination status is monitored through a service-wide immunization registry. Active Duty and Reserve (military) CG members are required to report any new positive test for COVID-19 to a centralized database.\n\nMethodsBetween May and August 2021, vaccination effectiveness (VE) against any new report of COVID-19 was calculated according to standard formulas, using registry immunization status of cases and monthly mid-point vaccine coverage data. CG members recorded as fully vaccinated with a two-dose vaccine were compared with those with any other vaccine status. Sub-analyses were also conducted according to geographic area (Atlantic vs Pacific), age, and type of vaccine received.\n\nResultsEffectiveness of full vaccination reached a peak of 89.0% in June, then declined over the rest of the study period to 62.7% in August. In July and August, steeper declines in VE were seen in the Atlantic region. The rate of breakthrough infections remained under 1% in two-dose vaccine recipients, and did not differ between those who received the Moderna or Pfizer vaccines. No hospitalizations or deaths due to COVID-19 disease were recorded in fully vaccinated Coast Guard members.\n\nConclusionCoincident with the national spread of the Delta variant of SARS-CoV-2, overall vaccine effectiveness among CG personnel decreased during the summer months of 2021, but continued to provide substantial protection, as well as full protection against the most serious outcomes. Policy initiatives and outreach intended to increase vaccine coverage within this and other military populations could extend the disease prevention benefits seen in this study.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "John Iskander", + "author_inst": "United States Coast Guard" + }, + { + "author_name": "Jamie K Frost", + "author_inst": "United States Coast Guard" + }, + { + "author_name": "Sharon Russell", + "author_inst": "United States Coast Guard" + }, + { + "author_name": "Jaspal Ahluwalia", + "author_inst": "United States Coast Guard" + }, + { + "author_name": "Emily Ward", + "author_inst": "United States Coast Guard" + }, + { + "author_name": "Shane Steiner", + "author_inst": "United States Coast Guard" + }, + { + "author_name": "Dana Thomas", + "author_inst": "United States Coast Guard" + }, + { + "author_name": "Paul Michaud", + "author_inst": "United States Coast Guard" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.19.21266547", "rel_title": "Protective characteristics of COVID-19 convalescent and post-vaccination IgG antibodies", @@ -519358,61 +520599,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.11.16.21266408", - "rel_title": "HLA-A*03:01 is associated with increased risk of fever, chills, and more severe reaction to Pfizer-BioNTech COVID-19 vaccination", - "rel_date": "2021-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.16.21266408", - "rel_abs": "COVID-19 vaccines are safe and highly effective, but some individuals experience unpleasant reactions to vaccination. As the majority of adults in the US have received a COVID-19 vaccine this year, there is an unprecedented opportunity to study the genetics of reactions to vaccination via surveys of individuals who are already part of genetic research studies. Here, we have queried 17,440 participants in the Helix DNA Discovery Project and Healthy Nevada Project about their reactions to COVID-19 vaccination. Our GWAS identifies an association between severe difficulties with daily routine after vaccination and HLA-A*03:01. This association was statistically significant only for those who received the Pfizer-BioNTech vaccine (BNT162b2; p=4.70E-11), but showed a trending association in those who received the Moderna vaccine (mRNA-1273; p=0.005) despite similar sample sizes for study. In Pfizer-BioNTech recipients, HLA-A*03:01 was associated with a two-fold increase in risk of severe vaccine reactions. The effect was consistent across ages, sexes, and whether the person had previously had a COVID-19 infection. The reactions experienced by HLA-A*03:01 carriers were driven by associations with chills, fever, fatigue, and in general feeling unwell.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alexandre Bolze", - "author_inst": "Helix" - }, - { - "author_name": "Iva Neveux", - "author_inst": "Desert Research Institute" - }, - { - "author_name": "Kelly M Schiabor Barrett", - "author_inst": "Helix" - }, - { - "author_name": "Simon White", - "author_inst": "Helix" - }, - { - "author_name": "Magnus Isaksson", - "author_inst": "Helix" - }, - { - "author_name": "Shaun Dabe", - "author_inst": "Renown Health" - }, - { - "author_name": "William Lee", - "author_inst": "Helix" - }, - { - "author_name": "Joseph J Grzymski", - "author_inst": "Desert Research Institute" - }, - { - "author_name": "Nicole L Washington", - "author_inst": "Helix" - }, - { - "author_name": "Elizabeth T Cirulli", - "author_inst": "Helix" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.17.21266410", "rel_title": "COVID-19 management in social care in England: a systematic review of changing policies and newspaper reported staff perspectives.", @@ -519732,6 +520918,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.18.21266558", + "rel_title": "Effectiveness of digital contact tracing for COVID-19 in New South Wales, Australia", + "rel_date": "2021-11-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.18.21266558", + "rel_abs": "BackgroundDigital proximity tracing applications were rolled out early in the COVID-19 pandemic in many countries to complement conventional contact tracing. Empirical evidence about their benefits for pandemic response remains scarce. We evaluated the effectiveness and usefulness of COVIDSafe, Australias national smartphone-based proximity tracing application for COVID-19.\n\nMethodsIn this prospective study, conducted in New South Wales, Australia between May and November 2020, we calculated the positive predictive value and sensitivity of COVIDSafe, its additional contact yield, and the number of averted public exposure events. Semi-structured interviews with public health staff were conducted to assess the applications usefulness.\n\nResultsThere were 619 confirmed COVID-19 cases and over 25,300 close contacts during the study period. COVIDSafe was used by 137 (22%) cases and detected 79 (0{middle dot}3%) close contacts. It had a positive predictive value of 39% and a sensitivity of 15%, and detected 17 (0{middle dot}07%) additional close contacts that were not identified by conventional contact tracing. The application generated a substantial additional workload for public health staff and was not considered useful.\n\nConclusionsCOVIDSafe was not sufficiently effective to make a meaningful contribution to the COVID-19 response in Australias most populous state over a 6-month period. This contrasts optimistic projections from modelling studies about the added value of digitally supported contact tracing. We found no evidence that it adds value to conventional contact tracing, and recommend that their implementation should always include comprehensive effectiveness evaluations.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Florian Vogt", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Bridget Haire", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Linda Selvey", + "author_inst": "University of Queensland" + }, + { + "author_name": "John Kaldor", + "author_inst": "University of New South Wales" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.17.21266404", "rel_title": "Care Models for Long COVID: A Rapid Systematic Review", @@ -520984,29 +522201,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.11.17.468929", - "rel_title": "Predicting SARS-CoV-2 epitope-specific TCR recognition using pre-trained protein embeddings", - "rel_date": "2021-11-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.17.468929", - "rel_abs": "The COVID-19 pandemic is ongoing because of the high transmission rate and the emergence of SARS-CoV-2 variants. The P272L mutation in SARS-Cov-2 S-protein is known to be highly relevant to the viral escape associated with the second pandemic wave in Europe. Epitope-specific T-cell receptor (TCR) recognition is a key factor in determining the T-cell immunogenicity of a SARS-CoV-2 epitope. Although several data-driven methods for predicting epitope-specific TCR recognition have been proposed, they remain challenging owing to the enormous diversity of TCRs and the lack of available training data. Self-supervised transfer learning has recently been demonstrated to be powerful for extracting useful information from unlabeled protein sequences and increasing the predictive performance of the fine-tuned models in downstream tasks.\n\nHere, we present a predictive model based on Bidirectional Encoder Representations from Transformers (BERT), employing self-supervised transfer learning, to predict SARS-CoV-2 T-cell epitope-specific TCR recognition. The fine-tuned model showed notably high predictive performance for independent evaluation using the SARS-CoV-2 epitope-specific TCR CDR3{beta} sequence datasets. In particular, we found the proline at position 4 corresponding to the P272L mutation in the SARS-CoV-2 S-protein269-277 epitope (YLQPRTFLL) may contribute substantially to TCR recognition of the epitope through interpreting the output attention weights of our model.\n\nWe anticipate that our findings will provide new directions for constructing a reliable data-driven model to predict the immunogenic T-cell epitopes using limited training data and help accelerate the development of an effective vaccine in response to SARS-CoV-2 variants.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Youngmahn Han", - "author_inst": "Korea Institute of Science and Technology Information" - }, - { - "author_name": "Aeri Lee", - "author_inst": "BioBrain Inc" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.11.15.468720", "rel_title": "Susceptibility of sheep to experimental co-infection with the ancestral lineage of SARS-CoV-2 and its alpha variant", @@ -521338,6 +522532,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.11.17.468942", + "rel_title": "IFITM dependency of SARS-CoV-2 variants of concern", + "rel_date": "2021-11-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.17.468942", + "rel_abs": "It has recently been shown that an early SARS-CoV-2 isolate (NL-02-2020) hijacks interferon-induced transmembrane proteins (IFITMs) for efficient replication in human cells. To date, several \"Variants of Concern\" (VOCs) showing increased infectivity and resistance to neutralization have emerged and globally replaced the early viral strains. Here, we determined whether the four SARS-CoV-2 VOCs (Alpha, Beta, Gamma and Delta) maintained the dependency on IFITM proteins for efficient replication. We found that depletion of IFITM2 strongly reduces viral RNA production by all four VOCs in the human epithelial lung cancer cell line Calu-3. Silencing of IFITM1 had little effect, while knock-down of IFITM3 resulted in an intermediate phenotype. Strikingly, depletion of IFITM2 generally reduced infectious virus production by more than four orders of magnitude. In addition, an antibody directed against the N-terminus of IFITM2 inhibited SARS-CoV-2 VOC replication in iPSC-derived alveolar epithelial type II cells thought to represent major viral target cells in the lung. In conclusion, endogenously expressed IFITM proteins (especially IFITM2) are critical cofactors for efficient replication of genuine SARS-CoV-2 VOCs, including the currently dominating Delta variant.\n\nIMPORTANCERecent results showed that an early SARS-CoV-2 isolate requires endogenously expressed IFITM proteins for efficient infection. However, whether IFITMs are also important cofactors for infection of emerging SARS-CoV-2 VOCs that out-competed the original strains and currently dominate the pandemic remained to be determined. Here, we demonstrate that depletion of endogenous IFITM2 expression almost entirely prevents the production of infectious Alpha, Beta, Gamma and Delta VOC SARS-CoV-2 virions in a human lung cell line. In comparison, silencing of IFITM1 had little impact, while knock-down of IFITM3 had intermediate effects on viral replication. Finally, an antibody targeting the N-terminus of IFITM2 inhibited SARS-CoV-2 VOC replication in iPSC-derived alveolar epithelial type II cells. Our results show that SARS-CoV-2 VOCs including the currently dominant Delta variant are dependent on IFITM2 for efficient replication suggesting that IFITM proteins play a key role in viral transmission and pathogenicity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rayhane Nchioua", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Annika Schundner", + "author_inst": "Institute of General Physiology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Dorota Kmiec", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Caterina Prelli Bozzo", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Fabian Zech", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Lennart Koepke", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Alexander Graf", + "author_inst": "Laboratory for Functional Genome Analysis and Gene Center, LMU Munich, 80539 Munich, Germany" + }, + { + "author_name": "Stefan Krebs", + "author_inst": "Laboratory for Functional Genome Analysis and Gene Center, LMU Munich, 80539 Munich, Germany" + }, + { + "author_name": "Helmut Blum", + "author_inst": "Laboratory for Functional Genome Analysis and Gene Center, LMU Munich, 80539 Munich, Germany" + }, + { + "author_name": "Manfred Frick", + "author_inst": "Institute of General Physiology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Konstantin MJ Sparrer", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + }, + { + "author_name": "Frank Kirchhoff", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.11.15.468737", "rel_title": "SARS-CoV-2 RdRp is a versatile enzyme with proofreading activity and ability to incorporate NHC into RNA by using diphosphate form molnupiravir as a substrate", @@ -522762,225 +524019,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.12.468428", - "rel_title": "#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol", - "rel_date": "2021-11-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.12.468428", - "rel_abs": "We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus ob-scure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.\n\nACM Reference FormatAbigail Dommer1{dagger}, Lorenzo Casalino1{dagger}, Fiona Kearns1{dagger}, Mia Rosenfeld1, Nicholas Wauer1, Surl-Hee Ahn1, John Russo,2 Sofia Oliveira3, Clare Morris1, AnthonyBogetti4, AndaTrifan5,6, Alexander Brace5,7, TerraSztain1,8, Austin Clyde5,7, Heng Ma5, Chakra Chennubhotla4, Hyungro Lee9, Matteo Turilli9, Syma Khalid10, Teresa Tamayo-Mendoza11, Matthew Welborn11, Anders Christensen11, Daniel G. A. Smith11, Zhuoran Qiao12, Sai Krishna Sirumalla11, Michael OConnor11, Frederick Manby11, Anima Anandkumar12,13, David Hardy6, James Phillips6, Abraham Stern13, Josh Romero13, David Clark13, Mitchell Dorrell14, Tom Maiden14, Lei Huang15, John McCalpin15, Christo- pherWoods3, Alan Gray13, MattWilliams3, Bryan Barker16, HarindaRajapaksha16, Richard Pitts16, Tom Gibbs13, John Stone6, Daniel Zuckerman2*, Adrian Mulholland3*, Thomas MillerIII11,12*, ShantenuJha9*, Arvind Ramanathan5*, Lillian Chong4*, Rommie Amaro1*. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. In Supercomputing 21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis. ACM, New York, NY, USA, 14 pages. https://doi.org/finalDOI", - "rel_num_authors": 51, - "rel_authors": [ - { - "author_name": "Abigail Dommer", - "author_inst": "UC San Diego" - }, - { - "author_name": "Lorenzo Casalino", - "author_inst": "UC San Diego" - }, - { - "author_name": "Fiona Kearns", - "author_inst": "UC San Diego" - }, - { - "author_name": "Mia Rosenfeld", - "author_inst": "UC San Diego" - }, - { - "author_name": "Nicholas Wauer", - "author_inst": "UC San Diego" - }, - { - "author_name": "Surl-Hee Ahn", - "author_inst": "UC San Diego" - }, - { - "author_name": "John Russo", - "author_inst": "OHSU" - }, - { - "author_name": "Sofia Oliveira", - "author_inst": "U Bristol" - }, - { - "author_name": "Clare Morris", - "author_inst": "UC San Diego" - }, - { - "author_name": "Anthony Bogetti", - "author_inst": "U Pittsburgh" - }, - { - "author_name": "Anda Trifan", - "author_inst": "University of Illinois at Urbana/ Champaign and Argonne National Lab" - }, - { - "author_name": "Alexander Brace", - "author_inst": "Argonne National Lab" - }, - { - "author_name": "Terra Sztain", - "author_inst": "Freie University Berlin" - }, - { - "author_name": "Austin Clyde", - "author_inst": "Argonne National Lab" - }, - { - "author_name": "Heng Ma", - "author_inst": "Argonne National Lab" - }, - { - "author_name": "Chakra Chennubhotla", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Hyungro Lee", - "author_inst": "Rutgers U" - }, - { - "author_name": "Matteo Turilli", - "author_inst": "Rutgers U" - }, - { - "author_name": "Syma Khalid", - "author_inst": "U Oxford" - }, - { - "author_name": "Teresa Tamayo-Mendoza", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Matthew Welborn", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Anders Christiansen", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Daniel G.A. Smith", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Zhuoran Qiao", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Sai Krishna Sirumalla", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Frederick Manby", - "author_inst": "Entos, Inc" - }, - { - "author_name": "Anima Anandkumar", - "author_inst": "California Institute of Technology & NVIDIA, Inc" - }, - { - "author_name": "David Hardy", - "author_inst": "University of Illinois at Urbana / Champaign" - }, - { - "author_name": "James Phillips", - "author_inst": "University of Illinois at Urbana / Champaign" - }, - { - "author_name": "Abraham Stern", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "Josh Romero", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "David Clark", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "Mitchell Dorrell", - "author_inst": "Pittsburgh Supercomputing Center" - }, - { - "author_name": "Tom Maiden", - "author_inst": "Pittsburgh Supercomputing Center" - }, - { - "author_name": "Lei Huang", - "author_inst": "Texas Advanced Computing Center" - }, - { - "author_name": "John McCalpin", - "author_inst": "Texas Advanced Computing Center" - }, - { - "author_name": "Christopher Woods", - "author_inst": "U Bristol" - }, - { - "author_name": "Alan Gray", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "Matt Williams", - "author_inst": "U Bristol" - }, - { - "author_name": "Bryan Barker", - "author_inst": "Oracle for Research" - }, - { - "author_name": "Harinda Rajapaksha", - "author_inst": "Oracle for Research" - }, - { - "author_name": "Richard Pitts", - "author_inst": "Oracle for Research" - }, - { - "author_name": "Tom Gibbs", - "author_inst": "NVIDIA Corp" - }, - { - "author_name": "John Stone", - "author_inst": "University of Illinois at Urbana/Champaign" - }, - { - "author_name": "Daniel Zuckerman", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Adrian Muholland", - "author_inst": "University of Bristol" - }, - { - "author_name": "Thomas Miller III", - "author_inst": "California Institute of Technology & Entos, Inc" - }, - { - "author_name": "Shantenu Jha", - "author_inst": "Rutgers University" - }, - { - "author_name": "Arvind Ramanathan", - "author_inst": "Argonne National Lab" - }, - { - "author_name": "Lillian Chong", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Rommie E Amaro", - "author_inst": "University of California San Diego" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.11.15.468283", "rel_title": "Mutagenic distinction between the receptor-binding and fusion subunits of the SARS-CoV-2 spike glycoprotein", @@ -523296,6 +524334,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.11.13.468472", + "rel_title": "A live attenuated influenza virus-vectored intranasal COVID-19 vaccine provides rapid, prolonged, and broad protection against SARS-CoV-2 infection", + "rel_date": "2021-11-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.13.468472", + "rel_abs": "Remarkable progress has been made in developing intramuscular vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, they are limited with respect to eliciting local immunity in the respiratory tract, which is the primary infection site for SARS-CoV-2. To overcome the limitations of intramuscular vaccines, we constructed a nasal vaccine candidate based on an influenza vector by inserting a gene encoding the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2, named CA4-dNS1-nCoV-RBD (dNS1-RBD). A preclinical study showed that in hamsters challenged 1 day and 7 days after single-dose vaccination or 6 months after booster vaccination, dNS1-RBD largely mitigated lung pathology, with no loss of body weight, caused by either the prototype-like strain or beta variant of SARS-CoV-2. Lasted data showed that the animals could be well protected against beta variant challenge 9 months after vaccination. Notably, the weight loss and lung pathological changes of hamsters could still be significantly reduced when the hamster was vaccinated 24 h after challenge. Moreover, such cellular immunity is relatively unimpaired for the most concerning SARS-CoV-2 variants. The protective immune mechanism of dNS1-RBD could be attributed to the innate immune response in the nasal epithelium, local RBD-specific T cell response in the lung, and RBD-specific IgA and IgG response. Thus, this study demonstrates that the intranasally delivered dNS1-RBD vaccine candidate may offer an important addition to fight against the ongoing COVID-19 pandemic, compensating limitations of current intramuscular vaccines, particularly at the start of an outbreak.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Junyu Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Pei Wang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Lunzhi Yuan", + "author_inst": "Xiamen University" + }, + { + "author_name": "Liang Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Limin Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Hui Zhao", + "author_inst": "National Institute for Food and Drug Control" + }, + { + "author_name": "Congjie Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yaode Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jinle Han", + "author_inst": "Beijing Wantai Biological Pharmacy Enterprise Co., Ltd" + }, + { + "author_name": "Jizong Jia", + "author_inst": "Beijing Wantai Biological Pharmacy Enterprise Co., Ltd" + }, + { + "author_name": "Zhen Lu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Junping Hong", + "author_inst": "Xiamen University" + }, + { + "author_name": "Liqiang Chen", + "author_inst": "Shantou University" + }, + { + "author_name": "Changfa Fan", + "author_inst": "National Institute for Food and Drug Control" + }, + { + "author_name": "Zicen Lu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Qian Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Rirong Chen", + "author_inst": "Shantou University" + }, + { + "author_name": "Mingping Cai", + "author_inst": "Shantou University" + }, + { + "author_name": "Ruoyao Qi", + "author_inst": "Xiamen University" + }, + { + "author_name": "Xijing Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jian Ma", + "author_inst": "Xiamen University" + }, + { + "author_name": "Min Zhou", + "author_inst": "Xiamen University" + }, + { + "author_name": "Huan Yu", + "author_inst": "Shantou University" + }, + { + "author_name": "Chualan Zhuang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Xiaohui Liu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Qiangyuan Han", + "author_inst": "Xiamen University" + }, + { + "author_name": "Guosong Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yingying Su", + "author_inst": "Xiamen University" + }, + { + "author_name": "Quan Yuan", + "author_inst": "National Institute of Diagnostics and Vaccine Development in Infectious Diseases" + }, + { + "author_name": "Tong Cheng", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ting Wu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Xiangzhong Ye", + "author_inst": "Beijing Wantai Biological Pharmacy Enterprise Co., Ltd" + }, + { + "author_name": "Changgui Li", + "author_inst": "National Institute for Food and Drug Control" + }, + { + "author_name": "Tianying Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jun Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Huachen Zhu", + "author_inst": "Shantou University" + }, + { + "author_name": "Yixin Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Hongling Chen", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ningshao Xia", + "author_inst": "Xiamen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2021.11.12.21266178", "rel_title": "The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA?", @@ -524836,113 +526045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.12.21266250", - "rel_title": "Protection offered by mRNA-1273 versus BNT162b2 vaccines against SARS-CoV-2 infection and severe COVID-19 in Qatar", - "rel_date": "2021-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.12.21266250", - "rel_abs": "BACKGROUNDGrowing evidence suggests that COVID-19 vaccines differ in effectiveness against breakthrough infection or severe COVID-19, but vaccines have yet to be investigated in controlled studies that head-to-head compare immunity of one to another. This study compared protection offered by the mRNA-1273 (Moderna) vaccine with that of the BNT162b2 (Pfizer-BioNTech) vaccine in Qatar.\n\nMETHODSIn a population of 1,531,736 vaccinated persons, two matched retrospective cohort studies were designed and used to investigate differences in mRNA-1273 and BNT162b2 vaccine protection, after the first and second doses, from December 21, 2020 to October 20, 2021.\n\nRESULTSAfter dose 1, cumulative incidence of breakthrough infection was 0.79% (95% CI: 0.75-0.83%) for mRNA-1273-vaccinated individuals and 0.86% (95% CI: 0.82-0.90%) for BNT162b2-vaccinated individuals, 21 days post-injection. Adjusted hazard ratio (AHR) for breakthrough infection was 0.89 (95% CI: 0.83-0.95; p=0.001). AHR was constant in the first two weeks at 1, but it declined to 0.67 (95% CI: 0.57-0.77; p<0.001) in the third week after dose 1. AHR for any severe, critical, or fatal COVID-19 was 0.71 (95% CI: 0.53-0.95; p=0.020). After dose 2, cumulative incidence was 0.59% (95% CI: 0.55-0.64%) for mRNA-1273-vaccinated individuals and 0.84% (95% CI: 0.79-0.89%) for BNT162b2-vaccinated individuals, 180 days post-injection. AHR for breakthrough infection was 0.69 (95% CI: 0.63-0.75; p<0.001) and was largely constant over time after dose 2. AHR for any severe, critical, or fatal COVID-19 was 0.37 (95% CI: 0.10-1.41; p=0.147).\n\nCONCLUSIONSmRNA-1273 vaccination is associated with lower SARS-CoV-2 breakthrough infection and COVID-19 hospitalization and death than BNT162b2 vaccination, but the number of hospitalizations and deaths was exceedingly small for both vaccines. Both vaccines demonstrated strikingly similar patterns of build-up of protection after the first dose and waning of protection after the second dose.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Houssein H. Ayoub", - "author_inst": "Qatar University" - }, - { - "author_name": "Patrick J Tang", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Mohammad Rubayet Hasan", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Peter Coyle", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "HADI M. YASSINE", - "author_inst": "Qatar University" - }, - { - "author_name": "Fatiha Benslimane", - "author_inst": "Qatar University" - }, - { - "author_name": "Hebah A. Al-Khatib", - "author_inst": "Qatar University" - }, - { - "author_name": "Zaina Al-Kanaani", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Einas Al Kuwari", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Andrew Jeremijenko", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Anvar Hassan Kaleeckal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali Nizar Latif", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Riyazuddin Mohammad Shaik", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hanan F. Abdul Rahim", - "author_inst": "Qatar University" - }, - { - "author_name": "Gheyath Nasrallah", - "author_inst": "Qatar University" - }, - { - "author_name": "Mohamed Ghaith Al Kuwari", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Adeel A Butt", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hamad Eid Al Romaihi", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Mohamed H. Al-Thani", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Abdullatif Al Khal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Roberto Bertollini", - "author_inst": "Ministry of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.10.467646", "rel_title": "Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens", @@ -525218,6 +526320,65 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.11.10.468168", + "rel_title": "Ensemble cryo-electron microscopy reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex", + "rel_date": "2021-11-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.10.468168", + "rel_abs": "The SARS-CoV-2 nonstructural proteins coordinate genome replication and gene expression. Structural analyses revealed the basis for coupling of the essential nsp13 helicase with the RNA dependent RNA polymerase (RdRp) where the holo-RdRp and RNA substrate (the replication-transcription complex, or RTC) associated with two copies of nsp13 (nsp132-RTC). One copy of nsp13 interacts with the template RNA in an opposing polarity to the RdRp and is envisaged to drive the RdRp backwards on the RNA template (backtracking), prompting questions as to how the RdRp can efficiently synthesize RNA in the presence of nsp13. Here, we use cryo-electron microscopy and molecular dynamics simulations to analyze the nsp132-RTC, revealing four distinct conformational states of the helicases. The results suggest a mechanism for the nsp132-RTC to turn backtracking on and off, using an allosteric mechanism to switch between RNA synthesis or backtracking in response to stimuli at the RdRp active site.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "James Chen", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Qi Wang", + "author_inst": "D. E. Shaw Research" + }, + { + "author_name": "Brandon Malone", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Eliza Llewellyn", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "Yakov Pechersky", + "author_inst": "D. E. Shaw Research" + }, + { + "author_name": "Kashyap Maruthi", + "author_inst": "The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center" + }, + { + "author_name": "Edward T Eng", + "author_inst": "New York Structural Biology Center" + }, + { + "author_name": "Jason K Perry", + "author_inst": "Gilead Sciences" + }, + { + "author_name": "Elizabeth A. Campbell", + "author_inst": "The Rockefeller University" + }, + { + "author_name": "David E. Shaw", + "author_inst": "D. E. Shaw Research" + }, + { + "author_name": "Seth A Darst", + "author_inst": "The Rockefeller University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.11.10.468173", "rel_title": "SARS-CoV-2 Envelope protein (E) binds and activates TLR2: A novel target for COVID-19 interventions", @@ -526554,41 +527715,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.10.21266139", - "rel_title": "The role of antiviral treatment in curbing the COVID-19 pandemic: a modeling study.", - "rel_date": "2021-11-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266139", - "rel_abs": "Despite the development of safe and effective vaccines, effective treatments for COVID-19 disease are still urgently needed. Several antiviral drugs have shown to be effective in reducing progression of COVID-19 disease. In the present work, we use an agent-based mathematical model to assess the potential population impact of the use of antiviral treatments in four countries with different demographic structure and current levels of vaccination coverage: Kenya, Mexico, United States (US) and Belgium. We analyzed antiviral effects on reducing hospitalization and death, and potential antiviral effects on reducing transmission. For each country, we varied daily treatment initiation rate (DTIR) and antiviral effect in reducing transmission (AVT). Irrespective of location and AVT, widespread antiviral treatment of symptomatic adult infections ([≥]20% DTIR) prevented the majority of COVID-19 deaths, and recruiting 6% of all adult symptomatic infections daily reduced mortality by a third in all countries. Furthermore, our model projected that targeting antiviral treatment to the oldest age group (65 years old and older, DTIR of 20%) can prevent over 47% of deaths. Our results suggest that early antiviral treatment (as soon as possible after inception of infection) is needed to mitigate transmission, preventing 50% more infections compared to late treatment (started 3 to 5 days after symptoms onset). Our results highlight the synergistic effect of vaccination and antiviral treatment: as the vaccination rate increases, antivirals have a larger relative impact on population transmission. These results suggest that antiviral treatments can become a strategic tool that, in combination with vaccination, can significantly reduce COVID-19 hospitalizations and deaths and can help control SARS-CoV-2 transmission.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Laura Matrajt", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Elizabeth R Brown", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Myron S Cohen", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Dobromir Dimitrov", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Holly Janes", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.10.21266195", "rel_title": "Disparities in COVID-19 Fatalities among Working Californians", @@ -527040,6 +528166,89 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2021.11.11.21266189", + "rel_title": "Tenofovir Disoproxil Fumarate and severity of COVID-19 in people with HIV infection", + "rel_date": "2021-11-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21266189", + "rel_abs": "BackgroundEffective, safe, and affordable antivirals are needed for COVID-19. Tenofovir has not been studied in randomized trials despite evidence consistent with its effectiveness against COVID-19.\n\nMethodsWe studied HIV-positive individuals on antiretroviral therapy (ART) in 2020 at 69 HIV clinics in Spain. We collected data on sociodemographics, ART, CD4-cell count, HIV-RNA viral load, comorbidities and the following outcomes: laboratory-confirmed SARS-CoV-2 infection, COVID-19 hospitalization, intensive care unit (ICU) admission and death. We compared the 48-week risks for individuals receiving tenofovir disoproxil fumarate (TDF)/emtricitabine (FTC), tenofovir alafenamide (TAF)/ FTC, abacavir (ABC)/lamivudine (3TC), and other regimes. All estimates were adjusted for clinical and sociodemographic characteristics via inverse probability weighting.\n\nResultsOf 51,558 eligible individuals, 39.6% were on TAF/FTC, 11.9% on TDF/FTC, 26.6% on ABC/3TC, 21.8% on other regimes. There were 2,402 documented SARS-CoV-2 infections (425 hospitalizations, 45 ICU admissions, 37 deaths). Compared with TAF/FTC, the estimated risk ratios (RR) (95% CI) of hospitalization were 0.66 (0.43, 0.91) for TDF/FTC and 1.29 (1.02, 1.58) for ABC/3TC, the RRs of ICU admission were 0.28 (0.11, 0.90) for TDF/FTC and 1.39 (0.70, 2.80) for ABC/3TC, and the RRs of death were 0.37 (0.23, 1.90) for TDF/FTC and 2.02 (0.88-6.12) for ABC/3TC. The corresponding RRs of hospitalization for TDF/FTC were 0.49 (0.24, 0.81) in individuals [≥]50 years and 1.15 (0.59, 1.93) in younger individuals.\n\nConclusionOur findings suggest that, compared with other antiretrovirals, TDF/FTC lowers COVID-19 severity among HIV-positive individuals with virological control. This protective effect may be restricted to individuals aged 50 years and older.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Julia DelAmo", + "author_inst": "Division of HIV, STI, Hepatitis and Tuberculosis. Ministry of Health, Madrid, Spain" + }, + { + "author_name": "Rosa Polo", + "author_inst": "Division of HIV, STI, Hepatitis and Tuberculosis. Ministry of Health, Madrid, Spain" + }, + { + "author_name": "Santiago Moreno", + "author_inst": "University Hospital Ramon y Cajal Madrid, Spain; HIV Network of Excellence, Spain" + }, + { + "author_name": "Esteban Martinez", + "author_inst": "HIV Network of Excellence, Spain; University Hospital Clinic, Barcelona, Spain" + }, + { + "author_name": "Alfonso Cabello", + "author_inst": "HIV Network of Excellence, Spain; University Hospital La Concepcion, Fundacion Jimenez Diaz, Madrid, Spain" + }, + { + "author_name": "Jose Antonio Iribarren", + "author_inst": "HIV Network of Excellence, Spain; University Hospital of Donosti, San Sebastian, Spain" + }, + { + "author_name": "Adria Curran", + "author_inst": "HIV Network of Excellence, Spain; University Hospital, Vall D'Hebron, Barcelona, Spain" + }, + { + "author_name": "Juan Macias", + "author_inst": "HIV Network of Excellence, Spain; University Hospital Virgen de Valme, Seville, Spain" + }, + { + "author_name": "Marta Montero", + "author_inst": "HIV Network of Excellence, Spain; University Hospital La Fe, Valencia, Spain" + }, + { + "author_name": "Carlos Duenas", + "author_inst": "University Clinical Hospital of Valladolid, Spain" + }, + { + "author_name": "Ana I Marino", + "author_inst": "HIV Network of Excellence, Spain; University Hospital El Ferrol, Spain" + }, + { + "author_name": "Santiago Perez de la Camara", + "author_inst": "HIV Network of Excellence, Spain; Telemedicine Unit, Institute of Health Carlos III, Madrid, Spain" + }, + { + "author_name": "Asuncion Diaz", + "author_inst": "HIV Network of Excellence, Spain; National Center for Epidemiology, Institute of Health Carlos III, Madrid, Spain" + }, + { + "author_name": "Jose Ramon Arribas", + "author_inst": "HIV Network of Excellence, Spain; University Hospital La Paz, IdiPAZ Madrid, Spain" + }, + { + "author_name": "Inma Jarrin", + "author_inst": "HIV Network of Excellence, Spain; National Center for Epidemiology, Institute of Health Carlos III, Madrid, Spain" + }, + { + "author_name": "Miguel A Hernan", + "author_inst": "CAUSALab, Harvard T.H. Chan School of Public Health, Boston, MA 02115; Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health," + }, + { + "author_name": "- The CoVIHd Collaboration in Spain", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2021.11.11.21266207", "rel_title": "ANALYSIS OF IMMUNE ESCAPE VARIANTS FROM ANTIBODY-BASED THERAPEUTICS AGAINST COVID-19.", @@ -528559,53 +529768,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.05.21265970", - "rel_title": "Exploring Associations with Severe Hypoxemic Respiratory Failure in COVID-19 Patients upon Admission: A Model for Severe Hypoxemic Respiratory Failure in 329 Unvaccinated, Hospitalized COVID-19 Patients.", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.05.21265970", - "rel_abs": "ObjectiveThe severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) has caused a pandemic claiming more than 4 million lives worldwide. Overwhelming Coronavirus-Disease-2019 (COVID-19) respiratory failure placed tremendous demands on healthcare systems increasing the death toll. Cost-effective prognostic tools to characterize COVID-19 patients likely to progress to severe hypoxemic respiratory failure are still needed.\n\nDesignWe conducted a retrospective cohort study to develop a model utilizing demographic and clinical data collected in the first 12-hours admission to explore associations with severe hypoxemic respiratory failure in unvaccinated and hospitalized COVID-19 patients.\n\nSettingUniversity based healthcare system including 6 hospitals located in the Galveston, Brazoria and Harris counties of Texas.\n\nParticipantsAdult patients diagnosed with COVID-19 and admitted to one of six hospitals between March 19th and June 31st, 2020.\n\nPrimary outcomeThe primary outcome was defined as reaching a WHO ordinal scale between 6-9 at any time during admission, which corresponded to severe hypoxemic respiratory failure requiring high-flow oxygen supplementation or mechanical ventilation.\n\nResultsWe included 329 participants in the model cohort and 62 (18.8%) met the primary outcome. Our multivariable regression model found that lactate dehydrogenase (OR 2.36), qSOFA score (OR: 2.26), and neutrophil to lymphocyte ratio (OR:1.15) were significant predictors of severe disease. The final model showed an area under curve (AUC) of 0.84. The sensitivity analysis and point of influence analysis did not reveal inconsistencies.\n\nConclusionsOur study suggests that a combination of accessible demographic and clinical information collected on admission may predict the progression to severe COVID-19 among adult patients with mild and moderate disease. This model requires external validation prior to its use.\n\nSTRENGTHS AND LIMITATIONS OF THIS STUDY Our study utilized objective and measurable demographic and clinical information regularly available in healthcare settings even among patients unable to communicate.\n Our primary outcome corresponds to WHO ordinal score which would allow compare our results to other studies and in other settings.\n Our model could serve as an effective point of service tool during early admission to assist in clinical management and allocation of resources to unvaccinated patients.\n Our study is a retrospective study of unvaccinated COVID19 patients, and validation of our prediction model in the rest of our study population is still needed.\n In addition, testing our model in a more recent cohort after emergence of new SARS-CoV-2 variants will be needed to assess its robustness.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "John W Davis", - "author_inst": "University Of Texas Medical Branch At Galveston" - }, - { - "author_name": "Beilin Wang", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Ewa Tomczak", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Chia-Chi Fu", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Wissam Harmouch", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "David Reynoso", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Philip Keiser", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Miguel Cabada", - "author_inst": "University of Texas Medical Branch at Galveston" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.04.21265951", "rel_title": "Validation of a rapid and sensitive SARS-CoV-2 screening system developed for pandemic-scale infection surveillance", @@ -528873,6 +530035,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.01.21265445", + "rel_title": "Delta subvariants of SARS-COV-2 in Israel, Qatar and Bahrain: Optimal vaccination as an effective strategy to block viral evolution and control the pandemic", + "rel_date": "2021-11-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265445", + "rel_abs": "{delta} variant has rapidly become the predominant pandemic driver and yielded four subvariants ({delta}1, {delta}2, {delta}3 and {delta}4). Among them, {delta}1 has been mainly responsible for the latest COVID-19 waves in India, Southeast Asia, Europe and the USA. A relevant question is how {delta} subvariants may have driven the pandemic in the rest of the world. In both Israel and Qatar, mRNA-based vaccination has been rolled out competitively, but the outcomes are quite different in terms of controlling the recent waves resulting from {delta} variant. This raises the question whether {delta} subvariants have acted differently in Israel and Qatar. In both countries, {delta} variant was first identified in April 2021 and {delta}1 subvariant constituted [~]50% {delta} genomes from April to May 2021. But the situation started to diverge in June 2021: In Israel, {delta}1 variant was encoded by 92.0% {delta} genomes, whereas this fraction was only 43.9% in Qatar. Moreover, a {delta}1 sublineage encoding spike T791I was identified in Israel but not Qatar. This sublineage accounted for 31.8% {delta} genomes sequenced in June 2021 and declined to 13.3% in October 2021. In August 2021, {delta}1 also became dominant in Qatar and a major sublineage encoding spike D1259H emerged. This sublineage has evolved further and acquired additional spike substitutions, including K97E, S255F, I693S, I712S, I1104L, E1258D and/or V1177I, in Qatar and other countries, such as Czech Republic, France and Mexico. Monthly distribution of the above sublineages suggests that the one from Qatar is much more of concern than that from Israel. Different from what was in Israel and Qatar, {delta}2 subvariant has also been important in Bahrain, whereas a {delta}2 sublineage encoding spike V1264L and A1736V of NSP3 was dominant in June 2021, but was gradually taken over by {delta}1 subvariant. These results suggest that {delta}1 and {delta}2 subvariants continue their evolution in different countries. The recent successful pandemic control in Israel, Qatar and Bahrain supports that {delta}1 and {delta}2 subvariants are still sensitive to timed vaccination, thereby urging the use of optimal immunity as a strategy to block SARS-COV-2 evolution and control the pandemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Xiang-Jiao Yang", + "author_inst": "McGill University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.05.21265849", "rel_title": "Humoral immune response to Covid-19 vaccination in diabetes: age-dependent but independent of type of diabetes and glycaemic control-the prospective COVAC-DM cohort study", @@ -530149,29 +531330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.08.21266099", - "rel_title": "A mathematical model for repetitive behaviors of Covid-19", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21266099", - "rel_abs": "Covid-19 pandemic waves have been hitting us again and again in the past couple years in many countries, while the reason why they come in such repetitive manners remains unexplained, which have brought us with lingering anxieties and economic stagnations.\n\nWe proposed a mathematical model to describe the mechanism of the repetitive appearance of the number of new cases based upon the SIQR model in which Q (quarantined infectors) were distinguished from I (un-quarantined ones). The repetitive behavior of the pandemic was simulated by an activator-inhibitor system around a fixed point in a phase space as a kind of self-organized oscillations. Periods between each wave were confirmed to be approximately similar. Repetitive behaviors were also observed in actual Covid-19 data.\n\nPractical policies and actions were discussed on the ways to effectively control the repetition of pandemic, and proactive PCR test especially after the peak-out stage is highly recommended.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yoshiro Nishimoto", - "author_inst": "Seishin Science Club" - }, - { - "author_name": "Kenichi Inoue", - "author_inst": "Seishin Science Club" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.08.467648", "rel_title": "Phage-like particle vaccines are highly immunogenic and protect against pathogenic coronavirus infection and disease", @@ -530407,6 +531565,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.11.09.467911", + "rel_title": "Evidence for a long-r ange RNA-RNA interaction between ORF8 and the downstream region of the Spike polybasic insertion of SARS-CoV-2", + "rel_date": "2021-11-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.09.467911", + "rel_abs": "SARS-CoV-2 has affected people worldwide as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV responsible for the 2002-2003 SARS outbreak in Asia. Research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Like other beta coronaviruses, RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into other viral proteins. In this work, we performed a comparative analysis for novel long-range RNA-RNA interactions that may involve the Spike region. Comparing predictions between reference sequences of SARS-CoV-1 and SARS-CoV-2 revealed several predictions amongst which a thermodynamically stable long-range RNA-RNA interaction between (23660-23703 Spike) and (28025-28060 ORF8) unique to SARS-CoV-2 was observed. Using data gathered worldwide, sequence variation patterns observed in the population support the in-silico RNA-RNA base-pairing predictions within these regions, suggesting further evidence for the interaction. The predicted interactions can potentially be related to the regulation of sub-genomic RNA production rates in SARS-CoV-2 and their subsequent accessibility to the host transcriptome.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Okiemute Beatrice Omoru", + "author_inst": "Indiana-University-Purdue-University-Indianapolis" + }, + { + "author_name": "Filipe Pereira", + "author_inst": "University of Coimbra: Universidade de Coimbra" + }, + { + "author_name": "Sarath Chandra Janga", + "author_inst": "Indiana University Purdue University Indianapolis (IUPUI)" + }, + { + "author_name": "Amirhossein Manzourolajdad", + "author_inst": "Indiana University Purdue University Indianapolis" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.11.02.21265805", "rel_title": "Causes, characteristics, and patterns of prolonged unplanned school closures prior to the COVID-19 pandemic - United States, 2011 - 2019", @@ -532159,61 +533348,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.08.21265888", - "rel_title": "SARS-CoV-2 Antibody Response is Associated with Age in Convalescent Outpatients", - "rel_date": "2021-11-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265888", - "rel_abs": "COVID-19 has had an unprecedented global impact on human health. Understanding the antibody memory responses to infection is one tool needed to effectively control the pandemic. Among 173 outpatients who had virologically confirmed SARS-CoV-2 infection, we evaluated serum antibody concentrations, microneutralization activity, and enumerated SARS-CoV-2 specific B cells in convalescent blood specimens. Serum antibody concentrations were variable, allowing for stratification of the cohort into high and low responders. Serum antibody concentration was positively associated with microneutralization activity and participant age, with participants under the age of 30 showing the lowest antibody level. Neither participant sex, the timing of blood sampling following the onset of illness, nor the number of SARS-CoV-2 spike protein specific B cells correlated with serum antibody concentration. These data suggest that young adult outpatients did not generate as robust antibody memory, compared with older adults. Further, serum antibody concentration or neutralizing activity trended but did not significantly correlate with the number of SARS-CoV-2 memory B cells. These findings have direct implications for public health policy and current vaccine efforts. Knowledge gained regarding antibody memory following infection will inform the need for vaccination in those previously infected and allow for a better approximation of population-wide protective immunity.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Bo Zhai", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - }, - { - "author_name": "Karen Clarke", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "David L Bauer", - "author_inst": "Tulane University School of Medicine" - }, - { - "author_name": "Saran Kupul", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - }, - { - "author_name": "Lucas J Schratz", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - }, - { - "author_name": "M Patricia Nowalk", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Anita K McElroy", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - }, - { - "author_name": "James B McLachlan", - "author_inst": "Tulane University School of Medicine" - }, - { - "author_name": "Richard K Zimmerman", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "John F Alcorn", - "author_inst": "UPMC Children's Hospital of Pittsburgh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.04.21265780", "rel_title": "Immunogenicity and safety of the homogenous booster shot of a recombinant fusion protein vaccine (V-01) against COVID-19 in healthy adult participants primed with a two-dose regimen", @@ -532525,6 +533659,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.04.21265945", + "rel_title": "Inhaled Corticosteroids for Outpatients with Covid-19: A Meta-Analysis", + "rel_date": "2021-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.04.21265945", + "rel_abs": "The role of inhaled corticosteroids for outpatient COVID-19 is evolving. We meta-analyzed reported clinical trials and estimated probability of any effect and number needed to treat of 50 or 20 for symptom resolution by day 14 [100%, 99.8%, 93.1%] and hospitalization [89.3%, 72.9%, 26.7%] respectively.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Todd C Lee", + "author_inst": "McGill University" + }, + { + "author_name": "Emilie Bortolussi-Courval", + "author_inst": "McGill University, Montreal, Canada" + }, + { + "author_name": "Sara Belga", + "author_inst": "University of British Columbia, Vancouver, Canada" + }, + { + "author_name": "Nick Daneman", + "author_inst": "Sunnybrook Health Sciences Centre, Toronto, Canada" + }, + { + "author_name": "Adrienne K Chan", + "author_inst": "Sunnybrook Health Sciences Centre, Toronto, Canada" + }, + { + "author_name": "Ryan Hanula", + "author_inst": "McGill University, Montreal, Canada" + }, + { + "author_name": "Nicole Ezer", + "author_inst": "McGill University, Montreal, Canada" + }, + { + "author_name": "Emily G McDonald", + "author_inst": "McGill University, Montreal, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.04.21265931", "rel_title": "Evaluation of a Machine Learning Approach Utilizing Wearable Data for Prediction of SARS-CoV-2 Infection in Healthcare Workers", @@ -534001,29 +535182,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.11.04.21265923", - "rel_title": "How Do College Students with Disabilities Feel About Taking COVID-19 Vaccines?", - "rel_date": "2021-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.04.21265923", - "rel_abs": "This survey explores attitudes of 245 currently enrolled college students with disabilities regarding their comfort taking a COVID-19 vaccine. Results suggest most college students with disabilities are willing to take a COVID-19 vaccine if their institution requires it to return to campus in subsequent semesters. However, many students with disabilities would not feel comfortable with a vaccine mandate mid-semester and would consider withdrawing, especially among older students with disabilities and first-generation college students with disabilities. Implications for postsecondary policy and leadership are addressed.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Z W. Taylor", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Chelseaia Charran", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2021.11.02.21265778", "rel_title": "Plasma markers of neurologic injury and systemic inflammation in individuals with self-reported neurologic post-acute sequelae of SARS-CoV-2 infection (PASC)", @@ -534331,6 +535489,33 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.11.02.463717", + "rel_title": "Comparing protein-protein interaction networks of SARS-CoV-2 and (H1N1) influenza using topological features", + "rel_date": "2021-11-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.02.463717", + "rel_abs": "BackgroundSARS-CoV-2 pandemic first emerged in late 2019 in China. It has since infected more than 183 million individuals and caused about 4 million deaths globally. A protein-protein interaction network (PPIN) and its analysis can provide insight into the behavior of cells and lead to advance the procedure of drug discovery. The identification of essential proteins is crucial to understand for cellular survival. There are many centrality measures to detect influential nodes in complex networks. Since SARS-CoV-2 and (H1N1) influenza PPINs pose 553 common proteins. Analyzing influential proteins and comparing these networks together can be an effective step helping biologists in drug design.\n\nResultsWe used 21 centrality measures on SARS-CoV-2 and (H1N1) influenza PPINs to identify essential proteins. PCA-based dimensionality reduction was applied on normalized centrality values. Some measures demonstrated a high level of contribution in comparison to others in both PPINs, like Barycenter, Decay, Diffusion degree, Closeness (Freeman), Closeness (Latora), Lin, Radiality, and Residual. Using validation measures, the appropriate clustering method was chosen for centrality measures. We also investigated some graph theory-based properties like the power law, exponential distribution, and robustness.\n\nConclusionsThrough analysis and comparison, both networks exhibited remarkable experimental results. The network diameters were equal and in terms of heterogeneity, SARS-CoV-2 PPIN tends to be more heterogeneous. Both networks under study display a typical power-law degree distribution. Dimensionality reduction and unsupervised learning methods were so effective to reveal appropriate centrality measures.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Hakimeh Khojasteh", + "author_inst": "University of Zanjan" + }, + { + "author_name": "Alireza Khanteymoori", + "author_inst": "University of Zanjan" + }, + { + "author_name": "Mohammad Hossein Olyaee", + "author_inst": "University of Gonabad" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.11.02.467026", "rel_title": "Marked enhancement of neutralizing antibody and IFN-\u03b3 T-cell responses by GX-19N DNA booster in mice primed with inactivated vaccine", @@ -536035,69 +537220,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.01.21265766", - "rel_title": "Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19", - "rel_date": "2021-11-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265766", - "rel_abs": "Type I interferon (IFN) is critical in our defense against viral infections. Increased type I IFN pathway activation is a genetic risk factor for systemic lupus erythematosus (SLE), and a number of common risk alleles contribute to the high IFN trait. We hypothesized that these common gain-of-function IFN pathway alleles may be associated with protection from mortality in acute COVID-19. We studied patients admitted with acute COVID-19 (756 European-American and 398 African-American ancestry). Ancestral backgrounds were analyzed separately, and mortality after acute COVID-19 was the primary outcome. In European-American ancestry, we found that a haplotype of interferon regulatory factor 5 (IRF5) and alleles of protein kinase cGMP-dependent 1 (PRKG1) were associated with mortality from COVID-19. Interestingly, these were much stronger risk factors in younger patients (OR=29.2 for PRKG1 in ages 45-54). Variants in the IRF7 and IRF8 genes were associated with mortality from COVID-19 in African-American subjects, and these genetic effects were more pronounced in older subjects. Combining genetic information with blood biomarker data such as C-reactive protein, troponin, and D-dimer resulted in significantly improved predictive capacity, and in both ancestral backgrounds the risk genotypes were most relevant in those with positive biomarkers (OR for death between 14 and 111 in high risk genetic/biomarker groups). This study confirms the critical role of the IFN pathway in defense against COVID-19 and viral infections, and supports the idea that some common SLE risk alleles exert protective effects in anti-viral immunity.\n\nBackgroundWe find that a number of IFN pathway lupus risk alleles significantly impact mortality following COVID-19 infection. These data support the idea that type I IFN pathway risk alleles for autoimmune disease may persist in high frequency in modern human populations due to a benefit in our defense against viral infections.\n\nTranslational SignificanceWe develop multivariate prediction models which combine genetics and known biomarkers of severity to result in greatly improved prediction of mortality in acute COVID-19. The specific associated alleles provide some clues about key points in our defense against COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Ilona Nln", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Ruth Fernandez-Ruiz", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Theresa L Wampler Muskardin", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Jacqueline L Paredes", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Ashira D Blazer", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Stephanie Tuminello", - "author_inst": "Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Mukundan Attur", - "author_inst": "Divison of Rheumatology, Department of Medicine, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Eduardo Iturrate", - "author_inst": "Department of Medicine, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Christopher M Petrilli", - "author_inst": "Department of Medicine, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Steven B Abramson", - "author_inst": "Department of Medicine, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Aravinda Chakravarti", - "author_inst": "Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Timothy B Niewold", - "author_inst": "Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.11.01.21265527", "rel_title": "Effectiveness, Explainability and Reliability of Machine Meta-Learning Methods for Predicting Mortality in Patients with COVID-19: Results of the Brazilian COVID-19 Registry", @@ -536785,6 +537907,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.11.01.21265775", + "rel_title": "Using portable air purifiers to reduce airborne transmission of infectious respiratory viruses - a computational fluid dynamics study", + "rel_date": "2021-11-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265775", + "rel_abs": "Aerosols and droplets generated from expiratory events play a critical role in the transmission of infectious respiratory viruses. Increasingly robust evidence has suggested the crucial role of fine aerosols in airborne transmission of respiratory diseases, which is now widely regarded as an important transmission path of COVID-19. In this report, we used CFD modelling to investigate the efficiency of using portable air purifiers containing HEPA filters to reduce airborne aerosols in hospitals and serve as a potential retrofit mitigation strategy. We used a consulting room to set up our simulations because currently the clearance time between consultations is the controlling factor that limits the patient turnover rate. The results suggest the inlet/suction of the air purifier unit should be lifted above the floor to achieve better clearance efficiency, with up to 40% improvement possible. If multiple air purifiers are used, the combined efficiency can increase to 62%. This work provides practical guidance on a mitigation strategy that can be easily implemented in an expedient, cost-effective and rapid manner, and paves the way for developing more science-informed strategies to mitigate the airborne transmission of respiratory infections in hospitals.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Liwei Guo", + "author_inst": "University College London" + }, + { + "author_name": "Ryo Torii", + "author_inst": "University College London" + }, + { + "author_name": "Ruth Epstein", + "author_inst": "Royal National Ear Nose and Throat & Eastman Dental Hospital" + }, + { + "author_name": "John Rubin", + "author_inst": "Royal National Ear Nose and Throat & Eastman Dental Hospital" + }, + { + "author_name": "Jonathan P Reid", + "author_inst": "University of Bristol" + }, + { + "author_name": "Haoran Li", + "author_inst": "University College London" + }, + { + "author_name": "Andrea Ducci", + "author_inst": "University College London" + }, + { + "author_name": "Ramanarayanan Balachandran", + "author_inst": "University College London" + }, + { + "author_name": "Manish K Tiwari", + "author_inst": "University College London" + }, + { + "author_name": "Yiannis Ventikos", + "author_inst": "University College London" + }, + { + "author_name": "Laurence B Lovat", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.01.21265742", "rel_title": "Examining the Unit Costs of COVID-19 Vaccine Delivery in Kenya", @@ -538189,93 +539370,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.10.31.466677", - "rel_title": "Multiple spillovers and onward transmission of SARS-Cov-2 in free-living and captive White-tailed deer (Odocoileus virginianus)", - "rel_date": "2021-11-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.31.466677", - "rel_abs": "Many animal species are susceptible to SARS-CoV-2 and could potentially act as reservoirs, yet transmission of the virus in non-human free-living animals has not been documented. White-tailed deer (Odocoileus virginianus), the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 may be circulating in deer, we tested 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through December of 2020 for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 deer (33.2%; 95% CI: 28, 38.9) samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, between November 23, 2020 and January 10, 2021, 80 of 97 (82.5%; 95% CI 73.7, 88.8) RPLN samples had detectable SARS-CoV-2 RNA by RT-PCR. Whole genome sequencing of the 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%), and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple zooanthroponotic spillover events and deer-to-deer transmission. The discovery of sylvatic and enzootic SARS-CoV-2 transmission in deer has important implications for the ecology and long-term persistence, as well as the potential for spillover to other animals and spillback into humans. These findings highlight an urgent need for a robust and proactive \"One Health\" approach to obtaining a better understanding of the ecology and evolution of SARS-CoV-2.\n\nOne-Sentence SummarySARS-CoV-2 was detected in one-third of sampled white-tailed deer in Iowa between September 2020 and January of 2021 that likely resulted from multiple human-to-deer spillover and deer-to-deer transmission events.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Suresh V Kuchipudi", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Meera Surendran-Nair", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Rachel M Ruden", - "author_inst": "Iowa State University" - }, - { - "author_name": "Michele Yon", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Ruth H Nissly", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Rahul K Nelli", - "author_inst": "Iowa State University" - }, - { - "author_name": "Lingling Li", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Bhushan M Jayarao", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Kurt Vandegrift", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Costas D Maranas", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Nicole Levine", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Katriina Willgert", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Andrew J.K Conlan", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Randall J Olsen", - "author_inst": "Houston Methodist Research Institute and Houston Methodist Hospital" - }, - { - "author_name": "James Davis", - "author_inst": "Argonne National Laboratory" - }, - { - "author_name": "James M. Musser", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Peter J Hudson", - "author_inst": "Pennsylvania State University University Park : Penn State" - }, - { - "author_name": "Vivek Kapur", - "author_inst": "Pennsylvania State University University Park : Penn State" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.10.29.466519", "rel_title": "A biosafety level 2 surrogate for studying SARS-CoV-2 survival in food processing environmental biofilms", @@ -538571,6 +539665,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.10.28.21265549", + "rel_title": "COVID-19 Vaccine Failure in Chronic Lymphocytic Leukemia and Monoclonal B-Lymphocytosis; Humoral and Cellular Immunity", + "rel_date": "2021-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265549", + "rel_abs": "Chronic lymphocytic leukemia (CLL) is associated with immunocompromise and high risk of severe COVID-19 disease and mortality. Monoclonal B-Lymphocytosis (MBL) patients also have immune impairment. We evaluated humoral and cellular immune responses in 181 patients with CLL (160) and MBL (21) to correlate failed seroconversion (<50AU/mL SARS-CoV-2 II IgG assay, antibody to spike protein, Abbott Diagnostics) following each of 2 vaccine doses with clinical and laboratory parameters. Following first and second doses, 79.2% then 45% of CLL, and 50% then 9.5% of MBL respectively remained seronegative, indicating 2 vaccine doses are crucial. There was significant association between post-dose 2 antibody level with pre-vaccination reduced IgM (p<0.0001), IgG2 (p<0.035), IgG3 (p<0.046), and CLL therapy within 12 months (p<0.001) in univariate analysis. By multivariate analysis, reduced IgM (p<0.0002) and active therapy (p<0.0002) retained significance. There was no significant correlation with age, gender, CLL duration, IgG, IgA or lymphocyte subsets. Anti-spike protein levels varied widely and were lower in CLL, than MBL, and both lower than normal donors. Neutralization activity showed anti-spike levels <1000AU/mL were usually negative for both an early viral clade and the contemporary Delta variant. There were 72.9% of CLL and 53.3% of MBL who failed to reach anti-spike levels >1000AU/mL. In a representative subset of 32 CLL patients, 80% had normal T-cell responses by IFN{gamma} and IL-2 FluoroSpot assay. Failed seroconversion occurred in 36.6%% of treatment-naive patients, 52.9% treatment-naive with reduced IgM, 78.1% on therapy, and 85.7% on ibrutinib. Vaccination failure is very common in CLL, including early-stage disease.\n\n6 Key Novel FindingsO_LIComparison CLL vs MBL vs normal\n- 45% of CLL and 9.5% of MBL fail to seroconvert with 2 doses of COVID-19 vaccine\n\nC_LIO_LINeutralization assay\n- SARS CoV-2 IgG levels <1000 AU/mL rarely associated with neutralization activity.\n\nC_LIO_LICOVID-19-specific T-cell function by FluoroSpot IFN-g and IL-2 production\nC_LIO_LIIgG, A, M class and IgG subclass: correlations by univariate and multivariate analysis\n- IgM (OR 7.29 p<0.0001), IgG2 and IgG3 subclass univariate significance\n\nC_LIO_LICorrelation with therapy - ICT, targeted therapies, and those on Ig replacement\nC_LIO_LIHigh risk of vaccination failure for all CLL, including early-stage disease, and MBL\nC_LI\n\nKey PointsCLL and MBL show significantly impaired anti-spike antibody, viral neutralization, with cellular immune response to COVID-19 vaccination\n\nFailure to seroconvert is associated with low IgM, IgG2, IgG3, and recent therapy; many CLL and MBL patients remain COVID-19 vulnerable", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Yanodng Shen", + "author_inst": "Royal North Shore Hospital" + }, + { + "author_name": "Jane A Freeman", + "author_inst": "Department of Haematology and Flow Cytometry, Laverty Pathology" + }, + { + "author_name": "Juliette Holland", + "author_inst": "Department of Microbiology, Laverty Pathology" + }, + { + "author_name": "Ann Solterbeck", + "author_inst": "Statistical Revelations Pty Ltd" + }, + { + "author_name": "Kartik Naidu", + "author_inst": "Department of Microbiology, Laverty Pathology" + }, + { + "author_name": "Asha Soosapilla", + "author_inst": "Department of Haematology and Flow Cytometry, Laverty Pathology" + }, + { + "author_name": "Paul Downe", + "author_inst": "Department of Haematology and Flow Cytometry, Laverty Pathology" + }, + { + "author_name": "Catherine Tang", + "author_inst": "Department of Haematology and Flow Cytometry, Laverty Pathology" + }, + { + "author_name": "Ian Kerridge", + "author_inst": "Department of Haematology, Royal North Shore Hospital" + }, + { + "author_name": "Lucinda Wallman", + "author_inst": "Department of Immunology, Laverty Pathology" + }, + { + "author_name": "Neena Van Bilsen", + "author_inst": "Department of Haematology and Flow Cytometry, Laverty Pathology" + }, + { + "author_name": "Vanessa Milogiannakis", + "author_inst": "Kirby Institute, University of New South Wales" + }, + { + "author_name": "Anouschka Akerman", + "author_inst": "Kirby Institute, University of New South Wales" + }, + { + "author_name": "Gabriela Martins Costa Gomes", + "author_inst": "Centre for Virology Research, Westmead Institute, Sydney Infectious Diseases University of Sydney" + }, + { + "author_name": "Kerrie Sandgren", + "author_inst": "Centre for Virology Research, Westmead Institute, Sydney Infectious Diseases University of Sydney" + }, + { + "author_name": "Anthony L Cunningham", + "author_inst": "Centre for Virology Research, Westmead Institute, Sydney Infectious Diseases University of Sydney" + }, + { + "author_name": "Stuart Turville", + "author_inst": "Kirby Institute, University of New South Wales" + }, + { + "author_name": "Stephen P Mulligan", + "author_inst": "Department of Haematology, Royal North Shore Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2021.10.28.21265622", "rel_title": "Vaccination of COVID-19 Convalescent Plasma Donors Increases Binding and Neutralizing Antibodies Against SARS-CoV-2 Variants", @@ -539799,61 +540980,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.10.28.21265588", - "rel_title": "Designing an evidence-based Bayesian network for estimating the risk versus benefits of AstraZeneca COVID-19 vaccine", - "rel_date": "2021-10-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265588", - "rel_abs": "Uncertainty surrounding the risk of developing and dying from Thrombosis and Thromobocytopenia Syndrome (TTS) associated with the AstraZeneca (AZ) COVID-19 vaccine may contribute to vaccine hesitancy. A model is urgently needed to combine and effectively communicate the existing evidence on the risks versus benefits of the AZ vaccine. We developed a Bayesian network to consolidate the existing evidence on risks and benefits of the AZ vaccine, and parameterised the model using data from a range of empirical studies, government reports, and expert advisory groups. Expert judgement was used to interpret the available evidence and determine the structure of the model, relevant variables, data to be included, and how these data were used to inform the model.\n\nThe model can be used as a decision support tool to generate scenarios based on age, sex, virus variant and community transmission rates, making it a useful for individuals, clinicians, and researchers to assess the chances of different health outcomes. Model outputs include the risk of dying from TTS following the AZ COVID-19 vaccine, the risk of dying from COVID-19 or COVID-19-associated atypical severe blood clots under different scenarios. Although the model is focused on Australia, it can be easily adaptable to international settings by re-parameterising it with local data. This paper provides detailed description of the model-building methodology, which can used to expand the scope of the model to include other COVID-19 vaccines, booster doses, comorbidities and other health outcomes (e.g., long COVID) to ensure the model remains relevant in the face of constantly changing discussion on risks versus benefits of COVID-19 vaccination.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Helen J Mayfield", - "author_inst": "School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Colleen L Lau", - "author_inst": "School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Jane E Sinclair", - "author_inst": "School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Samuel J Brown", - "author_inst": "School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Andrew Baird", - "author_inst": "St Kilda Medical Group, St Kilda, Melbourne, Victoria, Australia" - }, - { - "author_name": "John Litt", - "author_inst": "Discipline of General Practice, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia; Scientific Advisory Committee," - }, - { - "author_name": "Aapeli Vuorinen", - "author_inst": "Data Science Institute, Columbia University, New York, New York, U.S.A." - }, - { - "author_name": "Kirsty R Short", - "author_inst": "School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Michael Waller", - "author_inst": "School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia" - }, - { - "author_name": "Kerrie Mengersen", - "author_inst": "School of Mathematical Sciences, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.29.21265248", "rel_title": "Safety and immunogenicity of a high-dose quadrivalent influenza vaccine administered concomitantly with a third dose of the mRNA-1273 SARS-CoV-2 vaccine in adults >= 65 years of age: a Phase II, open-label study", @@ -540329,6 +541455,89 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.10.28.465226", + "rel_title": "A Potential Novel COVID-19 Vaccine With RBD-HR1/HR2 Hexamer Structure", + "rel_date": "2021-10-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.28.465226", + "rel_abs": "The COVID-19 pandemic and the continued spreading of the SARS-CoV-2 variants have brought a grave public health consequence and severely devastated the global economy with recessions. Vaccination is considered as one of the most promising and efficient methods to end the COVID-19 pandemic and mitigate the disease conditions if infected. Although a few vaccines have been developed with an unprecedented speed, scientists around the world are continuing pursuing the best possible vaccines with innovations. Comparing to the expensive mRNA vaccines and attenuated/inactivated SARS-CoV-2 vaccines, recombinant protein vaccines have certain advantages, including their safety (non-virus components), potential stronger immunogenicity, broader protection, ease of scaling-up production, reduced cost, etc. In this study, we reported a novel COVID-19 vaccine generated with RBD-HR1/HR2 hexamer that was creatively fused with the RBD domain and heptad repeat 1 (HR1) or heptad repeat 2 (HR2) to form a dumbbell-shaped hexamer to target the spike S1 subunit. The novel hexamer COVID-19 vaccine induced high titers of neutralizing antibody in mouse studies (>100,000), and further experiments also showed that the vaccine also induced an alternative antibody to the HR1 region, which probably alleviated the drop of immunogenicity from the frequent mutations of SARS-CoV-2.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Hongbo Liu", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Xiang Gao", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Guoyong Wang", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Jianjun Zhang", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Jiajie Zhou", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Tingting Wei", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Yu Zhang", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Yujiao Liu", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Jinhua Piao", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Qiulei Zhang", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Yayuan Wang", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Xin Ma", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Xiaoting Zhu", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Yikun Rao", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Wenjuan Xia", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Heng Xie", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + }, + { + "author_name": "Wei Zhang", + "author_inst": "Beijing Leto Laboratories Co., Ltd., Beijing, China." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.10.27.466055", "rel_title": "Phylogenetic analysis and in silico studies link spike Q675H mutation to SARS-CoV-2 adaptive evolution", @@ -541681,77 +542890,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.25.21265166", - "rel_title": "Regional probabilistic situational awareness and forecasting of COVID-19", - "rel_date": "2021-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265166", - "rel_abs": "Mathematical models and statistical inference are fundamental for surveillance and control of the COVID-19 pandemic. Several aspects cause regional heterogeneity in disease spread. Individual behaviour, mobility, viral variants and transmission vary locally, temporally and with season, and interventions and vaccination are often implemented regionally. Therefore, we developed a new regional changepoint stochastic SEIR metapopulation model. The model is informed by real-time mobility estimates from mobile phone data, laboratory-confirmed cases, and hospitalisation incidence. To estimate locally and time-varying transmissibility, case detection probabilities, and missed imported cases, we present a new sequential Approximate Bayesian Computation method allowing inference in useful time, despite the high parametric dimension. We test our approach on Norway and find that three-week-ahead predictions are precise and well-calibrated, suitable for real-time surveillance.\n\nSignificanceWe developed a regional infectious disease spread model focussing on operational usefulness in real time. The model is informed by near real-time mobile phone mobility data, laboratory-confirmed cases, and hospitalisation incidence. The model is used to estimate reproduction numbers and provide regional predictions of future hospital beds. Regional reproduction numbers are important due spatio-temporal heterogeneity due to for example local interventions. We assume different regional reproduction numbers for different periods of the epidemic. We propose a new calibration method to estimate the reproduction numbers and other parameters of the model, tailored to handle the increasingly high dimension of parameters over time. The model has been successfully used for local situational awareness and forecasting for the Norwegian health authorities during COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Solveig Engebretsen", - "author_inst": "SAMBA, Norwegian Computing Center" - }, - { - "author_name": "Alfonso Diz-Lois Palomares", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Gunnar \u00d8vind Isaksson R\u00f8", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Anja Br\u00e5then Kristoffersen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Jonas Christoffer Lindstr\u00f8m", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kenth Eng\u00f8-Monsen", - "author_inst": "Telenor Research, Telenor (Norway)" - }, - { - "author_name": "Louis Yat Hin Chan", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "\u00d8rjan Dale", - "author_inst": "Telenor (Norway)" - }, - { - "author_name": "J\u00f8rgen Eriksson Midtb\u00f8", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kristian Lindalen-Stenerud", - "author_inst": "Telenor (Norway)" - }, - { - "author_name": "Francesco Di Ruscio", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Richard Aubrey White", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Arnoldo Frigessi", - "author_inst": "University of Oslo//Oslo University Hospital" - }, - { - "author_name": "Birgitte Freiesleben de Blasio", - "author_inst": "Norwegian Institute of Public Health/University of Oslo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.23.21265429", "rel_title": "Use of serology immunoassays for predicting SARS-CoV-2 infection: a serology-based diagnostic algorithm", @@ -542055,6 +543193,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.22.21264941", + "rel_title": "Access and quality of sexual and reproductive health (SRH) services in Britain during the early stages of the COVID-19 pandemic: a qualitative interview study of patient experiences", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.22.21264941", + "rel_abs": "ObjectivesAccess to quality sexual and reproductive health (SRH) services remains imperative, even during a pandemic. Our objective was to understand experiences of delayed or unsuccessful access to SRH services in Britain during the early stages of COVID-19 pandemic.\n\nDesignSemi-structured qualitative follow-up interviews were conducted in October-November 2020 (six months after the first UK lockdown) with participants of Natsal-COVID, a quasi-representative web-panel survey of sexual health and behaviour during COVID-19 (n=6654). Inductive thematic analysis was used to identify lessons for future SRH service access and quality.\n\nSettingTelephone interviews with participants from the general population.\n\nParticipants14 women and 6 men (24-47-years-old) reporting unmet need for SRH services and agreeing to recontact (n=311) were selected for interview using socio-demographic quotas.\n\nResultsParticipant experiences spanned ten different SRH services, including contraception and antenatal/maternity services. At interview, ten participants still experienced unmet need. Participants reported hesitancy and self-censorship of need. Accessing services required tenacity. Challenges included navigating inconsistent information and changing procedures; perceptions of gatekeepers as obstructing access; and inflexible appointment systems. Concerns about reconfigured services included reduced privacy; decreased quality of interactions with professionals; reduced informal support due to lone attendance; and fewer routine physical checks. However, participants also described examples of more streamlined services and staff efforts to compensate for disruptions. Many viewed the blending of telemedicine with in-person care as a positive development.\n\nConclusionCOVID-19 impacted access and quality of SRH services. The accounts of those who struggled to access services revealed self-censorship of need, difficulty navigating shifting service configurations, and perceived reduction in quality due to a socially-distanced service model. Telemedicine offers potential for greater efficiency if blended intelligently with in-person care. We offer some initial data-based recommendations for promoting equitable access and quality in restoration and future adaption of SRH services.\n\nSUMMARY BOXO_ST_ABSWhat is already known on this topicC_ST_ABSAccess to quality sexual and reproductive health (SRH) services remains imperative, even during a pandemic. In response to the threat of COVID-19, SRH services limited in-person provision, introduced social distancing and mask wearing, and expanded remote consultations and postal services. There are no published qualitative community studies in Britain exploring service-user experiences of the rapid adaption and scaling-down of SRH services in response to COVID-19.\n\nWhat this study addsThis study provides important insights into how rapid contraction and adaptation of sexual and reproductive health services was experienced by service users. It adds the patient perspective to formal and informal learning and sharing of knowledge been practitioners and policy makers. The study highlights that difficulty accessing services, decreased quality of SRH interactions, reduced opportunity to receive informal support, and fewer routine physical checks were difficult for patients. Our data-driven recommendations - including cautious adoption of telemedicine and improving collaboration across services - have relevance across SRH services and may be useful to other primary and secondary care providers.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Raquel Boso Perez", + "author_inst": "MRC/CSO Social and Public Health Sciences Unit, University of Glasgow" + }, + { + "author_name": "David Reid", + "author_inst": "The National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections at University College London in pa" + }, + { + "author_name": "Karen Julia Maxwell", + "author_inst": "MRC/CSO Social and Public Health Sciences Unit, University of Glasgow" + }, + { + "author_name": "Jo Gibbs", + "author_inst": "Institute for Global Health, University College London" + }, + { + "author_name": "Emily Dema", + "author_inst": "Institute for Global Health, University College London" + }, + { + "author_name": "Chris Bonell", + "author_inst": "Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Catherine Heather Mercer", + "author_inst": "Institute for Global Health, University College London" + }, + { + "author_name": "Pam Sonnenberg", + "author_inst": "Institute for Global Health, University College London" + }, + { + "author_name": "Nigel Field", + "author_inst": "Institute for Global Health, University College London" + }, + { + "author_name": "Kirstin Rebecca Mitchell", + "author_inst": "MRC/CSO Social and Public Health Sciences Unit, University of Glasgow" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "sexual and reproductive health" + }, { "rel_doi": "10.1101/2021.10.22.21265309", "rel_title": "Occupational versus community risk of SARS-CoV-2 infection among employees of a long-term care facility: an observational study", @@ -543391,81 +544584,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.23.21265402", - "rel_title": "Severity of Illness Caused by Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern in Children: A Single-Center Retrospective Cohort Study", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.23.21265402", - "rel_abs": "BackgroundRecent surges in coronavirus 2019 disease (COVID-19) is attributed to the emergence of more transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs). However, the relative severity of SARS-CoV-2 VOCs in children is unknown.\n\nMethodsThis retrospective single-center cohort study was performed at the Ann & Robert H. Lurie Childrens Hospital of Chicago, academic free-standing childrens hospital. We included all children [≤] 18 years-old diagnosed with COVID-19 between October 15th, 2020 and August 31st, 2021 and whose SARS-CoV-2 isolate was sequenced using the Illumina platform. For each patient sample, we identified the SARS-CoV-2 lineage, which was assigned to one of the following groups: Non-VOC, alpha VOC, beta VOC, gamma VOC, or delta VOC. We measured frequency of 5 markers of COVID-19 severity: hospitalization; COVID-19 pharmacologic treatment; respiratory support; intensive care unit admission; and severe disease as classified by the COVID-19 World Health Organization (WHO) Clinical Progression Scale (severe disease; score [≥] 6). A series of logistic regression models were fitted to estimate odds of each severity marker with each VOC (in comparison to non-VOCs), adjusting for COVID-19 community incidence and demographic and clinical co-variates.\n\nResultsDuring the study period, 2,025 patients tested positive for SARS-CoV-2; 1,422 (70.2%) had sufficient viral load to permit sequencing. Among the 499 (35.1%) patients whose isolate was sequenced, median (inter-quartile range) age was 7 (1,12) years; 256 (51.3%) isolates were a VOC: 96 (37.5%) alpha, 38 (14.8%) gamma, and 119 (46.5%) delta. After adjusting for age, Black race, Hispanic ethnicity, high-risk medical conditions, and COVID-19 community incidence, neither alpha nor delta was associated with severe COVID-19. Gamma was independently associated with hospitalization (OR 5.9, 95% CI 1.6-21.5, p=0.007), respiratory support (OR 8.3, 95% CI 1.5-56.3, p=0.02), and severe disease as classified by the WHO Clinical Progression Scale (OR 7.7, 95% CI 1.0-78.1, p=0.05).\n\nConclusionsCompared to non-VOC COVID-19 infections, the gamma VOC, but not the alpha or delta VOCs, was associated with increased severity. These data suggest that recent increased in pediatric COVID-19 hospitalizations are related to increased delta COVID-19 incidence rather than increased delta virulence in children.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Priya R. Edward", - "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" - }, - { - "author_name": "Ramon Lorenzo-Redondo", - "author_inst": "Northwestern University" - }, - { - "author_name": "Megan E. Reyna", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Lacy M Simons", - "author_inst": "Northwestern University" - }, - { - "author_name": "Judd F. Hultquist", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Ami B. Patel", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Egon A Ozer", - "author_inst": "Northwestern University" - }, - { - "author_name": "William J Mullerr", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Taylor Heald-Sargent", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Matthew McHugh", - "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Taylor J. Dean", - "author_inst": "Northwestern University Feinberg School of Medicine," - }, - { - "author_name": "Raj M. Dalal", - "author_inst": "Northwestern University Feinberg School of Medicine," - }, - { - "author_name": "Jordan John", - "author_inst": "Northwestern University Feinberg School of Medicine," - }, - { - "author_name": "Shannon C. Manz", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Larry K. Kociolek", - "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.25.21265493", "rel_title": "Modeling the impact of vaccination strategies for nursing homes in the context of increased SARS-CoV-2 community transmission and variants", @@ -543709,6 +544827,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.25.21265484", + "rel_title": "Rapid surveillance platforms for key SARS-CoV-2 mutations in Denmark", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265484", + "rel_abs": "Multiple mutations in SARS-CoV-2 variants of concern (VOCs) may increase, transmission, disease severity, immune evasion and facilitate zoonotic or anthoprozoonotic infections. Four such mutations, {Delta}H69/V70, L452R, E484K and N501Y, occur in the SARS-CoV-2 spike glycoprotein in combinations that allow detection of the most important VOCs. Here we present two flexible RT-qPCR platforms for small-and large-scale screening to detect these mutations, and schemes for adapting the platforms for future mutations. The large-scale RT-qPCR platform, was validated by pair-wise matching of RT-qPCR results with WGS consensus genomes, showing high specificity and sensitivity. Detection of mutations using this platform served as an important interventive measure for the Danish public health system to delay the emergence of VOCs and to gain time for vaccine administration. Both platforms are valuable tools for WGS-lean laboratories, as well for complementing WGS to support rapid control of local transmission chains worldwide.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Katja Spiess", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Vithiagaran Gunalan", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Ellinor Marving", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Sofie Holdflod Nielsen", + "author_inst": "Test Center Danmark, Statens Serum Institut" + }, + { + "author_name": "Michelle G. P. Joergensen", + "author_inst": "Test Center Denmark, Statens Serum Institut" + }, + { + "author_name": "Anna S. Fomsgaard", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Line Nielsen", + "author_inst": "Test Center Denmark; Statens Serum Institut" + }, + { + "author_name": "Alonzo Alfaro-Nunez", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Soeren M. Karst", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Shila Mortensen", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "- The Danish COVID-19 Genome Consortium (DCGC)", + "author_inst": "" + }, + { + "author_name": "Morten Rasmussen", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Ria Lassauniere", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Maiken W. Rosenstierne", + "author_inst": "Qlife Aps." + }, + { + "author_name": "Charlotta Polacek", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Jannik Fonager", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Arieh S. Cohen", + "author_inst": "Test Center Denmark, Statens Serum Institut" + }, + { + "author_name": "Claus Nielsen", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + }, + { + "author_name": "Anders Fomsgaard", + "author_inst": "Virus Research and Development Department of Microbiological Diagnostics & Virology, Statens Serum Institut" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.25.21264964", "rel_title": "Nucleocapsid antibody positivity as a marker of past SARS-CoV-2 infection in population serosurveillance studies: impact of variant, vaccination, and choice of assay cut-off", @@ -545497,69 +546706,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.10.21.21265340", - "rel_title": "How different pre-existing mental disorders and their co-occurrence affects clinical outcomes of COVID-19? A study based on real-world data in the Southern United States", - "rel_date": "2021-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265340", - "rel_abs": "ImportanceA growing body of research focuses on the impact of pre-existing mental disorders on clinical outcomes of COVID-19 illness. Although a psychiatric history might be an independent risk factor for COVID-19 infection and mortality, no studies have systematically investigated how different clusters of pre-existing mental disorders may affect COVID-19 clinical outcomes or showed how the coexistence of mental disorder clusters is related to COVID-19 clinical outcomes.\n\nObjectiveTo explore how different pre-existing mental disorders and their co-occurrence affects COVID-19-related clinical outcomes based on real-world data.\n\nDesign, Setting, and ParticipantsUsing a retrospective cohort study design, a total of 476,775 adult patients with lab-confirmed and probable COVID-19 between March 06, 2020 and April 14, 2021 in South Carolina, United States were included in the current study. The electronic health record data of COVID-19 patients were linked to all payer-based claims data through the SC Revenue and Fiscal Affairs Office.\n\nMain Outcomes and MeasuresKey COVID-19 clinical outcomes included severity, hospitalization, and death. COVID-19 severity was defined as asymptomatic, mild, and moderate/severe. Pre-existing mental disorder diagnoses from Jan 2, 2019 to Jan 14, 2021 were extracted from the patients healthcare utilization data via ICD-10 codes. Mental disorders were categorized into internalizing disorders, externalizing disorders, and thought disorders.\n\nResultsOf the 476,775 COVID-19 patients, 55,300 had pre-existing mental disorders. There is an elevated risk of COVID-19-related hospitalization and death among participants with pre-existing mental disorders adjusting for key socio-demographic covariates (i.e., age, gender, race, ethnicity, residence, smoking). Co-occurrence of any two clusters was positively associated with COVID-19-related hospitalization and death. The odds ratio of being hospitalized was 2.50 (95%CI 2.284, 2.728) for patients with internalizing and externalizing disorders, 3.34 (95%CI 2.637, 4.228) for internalizing and thought disorders, 3.29 (95%CI 2.288, 4.733) for externalizing and thought disorders, and 3.35 (95%CI 2.604, 4.310) for three clusters of mental disorders.\n\nConclusions and RelevancePre-existing internalizing disorders, externalizing disorders, and thought disorders are positively related to COVID-19 hospitalization and death. Co-occurrence of any two clusters of mental disorders have elevated risk of COVID-19-related hospitalization and death compared to those with a single cluster.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina" - }, - { - "author_name": "jiajia zhang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Shujie Chen", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Bankole Olatosi", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Suzanne Hardeman", - "author_inst": "Prisma Health (Midland), South Carolina" - }, - { - "author_name": "Meera Narasimhan", - "author_inst": "Prisma Health (Midland), South Carolina" - }, - { - "author_name": "Larisa Bruner", - "author_inst": "Department of Health and Environment Control South Carolina" - }, - { - "author_name": "Diedhiou Abdoulaye", - "author_inst": "Department of Health and Environment Control South Carolina" - }, - { - "author_name": "Cheryl L. Scott", - "author_inst": "Department of Health and Environment Control South Carolina" - }, - { - "author_name": "Ali B. Mansaray", - "author_inst": "Department of Health and Environment Control South Carolina" - }, - { - "author_name": "Sharon Weissman", - "author_inst": "University of South Carolina School of Medicine" - }, - { - "author_name": "Xiaoming Li", - "author_inst": "University of South Carolina" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.22.21265371", "rel_title": "Social mixing patterns in the UK following the relaxation of COVID-19 pandemic restrictions: a cross-sectional online survey", @@ -545855,6 +547001,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.10.22.21265401", + "rel_title": "SARS-CoV-2 Receptor Binding Domain IgG Response to AstraZeneca (AZD1222) COVID-19 Vaccination, Jamaica", + "rel_date": "2021-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.22.21265401", + "rel_abs": "The Caribbean region is lacking an assessment of the antibody response and side effects experienced after AstraZeneca COVID-19 vaccination (AZD1222). We examined SARS-CoV-2 spike receptor binding domain (RBD) IgG levels and reported side effects in a Jamaican population after AZD1222 vaccination. Median RBD IgG levels for persons without evidence of previous SARS-CoV-2 infection were 43.1 bIU/mL after 3-7 weeks post first dose, rising to 100.1 bIU/mL 3-7 weeks post second dose, and falling 46.9 bIU/mL 16-22 weeks post second dose. The median RBD IgG level 2-8 weeks after symptom onset for unvaccinated SARS-CoV-2 infected persons of all disease severities was 411.6 bIU/mL. Common AZD1222 side effects after first dose were injection site pain, headache and chills. Most persons reported no side effects after second dose. AZD1222 is widely used across the English-speaking Caribbean and the study provides evidence for its continued safe and effective use in vaccination programs.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ynolde E Leys", + "author_inst": "University of the West Indies, Kingston, Jamaica" + }, + { + "author_name": "Magdalene Nwokocha", + "author_inst": "University of the West Indies, Kingston, Jamaica" + }, + { + "author_name": "Jerome P Walker", + "author_inst": "University of the West Indies, Kingston, Jamaica" + }, + { + "author_name": "Tiffany R Butterfield", + "author_inst": "University of the West Indies, Kingston, Jamaica" + }, + { + "author_name": "Velesha Frater", + "author_inst": "University of the West Indies, Kingston, Jamaica" + }, + { + "author_name": "Tamara K Thompson", + "author_inst": "University of the West Indies, Kingston, Jamaica" + }, + { + "author_name": "Mark Anderson", + "author_inst": "Abbott Laboratories" + }, + { + "author_name": "Gavin A Cloherty", + "author_inst": "Abbott Labs" + }, + { + "author_name": "Joshua J Anzinger", + "author_inst": "The University of the West Indies, Kingston, Jamaica" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.22.21265316", "rel_title": "The Impact of SARS-CoV-2 Lineages (Variants) on the COVID-19 Epidemic in South Africa", @@ -547747,85 +548944,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.20.21265295", - "rel_title": "Predictors of SARS-CoV-2 infection following high-risk exposure: a test-negative design case-control study", - "rel_date": "2021-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265295", - "rel_abs": "BackgroundNon-pharmaceutical interventions (NPIs) are recommended for COVID-19 mitigation. However, the effectiveness of NPIs in preventing SARS-CoV-2 transmission remains poorly quantified.\n\nMethodsWe conducted a test-negative design case-control study enrolling cases (testing positive for SARS-CoV-2) and controls (testing negative) with molecular SARS-CoV-2 diagnostic test results reported to California Department of Public Health between 24 February-26 September, 2021. We used conditional logistic regression to assess predictors of case status among participants who reported contact with an individual known or suspected to have been infected with SARS-CoV-2 (\"high-risk exposure\") within [≤]14 days of testing.\n\nResults643 of 1280 cases (50.2%) and 204 of 1263 controls (16.2%) reported high-risk exposures [≤]14 days before testing. Adjusted odds of case status were 2.94-fold (95% confidence interval: 1.66-5.25) higher when high-risk exposures occurred with household members (vs. other contacts), 2.06-fold (1.03-4.21) higher when exposures occurred indoors (vs. not indoors), and 2.58-fold (1.50-4.49) higher when exposures lasted [≥]3 hours (vs. shorter durations) among unvaccinated and partially-vaccinated individuals; excess risk associated with such exposures was mitigated among fully-vaccinated individuals. Mask usage by participants or their contacts during high-risk exposures reduced adjusted odds of case status by 48% (8-72%). Adjusted odds of case status were 68% (32-84%) and 77% (59-87%) lower for partially- and fully-vaccinated participants, respectively, than for unvaccinated participants. Benefits of mask usage were greatest when exposures lasted [≥]3 hours, occurred indoors, or involved non-household contacts.\n\nConclusionsNPIs reduced the likelihood of SARS-CoV-2 infection following high-risk exposure. Vaccine effectiveness was substantial for partially and fully vaccinated persons.\n\nKEY POINTSO_LISARS-CoV-2 infection risk was greatest for unvaccinated participants when exposures to known or suspected cases occurred indoors or lasted [≥]3 hours.\nC_LIO_LIFace mask usage when participants were exposed to a known or suspect case reduced odds of infection by 48%.\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Kristin L. Andrejko", - "author_inst": "University of California at Berkeley" - }, - { - "author_name": "Jake Pry", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Jennifer F. Myers", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "John Openshaw", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "James Watt", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Nozomi Birkett", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Jennifer L DeGuzman", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Sophia S. Li", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Camilla M. Barbaduomo", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Anna T. Fang", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Vivian H. Tran", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Mahsa H. Javadi", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Paulina M. Frost", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Zheng N. Dong", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Seema Jain", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Joseph A. Lewnard", - "author_inst": "University of California Berkeley" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.21.21265216", "rel_title": "Generation time of the Alpha and Delta SARS-CoV-2 variants", @@ -548109,6 +549227,69 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.10.21.21265314", + "rel_title": "Autoimmune conditions following mRNA (BNT162b2) and inactivated (CoronaVac) COVID-19 vaccination: a descriptive cohort study among 1.1 million vaccinated people in Hong Kong", + "rel_date": "2021-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265314", + "rel_abs": "BackgroundConcerns regarding the autoimmune safety of COVID-19 vaccines may negatively impact vaccine uptake. We aimed to describe the incidence of autoimmune conditions following BNT162b2 and CoronaVac vaccination and compare these with age-standardized incidence rates in non-vaccinated individuals.\n\nMethodsThis is a descriptive cohort study conducted in public healthcare service settings. Territory-wide longitudinal electronic medical records of Hong Kong Hospital Authority users ([≥]16 years) were linked with COVID-19 vaccination records between February 23, 2021 and June 30, 2021. We classified participants into first/second dose BNT162b2 groups, first/second dose CoronaVac groups and non-vaccinated individuals for incidence comparison. The study outcomes include hospitalized autoimmune diseases (16 types of immune-mediated diseases across six body systems) within 28 days after first and second dose of vaccination. Age-standardized incidence rate ratios (IRRs) with exact 95% confidence intervals (CIs) were estimated using Poisson distribution.\n\nResultsThis study included around 3.9 million Hong Kong residents, of which 1,122,793 received at least one dose of vaccine (BNT162b2: 579,998; CoronaVac: 542,795), and 721,588 completed two doses (BNT162b2: 388,881; CoronaVac: 332,707). Within 28 days following vaccination, cumulative incidences for all autoimmune conditions were below 9 per 100,000 persons, for both vaccines and both doses. None of the age-standardized incidence rates were significantly higher than the non-vaccinated individuals, except for an observed increased incidence of hypersomnia following the first dose of BNT162b2 (standardized IRR: 1.47; 95% CI: 1.10-1.94).\n\nConclusionsAutoimmune conditions requiring hospital care are rare following mRNA and inactivated virus COVID-19 vaccination with similar incidence to non-vaccinated individuals. The association between first dose BNT162b2 vaccination and immune-related sleeping disorders requires further research. Population-based robust safety surveillance is essential to detect rare and unexpected vaccine safety events.\n\nFundingResearch Grant from the Food and Health Bureau, the Government of the Hong Kong Special Administrative Region (Ref. No. COVID19F01).", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Xue Li", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Le Gao", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Xinning Tong", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Vivien K.Y. Chan", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Celine S.L. Chui", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Francisco Lai", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Carlos Wong", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Eric Y.F. Wan", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Esther W.Y. Chan", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Kui Kai Lau", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Chak Sing Lau", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Ian C.K. Wong", + "author_inst": "University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.20.21265284", "rel_title": "Effect of SARS-CoV-2 infection on outcome of cancer patients: A systematic review and meta-analysis of studies of unvaccinated patients", @@ -549544,37 +550725,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2021.10.20.21265283", - "rel_title": "Food Security Impacts of the COVID-19 Pandemic: Following a Cohort of Vermonters During the First Year", - "rel_date": "2021-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265283", - "rel_abs": "ObjectiveThis study assessed changes in household food insecurity throughout the first year of the COVID-19 pandemic in a cohort of Vermonters and examined the socio-demographic characteristics associated with increased odds of experiencing food insecurity during the pandemic.\n\nDesignWe conducted three online surveys with a cohort of Vermonters between March 2020 and March 2021 to collect longitudinal data on food security, food access, and job disruptions during the COVID-19 pandemic. Food security was measured using the USDA six-item module. We used t-tests and chi-square tests to determine statistically significant differences between groups and multivariate logistic regression models to determine the factors correlated with food insecurity.\n\nParticipants441 adults (18 years and older)\n\nSettingVermont, United States\n\nResultsFood insecurity rates increased significantly during the pandemic and remained above pre-pandemic levels a year after the start of the pandemic. Nearly a third (31.6%) of respondents experienced food insecurity at some point during the first year of the pandemic. Certain demographic groups were at significantly higher odds of experiencing food insecurity during the first year of the COVID-19 pandemic including households with children (OR 5.1, p < 0.01), women (OR 7.3, p < 0.05), BIPOC/Hispanic respondents (OR 10.4, p < 0.05), and households experiencing a job disruption (OR 4.6, p <0.01).\n\nConclusionThe prevalence of food insecurity increased during the first year of the COVID-19 pandemic and remained higher than pre-pandemic levels a year after the pandemic began. Odds of experiencing food insecurity during the pandemic vary based on socio-demographic factors.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ashley C McCarthy", - "author_inst": "University of Vermont" - }, - { - "author_name": "Emily H Belarmino", - "author_inst": "University of Vermont" - }, - { - "author_name": "Farryl MW Bertmann", - "author_inst": "University of Vermont" - }, - { - "author_name": "Meredith T. Niles", - "author_inst": "University of Vermont" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.20.21265269", "rel_title": "Effect of the third dose of BNT162b2 vaccine in quantitative SARS-CoV-2 spike 1-2 IgG antibody titers in healthcare workers", @@ -549942,6 +551092,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.19.21265208", + "rel_title": "Airborne transmission of SARS-CoV-2 over distances greater than two metres: a rapid systematic review", + "rel_date": "2021-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.19.21265208", + "rel_abs": "ObjectiveTo evaluate the potential for long-distance (over two metres) airborne transmission of SARS-CoV-2 in indoor community settings and investigate factors which may impact this transmission.\n\nDesignSystematic review and narrative synthesis.\n\nData sourceMEDLINE, Embase, medRxiv, Arxiv and WHO COVID-19 Research Database for studies published from 27 July 2020 to 21 April 2021; existing relevant rapid systematic reviews for studies published between 1 January to 27 July 2020.\n\nEligibility criteria for study selectionObservational studies that included a thorough epidemiological assessment of routes of transmission and which reported on the likelihood of airborne transmission of SARS-CoV-2 at a distance greater than two metres in indoor community settings.\n\nData extraction and synthesisData extraction was completed by one reviewer and independently checked by a second reviewer. Primary outcomes were COVID-19 infections via airborne transmission over distances greater than two metres and any factors that may have modified transmission risk. Included studies were rated using a quality criteria checklist (QCC) for primary research and certainty of key outcomes was determined using GRADE. Narrative synthesis was themed by setting.\n\nResultsOf the 3,780 articles screened for inclusion, 15 publications reporting on 13 epidemiological investigations were included (three high, six medium and four low quality). Airborne transmission at distances greater than two metres was likely to have occurred for some or all transmission events in 12 studies and was unclear in one study (GRADE: very low certainty). In all studies, one or more factors plausibly increased the likelihood of long-distance airborne transmission occurring, particularly insufficient air replacement (GRADE: very low certainty), recirculating air flow (GRADE: very low certainty) and singing (GRADE: very low certainty). In nine studies, the primary cases were reported as being asymptomatic, presymptomatic or around symptom onset at the time of transmission.\n\nConclusionThis rapid systematic review found evidence of long-distance airborne transmission of SARS-CoV-2 in indoor community settings and identified factors that likely contributed to this transmission in all included studies. These results strengthen the need for adequate mitigation measures in indoor community settings, particularly adequate ventilation with fresh air, and caution required with the use of recirculating air flow systems.\n\nSystematic review registrationPROSPERO CRD42021236762", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jennifer C Palmer", + "author_inst": "COVID-19 Rapid Evidence Service, UK Health Security Agency (UKHSA), UK; MRC Integrative Epidemiology Unit at the University of Bristol, UK; Population Health Sc" + }, + { + "author_name": "Daphne Duval", + "author_inst": "COVID-19 Rapid Evidence Service, UK Health Security Agency (UKHSA)" + }, + { + "author_name": "Isobel Tudge", + "author_inst": "COVID-19 Rapid Evidence Service, UK Health Security Agency (UKHSA)" + }, + { + "author_name": "Jason Kwasi Sarfo-Annin", + "author_inst": "COVID-19 Rapid Evidence Service, UK Health Security Agency (UKHSA)" + }, + { + "author_name": "Nicola Pearce-Smith", + "author_inst": "COVID-19 Rapid Evidence Service, UK Health Security Agency (UKHSA)" + }, + { + "author_name": "Emer O'Connell", + "author_inst": "COVID-19 Advice and Guidance, UK Health Security Agency (UKHSA)" + }, + { + "author_name": "Allan Bennett", + "author_inst": "Research and Evaluation, UK Health Security Agency (UKHSA)" + }, + { + "author_name": "Rachel Clark", + "author_inst": "COVID-19 Rapid Evidence Service, UK Health Security Agency (UKHSA)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.20.21265137", "rel_title": "Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts", @@ -551710,49 +552907,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.14.21264762", - "rel_title": "Longitudinal and comparative analysis of humoral response upon COVID-19 vaccination", - "rel_date": "2021-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21264762", - "rel_abs": "The emergence of COVID-19 has led to a worldwide challenge for the rapid development of vaccines. Several types of safe and effective vaccines have been available in a time frame never seen before. Comparative studies to know the extent of protection and the immune response elicited by the different vaccines are of outstanding utility. Here, as a correlate for protection, we perform a comparative study of the humoral response to three vaccines, ChAdOx1 (Oxford-AstraZeneca), mRNA-1273 (Moderna), and BNT162b2 (Pfizer-BioNTech) by applying a flow cytometry-based highly sensitive method that we had previously developed. We have found that mRNA vaccines (mRNA-1273 and BNT162b2) induce a stronger humoral response that lasts for at least 6 months after vaccination. We also show that only one dose of BNT162b2 is enough to achieve the maximum response in seropositive pre-vaccination donors.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Salvador Romero-Pinedo", - "author_inst": "VITRO SA" - }, - { - "author_name": "Marina Quesada", - "author_inst": "VITRO SA" - }, - { - "author_name": "Stela \u00c1lvarez-Fern\u00e1ndez", - "author_inst": "VITRO SA" - }, - { - "author_name": "Asunci\u00f3n Olmo", - "author_inst": "VITRO SA" - }, - { - "author_name": "David Abia", - "author_inst": "Centro de Biolog\u00eda Molecular Severo Ochoa" - }, - { - "author_name": "Balbino Alarc\u00f3n", - "author_inst": "Centro de Biolog\u00eda Molecular Severo Ochoa" - }, - { - "author_name": "Pilar Delgado", - "author_inst": "Centro de Biolog\u00eda Molecular Severo Ochoa" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.11.21264694", "rel_title": "A cohort of 222 anti-CD20 treated patients with multiple sclerosis followed through the COVID-19 pandemic: Attenuated humoral but robust cellular immune responses after vaccination and infection", @@ -552036,6 +553190,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2021.10.18.464900", + "rel_title": "Preclinical Efficacy of IMM-BCP-01, a Highly Active Patient-Derived Anti-SARS-CoV-2 Antibody Cocktail", + "rel_date": "2021-10-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.18.464900", + "rel_abs": "Using an unbiased interrogation of the memory B cell repertoire of convalescent COVID-19 patients, we identified human antibodies that demonstrated robust antiviral activity in vitro and efficacy in vivo against all tested SARS-CoV-2 variants. Here, we describe the pre-clinical characterization of an antibody cocktail, IMM-BCP-01, that consists of three unique, patient-derived recombinant neutralizing antibodies directed at non-overlapping surfaces on the SARS-CoV-2 spike protein. Two antibodies, IMM20184 and IMM20190 directly block spike binding to the ACE2 receptor. Binding of the third antibody, IMM20253, to its unique epitope on the outer surface of RBD, alters the conformation of the spike trimer, promoting release of spike monomers. These antibodies decreased SARS-CoV-2 infection in the lungs of Syrian golden hamsters, and efficacy in vivo efficacy was associated with broad antiviral neutralizing activity against multiple SARS-CoV-2 variants and robust antiviral effector function response, including phagocytosis, ADCC, and complement pathway activation. Our pre-clinical data demonstrate that the three antibody cocktail IMM-BCP-01 shows promising potential for preventing or treating SARS-CoV-2 infection in susceptible individuals.\n\nOne sentence summaryIMM-BCP-01 cocktail triggers Spike Trimer dissociation, neutralizes all tested variants in vitro, activates a robust effector response and dose-dependently inhibits virus in vivo.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Pavel A Nikitin", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Jillian M DiMuzio", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "John P Dowling", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Nirja B Patel", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Jamie L Bingaman-Steele", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Chris Nicolescu", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Baron C Heimbach", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Noeleya Henriquez", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Eden L Sikorsky", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Antonio Polley", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Raymond J Howanski", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Mitchell Nath", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Halley Shukla", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Suzanne M. Scheaffer", + "author_inst": "Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine" + }, + { + "author_name": "James P Finn", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Li-fang Liang", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Todd Smith", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Nadia Storm", + "author_inst": "Boston University School of Medicine and National Emerging Infectious Diseases Laboratories" + }, + { + "author_name": "Lindsay G.A. McKay", + "author_inst": "Boston University School of Medicine and National Emerging Infectious Diseases Laboratories" + }, + { + "author_name": "Rebecca I Johnson", + "author_inst": "Boston University School of Medicine and National Emerging Infectious Diseases Laboratories" + }, + { + "author_name": "Lauren E Malsick", + "author_inst": "Boston University School of Medicine and National Emerging Infectious Diseases Laboratories" + }, + { + "author_name": "Anna N Honko", + "author_inst": "Boston University School of Medicine and National Emerging Infectious Diseases Laboratories" + }, + { + "author_name": "Anthony Griffiths", + "author_inst": "Boston University School of Medicine and National Emerging Infectious Diseases Laboratories" + }, + { + "author_name": "Michael S Diamond", + "author_inst": "Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine" + }, + { + "author_name": "Purnanand Sarma", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Dennis H Geising", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Michael J Morin", + "author_inst": "Immunome, Inc" + }, + { + "author_name": "Matthew K Robinson", + "author_inst": "Immunome, Inc" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.10.16.464641", "rel_title": "SARS-COV-2 \u03b3 variant acquires spike P681H or P681R for improved viral fitness", @@ -553279,49 +554560,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.15.21265006", - "rel_title": "Vaccine effectiveness of Ad26.COV2.S against symptomatic COVID-19 and clinical outcomes in Brazil: a test-negative study design", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.15.21265006", - "rel_abs": "We used a test-negative design to estimate the vaccine effectiveness of Ad26.COV2.S (Janssen) against symptomatic COVID-19 and clinical outcomes in Mato-Grosso do Sul, Brazil. We analyzed 11,817 RT-PCR tests. The mean age was 37 (SD=17) years, 2,308 (20%) of individuals more or equal than 50 years and almost two-thirds of the population was Brown/Pardo. Adjusted effectiveness against symptomatic COVID-19 after 28 days of the single dose was 50.9% (95% CI, 35.5-63.0). Adjusted effectiveness against clinical outcomes was 72.9% (95% CI, 35.1-91.1) for hospitalization, 92.5% (95% CI, 54.9-99.6) for ICU admission, 88.7% (95% CI, 17.9-99.5) for mechanical ventilation and 90.5% (95% CI, 31.5-99.6) for death. Despite lacking precision on some estimates, a single dose of Ad26.COV2.S vaccine continues to protect specially for severe forms of COVID-19 in the context of new variants.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Otavio T Ranzani", - "author_inst": "Barcelona Institute for Global Health, ISGlobal, Spain / Pulmonary Division, University of Sao Paulo" - }, - { - "author_name": "Rog\u00e9rio dos Santos Leite", - "author_inst": "Secretaria Municipal de Sa\u00fade de Corumb\u00e1, Corumb\u00e1, Brazil" - }, - { - "author_name": "Larissa Domingues Castilho", - "author_inst": "Secretaria de Sa\u00fade do estado de Mato Grosso do Sul, Campo Grande, Brazil" - }, - { - "author_name": "Crhistinne Cavalheiro Maymone Gon\u00e7alves", - "author_inst": "Secretaria de Sa\u00fade do estado de Mato Grosso do Sul, Campo Grande, Brazil/ Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil" - }, - { - "author_name": "Geraldo Resende", - "author_inst": "Secretaria de Sa\u00fade do estado de Mato Grosso do Sul, Campo Grande, Brazil" - }, - { - "author_name": "Rosana Leite de Melo", - "author_inst": "Secretaria Extraordin\u00e1ria de Enfrentamento \u00e0 Covid-19, Ministerio da Sa\u00fade, Bras\u00edlia, Brazil" - }, - { - "author_name": "Julio Croda", - "author_inst": "Fiocruz Mato Grosso do Sul, Funda\u00e7\u00e3o Oswaldo Cruz, Campo Grande, Brazil/ Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil/ Department of Epidemi" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.15.21265059", "rel_title": "CoWWAn: Model-based assessment of COVID-19 epidemic dynamics by wastewater analysis", @@ -553505,6 +554743,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.14.21264918", + "rel_title": "Back to the medical classes-Part I- Strategy for return to the presential practices during COVID-19 pandemics in a Brazilian Medical School", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21264918", + "rel_abs": "IntroductionIn Brazil, practices of medical students have been interrupted due to COVID-19 to meet emergency demands.\n\nAimTo describe a strategy for a controlled return to the presential practices for medical students.\n\nMethodsWe developed a standardized protocol to be applied before and during the return of the practical classes in medical students of Universidade Federal Fluminense, in the follow months after COVID-19 pandemic beginning. The protocol was comprised in three parts: Remote training on COVID-19 prevention; Face-to-face training focused in COVID-19 prevention, handwashing and personal protective equipment use; Investigation of students COVID-19 status before starting practical activities and weekly monitoring for COVID-19 during seven weeks. The training was done by medical teachers in small groups for medical students of the last lective semester.\n\nResultsThe classes were interrupted on March 12, 2020 and returned in August 10, 2020. Seventy-one students were trained and followed. The mean age was 26.6 years (26.7 {+/-}0.835) and 54% were female. Forty-nine (69%) students over 71 had a private health insurance, 60 (84.5%) shared a house/apartment with one or more person and 12(16.9%) reported a previous comorbidity. Eighteen (25.4%) over 71 reported previous symptoms of COVID-19, being positive in two students. During the follow-up, fourteen (19.7%) over 71 students were placed in quarantine due to signals/symptoms compatible with COVID-19 or contact with symptomatic case. Only two cases (2.8%) were confirmed and occurred in Brazilian epidemiological week 37.\n\nConclusionThe protocol was successful in minimizing COVID-19 acquisition during practical classes of medical students.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Maria Auxiliadora Nogueira Saad", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Vinicius Cesar Jardim Pereira", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Arnaldo Costa Bueno", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Alan Araujo Vieira", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Maria de Fatima Pombo March", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Maria Dolores Salgado Quintans", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Bruno Mendonca Barcellos", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Laura da Cunha Ferreira", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Karla Regina Oliveira Moura Ronchini", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Luis Guillermo Coca Velarde", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Claudete Aparecida Araujo Cardoso", + "author_inst": "Universidade Federal Fluminense" + }, + { + "author_name": "Andre Ricardo Araujo da Silva", + "author_inst": "Universidade Federal Fluminense" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2021.10.15.21264977", "rel_title": "Efficacy and safety of a third SARS-CoV-2 vaccination in multiple sclerosis vaccine non-responders", @@ -554897,37 +556198,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.10.13.21264855", - "rel_title": "\"I had no life. I was only existing\". Factors shaping the mental health and wellbeing of people experiencing long Covid: a qualitative study.", - "rel_date": "2021-10-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264855", - "rel_abs": "BackgroundAround one in 10 people who have COVID-19 report persistent symptoms or long Covid. Impaired mental health and wellbeing is commonly reported including anxiety, depression and reduced quality of life. There is however, limited in-depth research exploring why mental health and wellbeing have been impacted among people experiencing long Covid.\n\nAimsTo explore factors impacting mental health and wellbeing, from the perspective of people with long Covid.\n\nMethodSemi-structured qualitative interviews that were audio-recorded and transcribed. Data were analysed using reflexive thematic analysis. 21 people with long Covid participated in the study. Participants were eligible to take part if they self-reported a positive swab test/antibody test, or one or more commonly reported COVID-19 symptoms at illness onset and experiences of one or more long Covid symptom three or more weeks following illness onset.\n\nResultsFive themes were identified across participant accounts regarding factors impacting mental health and wellbeing including i) experiences of care and understanding from others; ii) lack of service and treatment options; iii) severe disruption to daily life iv) uncertainty of illness trajectories and v) changes to identity.\n\nConclusionsPeople with long Covid experience a range of factors that negatively impact their mental health and wellbeing. Providing patient centred health services that integrate the rapidly evolving research in this area is important, as are peer support groups and supported approaches to self-management.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Alexandra Burton", - "author_inst": "University College London" - }, - { - "author_name": "Henry Aughterson", - "author_inst": "UCL" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Keir Elmslie James Philip", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.10.13.21264894", "rel_title": "Memory B cell and humoral responses elicited by Sputnik V in nai\u0308ve and COVID-19-recovered vaccine recipients", @@ -555134,6 +556404,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.12.21264913", + "rel_title": "Psychiatric Manifestations and Associated Risk Factors among Hospitalized Patients with COVID-19 in Edo State, Nigeria.", + "rel_date": "2021-10-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264913", + "rel_abs": "ObjectiveThe Coronavirus Disease 2019 (COVID-19) has had devastating effects globally. These effects are likely to result in mental health problems at different levels. Although studies have reported the mental health burden of the pandemic on the general population and frontline health workers, the impact of the disease on the mental health of patients in COVID-19 treatment and isolation centres have been understudied in Africa. We estimated the prevalence of depression and anxiety and associated risk factors in hospitalized persons with COVID-19.\n\nMethodsA cross-sectional survey was conducted among 489 patients with COVID-19 at the three government designated treatment and isolation centres in Edo State, Nigeria. The 9-item Patient Health Questionnaire (PHQ-9) and the Generalized Anxiety Disorder-7 (GAD-7) tool were used to assess depression and anxiety respectively. Binary logistic regression was applied to determine risk factors of depression and anxiety.\n\nResultsOf the 489 participants, 49.1% and 38.0% had depressive and anxiety symptoms respectively. The prevalence of depression, anxiety, and combination of both were 16.2%, 12.9% and 9.0% respectively. Moderate-severe symptoms of COVID-19, [≥]14 days in isolation, worrying about the outcome of infection and stigma increased the risk of having depression and anxiety. Additionally, being separated/divorced increased the risk of having depression and having comorbidity increased the risk of having anxiety.\n\nConclusionA substantial proportion of our participants experienced depression, anxiety and a combination of both especially in those who had the risk factors we identified. The findings underscore the need to address these risk factors early in the course of the disease and integrate mental health interventions into COVID-19 management guidelines.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Esther O Okogbenin", + "author_inst": "Department of Mental Health, Irrua Specialist Teaching Hospital, Irrua, Edo State , Nigeria" + }, + { + "author_name": "Omonefe J Seb-Akahomen", + "author_inst": "Department of Mental Health, Irrua Specialist Teaching Hospital, Irrua, Edo State , Nigeria" + }, + { + "author_name": "Osahogie I. Edeawe", + "author_inst": "Institute of Lassa Fever Research and Control Irrua Specialist Teaching Hospital, Edo State, Nigeria" + }, + { + "author_name": "Mary Ehimigbai", + "author_inst": "Department of Mental Health, University of Benin Teaching Hospital, Benin City, Edo State, Nigeria" + }, + { + "author_name": "Helen Eboreime", + "author_inst": "Department of Hospital Services, Health Management Board, Ministry of Health, Edo State, Nigeria" + }, + { + "author_name": "Angela Odike", + "author_inst": "Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Edo State , Nigeria" + }, + { + "author_name": "Micheal O Obagaye", + "author_inst": "Department of Mental Health, Irrua Specialist Teaching Hospital, Irrua, Edo State , Nigeria" + }, + { + "author_name": "Benjamin E Aweh", + "author_inst": "Department of Mental Health, Irrua Specialist Teaching Hospital, Irrua, Edo State , Nigeria" + }, + { + "author_name": "Paul Erohubie", + "author_inst": "Department of Mental Health, Irrua Specialist Teaching Hospital, Irrua, Edo State , Nigeria" + }, + { + "author_name": "Williams Eriyo", + "author_inst": "Department of Mental Health, Irrua Specialist Teaching Hospital, Irrua, Edo State , Nigeria" + }, + { + "author_name": "Chinwe F Inogbo", + "author_inst": "Department of Clinical Services, Federal Neuro-Psychiatric Hospital, Uselu, Edo State, Nigeria" + }, + { + "author_name": "Peter Akhideno", + "author_inst": "Institute of Lassa Fever Research and Control Irrua Specialist Teaching Hospital, Edo State, Nigeria" + }, + { + "author_name": "Gloria Eifediyi", + "author_inst": "Institute of Lassa Fever Research and Control Irrua Specialist Teaching Hospital, Edo State, Nigeria" + }, + { + "author_name": "Reuben Eifediyi", + "author_inst": "Institute of Lassa Fever Research and Control Irrua Specialist Teaching Hospital, Edo State, Nigeria" + }, + { + "author_name": "Danny Asogun", + "author_inst": "Institute of Lassa Fever Research and Control Irrua Specialist Teaching Hospital, Edo State, Nigeria" + }, + { + "author_name": "Sylvanus A Okogbenin", + "author_inst": "Institute of Lassa Fever Research and Control Irrua Specialist Teaching Hospital, Edo State, Nigeria" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.10.13.21264956", "rel_title": "Changes in paediatric respiratory infections at a UK teaching hospital 2016-2021; impact of the SARS-CoV-2 pandemic.", @@ -556962,73 +558311,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.12.21264860", - "rel_title": "SARS-CoV-2 vaccine antibody response and breakthrough infections in patients receiving dialysis", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264860", - "rel_abs": "BackgroundPatients receiving dialysis are a sentinel population for groups at high risk for death and disability from COVID-19. Understanding correlates of protection post-vaccination can inform immunization and mitigation strategies.\n\nMethodsMonthly since January 2021, we tested plasma from 4791 patients receiving dialysis for antibodies to the receptor-binding domain (RBD) of SARS-CoV-2 using a high-throughput assay. We qualitatively assessed the proportion without a detectable RBD response and among those with a response, semiquantitative median IgG index values. Using a nested case-control design, we matched each breakthrough case to five controls by age, sex, and vaccination-month to determine whether peak and pre-breakthrough RBD IgG index values were associated with risk for infection post-vaccination.\n\nResultsAmong 2563 vaccinated patients, the proportion without a detectable RBD response increased from 6.6% [95% CI 5.5-8.1] in 14-30 days post-vaccination to 20.2% [95% CI 17.1-23.8], and median index values declined from 92.7 (95% CI 77.8-107.5) to 3.7 (95% CI 3.1-4.3) after 5 months. Persons with SARS-CoV-2 infection prior-to-vaccination had higher peak index values than persons without prior infection, but values equalized by 5 months (p=0.230). Breakthrough infections occurred in 56 patients, with samples collected a median of 21 days pre-breakthrough. Peak and pre-breakthrough RBD values <23 (equivalent to <506 WHO BAU/mL) were associated with higher odds for breakthrough infection (OR: 3.7 [95% CI 2.0-6.8] and 9.8 [95% CI 2.9-32.8], respectively).\n\nConclusionsThe antibody response to SARS-CoV-2 vaccination wanes rapidly, and in persons receiving dialysis, the persisting antibody response is associated with risk for breakthrough infection.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Shuchi Anand", - "author_inst": "Stanford University" - }, - { - "author_name": "Maria E Montez-Rath", - "author_inst": "Stanford University" - }, - { - "author_name": "Jialin Han", - "author_inst": "Stanford University" - }, - { - "author_name": "Pablo Garcia", - "author_inst": "Stanford University" - }, - { - "author_name": "LinaCel Cadden", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Patti Hunsader", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Curt Morgan", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Russell Kerschmann", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Paul Beyer", - "author_inst": "Ascend Clinical Lab" - }, - { - "author_name": "Mary Dittrich", - "author_inst": "US Renal Care" - }, - { - "author_name": "Geoffrey A Block", - "author_inst": "US Renal Care" - }, - { - "author_name": "Glenn M Chertow", - "author_inst": "Stanford University" - }, - { - "author_name": "Julie Parsonnet", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.11.21264869", "rel_title": "Modeling and analysis of COVID-19 infected persons during repeated waves in Japan", @@ -557292,6 +558574,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.10.13.21264961", + "rel_title": "Examining the Association between the COVID-19 Pandemic and Self-Harm Death Counts in Four Canadian Provinces", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264961", + "rel_abs": "Governments implemented lockdowns and other physical distancing measures to stop the spread of SARS-CoV-2 (COVID-19). Resulting unemployment, income loss, poverty, and social isolation, coupled with daily reports of dire news about the COVID-19 pandemic, could serve as catalysts for increased self-harm deaths (SHD). This ecological study examined whether observed SHD counts were higher than predicted SHD counts during the pandemic period in the Canadian provinces of Alberta, British Columbia, Ontario, and Quebec. The study also explored whether SHD counts during the pandemic were affected by lockdown severity (measured using the lockdown stringency index [LSI]) and COVID-19 case numbers. We utilized publicly available SHD data from January 2018 through November 2020, and employed AutoRegressive Integrated Moving Average (ARIMA) modelling, to predict SHD during the COVID-19 period (March 21 to November 28, 2020). We used Poisson and negative binomial regression to assess ecological associations between the LSI and COVID-19 case numbers, controlling for seasonality, and SHD counts during the COVID-19 period. On average, observed SHD counts were lower than predicted counts during this period (p < 0.05 [except Alberta]). Additionally, LSI and COVID-19 case numbers were not statistically significantly associated with SHD counts.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Shelly Isnar", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Mark Oremus", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.10.13.464254", "rel_title": "Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry", @@ -558892,65 +560197,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.10.21264825", - "rel_title": "Effects of Age, Sex, Serostatus and Underlying Comorbidities on Humoral Response Post-SARS-CoV-2 Pfizer-BioNTech Vaccination: A Systematic Review", - "rel_date": "2021-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.10.21264825", - "rel_abs": "With the advent of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, several vaccines have been developed to mitigate its spread and prevent adverse consequences of the Coronavirus Disease 2019 (COVID-19). The mRNA technology is an unprecedented vaccine, usually given in two doses to prevent SARS-CoV-2 infections. Despite effectiveness and safety, inter-individual immune response heterogeneity has been observed in recipients of mRNA-based vaccines. As a novel disease, the specific immune response mechanism responsible for warding off COVID-19 remains unclear at this point. However, significant evidence suggests that humoral response plays a crucial role in affording immunoprotection and preventing debilitating sequelae from COVID-19. As such this paper focused on the possible effects of age, sex, serostatus, and comorbidities on humoral response (i.e., total antibodies, IgG and/or IgA) of different populations post-mRNA-based Pfizer-BioNTech vaccination. A systematic search of literature was performed through PubMed, Cochrane CENTRAL, and Google Scholar. Studies were included if they reported humoral response to COVID-19 mRNA vaccines. A total of 32 studies was identified and reviewed, and the percent difference of means of reported antibody levels were calculated for comparison. Findings revealed that older individuals, the male sex, seronegativity, and those with more comorbidities mounted less humoral immune response. Given these findings, several recommendations were proposed regarding the current vaccination practices. These include giving additional doses of vaccination for immunocompromised and elderly populations. Another recommendation is conducting clinical trials in giving a combined scheme of mRNA vaccines, protein vaccines, and vector-based vaccines.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kin Israel Notarte", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Abbygail Therese Ver", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Jacqueline Veronica Velasco", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Adriel Pastrana", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Jesus Alfonso Catahay", - "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines" - }, - { - "author_name": "Gian Luca Salvagno", - "author_inst": "Service of Laboratory Medicine, Pederzoli Hospital, Peschiera del Garda, Italy" - }, - { - "author_name": "Eric Peng Huat Yap", - "author_inst": "Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore" - }, - { - "author_name": "Luis Martinez-Sobrido", - "author_inst": "Host-Pathogens Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA" - }, - { - "author_name": "Jordi Torrelles", - "author_inst": "Host-Pathogens Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA" - }, - { - "author_name": "Giuseppe Lippi", - "author_inst": "Section of Clinical Biochemistry, University of Verona, Verona, Italy" - }, - { - "author_name": "Brandon Michael Henry", - "author_inst": "Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Ohio, USA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.10.21264821", "rel_title": "Modelling the effect of COVID-19 mass vaccination on acute admissions in a major English healthcare system", @@ -559250,6 +560496,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.12.464114", + "rel_title": "A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy", + "rel_date": "2021-10-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.12.464114", + "rel_abs": "Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the \"class 3\" epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Allison J Greaney", + "author_inst": "University of Washington" + }, + { + "author_name": "Tyler N Starr", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Rachel T Eguia", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Andrea N Loes", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Khadija Khan", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Farina Karim", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Sandile Cele", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "John E Bowen", + "author_inst": "University of Washington" + }, + { + "author_name": "Jennifer K Logue", + "author_inst": "University of Washington" + }, + { + "author_name": "Davide Corti", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Helen Y Chu", + "author_inst": "University of Washington" + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.10.12.464150", "rel_title": "AUG-3387, a Human-Derived Monoclonal Antibody Neutralizes SARS-CoV-2 Variants and Reduces Viral Load from Therapeutic Treatment of Hamsters In Vivo", @@ -560541,57 +561858,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.10.07.21264204", - "rel_title": "Decreased hospital visits and increased mortality rate in the emergency department during the COVID-19 pandemic: Evidence from Albania.", - "rel_date": "2021-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21264204", - "rel_abs": "ObjectiveTo investigate the hospital visits and mortality rate during the COVID-19 in emergency department of Vlora regional hospital in Albania and to compare with the three previous years (2017-2019).\n\nData sourcesSecondary data of patients that visited emergency department of Vlora Regional hospital Albania (largest hospital in the south of the country), since January 1, 2017 till December 31, 2020.\n\nStudy DesignThis is a retrospective study. We used the hard copy of the patients health register records.\n\nExtraction methodsThe data extraction was conducted during March 2021 till June 2021. Eligible were all patients admitted and recorded in the registry of the Emergency department. The causes of admission were categorized in 14 different disease categories. All registered patient admitted to the Vlora regional hospital were included in the study. Patients that all data were not recorded and patients that data were not possible to be read were excluded.\n\nPrincipal FindingsStudy population included 44.917 patients during 2017-2020. Mean age of patients was 51.5 years, while 53.6% were females. The highest number of patients was in 2017 (n=12.407) and the lowest in 2020 (n=9.266). Increase of patients presented with cardiovascular, psychiatric and renal/urinary tract were observed in 2020 in comparison to 2019. Patients decreased over time with an average annual percent decrease of -7% (p-value=0.22). Joinpoint analysis revealed that mortality rate increased over time with an average annual percent increase of 34.3% (95% confidence interval= -42.7% to 214.8%, p-value=0.27).\n\nConclusionsDuring the study years the number of patients visiting emergency department decreased while mortality rate increased. Educating and raising awareness of patient to seek medical assistance should be a key objective of health policy makers and health personnel. A specific focus should be put on the more vulnerable (elderly and unemployed) as their health status is in higher risk.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jorgjia Bucaj", - "author_inst": "Department of Healthcare, Faculty of Health, University of Vlora, Vlora, Albania" - }, - { - "author_name": "Enkeleint A. Mechili", - "author_inst": "Department of Healthcare, Faculty of Health, University of Vlora" - }, - { - "author_name": "Petros Galanis", - "author_inst": "Faculty of Nursing, Center for Health Services Management and Evaluation, National and Kapodistrian University of Athens, Athens, Greece" - }, - { - "author_name": "Bruna Mersini", - "author_inst": "Vlora Regional Hospital, Vlora, Albania" - }, - { - "author_name": "Sonila Nika", - "author_inst": "Department of Nursing, Faculty of Health, University of Vlora, Vlora, Albania" - }, - { - "author_name": "Inis Hoxhaj", - "author_inst": "Department of Nursing, Faculty of Health, University of Vlora, Vlora, Albania" - }, - { - "author_name": "Stefano Likaj", - "author_inst": "Department of Nursing, Faculty of Health, University of Vlora, Vlora, Albania" - }, - { - "author_name": "Athina E. Patelarou", - "author_inst": "Faculty of Nursing, Hellenic Mediterranean University, Crete, Greece" - }, - { - "author_name": "Evridiki Patelarou", - "author_inst": "Faculty of Nursing, Hellenic Mediterranean University, Crete, Greece" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.10.08.21264765", "rel_title": "The impact of heating, ventilation, and air conditioning design features on the transmission of viruses, including the 2019 novel coronavirus: a systematic review of ventilation and coronavirus", @@ -560803,6 +562069,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.07.21264713", + "rel_title": "Monitoring and forecasting the COVID-19 epidemic in Moscow: model selection by balanced identification technology - version: September 2021", + "rel_date": "2021-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21264713", + "rel_abs": "A mathematical model is a reflection of knowledge on the real object studied. The paper shows how the accumulation of data (statistical data and knowledge) about the COVID-19 pandemic lead to gradual refinement of mathematical models, to the expansion of the scope of their use. The resulting model satisfactorily describes the dynamics of COVID-19 in Moscow from 19.03.2020 to 01.09.2021 and can be used for forecasting with a horizon of several months. The dynamics of the model is mainly determined by herd immunity. Monitoring the situation in Moscow has not yet (as of 01.09.2021) revealed noticeable seasonality of the disease nor an increase in infectivity (due to the Delta strain). The results of using balanced identification technology to monitor the COVID-19 pandemic are:\n\nO_LImodels corresponding to the data available at different points in time (from March 2020 to August 2021);\nC_LIO_LInew knowledge (dependencies) acquired;\nC_LIO_LIforecasts for the third and fourth waves in Moscow.\nC_LI\n\nDiscrepancies that manifested after 01.09.2021 and possible further modifications of the model are discussed", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alexander Sokolov", + "author_inst": "Institute for information transmission problem RAS" + }, + { + "author_name": "Lyubov Sokolova", + "author_inst": "Federal Research Center Computer Science and Control of the Russian Academy of Sciences, Russia, Moscow" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.08.21264718", "rel_title": "The impact of mandatory COVID-19 certificates on vaccine uptake: Synthetic Control Modelling of Six Countries", @@ -562507,37 +563796,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.08.21264716", - "rel_title": "COVID-19 Pandemic Impact on Sexually Transmitted Infection Testing in a College Setting", - "rel_date": "2021-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264716", - "rel_abs": "ObjectiveAssess the impact of the pandemic on STI (sexually transmitted infections) testing in a college health setting.\n\nDesignExploratory analysis of the number of STI tests done, positive rates for those tests and of percentage of \"compliance to follow-up\" from March to December 2020 and its comparison with historical data at the University Health Services, UW-Madison.\n\nSamplestudents STI tests during the analyzed period.\n\nMeasurementObserved (2020) vs Expected (2015-2019, average) number of STI tests, positive rate, compliance to follow-up testing for STIs.\n\nResultsThere was a significant decrease in the number of tests done and increase of positive rate when compared to historical for total sample and per sex. There was a decrease in the percentage of follow-up for the entire sample and females and an increase for males.\n\nConclusionsConsidering the three outcomes assessed, we observe an impact in STI testing during the pandemic. In concordance with national data, our analysis shows significant declines in STI testing and follow-up during 2020 compared to previous years and an increase in positivity rate. The finding of higher positivity with lower number of tests is likely due to triaging patients, facilitating testing for those at highest risk of infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Agustina M Marconi", - "author_inst": "UW-Madison" - }, - { - "author_name": "Elizabeth C Falk-Hanson", - "author_inst": "UW-Madison" - }, - { - "author_name": "Megan E Crass", - "author_inst": "UW-Madison" - }, - { - "author_name": "Peter Campbell", - "author_inst": "UW-Madison" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.09.21264771", "rel_title": "Taste loss as a distinct symptom of COVID-19: A systematic review and meta-analysis", @@ -562833,6 +564091,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.10.07.463533", + "rel_title": "Angiotensin converting enzyme 2 (ACE2) is expressed in murine cutaneous under single-cell transcriptome resolution", + "rel_date": "2021-10-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.07.463533", + "rel_abs": "Angiotensin converting enzyme 2 (Ace2) is widely distributed in human organs, which was identified as a functional receptor for severe acute respiratory syndrome (SARS) coronavirus in human beings. It was also confirmed that SARS-CoV-2 uses the same cell entry receptor, ACE2, as SARS-CoV. However, related research still not discover the expression data associated with murine skin under single cell RNA resolution. In this study, we performed single-cell RNA sequencing (scRNA-seq) on unsorted cells from mouse dorsal skin after 7 days post-wounding. 8312 sequenced cells from four skin samples met quality control metrics and were analyzed.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Chenyu Chu", + "author_inst": "State Key Laboratory of Oral Diseases" + }, + { + "author_name": "Chen Hu", + "author_inst": "Sichuan University" + }, + { + "author_name": "Li Liu", + "author_inst": "Sichuan University" + }, + { + "author_name": "Yuanjing Wang", + "author_inst": "Sichuan University" + }, + { + "author_name": "Yili Qu", + "author_inst": "Sichuan University" + }, + { + "author_name": "Yi Man", + "author_inst": "Sichuan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.10.04.21262827", "rel_title": "A twelve-month projection to September 2022 of the Covid-19 epidemic in the UK using a Dynamic Causal Model", @@ -564573,101 +565870,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.05.21264559", - "rel_title": "Effectiveness and Safety of MSC Cell Therapies for Hospitalized Patients with COVID-19: A Systematic Review and Meta-analysis", - "rel_date": "2021-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264559", - "rel_abs": "MSC (a.k.a. mesenchymal stem cell or medicinal signaling cell) cell therapies have shown promise in decreasing mortality in ARDS and suggest benefits in treatment of COVID-19 related ARDS. We performed a meta-analysis of published trials assessing the effectiveness and adverse events (AE) of MSC cell therapy in individuals hospitalized for COVID-19. Systematic searches were performed in multiple databases through April 8th, 2021. Reports in all languages including randomized clinical trials (RCTs), comparative observational studies, and case series/case reports were included. Random effects model was used to pool outcomes from RCTs and comparative observational studies. Outcome measures included all-cause mortality, serious adverse events (SAEs), AEs, pulmonary function, laboratory and imaging findings. A total of 413 patients were identified from 25 studies, which included 8 controlled trials (3 RCTs), 5 comparative observational studies, (n=300) and 17 case-series/case reports (n=113). The patients age was 60.5 years (mean), 33.7% were women. When compared with the control group, MSC cell therapy was associated with reduction in all-cause mortality (RR=0.31, 95% CI: 0.12 to 0.75, I2=0.0%; 3 RCTs and 5 comparative observational studies, 300 patients), reduction in SAEs (IRR=0.36, 95% CI: 0.14 to 0.90, I2=0.0%; 3 RCTs and 2 comparative studies, n=219), no significant difference in AE rate. A sub-group with pulmonary function studies suggested improvement in patients receiving MSC. These findings support the potential for MSC cell therapy to decrease all-cause mortality, reduce SAEs, and improve pulmonary function compared to conventional care. Large scale double-blinded, well-powered RCTs should be conducted to further explore these results.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Wenchun Qu", - "author_inst": "Department of Pain Medicine, Mayo Clinic, Jacksonville, Florida; Center for Regenerative Medicine, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Zhen Wang", - "author_inst": "Evidence-Based Practice Center, Mayo Clinic, Rochester, Minnesota; Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, R" - }, - { - "author_name": "Erica Engelberg Cook", - "author_inst": "Department of Neuroscience, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Abu Bakar Siddik", - "author_inst": "Department of Pain Medicine, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Guojun Bu", - "author_inst": "Center for Regenerative Medicine, Mayo Clinic, Jacksonville, Florida; Department of Neuroscience, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Julie G Allickson", - "author_inst": "Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota" - }, - { - "author_name": "Eva Kubrova", - "author_inst": "Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, Minnesota" - }, - { - "author_name": "Arnold I Caplan", - "author_inst": "Skeletal Research Center, Biology Department, Case Western Reserve University, Cleveland, Ohio" - }, - { - "author_name": "Joshua M Hare", - "author_inst": "Interdisciplinary Stem Cell Institute and Cardiology Division, Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida" - }, - { - "author_name": "Calillo Ricordi", - "author_inst": "Department of Surgery, Diabetes Research Institute and Cell Transplant Center, University of Miami Miller School of Medicine" - }, - { - "author_name": "Carl J Pepine", - "author_inst": "Division of Cardiovascular Medicine, and Center for Regenerative Medicine, University of Florida, Gainesville, Florida" - }, - { - "author_name": "Joanne Kurtzberg", - "author_inst": "Marcus Center for Cellular Cures, Duke University School of Medicine" - }, - { - "author_name": "Jorge M Pascual", - "author_inst": "Division of Pulmonary, Allergy and Sleep Medicine, Department of Medicine, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Jorge M Mallea", - "author_inst": "Division of Pulmonary, Allergy and Sleep Medicine, Department of Medicine, Mayo Clinic, Jacksonville, Florida" - }, - { - "author_name": "Ricardo L Rodriguez", - "author_inst": "Co-Chair Regenerative Medicine Committee, American Society Plastic Surgeons" - }, - { - "author_name": "Tarek Nayfeh", - "author_inst": "Evidence-Based Practice Center, Mayo Clinic, Rochester, Minnesota; Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, R" - }, - { - "author_name": "Samer Saadi", - "author_inst": "Evidence-Based Practice Center, Mayo Clinic, Rochester, Minnesota; Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, R" - }, - { - "author_name": "Elaine M Richards", - "author_inst": "Department of Physiology and Functional Genomics, Center of Regenerative Medicine, University of Florida, Gainesville, Florida" - }, - { - "author_name": "Keith March", - "author_inst": "Division of Cardiovascular Medicine, Center for Regenerative Medicine, University of Florida, Gainesville, Florida" - }, - { - "author_name": "Fred P Sanfilippo", - "author_inst": "Department of Pathology and Laboratory Medicine, Department of Health Policy and Management, Emory University, Atlanta, Georgia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.10.05.21264597", "rel_title": "Effect of workplace infection control practices on workers' psychological distress: a large-scale cohort study during the COVID-19 second state of emergency in Japan", @@ -564923,6 +566125,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.06.21264616", + "rel_title": "Evolution of SARS-CoV-2 immune responses in nursing home residents following full dose of the Comirnaty COVID-19 vaccine", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264616", + "rel_abs": "ObjectivesThere is scarce information as to the durability of immune responses elicited by the Comirnaty(R) COVID-19 vaccine in nursing home residents. Here, we assessed SARS-CoV-2-Spike (S)-targeted antibody and functional T cell responses at around 6 months after complete vaccination.\n\nMethodsThe sample comprised 46 residents (34 females; age, 60-100 years), of whom 10 had COVID-19 prior to vaccination. Baseline (median of 17.5 days after vaccination) and follow-up (median, 195 days) plasma specimens were available for quantitation of SARS-CoV-2-S antibodies and enumeration of SARS-CoV-2-S-reactive IFN-{gamma} CD4+ and CD8+ T cells by flow cytometry.\n\nResultsIn total, 44/45 participants had detectable SARS-CoV-2-S antibodies at follow-up. Overall, antibody levels were found to decrease (median, 4.8 fold). Antibodies waning was more frequent (P<0.001) in SARS-CoV-2 naive (29/35) than in recovered (1/10) residents. SARS-CoV-2-S IFN-{gamma} CD8+ T cells were detected in 33/46 and 24/46 at baseline and follow-up, respectively. The figures for CD4+ T cell counterparts were 12/46 and 30/46. Detectable SARS-CoV-2 IFN-{gamma} CD8+ and CD4+ T cell responses at follow-up were more common in recovered (8/10 and 7/10, respectively) than in naive residents (9/36 and 25/36, respectively). For those with detectable responses at both time points, SARS-CoV-2-S IFN-{gamma} CD8+ T cell frequencies decreased significantly (P=0.001) over time whereas the opposite (P=0.01) was observed in CD4+ T cells.\n\nConclusionAlmost all residents displayed detectable SARS-CoV-2-S-reactive antibodies and T cell responses, respectively, by around 6 months after complete vaccination with Comirnaty(R) COVID-19 vaccine, albeit generally waning in magnitude over time.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Estela Gimenez", + "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." + }, + { + "author_name": "Juan Alberola", + "author_inst": "Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain" + }, + { + "author_name": "Ignacio Torres", + "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain" + }, + { + "author_name": "Eliseo Albert", + "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain" + }, + { + "author_name": "Maria Jesus Alcaraz", + "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain" + }, + { + "author_name": "Pilar Botija", + "author_inst": "Direccion de Atencion Primaria, Departamento de Salud Clinico-Malvarrosa, Hospital Clinico Universitario de Valencia, Valencia, Spain" + }, + { + "author_name": "Paula Amat", + "author_inst": "Hematology Service Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain" + }, + { + "author_name": "Maria Jose Remigia", + "author_inst": "Hematology Service Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain" + }, + { + "author_name": "Maria Jose Beltran", + "author_inst": "Direccion de Enfermeria, Departamento de Salud Clinico-Malvarrosa, Hospital Clinico Universitario de Valencia, Valencia, Spain" + }, + { + "author_name": "Celia Rodado", + "author_inst": "Comision Departamental de control de Residencias. Departamento de Salud Valencia Clinico Malvarrosa." + }, + { + "author_name": "Dixie Huntley", + "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain" + }, + { + "author_name": "Beatriz Olea", + "author_inst": "1icrobiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain" + }, + { + "author_name": "David Navarro", + "author_inst": "Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.05.21264543", "rel_title": "Higher Hospitalization and Mortality Rates Among SARS-CoV-2 infected Persons in Rural America", @@ -566783,93 +568052,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.10.06.21263384", - "rel_title": "SARS-CoV-2 RNA and antibody dynamics in a Dutch household study with dense sampling frame", - "rel_date": "2021-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21263384", - "rel_abs": "This study investigated the dynamics of SARS-CoV-2 infection and diagnostics in household members of different ages and with different symptom severity after SARS-CoV-2 exposure during the early phase of the pandemic. Households with a SARS-CoV-2 confirmed positive case and at least one child in the Netherlands were followed for 6 weeks. Naso (NP)- and oropharyngeal (OP) swabs, oral fluid and feces specimens were analyzed for SARS-CoV-2 RNA and serum for SARS-CoV-2-specific antibodies. The dynamics of the presence of viral RNA and the serological response was modeled to determine the sampling time-frame and sample type with the highest sensitivity to confirm or reject a SARS-CoV-2 diagnosis. Transmission of SARS-CoV-2 between adults and children within a household was correlated with symptom severity of index cases. In children higher viral loads compared to adults were detected at symptom onset. Early in infection, higher viral loads were detected in NP and OP specimens, while RNA in especially feces were longer detectable. SARS-CoV-2-specific antibodies have a 90% probability of detection from 7 days (total Ig) and 18 days (IgG) since symptom onset. In conclusion this study has shown that on average, children carry higher loads of virus as compared to adults early after infection. For highest probability of detection in SARS-CoV-2 diagnostics early in infection, RT-PCR on NP and OP specimens are more sensitive than on oral fluid and feces. For SARS-CoV-2 diagnostics late after infection, RT-PCR on feces specimens and serology are more valuable.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Wanda G.H. Han", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Arno Swart", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Axel Bonacic Marinovic", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Dirk Eggink", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Johan Reimerink", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Lisa A Wijsman", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Bas van der Veer", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Sharon van den Brink", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Anne-Marie van den Brandt", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Sophie van Tol", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Gert-Jan Godeke", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Fion Brouwer", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Marieke Hoogerwerf", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "- the Dutch FFX-COVID-19 research group", - "author_inst": "" - }, - { - "author_name": "Daphne F.M. Reukers", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Nynke Rots", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Chantal Reusken", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Adam Meijer", - "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.02.21264267", "rel_title": "Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion", @@ -567361,6 +568543,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.04.21264500", + "rel_title": "Increase in preterm stillbirths and reduction in iatrogenic preterm births for fetal compromise: a multi-centre cohort study of COVID-19 lockdown effects in Melbourne, Australia", + "rel_date": "2021-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.04.21264500", + "rel_abs": "ObjectivesThe COVID-19 pandemic has been associated with a worsening of perinatal outcomes in many settings due to the combined impacts of maternal COVID-19 disease, disruptions to maternity care, and overloaded health systems. In 2020, Melbourne endured a unique natural experiment where strict lockdown conditions were accompanied by very low COVID-19 case numbers and the maintenance of health service capacity. The aim of this study was to compare stillbirth and preterm birth rates in women who were exposed or unexposed to lockdown restrictions during pregnancy.\n\nDesignRetrospective multi-centre cohort study of perinatal outcomes before and during COVID-19 lockdown\n\nSettingBirth outcomes from all 12 public maternity hospitals in metropolitan Melbourne\n\nInclusion criteriaSingleton births without congenital anomalies from 24 weeks gestation. The lockdown-exposed cohort were those women for whom weeks 20- 40 of gestation would have occurred during the lockdown period of 23 March 2020 to 14 March 2021. The control cohort comprised all pregnancies in the corresponding periods one and two years prior to the exposed cohort.\n\nMain outcome measuresOdds of stillbirth, preterm birth (PTB), birth weight < 3rd centile, and iatrogenic PTB for fetal compromise, adjusting for multiple covariates.\n\nResultsThere were 24,017 births in the exposed and 50,017 births in the control group. There was a significantly higher risk of preterm, but not term, stillbirth in the exposed group compared with the control group (0.26% vs 0.18%, aOR 1.49, 95%CI 1.08 to 2.05, P = 0.015). There was also a significant reduction in preterm birth < 37 weeks (5.93% vs 6.23%, aOR 0.93, 95%CI 0.87 to 0.99, P=0.03), largely mediated by a reduction in iatrogenic PTB for live births (3.01% vs 3.27%, aOR 0.89, 95%CI 0.81 to 0.98, P = 0.015), including iatrogenic PTB for suspected fetal compromise (1.25% vs 1.51%, aOR 0.79, 95%CI 0.69 to 0.91, P= 0.001). There was no significant difference in the spontaneous PTB rate between the exposed and control groups (2.69% vs 2.82%, aOR 0.94, 95%CI 0.86 to 0.1.03, P=0.25).\n\nConclusionsLockdown restrictions in a high-income setting, in the absence of high rates of COVID-19 disease, were associated with a significant increase in preterm stillbirths, and a significant reduction in iatrogenic PTB for suspected fetal compromise.\n\nTrial registrationThis study was registered as an observational study with the Australian and New Zealand Clinical Trials Registry (ACTRN12620000878976).", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Lisa Hui", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Melvin B Marzan", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Stephanie Potenza", + "author_inst": "Mercy Hospital for Women" + }, + { + "author_name": "Daniel Lorber Rolnik", + "author_inst": "Monash University" + }, + { + "author_name": "Natasha Pritchard", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Joanne M Said", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Kirsten R Palmer", + "author_inst": "Monash University" + }, + { + "author_name": "Clare L Whitehead", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Penelope M Sheehan", + "author_inst": "Eastern Health" + }, + { + "author_name": "Jolyon Ford", + "author_inst": "Peninsula Health" + }, + { + "author_name": "Ben W Mol", + "author_inst": "Monash University" + }, + { + "author_name": "Susan P Walker", + "author_inst": "University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.10.01.21264393", "rel_title": "Adverse events following COVID-19 vaccination in young Japanese people: A case-control study of the risk of systemic adverse events by a questionnaire surveyShort title: COVID-19 vaccine adverse events in young Japanese", @@ -568837,25 +570082,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.10.03.21264494", - "rel_title": "Why a Globally Fair COVID-19 Vaccination? An Analysis based on Agent-Based Simulation", - "rel_date": "2021-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.03.21264494", - "rel_abs": "In this paper, an Agent-Based Model (ABM) is proposed to evaluate the impact of COVID-19 vaccination drive in different settings. The main focus is to evaluate the counter-effectiveness of disparity in vaccination drive among different regions / countries. The model proposed is simple yet novel in the sense that it captures the spatial transmission-induced activity into consideration, through which we are able to relate transmission model to the mutated variations of the virus. Some important what-if questions are asked in terms of number of deaths, and time required and percentage of population needed to be vaccinated before the pandemic is eradicate. The simulation results have revealed that it is necessary to maintain a global (rather than regional or country oriented) vaccination drive in case of a new pandemic or continual efforts against COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Kashif Zia", - "author_inst": "Sohar University, Oman" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.02.21264454", "rel_title": "COVID-19 Vaccine: Newspaper Coverage of the side effects of the vaccine in Nigeria", @@ -569091,6 +570317,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.03.21264476", + "rel_title": "Determination of utility of 3 minute and 6 minute walk tests in assessment of progression of mild COVID-19 infection at a tertiary hospital in North India", + "rel_date": "2021-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.03.21264476", + "rel_abs": "IntroductionThere have been 214 million confirmed cases of COVID-19 worldwide with a total death tally of 4.4 million. The current study aims to determine the predictive value of 3 minute and 6-minute walk tests in assessment of progression of mild COVID-19 infection at a tertiary care hospital in North India.\n\nMethodsThe study population consisted of adults (age more than 18 years) with a confirmed diagnosis of Covid-19 by RT-PCR on nasopharyngeal specimens. Patients with only mild illness were enrolled. After the patients were admitted to the isolation ward, the presenting history, comorbidity status, vital signs and laboratory parameters were recorded. The 3 and 6 minute walk test was performed daily from admission till discharge or progression of severity of COVID-19 and it was used to calculate BDS and NEWS2 scores.\n\nResultsOur study consisted of 50 patients with 34 (68%) males and the mean (SD) age of the patient population being 28.1 (6.4) years. The most common symptoms were fever, sore throat, and cough. All laboratory parameters were within normal ranges for all the patients. 96% recovered without progression, while only 4% of them progressed to moderate illness. Results of the 3 and 6 minutes walk tests, BDS and NEWS2 scores showed improvement over the course of hospital stay.\n\nConclusionsAlthough the walk tests and the scores improved over time, they failed to predict the disease progression.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Aastha Goel", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Souradeep Chowdhury", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Tamoghna Ghosh", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Anupam Singh", + "author_inst": "Santosh Medical College" + }, + { + "author_name": "Arvind Kumar", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Naveet Wig", + "author_inst": "All India Institute Of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.03.21264320", "rel_title": "Humoral immune responses to COVID-19 vaccination in people living with HIV on suppressive antiretroviral therapy", @@ -570651,109 +571916,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.01.21264408", - "rel_title": "Reduced amplification efficiency of the RNA-dependent-RNA-polymerase (RdRp) target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests", - "rel_date": "2021-10-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264408", - "rel_abs": "Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced PCR amplification efficiency of the RdRp gene target of the Seegene, Allplex 2019-nCoV diagnostic assay when detecting the Delta variant. We propose that this can be used as a surrogate for variant detection.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Ziyaad Valley-Omar", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Kruger Marais", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Arash Iranzadeh", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Michelle Naidoo", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Stephen Korsman", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Tongai Maponga", - "author_inst": "Division of Medical Virology, Stellenbosch University, Western Cape, South Africa" - }, - { - "author_name": "Hannah Hussey", - "author_inst": "Centre Health Intelligence, Western Cape Government: Health, South Africa" - }, - { - "author_name": "Mary-Ann Davies", - "author_inst": "Centre for Infectious Disease Epidemiology and Research, School of Public health, University of Cape Town, Western Cape South Africa" - }, - { - "author_name": "Andrew Boulle", - "author_inst": "Centre for Infectious Disease Epidemiology and Research, School of Public health, University of Cape Town, Western Cape South Africa" - }, - { - "author_name": "Deelan Doolabh", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Mariska Laubscher", - "author_inst": "Lancet laboratories, South Africa" - }, - { - "author_name": "JD Deetlefs", - "author_inst": "Ampath Laboratories, South Africa" - }, - { - "author_name": "Jean Maritz", - "author_inst": "PathCare Laboratories, South Africa" - }, - { - "author_name": "Lesley Scott", - "author_inst": "Research diagnostic Laboratories, School of Pathology, University of the Witwatersrand, South Africa" - }, - { - "author_name": "Nokukhanya Msomi", - "author_inst": "Discipline of Virology, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Jinal Bhiman", - "author_inst": "National institute for Communicable Diseases, Johannesburg, South Africa" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Wolfgang Preiser", - "author_inst": "Division of Medical Virology, Stellenbosch University, Western Cape, South Africa" - }, - { - "author_name": "Diana Ruth Hardie", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - }, - { - "author_name": "Nei-yuan Hsiao", - "author_inst": "Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.29.21264199", "rel_title": "Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants", @@ -571029,6 +572191,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.29.21264295", + "rel_title": "Neonatal outcomes of preterm infants born during COVID-19 community lockdowns in Melbourne, Australia", + "rel_date": "2021-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264295", + "rel_abs": "BackgroundCommunity lockdowns during the COVID-19 pandemic may influence preterm birth rates, but mechanisms are unclear.\n\nMethodsWe compared neonatal outcomes of preterm infants born to mothers exposed to community lockdowns in 2020 (exposed group) to those born in 2019 (control group). Main outcome studied was composite of significant neonatal morbidity or death.\n\nResultsMedian gestational age was 35+4 weeks (295 infants, exposed group) vs. 35+0 weeks (347 infants, control group) (p = 0.108). The main outcome occurred in 36/295 (12.2%) infants in exposed group vs. 46/347 (13.3%) in control group (p = 0.69). Continuous positive airway pressure (CPAP) use, jaundice requiring phototherapy, hypoglycaemia requiring treatment, early neonatal white cell and neutrophil counts were significantly reduced in the exposed group.\n\nConclusionsCOVID-19 community lockdowns did not alter composite neonatal outcomes in preterm infants, but reduced rates of some common outcomes, and early white cell and neutrophil counts.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Brendan Mulcahy", + "author_inst": "Monash Health" + }, + { + "author_name": "Daniel Rolnik", + "author_inst": "Monash University" + }, + { + "author_name": "Alexia Matheson", + "author_inst": "Monash Health" + }, + { + "author_name": "Yizhen Liu", + "author_inst": "Monash Health" + }, + { + "author_name": "Kirsten Palmer", + "author_inst": "Monash University" + }, + { + "author_name": "Ben W. Mol", + "author_inst": "Monash University" + }, + { + "author_name": "Atul Malhotra", + "author_inst": "Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.10.01.21264409", "rel_title": "Mental Health and Time Management Behavior among Students During COVID-19 Pandemic: Towards Persuasive Technology Design", @@ -572449,45 +573654,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.29.21264305", - "rel_title": "Determinants of sleep quality in adults during the COVID-19 pandemic: COVID-Inconfidentes, a population-based study", - "rel_date": "2021-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264305", - "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has had a negative effect on the health and behavior of the worlds population.\n\nObjectivesTo evaluate sleep quality and its associated factors in adults during the COVID-19 pandemic in Brazil.\n\nMethodsThis is a population-based serological survey of 1762 adults collected from October to December 2020 in the Iron Quadrangle region, Brazil. To measure sleep quality, we used the Pittsburgh Sleep Quality Index questionnaire and socio-demographic, health, health related behaviors, anxiety, vitamin D, weight gain/loss, and pandemic characteristics were assessed using a structured questionnaire. Univariate and multivariate analyses were performed to identify the factors associated with sleep quality.\n\nResultsMore than half of the individuals evaluated had poor sleep quality (52.5%). In multivariate analysis, factors related to sleep quality included living alone (OR=2.36; 95%CI: 1.11-5.00), anxiety disorder (OR=2.22; 95%CI: 1.20-4.14), 5.0% weight loss during the pandemic (OR=1.66; 95%CI: 1.01-2.76), weight gain of 5.0% (OR=1.90; 95%CI: 1.08-3.34), insufficient vitamin D scenario (OR=1.47; 95%CI: 1.01-2.12), and symptoms of COVID-19 (OR=1.94; 95%CI: 1.25-3.01).\n\nConclusionsOur study revealed that more than half of the participants had poor sleep quality during the COVID-19 outbreak, and the factors associated with poor sleep quality were related to the pandemic, such as insufficient vitamin D scenario and weight change.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Luiz Antonio Alves Menezes-Junior", - "author_inst": "Federal University of Ouro Preto" - }, - { - "author_name": "Luciano Garcia Lourencao", - "author_inst": "Federal University of Rio Grande" - }, - { - "author_name": "Amanda Cristina de Souza Andrade", - "author_inst": "Federal University of Mato Grosso" - }, - { - "author_name": "Julia Cristina Cardoso Carraro", - "author_inst": "Federal University of Ouro Preto" - }, - { - "author_name": "George Luiz Lins Machado-Coelho", - "author_inst": "Federal University of Ouro Preto" - }, - { - "author_name": "Adriana Lucia Meireles", - "author_inst": "Federal Univeristy of Ouro Preto" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.30.462449", "rel_title": "Pyronaridine Protects Against SARS-CoV-2 in Mouse", @@ -572927,6 +574093,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.26.21263756", + "rel_title": "Methods for Estimation of SARS-CoV-2 Seroprevalence and Reported COVID-19 Cases in U.S. Children, August 2020 - May 2021", + "rel_date": "2021-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21263756", + "rel_abs": "Background and ObjectivesCase-based surveillance of pediatric COVID-19 cases underestimates the prevalence of SARS-CoV-2 infections among children and adolescents. Our objectives were to: 1) estimate monthly SARS-CoV-2 antibody seroprevalence among children aged 0-17 years and 2) calculate ratios of SARS-CoV-2 infections to reported COVID-19 cases among children and adolescents in 14 U.S. states.\n\nMethodsUsing data from commercial laboratory seroprevalence surveys, we estimated monthly SARS-CoV-2 antibody seroprevalence among children aged 0-17 years from August 2020 through May 2021. Seroprevalence estimates were based on SARS-CoV-2 anti-nucleocapsid immunoassays from February to May 2021. We compared estimated numbers of children infected with SARS-CoV-2 by May 2021 to cumulative incidence of confirmed and probable COVID-19 cases from case-based surveillance, and calculated infection: case ratios by state and type of anti-SARS-CoV-2 nucleocapsid immunoassay used for seroprevalence testing.\n\nResultsAnalyses included 67,321 serum specimens tested for SARS-CoV-2 antibodies among children in 14 U.S. states. Estimated ratios of SARS-CoV-2 infections to reported confirmed and probable COVID-19 cases among children and adolescents varied by state and type of immunoassay, ranging from 0.8-13.3 in May 2021.\n\nConclusionsThrough May 2021, the majority of children in selected states did not have detectable SARS-CoV-2 nucleocapsid antibodies. Case-based surveillance underestimated the number of children infected with SARS-CoV-2, however the predicted extent of the underestimate varied by state, immunoassay, and over time. Continued monitoring of pediatric SARS-CoV-2 antibody seroprevalence should inform prevention and vaccination strategies.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Alexia Couture", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "B. Casey Lyons", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Megha L Mehrotra", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Lynn Sosa", + "author_inst": "Connecticut Department of Public Health" + }, + { + "author_name": "Ngozi Ezike", + "author_inst": "Illinois Department of Public Health" + }, + { + "author_name": "Farah Ahmed", + "author_inst": "Kansas Department of Health and Environment" + }, + { + "author_name": "Catherine M Brown", + "author_inst": "Massachusetts Departmet of Public Health" + }, + { + "author_name": "Stephanie Yendell", + "author_inst": "Minnesota Department of Health" + }, + { + "author_name": "Anna Cope", + "author_inst": "North Carolina Department of Health and Human Services" + }, + { + "author_name": "Bozena J Katic", + "author_inst": "New Jersey Department of Health" + }, + { + "author_name": "Ihsan A Azzam", + "author_inst": "Nevada Division of Public and Behavioral Health" + }, + { + "author_name": "Kristen Dickerson", + "author_inst": "Ohio Department of Health" + }, + { + "author_name": "Jolianne Stone", + "author_inst": "Oklahoma State Department of Health" + }, + { + "author_name": "L. Brannon Traxler", + "author_inst": "South Carolina Department of Health and Environmental Control" + }, + { + "author_name": "John Dunn", + "author_inst": "Tennessee Department of Health" + }, + { + "author_name": "Lora B Davis", + "author_inst": "Washington State Department of Health" + }, + { + "author_name": "Carrie Reed", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Kristie EN Clarke", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Brendan Flannery", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Myrna D Charles", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.09.27.21264070", "rel_title": "Secondary infections modify the overall course of hospitalized COVID-19 patients: A retrospective study from a network of hospitals across North India", @@ -574439,257 +575700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.09.28.21264207", - "rel_title": "Durability of ChAdOx1 nCov-19 (AZD1222) vaccination in people living with HIV - responses to SARS-CoV-2, variants of concern and circulating coronaviruses", - "rel_date": "2021-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264207", - "rel_abs": "Duration of protection from SARS-CoV-2 infection in people with HIV (PWH) following vaccination is unclear. In a sub-study of the phase 2/3 the COV002 trial (NCT04400838), 54 HIV positive male participants on antiretroviral therapy (undetectable viral loads, CD4+ T cells >350 cells/ul) received two doses of ChAdOx1 nCoV-19 (AZD1222) 4-6 weeks apart and were followed for 6 months. Responses to vaccination were determined by serology (IgG ELISA and MesoScale Discovery (MSD)), neutralisation, ACE-2 inhibition, gamma interferon ELISpot, activation-induced marker (AIM) assay and T cell proliferation. We show that 6 months after vaccination the majority of measurable immune responses were greater than pre-vaccination baseline, but with evidence of a decline in both humoral and cell mediated immunity. There was, however, no significant difference compared to a cohort of HIV-uninfected individuals vaccinated with the same regimen. Responses to the variants of concern were detectable, although were lower than wild type. Pre-existing cross-reactive T cell responses to SARS-CoV-2 spike were associated with greater post-vaccine immunity and correlated with prior exposure to beta coronaviruses. These data support the on-going policy to vaccinate PWH against SARS-CoV-2, and underpin the need for long-term monitoring of responses after vaccination.", - "rel_num_authors": 59, - "rel_authors": [ - { - "author_name": "Ane Ogbe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Matthew Pace", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mustapha Bittaye", - "author_inst": "University of Oxford" - }, - { - "author_name": "Timothy Tipoe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sandra Adele", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jasmini Alagaratnam", - "author_inst": "Imperial College" - }, - { - "author_name": "Parvinder K. Aley", - "author_inst": "University of Oxford" - }, - { - "author_name": "M. Azim Ansari", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anna Bara", - "author_inst": "Imperial College Healthcare NHS trust" - }, - { - "author_name": "Samantha Broadhead", - "author_inst": "NIHR Guys and St Thomas Biomedical Research Centre" - }, - { - "author_name": "Anthony Brown", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen Brown", - "author_inst": "University of Oxford" - }, - { - "author_name": "Wanwisa Dejnirattisai", - "author_inst": "University of Oxford" - }, - { - "author_name": "Federica Cappuccini", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paola Cinardo", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Katie J. Ewer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Henry Fok", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Pedro M. Folegatti", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jamie Fowler", - "author_inst": "University of Oxford" - }, - { - "author_name": "Leila Godfrey", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anna L. Goodman", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Bethany Jackson", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Daniel Jenkin", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mathew Jones", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephanie Longet", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rebecca Makinson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Natalie G. Marchevsky", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mathew Moncy", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Andrea Mazzella", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Yama F. Mujadidi", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lucia Parolini", - "author_inst": "University of Oxford" - }, - { - "author_name": "Claire Petersen", - "author_inst": "Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK" - }, - { - "author_name": "Emma Plested", - "author_inst": "University of Oxford" - }, - { - "author_name": "Katrina M Pollock", - "author_inst": "NIHR Imperial Clinical Research Facility and NIHR Imperial Biomedical Research Centre, London, UK" - }, - { - "author_name": "Thurkka Rajeswaran", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Maheshi N. Ramasamy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Rhead", - "author_inst": "University of Oxford" - }, - { - "author_name": "Hannah Robinson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicola Robinson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sonia Serrano", - "author_inst": "NIHR Guys and St Thomas Biomedical Research Centre" - }, - { - "author_name": "Helen Stockmann", - "author_inst": "Department of HIV Medicine, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK" - }, - { - "author_name": "Tom Tipton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anele Waters", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Helen Sanders", - "author_inst": "University of Oxford" - }, - { - "author_name": "Panagiota Zacharopoulou", - "author_inst": "University of Oxford" - }, - { - "author_name": "Eleanor Barnes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susanna Dunachie", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philip Goulder", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul Klenerman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gavin R. Screaton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alan Winston", - "author_inst": "Imperial College London" - }, - { - "author_name": "Adrian V. S. Hill", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah C. Gilbert", - "author_inst": "University of Oxford" - }, - { - "author_name": "Miles Carroll", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrew J. Pollard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Fidler", - "author_inst": "Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK" - }, - { - "author_name": "Julie Fox", - "author_inst": "Department of Infection, Harrison Wing and NIHR Clinical Research Facility, Guys and St Thomas NHS Trust, London, UK" - }, - { - "author_name": "Teresa Lambe", - "author_inst": "University of Oxford" - }, - { - "author_name": "John Frater", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2021.09.28.21264250", "rel_title": "Reduced antibody activity against SARS-CoV-2 B.1.617.2 Delta virus in serum of mRNA-vaccinated patients receiving TNF-alpha inhibitors", @@ -575165,6 +576175,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.28.21264266", + "rel_title": "Excess Deaths associated with the COVID-19 Pandemic in Ukraine in 2020", + "rel_date": "2021-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264266", + "rel_abs": "COVID-19 related mortality has been understudied in Ukraine. As part of a World Bank project, we estimated excess mortality in Ukraine during 2020. Data on all deaths registered in government-controlled Ukraine from 2016-2020 (N=2,946,505) were utilized. We predicted deaths in 2020 by five-year age groups, sex, and month and calculated the number of deaths that deviated from expected levels (excess deaths). We compared excess deaths with the number of recorded COVID-19 deaths on death certificates and with published estimates for 30 European countries. We estimated 38,095 excess deaths in 2020 (6% of all deaths). Death rates were above expected levels in February and from June-December and lower in January and March-May. From June-December, we estimated 52,124 excess deaths with a peak in November (16,891 deaths). COVID-19 recorded deaths were approximately one-third of excess deaths in June-December (18,959 vs. 52,124). Higher than expected mortality was detected for all age groups 40-44 years and above and for those ages 0-4, 15-19, and 20-24. Ukraines excess mortality was about average compared to 30 other European countries. Excess deaths may be attributed directly to SARS-COV2 infection or indirectly to death causes associated with social and economic upheavals resulting in from the pandemic. Lower than expected mortality during the early part of 2020 is consistent with low influenza activity and reductions in deaths from restricted movement. Further studies are required to examine the causes of death that have contributed to positive excess mortality, particularly among younger aged groups.\n\nKey MessagesO_LIUkraine has experienced sizeable changes in its recent demography and the impact of the COVID-19 pandemic on the countrys aggregate mortality patterns is understudied\nC_LIO_LIBased on recent death trends, we found that Ukraine experienced lower than expected mortality during the early part of 2020 and consistently higher than expected mortality from June-December with peak levels occurring in November\nC_LIO_LIPositive excess mortality was observed for all age groups beginning at ages 40-44 as well as some younger age groups.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Neil Mehta", + "author_inst": "The University of Texas Medical Branch" + }, + { + "author_name": "Ihor Honchar", + "author_inst": "Taras Shevchenko National University of Kyiv" + }, + { + "author_name": "Olena Doroshenko", + "author_inst": "World Bank Group" + }, + { + "author_name": "Igor Brovenchko", + "author_inst": "National Academy of Science of Ukraine" + }, + { + "author_name": "Khrystyna Pak", + "author_inst": "World Bank Group" + }, + { + "author_name": "Maria Danyuk", + "author_inst": "Modern Marketing Communications LTD" + }, + { + "author_name": "Pavlov Polikarchuk", + "author_inst": "Modern Marketing Communications LTD" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.28.21264244", "rel_title": "Contribution of Schools to Covid-19 Pandemic: Evidence from Czechia", @@ -576609,33 +577662,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.26.21264153", - "rel_title": "COVID-19 Vaccination Strategies Considering Hesitancy Using Particle-Based Epidemic Simulation", - "rel_date": "2021-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21264153", - "rel_abs": "Vaccine hesitancy is one of the critical factors in achieving herd immunity and suppressing the COVID-19 epidemic. Many countries face this as an acute public health issue that diminishes the efficacy of their vaccination campaigns. Epidemic modeling and simulation can be used to predict the effects of different vaccination strategies. In this work, we present an open-source particle-based COVID-19 simulator with a vaccination module capable of taking into account the vaccine hesitancy of the population. To demonstrate the efficacy of the simulator, we conducted extensive simulations for the province of Lecco, Italy. The results indicate that the combination of both high vaccination rate and low hesitancy leads to faster epidemic suppression.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Aknur Karabay", - "author_inst": "Institute of Smart Systems and Artificial Intelligence" - }, - { - "author_name": "Askat Kuzdeuov", - "author_inst": "Institute of Smart Systems and Artificial Intelligence" - }, - { - "author_name": "Huseyin Atakan Varol", - "author_inst": "Institute of Smart Systems and Artificial Intelligence" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.25.21264106", "rel_title": "Functional Data Analysis: Transition from Daily Observation of COVID-19 Prevalence in France to Functional Curves", @@ -576879,6 +577905,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.26.21264150", + "rel_title": "Changes in dispensing of medicines proposed for re-purposing in the first year of the COVID-19 pandemic in Australia", + "rel_date": "2021-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21264150", + "rel_abs": "ObjectiveWe quantified changes in dispensing of common medicines proposed for \"re-purposing\" due to their perceived benefits as therapeutic or preventive for COVID-19 in Australia, a country with relatively low COVID-19 incidence in the first year of the pandemic.\n\nMethodsWe performed an interrupted time series analysis and cross-sectional study using nationwide dispensing claims data (January 2017-November 2020). We focused on six subsidised medicines proposed for re-purposing: hydroxychloroquine, azithromycin, ivermectin, colchicine, corticosteroids, and calcitriol (Vitamin D analogue). We quantified changes in monthly dispensing and initiation trends during COVID-19 (March-November 2020) using autoregressive integrated moving average models (ARIMA) and compared characteristics of initiators in 2020 and 2019.\n\nResultsIn March 2020, we observed a 99% (95%CI 96%-103%) increase in hydroxychloroquine dispensing (of which approximately 22% attributable to new use), and a 199% increase (95%CI 184%-213%) in initiation, with a shift towards prescribing by general practitioners (42% in 2020 vs 25% in 2019) rather than specialists. These increases subsided following regulatory restrictions on prescribing to relevant specialties. There was a small but sustained increase in ivermectin dispensing over multiple months, with a 80% (95%CI 42%-118%) increase in initiation in May 2020 following its first identification as potentially disease-modifying in April. Other than increases in March related to stockpiling, we observed no increases in initiation of calcitriol or colchicine during COVID-19. Dispensing of corticosteroids and azithromycin remained lower than expected in April through November 2020.\n\nConclusionsWhile most increases in dispensing observed early on during COVID-19 were temporary and appear to be related to stockpiling among existing users, we did observed increases in initiation of hydroxychloroquine and ivermectin and a shift in prescribing patterns which may be related to media hype around these medicines. A quick response by regulators can help limit inappropriate repurposing to lessen the impact on medicine supply and patient harms.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andrea L Schaffer", + "author_inst": "University of New South Wales" + }, + { + "author_name": "David Henry", + "author_inst": "Bond University" + }, + { + "author_name": "Helga Zoega", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Julian Elliott", + "author_inst": "Monash University" + }, + { + "author_name": "Sallie-Anne Pearson", + "author_inst": "University of New South Wales" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.27.462006", "rel_title": "The BNT162b2 mRNA vaccine induces polyfunctional T cell responses with features of longevity.", @@ -578287,109 +579348,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.09.24.21263766", - "rel_title": "The Report on China-Spain Joint Clinical Testing for Rapid COVID-19 Risk Screening by Eye-region Manifestations", - "rel_date": "2021-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.24.21263766", - "rel_abs": "BackgroundThe worldwide surge in coronavirus cases has led to the COVID-19 testing demand surge. Rapid, accurate, and cost-effective COVID-19 screening tests working at a population level are in imperative demand globally.\n\nMethodsBased on the eye symptoms of COVID-19, we developed and tested a COVID-19 rapid prescreening model using the eye-region images captured in China and Spain with cellphone cameras. The convolutional neural networks (CNNs)-based model was trained on these eye images to complete binary classification task of identifying the COVID-19 cases. The performance was measured using area under receiver-operating-characteristic curve (AUC), sensitivity, specificity, accuracy, and F1. The application programming interface was open access.\n\nFindingsThe multicenter study included 2436 pictures corresponding to 657 subjects (155 COVID-19 infection, 23{middle dot}6%) in development dataset (train and validation) and 2138 pictures corresponding to 478 subjects (64 COVID-19 infections, 13{middle dot}4%) in test dataset. The image-level performance of COVID-19 prescreening model in the China-Spain multicenter study achieved an AUC of 0{middle dot}913 (95% CI, 0{middle dot}898-0{middle dot}927), with a sensitivity of 0{middle dot}695 (95% CI, 0{middle dot}643-0{middle dot}748), a specificity of 0{middle dot}904 (95% CI, 0{middle dot}891-0{middle dot}919), an accuracy of 0{middle dot}875(0{middle dot}861-0{middle dot}889), and a F1 of 0{middle dot}611(0{middle dot}568-0{middle dot}655).\n\nInterpretationThe CNN-based model for COVID-19 rapid prescreening has reliable specificity and sensitivity. This system provides a low-cost, fully self-performed, non-invasive, real-time feedback solution for continuous surveillance and large-scale rapid prescreening for COVID-19.\n\nFundingThis project is supported by Aimomics (Shanghai) Intelligent", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Yanwei Fu", - "author_inst": "School of Data Science, Fudan University," - }, - { - "author_name": "Feng Li", - "author_inst": "Shanghai Public Health Clinical Center" - }, - { - "author_name": "Paula boned Fustel", - "author_inst": "University and Polytechnic Hospital La Fe" - }, - { - "author_name": "Lei Zhao", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Lijie Jia", - "author_inst": "Department of Anesthesia, the International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Haojie Zheng", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Qiang Sun", - "author_inst": "Academy for Engineering & Technology, Fudan University" - }, - { - "author_name": "Shisong Rong", - "author_inst": "Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear" - }, - { - "author_name": "Haicheng Tang", - "author_inst": "Shanghai Public Health Clinical Center" - }, - { - "author_name": "Xiangyang Xue", - "author_inst": "Academy for Engineering & Technology, Fudan University" - }, - { - "author_name": "Li Yang", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Hong Li", - "author_inst": "Medical Examination Center,Hubei Provincial Hospital of Traditional Chinese Medicine" - }, - { - "author_name": "Jiao Xie", - "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Wenxuan Wang", - "author_inst": "School of Computer Science, Fudan University" - }, - { - "author_name": "Yuan Li", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Wei Wang", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Yantao Pei", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "JIamin Wang", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Xiuqi Wu", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Yanhua Zheng", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Hongxia Tian", - "author_inst": "The Fifth Hospital of Shijiazhuang" - }, - { - "author_name": "Mengwei Gu", - "author_inst": "Aimomics (Shanghai) Intelligent Technology Co., Ltd." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "ophthalmology" - }, { "rel_doi": "10.1101/2021.09.23.21264036", "rel_title": "Diagnostic Yield of Screening for SARS-CoV-2 among Patients Admitted for Alternate Diagnoses", @@ -578945,6 +579903,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.24.21264045", + "rel_title": "Non-invasive Vagus Nerve Stimulation for Respiratory Symptoms of COVID-19: Results From a Randomized Controlled Trial (SAVIOR I)", + "rel_date": "2021-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.24.21264045", + "rel_abs": "BackgroundSevere coronavirus disease 2019 (COVID-19) is characterized, in part, by an excessive inflammatory response. Evidence from animal and human studies suggests that vagus nerve stimulation can lead to reduced levels of various pro-inflammatory cytokines. We conducted a prospective randomized controlled study (SAVIOR-I) to assess the feasibility, efficacy, and safety of non-invasive vagus nerve stimulation (nVNS) for the treatment of respiratory symptoms and inflammatory markers among patients who were hospitalized for COVID-19 (ClinicalTrials.gov identifier: NCT04368156).\n\nMethodsParticipants were randomly assigned in a 1:1 allocation to receive either the standard of care (SoC) alone or nVNS therapy plus the SoC. The nVNS group received 2 consecutive 2-minute doses of nVNS 3 times daily as prophylaxis. Efficacy and safety were evaluated via the incidence of specific clinical events, inflammatory biomarker levels, and the occurrence of adverse events.\n\nResultsOf the 110 participants who were enrolled and randomly assigned, 97 (nVNS, n=47; SoC, n=50) had sufficient available data and comprised the evaluable population. C-reactive protein (CRP) levels decreased from baseline to a significantly greater degree in the nVNS group than in the SoC group at day 5 and overall (ie, all postbaseline data points collected through day 5, combined). Procalcitonin level also showed significantly greater decreases from baseline to day 5 in the nVNS group than in the SoC group. D-dimer levels were decreased from baseline for the nVNS group and increased from baseline for the SoC group at day 5 and overall, although the difference between the treatment groups did not reach statistical significance. No significant treatment differences were seen for clinical respiratory outcomes or any of the other biochemical markers evaluated. No serious nVNS-related adverse events occurred during the study.\n\nConclusionsnVNS therapy led to significant reductions in levels of inflammatory markers, specifically CRP and procalcitonin. Because nVNS has multiple mechanisms of action that may be relevant to COVID-19, additional research into its potential to be used earlier in the course of COVID-19 and possibly mitigate some of the symptoms associated with post-acute COVID-19 syndrome is warranted.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Carlos Tornero", + "author_inst": "Hospital Clinico Universitario de Valencia, Anesthesia, Critical Care and Pain Management Unit; Catedra Dolor, UFV-Fundacion Vithas" + }, + { + "author_name": "Ernesto Pastor", + "author_inst": "Hospital Clinico Universitario de Valencia, Anesthesia, Critical Care and Pain Management Unit" + }, + { + "author_name": "Maria del Mar Garzando", + "author_inst": "Hospital Clinico Universitario de Valencia, Anesthesia, Critical Care and Pain Management Unit" + }, + { + "author_name": "Jorge Orduna", + "author_inst": "Hospital Clinico Universitario de Valencia, Anesthesia, Critical Care and Pain Management Unit" + }, + { + "author_name": "Maria Jose Forner", + "author_inst": "Hospital Clinico Universitario de Valencia, Internal Medicine Department" + }, + { + "author_name": "Irene Bocigas", + "author_inst": "Hospital Clinico Universitario de Valencia, Pulmonary Department" + }, + { + "author_name": "David Cedeno", + "author_inst": "Department of Basic Science, Millennium Pain Center; Department of Psychology, Illinois Wesleyan University" + }, + { + "author_name": "Ricardo Vallejo", + "author_inst": "Department of Basic Science, Millennium Pain Center; Department of Psychology, Illinois Wesleyan University" + }, + { + "author_name": "Peter Staats", + "author_inst": "electroCore, Inc." + }, + { + "author_name": "Eric Liebler", + "author_inst": "electroCore, Inc" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.09.26.21264023", "rel_title": "CD19 B cell repopulation after ocrelizumab, alemtuzumab and cladribine: Implications for SARS-CoV-2 vaccinations in multiple sclerosis", @@ -580325,57 +581338,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.14.21263403", - "rel_title": "Evaluation Of A New All In One Sars-Cov-2 Antigen-Detecting Rapid Diagnostic Test And Self-Test: Diagnostic Performance And Usability On Child And Adult Population", - "rel_date": "2021-09-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263403", - "rel_abs": "The control of the COVID-19 epidemics has been one of top global health priorities for the last eighteen months. To that end, more reliable and easy-to-use diagnostic tests are necessary. Young children are still not eligible to vaccination and it is important to find a way to easily test this key population regularly. With that in mind, we evaluated a new innovative easy two-step self-test named COVID-VIRO ALL IN(R) developed by AAZ that uses a sampling nasal sponge instead of a classic nasal swab. Mirroring the previous study conducted on the first generation of COVID-VIRO(R) antigenic self-test, we first performed a multicentre, prospective study on 124 adults and children, in a point-of-care setting. Sensitivity, specificity and overall acceptance of the COVID-VIRO ALL IN(R) antigen self-test compared to RT-PCR on nasopharyngeal samples were evaluated at 93.02%, 100% and 97,5%, respectively. We then performed a multicentre, prospective, usability study to evaluate the ease of use of COVID-VIRO ALL IN(R) in real life on 68 laypersons, all adults. Globally, 99% of them considered the instructions material good, 98% executed the procedure well, and all of them interpreted the results correctly. The usability was then specifically investigated on 40 children and teenagers participants, comparing both COVID-VIRO(R) first generation and the new COVID-VIRO ALL IN(R). All of them found COVID-VIRO ALL IN(R) much easier to use and much more comfortable. For young children, the COVID-VIRO ALL IN(R) self-test appears to be safer (less risk of trauma compare to nasal swabs and no liquid exposure) easier to use than classic COVID self-tests and giving immediate result which is not the case for RT-PCR done on saliva samples (currently done in routine for kids in French schools). It could be an adapted tool for future mass screening campaigns in schools or at home under adult supervision for kids from the age of 3.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "thierry prazuck", - "author_inst": "CHR Orleans" - }, - { - "author_name": "Anne Gravier", - "author_inst": "Centre gratuit d information de depistage et de diagnostic Orleans" - }, - { - "author_name": "Daniela Pires-Roteira", - "author_inst": "Centre hospitalier d Orleans, service des maladies infectieuses et tropicales" - }, - { - "author_name": "Aurelie Theillay", - "author_inst": "Centre hospitalier regional d Orleans service des maladies infectieuses et tropicales" - }, - { - "author_name": "Sandra Pallay", - "author_inst": "Centre hospitalier regional d Orleans service des maladies infectieuses et tropicales" - }, - { - "author_name": "Mathilda Colin", - "author_inst": "Centre hospitalier regional d Orleans service des maladies infectieuses et tropicales" - }, - { - "author_name": "Raphael Serreau", - "author_inst": "Service de medecine preventive Orleans metropole" - }, - { - "author_name": "Laurent Hocqueloux", - "author_inst": "Centre hospitalier regional d Orleans service des maladies infectieuses et tropicales" - }, - { - "author_name": "Nino Guy Cassuto", - "author_inst": "Laboratoires Drouot" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.26.461851", "rel_title": "Cytotoxic T-cell-based vaccine against SARS-CoV2: a hybrid immunoinformatic approach", @@ -580539,6 +581501,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.22.21263976", + "rel_title": "Covid-19 Per Capita Fatality Rate: A Path Analysis Model", + "rel_date": "2021-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.22.21263976", + "rel_abs": "ObjectivesVarious individual factors have been shown to influence Covid-19 mortalities, but these factors do not exist in isolation. Unique to this study is a multivariate approach that has yet to be fully explored by previous research. Using an interconnected multifactor model, this work investigated social determinant, geographic, prior health, and political behavioral factors likely to influence Covid-19 per capita fatalities in Texas.\n\nMethodsCounty-level income, rurality, insurance, health status, 2020 presidential vote percentage, and fatality rate data were collected and analyzed in a path analysis model with Covid-19 per capita fatalities as the key variable of interest.\n\nResultsThe analysis found strong support for the proposed model structure (R2 = 37.6%). The strongest overall effects on the Covid-19 per capita fatality rate came from income levels and voting behaviors.\n\nConclusionThe model explained a substantial amount of variability in mortalities attributed to Covid-19. Socioeconomic and political factors provided the strongest contribution to the per-capita Covid-19 death rate, controlling for the other variables studied. The Covid-19 pandemic was highly politicized by various leaders and media outlets. The current analysis showed that political trends were one of the key overall factors related to Covid-19 mortality. The strongest overall factor was median income. Income is used to enhance ones current health or acquire adequate treatment which may safeguard people from the most severe effects of Covid-19. Counties with lower income levels had higher rates of Covid-19 per capita fatalities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Michael S Penuliar", + "author_inst": "Texas Tech University - Health Sciences Center" + }, + { + "author_name": "Candice Clark", + "author_inst": "Texas Tech University Health Sciences Center" + }, + { + "author_name": "Debra Curti", + "author_inst": "Texas Tech University Health Sciences Center" + }, + { + "author_name": "Miguel Carrasco", + "author_inst": "Texas Tech University Health Sciences Center" + }, + { + "author_name": "Catherine Hudson", + "author_inst": "Texas Tech University Health Sciences Center" + }, + { + "author_name": "Billy Philips", + "author_inst": "Texas Tech University Health Sciences Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.22.21263711", "rel_title": "Comparison of adverse events between COVID-19 and Flu vaccines", @@ -582223,93 +583224,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.19.21263807", - "rel_title": "RNA-extraction-free diagnostic method to detect SARS-CoV-2: an assessment from two States, India", - "rel_date": "2021-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.19.21263807", - "rel_abs": "With increasing demand for large numbers of testing during COVID-19 pandemic, came alternative protocols with shortened turn-around time. We evaluated the performance of such an approach wherein 1138 consecutive clinic attendees were enrolled; 584 and 554 respectively from two independent study sites in the cities of Pune and Kolkata. Paired nasopharyngeal and oropharyngeal swabs were tested by using both reference and index methods in blinded fashion. Prior to conducting RT-PCR, swabs collected in viral transport medium (VTM) were processed for RNA extraction (reference method) and swabs collected in dry tube without VTM were incubated in Tris-EDTA-Proteinase K buffer for 30 minutes and heat inactivated at 98{degrees}C for 6 minutes (index method). Overall sensitivity and specificity of the index method were 78.9% (95% CI 71% to 86%) and 99 % (95% CI 98% to 99.6%) respectively. Agreement between the index and reference method was 96.8 % (k = 0.83, SE=0.030). The reference method exhibited enhanced detection of viral genes (E, N and RdRP) with lower Ct values compared to the index method. The index method can be used for detecting SARS-CoV-2 infection with appropriately chosen primer-probe set and heat treatment approach in pressing time; low sensitivity constrains its potential wider use.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Madhumathi Jayaprakasam", - "author_inst": "Indian Council of Medical Research (ICMR), Ansari Nagar, New Delhi-110029" - }, - { - "author_name": "Sumit Aggarwal", - "author_inst": "Indian Council of Medical Research (ICMR), Ansari Nagar, New Delhi-110029" - }, - { - "author_name": "Arati Mane", - "author_inst": "ICMR-National AIDS Research Institute (ICMR-NARI), Pune" - }, - { - "author_name": "Vandana Saxena", - "author_inst": "ICMR-National AIDS Research Institute (ICMR-NARI), Pune" - }, - { - "author_name": "Amrita Rao", - "author_inst": "ICMR-National AIDS Research Institute (ICMR-NARI), Pune" - }, - { - "author_name": "Bhaswati Bandopadhyay", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Banya Chakraborty", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Subhasish Kamal Guha", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Mekhala Taraphdar", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Alisha Acharya", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Bishal Gupta", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Sonia Deb", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Aparna Chowdhury", - "author_inst": "School of Tropical Medicine, Kolkata" - }, - { - "author_name": "Kh Jitenkumar Singh", - "author_inst": "ICMR-National Institute of Medical Statistics (NIMS-ICMR), New Delhi" - }, - { - "author_name": "Prashant Tapase", - "author_inst": "ICMR-National Institute of Medical Statistics (NIMS-ICMR), New Delhi" - }, - { - "author_name": "Ravindra M Pandey", - "author_inst": "All India Institute of Medical Sciences (AIIMS), New Delhi" - }, - { - "author_name": "Balram Bhargava", - "author_inst": "Secretary, Department of Health Research (DHR) and Director General, ICMR" - }, - { - "author_name": "Samiran Panda", - "author_inst": "Indian Council of Medical Research (ICMR), Ansari Nagar, New Delhi-110029" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.21.21263457", "rel_title": "Real-world Effectiveness of 2-dose SARS-CoV-2 Vaccination in Kidney Transplant Recipients", @@ -582521,6 +583435,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.09.21.21263627", + "rel_title": "The slower antibody response in myelofibrosis patients after two doses of mRNA SARS-CoV-2 vaccine calls for a third dose", + "rel_date": "2021-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21263627", + "rel_abs": "Immunization with mRNA SARS-CoV-2 vaccines has been highly recommended and prioritized in fragile categories with higher risk of mortality after COVID-19 disease compared to healthy people, including patients with myelofibrosis (MF). Available data on the vaccine immune response developed by MF patients, and the impact of the treatment with the inhibitor of JAK-STAT signaling ruxolitimib, are still fragmented to support an informed decision for a third dose for this category of subjects. Here, we show that 76% of MF patients develop spike-specific IgG after the second vaccine dose, but the response has a slower kinetic compared to healthy subjects, suggesting a reduced capability of their immune system to promptly react to vaccination. A reduced ACE2/RBD inhibition binding activity of spike-specific antibodies was also observed, especially in ruxolitimib treated patients. Our results contribute to answer the open question on the induction of the antibody responses in MF patients following vaccination with COVID-19 mRNA vaccines, showing a slow kinetic that support the need for a third dose of SARS-CoV-2 mRNA vaccines.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Fabio Fiorino", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Anna Sicuranza", + "author_inst": "Hematology Unit, Department of Medical Science, Surgery and Neuroscience, University of Siena, Azienda Ospedaliero Universitaria Senese, Italy" + }, + { + "author_name": "Annalisa Ciabattini", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Adele Santoni", + "author_inst": "Hematology Unit, Department of Medical Science, Surgery and Neuroscience, University of Siena, Azienda Ospedaliero Universitaria Senese, Italy" + }, + { + "author_name": "Gabiria Pastore", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Martina Simoncelli", + "author_inst": "Hematology Unit, Department of Medical Science, Surgery and Neuroscience, University of Siena, Azienda Ospedaliero Universitaria Senese, Italy" + }, + { + "author_name": "Jacopo Polvere", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Sara Galimberti", + "author_inst": "Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy" + }, + { + "author_name": "Stefano Auddino", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + }, + { + "author_name": "Claudia Barate'", + "author_inst": "Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy" + }, + { + "author_name": "Francesca Montagnani", + "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hospital of Siena; Siena, Italy; Department of Medical Biotechnologies, Univer" + }, + { + "author_name": "Vincenzo Sammartano", + "author_inst": "Hematology Unit, Department of Medical Science, Surgery and Neuroscience, University of Siena, Azienda Ospedaliero Universitaria Senese, Italy" + }, + { + "author_name": "Monica Bocchia", + "author_inst": "Hematology Unit, Department of Medical Science, Surgery and Neuroscience, University of Siena, Azienda Ospedaliero Universitaria Senese, Italy" + }, + { + "author_name": "Donata Medaglini", + "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2021.09.22.461342", "rel_title": "Demographic Analysis of Mutations in Indian SARS-CoV-2 Isolates", @@ -583693,93 +584678,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.20.21263566", - "rel_title": "Health-care workers in gastrointestinal endoscopy are at higher risk for SARS-CoV-2 infection compared to other aerosol-generating disciplines", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263566", - "rel_abs": "ObjectiveHealthcare workers (HCW) are at high risk of SARS-CoV-2 infection due to exposure to potentially infectious material, especially during aerosol-generating procedures (AGP). We aimed to investigate the prevalence of infection among HCW in medical disciplines with AGP.\n\nDesignA nationwide questionnaire-based study in in- and outpatient settings was conducted between 12/16/2020 and 01/24/2021. Data on SARS-CoV-2 infections among HCW and potential risk factors were investigated.\n\nResults2,070 healthcare facilities with 25,113 employees were included in the study. Despite a higher rate of pre-interventional testing, clinics treated three times more confirmed SARS-CoV-2 cases than private practices (28.8% vs. 88.4%, p<0.001). Overall infection rate among HCW accounted for 4.7%. Multivariate analysis revealed that ZIP-regions having comparably higher incidences were significantly associated with increased risk of infection. Furthermore, clinical setting and the GIE specialty have more than double the risk of infection (OR 2.63; 95% CI 2.501-2.817, p<0.01 and OR 2.35; 95% CI 2.245-2.498, p<0.01). The number of procedures performed per day was also significantly associated with an increased risk of infection (OR 1.01; 95% CI 1.007-1.014), p<0.01). No treatment of confirmed SARS-CoV-2 cases was tending to lower the risk of infection (OR 0.72; 95% CI 0.507-1.025, p=0.068).\n\nConclusionHCW in GIE seem to be at higher risk of infection than those in other AGP, especially in the clinical setting. Regions having comparably higher incidences as well as the number of procedures performed per day were also significantly associated with increased risk of infection.\n\nSignificance of this studyO_ST_ABSWhat is already known on this subject?C_ST_ABSHealth care workers, especially those exposed to aerosol generating procedures, are assumed to have an increased risk of SARS-CoV-2 infection. However, data confirming this are lacking, especially for the outpatient care setting.\n\nWhat are the new findings?Health care workers in gastrointestinal endoscopy have a higher risk of SARS-CoV-2-infection than in other AGPs. This risk is particularly higher\n\n- in clinical settings compared to private practices\n- in regions having comparably higher incidences\n- the more procedures are performed per day\n\n\nHow might it impact on clinical practice in the foreseeable future?Our study suggests making additional efforts to protect HCW in the gastrointestinal work field.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Christoph Roemmele", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Alanna Ebigbo", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Maria Kahn", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Stephan Zellmer", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Anna Muzalyova", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Gertrud Hammel", - "author_inst": "Institute of Environmental Medicine, Helmholtz Zentrum Munich, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany" - }, - { - "author_name": "Christina Bartenschlager", - "author_inst": "Chair of Health Care Operations/Health Information Management, University Augsburg, Neusaesser Strasse 47, 86156 Augsburg, Germany" - }, - { - "author_name": "Albert Beyer", - "author_inst": "Medical Practice for Gastroenterology and Gastrointestinal Oncology, Altoetting, Germany" - }, - { - "author_name": "Jonas Rosendahl", - "author_inst": "Clinic for Internal Medicine - Gastroenterology and Pneumology, University Hospital Halle" - }, - { - "author_name": "Tilo Schlittenbauer", - "author_inst": "Department of Oral and Maxillofacial Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Johannes Zenk", - "author_inst": "Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - }, - { - "author_name": "Bilal Al-Nawas", - "author_inst": "Clinic and Polyclinic for Oral and Maxillofacial Surgery, Plastic Surgery, University Hospital Mainz, Augustusplatz 2, 55131 Mainz, Germany" - }, - { - "author_name": "Roland Frankenberger", - "author_inst": "Department for Operative Dentistry, Endodontics, and Pediatric Dentistry, Philipps University Marburg and University Hospital Giessen and Marburg, Campus Marbur" - }, - { - "author_name": "Juergen Hoffmann", - "author_inst": "Department of Oral and Maxillofacial Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany" - }, - { - "author_name": "Christoph Arens", - "author_inst": "Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany" - }, - { - "author_name": "Frank Lammert", - "author_inst": "Saarland University Medical Center" - }, - { - "author_name": "Claudia Traidl-Hoffmann", - "author_inst": "Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Neusaesser Strasse 47, 86156 Augsburg, Germany" - }, - { - "author_name": "Helmut Messmann", - "author_inst": "Clinic for Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, Stenglinstrasse 2, 86156 Augsburg, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2021.09.20.21263808", "rel_title": "Human Milk Antibodies Elicited by BNT162b2 Vaccination Target have reduced activity against SARS-CoV-2 Variants of Concern", @@ -584179,6 +585077,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.09.15.21263559", + "rel_title": "COVID-19 vaccine hesitancy and vaccine passports: Vaccination or restriction?", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.15.21263559", + "rel_abs": "ObjectivesWhile the development of vaccines against the novel coronavirus (COVID-19) brought the hope of establishing herd immunity, which might help end the global pandemic, vaccine hesitancy can hinder the progress towards herd immunity. In this study, we assess the determinants of vaccine hesitancy, reasons for hesitation, and effectiveness of vaccine passports in relaxing public health restrictions.\n\nMethodsThrough an online survey that includes a conjoint experiment of a demographically representative sample of 5,000 Japanese adults aged 20-74, we assess the determinants of vaccine hesitancy, reasons for hesitation, and effectiveness of hypothetical vaccine passports.\n\nResultsWe found that about 30% of respondents did not intend to vaccinate or have not yet decided, with major reasons for vaccine hesitancy being related to concerns about the safety and side effects of the vaccine. In line with previous findings, younger age, lower socioeconomic status, and psychological factors such as weaker COVID-19 fear were associated with vaccine hesitancy. The easing of public health restrictions such as travel, wearing face masks, and dining out at night was associated with an increase in vaccine acceptance by 4-10%.\n\nConclusionVaccine hesitancy can be reduced by mitigating the concerns about vaccine safety and side effects, as well as by relaxing public health restrictions. However, the feasibility of vaccine passports needs to be sufficiently assessed, taking the ethical issues of passports and the public health impacts of the relaxation of restrictions into careful consideration.\n\nStrengths and limitations of this study{square} This study includes timely data on COVID-19 vaccine hesitancy, obtained from a demographically representative sample of 5,000 Japanese adults.\n{square}A conjoint experiment allows assessing the effectiveness of easing public health restrictions on vaccine acceptance.\n{square}Actual behaviour may diverge from the survey responses or fluctuate due to the pandemic situation and the timing of the survey.\n{square}Results may not be applicable in other countries, since the pandemic situation, government responses to the pandemic, and reasons for vaccine hesitancy can vary across countries.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shohei Okamoto", + "author_inst": "Research Team for Social Participation and Community Health, Tokyo Metropolitan Institute of Gerontology" + }, + { + "author_name": "Kazuki Kamimura", + "author_inst": "Hirao School of Management, Konan University" + }, + { + "author_name": "Kohei Komamura", + "author_inst": "Faculty of Economics, Keio University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.09.20.21263777", "rel_title": "University patenting and licensing practices in the United Kingdom during the COVID-19 pandemic - implications for global equitable access to COVID-19 health technologies", @@ -585496,49 +586421,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.14.21263300", - "rel_title": "Predictors of COVID-19 vaccine uptake in healthcare workers: a cross-sectional study in Greece", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263300", - "rel_abs": "BackgroundThe role of healthcare workers (HCWs) in the general public health is crucial and their decision to vaccinate against the COVID-19 can have a positive impact on the general population facilitating widespread COVID-19 vaccine uptake.\n\nObjectiveTo estimate the uptake of a COVID-19 vaccine in HCWs and to expand our knowledge regarding the predictors of COVID-19 vaccine uptake.\n\nMethodsAn on-line cross-sectional study was conducted in Greece during August 2021. We collected socio-demographic data of HCWs and we measured attitudes towards vaccination and COVID-19, knowledge and trust. We used a convenience sample since we distributed the questionnaire through social media and e-mails.\n\nResultsStudy population included 855 HCWs. The majority of HCWs were vaccinated against the COVID-19 (91.5%). According to multivariate analysis, females, HCWs without a previous COVID-19 diagnosis, and HCWs with previous seasonal influenza vaccination history had a greater probability to take a COVID-19 vaccine. Also, increased self-perceived knowledge regarding COVID-19 and increased trust in COVID-19 vaccines and government regarding the information about the COVID-19 vaccines were associated with COVID-19 vaccine uptake. On the other hand, HCWs with more concerns about the side-effects of COVID-19 vaccination were more reluctant to take a COVID-19 vaccine.\n\nConclusionsOur study provides a timely assessment of COVID-19 vaccination status among HCWs and identifies specific factors associated with COVID-19 vaccine uptake. By understanding these factors, policy makers and scientists will be able to develop novel strategies to improve COVID-19 vaccine uptake among HCWs.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Petros A Galanis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Ioannis Moisoglou", - "author_inst": "General Hospital of Lamia" - }, - { - "author_name": "Irene Vraka", - "author_inst": "P & A Kyriakou Children's Hospital" - }, - { - "author_name": "Olga Siskou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Olympia Konstantakopoulou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Aglaia Katsiroumpa", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Daphne Kaitelidou", - "author_inst": "National and Kapodistrian University of Athens" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.14.21263467", "rel_title": "Information Theoretic Model Selection for Accurately Estimating Unreported COVID-19 Infections", @@ -585878,6 +586760,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.09.16.21263170", + "rel_title": "Characterisation of the blood RNA host response underpinning severity in COVID-19 patients", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263170", + "rel_abs": "Infection with SARS-CoV-2 has highly variable clinical manifestations, ranging from asymptomatic infection through to life-threatening disease. Host whole blood transcriptomics can offer unique insights into the biological processes underpinning infection and disease, as well as severity. We performed whole blood RNA Sequencing of individuals with varying degrees of COVID-19 severity. We used differential expression analysis and pathway enrichment analysis to explore how the blood transcriptome differs between individuals with mild, moderate, and severe COVID-19, performing pairwise comparisons between groups. Increasing COVID-19 severity was characterised by an abundance of inflammatory immune response genes and pathways, including many related to neutrophils and macrophages, in addition to an upregulation of immunoglobulin genes. Our insights into COVID-19 severity reveal the role of immune dysregulation in the progression to severe disease and highlight the need for further research exploring the interplay between SARS-CoV-2 and the inflammatory immune response.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Heather Jackson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Irene Rivero Calle", + "author_inst": "Hospital Clinico Universitario Santiago de Compostela" + }, + { + "author_name": "Claire Broderick", + "author_inst": "Imperial College London" + }, + { + "author_name": "Dominic Habgood-Coote", + "author_inst": "Imperial College London;" + }, + { + "author_name": "Giselle D'Souza", + "author_inst": "Imperial College London" + }, + { + "author_name": "Samuel Nichols", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jose G\u00f3mez Rial", + "author_inst": "Hospital Clinico Universitario Santiago de Compostela" + }, + { + "author_name": "Carmen Rivero-Velasco", + "author_inst": "Hospital Clinico Universitario Santiago de Compostela" + }, + { + "author_name": "Nuria Rodr\u00edguez-N\u00fa\u00f1ez", + "author_inst": "Hospital Clinico Universitario de Santiago de Compostela" + }, + { + "author_name": "Gema Barbeito-Casti\u00f1eiras", + "author_inst": "Hospital Clinico Universitario de Santiago de Compostela" + }, + { + "author_name": "Hugo P\u00e9rez-Freixo", + "author_inst": "Hospital Clinico Universitario de Santiago de Compostela" + }, + { + "author_name": "Manuel Barreiro-de Acosta", + "author_inst": "Hospital Clinico Universitario de Santiago de Compostela" + }, + { + "author_name": "Aubrey Cunnington", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jethro Herberg", + "author_inst": "Imperial College London" + }, + { + "author_name": "Victoria Wright", + "author_inst": "Imperial College London" + }, + { + "author_name": "Alberto G\u00f3mez-Carballa", + "author_inst": "Hospital Clinico Universitario Santiago de Compostela" + }, + { + "author_name": "Antonio Salas", + "author_inst": "Universidad de Santiago de Compostela" + }, + { + "author_name": "Michael Levin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Federico Martinon-Torres", + "author_inst": "Hospital Clinico Universitario de Santiago" + }, + { + "author_name": "Myrsini Kaforou", + "author_inst": "Imperial College London" + }, + { + "author_name": "- PERFORM consortium", + "author_inst": "" + }, + { + "author_name": "- GEN-COVID study group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.16.21263675", "rel_title": "Blood biochemical parameters as predictors of disease severity and mortality in COVID-19 patients- an updated systematic review and meta-analysis", @@ -586958,73 +587943,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.09.17.21263528", - "rel_title": "Dichotomy between the humoral and cellular responses elicited by mRNA and adenoviral vector vaccines against SARS-CoV-2.", - "rel_date": "2021-09-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.17.21263528", - "rel_abs": "Protection from severe disease and hospitalization by SARS-CoV-2 vaccination has been amply demonstrated by real-world data. However, the rapidly evolving pandemic raises new concerns. One pertains efficacy of adenoviral vector-based vaccines, particularly the single-dose Ad26.COV2.S, relative to mRNA vaccines. We investigated the immunogenicity of Ad26.COV2.S and mRNA vaccines in 33 subjects vaccinated with either vaccine class five months earlier on average. After controlling for time since vaccination, Spike-binding antibody and neutralizing antibody levels were higher in the mRNA-vaccinated subjects, while no significant differences in antigen-specific B cell and T cell responses were observed between the two groups. Thus, a dichotomy exists between humoral and cellular responses elicited by the two vaccine classes. Our results have implications for the need of booster doses in vaccinated subjects and might explain the dichotomy reported between the waning protection from symptomatic infection by SARS-CoV-2 vaccination and its persisting efficacy in preventing hospitalization and death.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Rahul Ukey", - "author_inst": "PHRI, Rutgers NJMS, Newark, NJ" - }, - { - "author_name": "Natalie Bruiners", - "author_inst": "PHRI, Rutgers NJMS, Newark, NJ" - }, - { - "author_name": "Hridesh Mishra", - "author_inst": "PHRI, Rutgers NJMS, Newark,NJ" - }, - { - "author_name": "Pankaj K Mishra", - "author_inst": "PHRI, Rutgers NJMS, Newark, NJ" - }, - { - "author_name": "Deborah McCluskey", - "author_inst": "Clinical Reserach Center, Rutgers RWJMS, New Brunswick, NJ" - }, - { - "author_name": "Alberta Onyuka", - "author_inst": "Global Tuberculosis Institute, Rutgers NJMS,Newark,NJ" - }, - { - "author_name": "Fei Chen", - "author_inst": "Clinical Reserach Center, Rutgers RWJMS, New Brunswick, NJ" - }, - { - "author_name": "Abraham Pinter", - "author_inst": "Rutgers University" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute For Allergy & Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Allergy & Immunology" - }, - { - "author_name": "Jason Roy", - "author_inst": "Department of Biostatistics, Rutgers University School of Public Health, NJ" - }, - { - "author_name": "Sunanda Gaur", - "author_inst": "Rutgers, Robert Wood Johnson Medical School" - }, - { - "author_name": "Maria Laura Gennaro", - "author_inst": "PHRI, Rutgers NJMS, Newark, NJ" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.17.21263532", "rel_title": "Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a sixteen-week interval between doses", @@ -587344,6 +588262,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.09.09.21262448", + "rel_title": "An Analysis of SARS-CoV-2 Vaccine Breakthrough Infections and Associated Clinical Outcomes", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21262448", + "rel_abs": "Understanding the rate and clinical features associated with vaccine breakthrough infections (VBT) is of critical public health importance. Recent evidence on VBT in Barnstable County, Massachusetts, has prompted guidance on masking for vaccinated individuals in areas of high community-level transmission.1 Additional data is needed to better understand the prevalence and rate of VBT infections. Using detailed disease investigation data from Washoe County, Nevada we sought to assess the rate of symptomatic infection and serious illness among VBT cases compared to non-vaccinated individuals with COVID-19. From February 12 - July 29, 2021, the Washoe County Health District identified and traced 6,128 out of 6,399 reported cases across the sample period. 338 (5.5%) of all cases were identified as breakthrough infections, and 289 (86%) vaccinated individuals had symptomatic infections. Severe clinical outcomes were infrequent with 17 hospitalizations (5% of VBT) and no deaths. Cycle threshold values were not statistically different between vaccinated and unvaccinated individuals.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Heather Kerwin", + "author_inst": "Washoe County Health District" + }, + { + "author_name": "Rex Briggs", + "author_inst": "Ad Council" + }, + { + "author_name": "Sameer Nair-Desai", + "author_inst": "Brown University School of Public Health" + }, + { + "author_name": "Andrew Gorzalski", + "author_inst": "Nevada State Public Health Laboratory" + }, + { + "author_name": "Mark Pandori", + "author_inst": "Nevada State Public Health Laboratory" + }, + { + "author_name": "Stefanie Friedhoff", + "author_inst": "Brown University School of Public Health" + }, + { + "author_name": "Thomas Tsai", + "author_inst": "Harvard T.H. Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.11.21263419", "rel_title": "Characteristics and outcomes of an international cohort of 400,000 hospitalised patients with Covid-19", @@ -588972,33 +589933,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.16.460716", - "rel_title": "The supramolecular organization of SARS-CoV and SARS-CoV-2 virions revealed by coarse-grained models of intact virus envelopes", - "rel_date": "2021-09-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.16.460716", - "rel_abs": "The coronavirus disease 19 (COVID-19) pandemic is causing a global health crisis and has already caused a devastating societal and economic burden. The pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has a high sequence and architecture identity with SARS-CoV, but far more people have been infected by SARS-CoV-2. Here, combining structural data from cryo-EM and structure prediction, we constructed bottom-up Martini coarse-grained models of intact SARS-CoV and SARS-CoV-2 envelopes. Microsecond molecular dynamics simulations were performed, allowing us to explore their dynamics and supramolecular organization. Both SARS-CoV and SARS-CoV-2 envelopes present a spherical morphology with structural proteins forming multiple string-like islands in the membrane and clusters between heads of spike proteins. Critical differences between the SARS-CoV and SARS-CoV-2 envelopes are the interaction pattern between spike proteins and the flexibility of spike proteins. Our models provide structural and dynamic insights in the SARS virus envelopes, and could be used for further investigation, such as drug design, and fusion and fission processes.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Beibei Wang", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Changqing Zhong", - "author_inst": "University of Electronic Science and Technology of China" - }, - { - "author_name": "D. Peter Tieleman", - "author_inst": "University of Calgary" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.09.15.21263654", "rel_title": "Correlates of COVID-19 vaccination status among college students", @@ -589510,6 +590444,121 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2021.09.17.460777", + "rel_title": "Altered fibrin clot structure contributes to thrombosis risk in severe COVID-19", + "rel_date": "2021-09-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.17.460777", + "rel_abs": "The high incidence of thrombotic events suggests a possible role of the contact system pathway in COVID-19 pathology. Here, we demonstrate altered levels of factor XII (FXII) and its activation products in two independent cohorts of critically ill COVID-19 patients in comparison to patients suffering from severe acute respiratory distress syndrome due to influenza virus (ARDS-influenza). Compatible with this data, we report rapid consumption of FXII in COVID-19, but not in ARDS-influenza, plasma. Interestingly, the kaolin clotting time was not prolonged in COVID-19 as compared to ARDS-influenza. Using confocal and electron microscopy, we show that increased FXII activation rate, in conjunction with elevated fibrinogen levels, triggers formation of fibrinolysis-resistant, compact clots with thin fibers and small pores in COVID-19. Accordingly, we observed clot lysis in 30% of COVID-19 patients and 84% of ARDS-influenza subjects. Analysis of lung tissue sections revealed wide-spread extra- and intra-vascular compact fibrin deposits in COVID-19. Together, our results indicate that elevated fibrinogen levels and increased FXII activation rate promote thrombosis and thrombolysis resistance via enhanced thrombus formation and stability in COVID-19.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Malgorzata Wygrecka", + "author_inst": "Justus-Liebig University Giessen" + }, + { + "author_name": "Anna Birnhuber", + "author_inst": "Ludwig Boltzmann Institute for Lung Vascular Research" + }, + { + "author_name": "Benjamin Seeliger", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Laura Michalick", + "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Oleg Pak", + "author_inst": "Universities of Giessen and Marburg Lung Center" + }, + { + "author_name": "Astrid-Solveig Schultz", + "author_inst": "Justus-Liebig University Giessen" + }, + { + "author_name": "Fabian Schramm", + "author_inst": "Justus-Liebig University Giessen" + }, + { + "author_name": "Martin Zacharias", + "author_inst": "Medical University Graz" + }, + { + "author_name": "Gregor Gorkiewicz", + "author_inst": "Medical University Graz" + }, + { + "author_name": "Sascha David", + "author_inst": "University Hospital Zurich" + }, + { + "author_name": "Tobias Welte", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Julius J. Schmidt", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Norbert Weissmann", + "author_inst": "Justus Liebig University Giessen" + }, + { + "author_name": "Ralph T Schermuly", + "author_inst": "Justus-Liebig-Universit\u00e4t Giessen" + }, + { + "author_name": "Guillermo Barreto", + "author_inst": "Max-Planck-Institute for Heart and Lung Research" + }, + { + "author_name": "Liliana Sch\u00e4fer", + "author_inst": "Goethe University Frankfurt" + }, + { + "author_name": "Philipp Markart", + "author_inst": "Fulda Hospital" + }, + { + "author_name": "Markus C. Brack", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Stefan Hippenstiel", + "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Florian Kurth", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Leif E Sander", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Martin Witzenrath", + "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Wolfgang M. Kuebler", + "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Grazyna Kwapiszewska", + "author_inst": "Ludwig Boltzmann Institute for Lung Vascular Research" + }, + { + "author_name": "Klaus T Preissner", + "author_inst": "Justus-Liebig-University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.09.16.460594", "rel_title": "3D virtual Histopathology of Cardiac Tissue from Covid-19 Patients based on Phase-Contrast X-ray Tomography", @@ -591134,37 +592183,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.13.21263497", - "rel_title": "Factors Influencing The First and Second Peak of COVID-19 Global Cases: A Survival Analysis", - "rel_date": "2021-09-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263497", - "rel_abs": "ObjectivesThe number of reported cases continues to increase everyday, since the first case of COVID-19 was detected in Wuhan, China in December 2019. Using the global COVID-19 data of 188 countries extracted from the Our World in Data between January 22, 2020-January 18, 2021, this study attempts to explore the potential determinants of the number of days to reach the first and second peak of COVID-19 cases for all 188 countries.\n\nMethodsA semi-parametric Cox proportional hazard (PH) model has been used to explore the covariates that are associated with the number of days to reach the first and second peak of global COVID-19 cases.\n\nResultsAs of January 18, 2021, the first and second peak were found in 175 and 59 countries, out of 188 countries, respectively. The median number of days to hit the first peak was 60 days for countries which have median age above 40 while the median number of days to hit the second peak was 267 days for countries which have population density above 500 per square kilometer. Countries having population density between 250 and 500 were 2.25 times more likely to experience the first peak of COVID-19 cases (95% CI: 1.15-4.45, P < 0.05) than countries which have population density below 25. Countries having population density between 100 and 250 were 67% less likely to get the second peak (95% CI: 0.119-0.908, P < 0.05) compared to countries which have population density below 25. Countries having cardiovascular death rates above 350 were 2.94 times more likely to get the first peak (95% CI: 1.59-5.43, P < 0.001). In contrast, countries having diabetes prevalence rate 3 to 12 were 85% less likely to experience the second peak of COVID-19 cases (95% CI: 0.036-0.680, P < 0.05) than countries which have diabetes prevalence rate below 3. Besides, highly significant difference is found in the Kaplan-Meier plots of the number of days to reach both peaks across different categories of the countrys Human Development Index.\n\nConclusionsThe number of days to the first peak was considerably small in Asian & European countries but that to the second peak in the countries where diabetes prevalence was very higher. Countrys life expectancy had a significant effect on determining the first peak and so was the case for two other variables-the cardiovascular death rate and hospital beds per thousand. A contrast result was found for Human Development Index factor under the second peak. Additionally, it was found that the second peak was more likely to occur in more densely populated countries.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Yesar Ahmed Oshan", - "author_inst": "ISRT, University of Dhaka" - }, - { - "author_name": "Begum Zainab", - "author_inst": "ISRT, University of Dhaka" - }, - { - "author_name": "Dipankar Bandyopadhyay", - "author_inst": "Department of Biostatistics, Virginia Commonwealth University" - }, - { - "author_name": "Hasinur Rahaman Khan", - "author_inst": "University of Dhaka, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.13.21262182", "rel_title": "mRNA COVID-19 Vaccination and Development of CMR-confirmed Myopericarditis", @@ -591604,6 +592622,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.09.13.21263511", + "rel_title": "Using Artificial Intelligence-based models to predict the risk of Mucormycosis among COVID-19 Survivors: An Experience from India", + "rel_date": "2021-09-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263511", + "rel_abs": "IntroductionIndia reported a severe public health challenge not only due to the COVID-19 outbreak but also the increasing number of associated mucormycosis cases since 2021. This study aimed at developing artificial intelligence-based models to predict the risk of mucormycosis among the patients at the time of discharge from the hospital.\n\nMethodsThe dataset included 1229 COVID-19 positive patients, and additional 214 inpatients, COVID-19 positive as well as infected with mucormycosis. We used logistic regression, decision tree, and random forest, and the extreme gradient boosting algorithm. All our models were evaluated with 5-fold validation to derive a reliable estimate of the model error.\n\nResultsThe logistic regression, XGBoost, and random forest performed equally well with AUROC 95.0, 94.0, and 94.0 respectively. This study also determined the top five variables namely obesity, anosmia, de novo diabetes, myalgia, and nasal discharge, which showed a positive impact on the risk of mucormycosis.\n\nConclusionThe developed model has the potential to predict the patients at high risk and thus, consequently initiating preventive care or aiding in early detection of mucormycosis infection. Thus, this study holds potential for early treatment and better management of patients suffering from COVID-19 associated mucormycosis.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Shabbir Syed-Abdul", + "author_inst": "Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan." + }, + { + "author_name": "A. Shoban Babu", + "author_inst": "Department of ENT, Gandhi Medical College and Hospital, Secunderabad, Telangana, India." + }, + { + "author_name": "Raja Shekhar Bellamkonda", + "author_inst": "School of Management Studies, University of Hyderabad, Hyderabad, Telangana, India" + }, + { + "author_name": "Ramaiah Itumalla", + "author_inst": "Department of Health Management, College of Public Health and Health Informatics, University of Hail, Hail, Kingdom of Saudi Arabia." + }, + { + "author_name": "GVRK Acharyulu", + "author_inst": "School of Management Studies, University of Hyderabad, Hyderabad, Telangana, India" + }, + { + "author_name": "Surya Krishnamurthy", + "author_inst": "iQGateway" + }, + { + "author_name": "Y. Venkat Santosh Ramana", + "author_inst": "Department of Hospital Administration, Gandhi Hospital, Secunderabad, Telangana, India." + }, + { + "author_name": "Naresh Mogilicharla", + "author_inst": "Department of ENT, Gandhi Medical College and Hospital, Secunderabad, Telangana, India" + }, + { + "author_name": "Shwetambara Malwade", + "author_inst": "International Center for Health Information Technology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan." + }, + { + "author_name": "Yu-Chuan (Jack) Li", + "author_inst": "Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.09.13.21263430", "rel_title": "Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage", @@ -593100,57 +594173,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.09.13.21263476", - "rel_title": "Association between work attendance when experiencing fever or cold symptoms and company characteristics and socioeconomic status in the COVID-19 pandemic in Japanese workers: a cross-sectional study", - "rel_date": "2021-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263476", - "rel_abs": "ObjectiveThis study investigated the association between attending work while experiencing fever or cold symptoms and workers socioeconomic background and company characteristics during the COVID-19 pandemic.\n\nMethodsA cross-sectional online survey was performed. Of a total of 33,302 participants, 3,676 workers who experienced fever or cold symptoms after April 2020 were included. The odds ratios (ORs) of attending work while sick associated with workers socioeconomic background and company characteristics were evaluated using a multilevel logistic model.\n\nResultsThe OR of attending work while sick associated with a lack of policy prohibiting workers from working when ill was 2.75 (95%CI: 2.28-3.20, P<0.001).\n\nConclusionThis study suggests that clear company policies on work and illness can be effective for preventing employees from attending work while sick.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kazuyoshi Mizuki", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Makoto Okawara", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Ayako Hino", - "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hajime Ando", - "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.09.12.21263475", "rel_title": "Spike Protein NTD mutation G142D in SARS-CoV-2 Delta VOC lineages is associated with frequent back mutations, increased viral loads, and immune evasion", @@ -593526,6 +594548,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.11.21263211", + "rel_title": "Early immunologic response to mRNA COVID-19 vaccine in patients receiving biologics and/or immunomodulators.", + "rel_date": "2021-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.11.21263211", + "rel_abs": "Patients with immune conditions and immune-modifying therapies were excluded from the Covid-19 vaccine trials. Studies have shown conflicting response to different vaccines in persons receiving immune suppressors or biologics. The aim of this study is to evaluate humoral and cellular response to Covid-19 vaccines in patients with Inflammatory Bowel Disease (IBD) using biologic and/or immunomodulatory (IMM) therapies.\n\nMethodsParticipants are adults with IBD receiving biologics or IMM planning to receive a Covid 19 vaccine. Cellular immunity (CD4+ and CD8+ T cell levels) with flow cytometry are measured at baseline and 2 weeks after each vaccine dose. Humoral immunity (antibody titers and neutralizing capacity,VNT%) is analyzed by ELISA at baseline, 2 weeks after each dose, and 6 and 12 months after vaccine. We present the early results of the first 19 subjects. The study is approved by the IRB.\n\nResults19 subjects (18 in biologics and 1 in IMM) who received 2 doses of the Pfizer-BioNTech vaccine are included. Total IgG antibodies increased 21.13 times after the first dose and 90 times after the second dose. VTN% increased 11.92 times after the first dose and 53.79 times after the second dose. When compared with a healthy control cohort, total IgG antibodies and VTN% were lower in the subjects after the first dose. After the second dose, IgG antibodies increased but remained lower than controls, but VTN% were similar to controls. CD4 and CD8 mean levels had an upward trend after vaccination.\n\nConclusionsNeutralizing capacity response to the vaccine in subjects was similar to a healthy cohort in spite of lower increases in total IgG antibodies. The CD4 and CD8 results observed may support the capacity to mount an effective cellular response in patients on biologics. Larger studies are needed to determine vaccine efficacy in these patients.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Esteban Rodriguez-Marrtino", + "author_inst": "Division of Gastroenterology, Department of Medicine, University of Puerto Rico School of Medicine, San Juan, Puerto Rico" + }, + { + "author_name": "Rafael Medina-Prieto", + "author_inst": "Division of Gastroenterology, Department of Medicine, University of Puerto Rico School of Medicine, San Juan, Puerto Rico" + }, + { + "author_name": "Jorge Santana-Bagur", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Puerto Rico School of Medicine, San Juan" + }, + { + "author_name": "Maria Sante", + "author_inst": "Department of Pathology, University of Puerto Rico School of Medicine, San Juan" + }, + { + "author_name": "Petraleigh Pantoja", + "author_inst": "Unit of Comparative Medicine, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico" + }, + { + "author_name": "Ana M Espino", + "author_inst": "Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico." + }, + { + "author_name": "Carlos A Sariol", + "author_inst": "Unit of Comparative Medicine, Department of Medicine, Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, San Juan, Pu" + }, + { + "author_name": "Esther A Torres", + "author_inst": "Division of Gastroenterology, Department of Medicine, University of Puerto Rico School of Medicine, San Juan, Puerto Rico" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2021.09.11.21262855", "rel_title": "Safety, Immunogenicity, and Efficacy of COVID-19 Vaccine in Children and Adolescents: A Systematic Review", @@ -595182,57 +596251,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.09.04.21262932", - "rel_title": "A Comparative Study Between Nasopharyngeal/Oropharyngeal, Faecal and Saliva Viral Shedding In Ghanaian COVID-19 Patients attending KATH from October-December, 2020", - "rel_date": "2021-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.04.21262932", - "rel_abs": "BackgroundDiagnostic testing for the current SARS-CoV-2 infections involves the collection and testing of invasive pharyngeal specimens by qualified Health workers. Though fully clad in personal protective equipment, the concern is that sampling in close proximity to the patient poses as a major health hazard. The present study sought to verify if saliva or faeces could become a possible surrogate for pharyngeal samples for SARS-CoV 2 testing in suspected Ghanaian COVID-19 patients.\n\nObjectivesTo ascertain if there is SARS-CoV 2 viral shedding in the saliva and faecal samples of Ghanaian COVID-19 patients, their sensitivity and specificity as compared to pharyngeal samples.\n\nMethodFifty (50) recruited COVID-19 patients who have been confirmed via RT-PCR using their nasopharyngeal/oropharyngeal samples and twenty (20) SARS-CoV 2 negative suspected patients each provided some faecal and saliva sample for RT-PCR analysis for SARS-CoV 2.\n\nResultsForty-three (43) out of the fifty (50) COVID-19 patients recruited representing 86% tested positive for SARS-CoV 2 via their saliva sample whiles all their faecal samples tested positive for SARS-CoV 2 representing 100%. The sensitivity of saliva samples was 86% whiles the specificity was 100% but the sensitivity and specificity of the faecal samples were all 100%.\n\nConclusionThere is indeed viral shedding of SARS-CoV 2 in the saliva and faeces of Ghanaian COVID-19 patients just like their counterparts in other parts of the world. Saliva and faeces could possibly become an alternative sample to the current in place of the invasive pharyngeal samples for SARS-CoV 2 testing in resource limited settings. Further research to explore this possibility at different testing sites with larger sample size is recommended.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ernest Badu-Boateng", - "author_inst": "Komfo Anokye Teaching Hospital / Catholic University College of Ghana-Fiapre, Sunyani" - }, - { - "author_name": "Lydia Sarponmaa Asante", - "author_inst": "Catholic University College of Ghana" - }, - { - "author_name": "Albert Dompreh", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Laud Anthony Basing Wihibeturo", - "author_inst": "KNUST" - }, - { - "author_name": "Kwabena Adjei Asante", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Sylvia Karikari", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Albert Adubofour", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Chris Oppong", - "author_inst": "Komfo Anokye Teaching Hospital" - }, - { - "author_name": "Faustina Acheampong", - "author_inst": "Komfo Anokye Teaching Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.03.21262757", "rel_title": "Asymptomatic SARS-CoV-2 infection and the demography of COVID-19", @@ -595612,6 +596630,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.14.460275", + "rel_title": "SARS-CoV-2 Spike Protein Regulation of Angiotensin Converting Enzyme 2 and Tissue Renin-Angiotensin Systems: Influence of Biologic Sex", + "rel_date": "2021-09-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.14.460275", + "rel_abs": "Angiotensin converting enzyme 2 (ACE2) is an enzyme that limits activity of the renin-angiotensin system (RAS) and also serves as a receptor for the SARS-CoV-2 Spike (S) protein. Binding of S protein to ACE2 causes internalization which activates local RAS. ACE2 is on the X chromosome and its expression is regulated by sex hormones. In this study, we defined ACE2 mRNA abundance and examined effects of S protein on ACE2 activity and/or angiotensin II (AngII) levels in pivotal tissues (lung, adipose) from male and female mice. In lung, ACE2 mRNA abundance was reduced following gonadectomy (GDX) of male and female mice and was higher in XX than XY mice of the Four Core Genotypes (FCG). Reductions in lung ACE2 mRNA abundance by GDX occurred in XX, but not XY FCG female mice. Lung mRNA abundance of ADAM17 and TMPRSS2, enzymes that shed cell surface ACE2 and facilitate viral cell entry, was reduced by GDX in male but not female mice. For comparison, adipose ACE2 mRNA abundance was higher in female than male mice and higher in XX than XY FCG mice. Adipose ADAM17 mRNA abundance was increased by GDX of male and female mice. S protein reduced ACE2 activity in alveolar type II epithelial cells and 3T3-L1 adipocytes. Administration of S protein to male and female mice increased lung AngII levels and decreased adipose ACE2 activity in male but not female mice. These results demonstrate that sex differences in ACE2 expression levels may impact local RAS following S protein exposures.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Charles M. Ensor", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Yasir AlSiraj", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Robin Shoemaker", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Jamie Sturgill", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Suresh Keshavamurthy", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Elizabeth Gordon", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Brittany Dong", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Christopher M Waters", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Lisa C Cassis", + "author_inst": "University of Kentucky" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "physiology" + }, { "rel_doi": "10.1101/2021.09.13.460163", "rel_title": "BNT162b2-Elicited Neutralization of Delta Plus, Lambda, and Other Variants", @@ -597044,65 +598113,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.06.21262027", - "rel_title": "A simple, sensitive and quantitative FACS-based test for SARS-CoV-2 serology in humans and animals", - "rel_date": "2021-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.06.21262027", - "rel_abs": "Serological tests are important for understanding the physiopathology and following the evolution of the Covid-19 pandemic. Assays based on flow cytometry (FACS) of tissue culture cells expressing the spike (S) protein of SARS-CoV-2 have repeatedly proven to perform slightly better than the plate-based assays ELISA and CLIA (chemiluminescent immuno-assay), and markedly better than lateral flow immuno-assays (LFIA).\n\nHere, we describe an optimized and very simple FACS assay based on staining a mix of two Jurkat cell lines, expressing either high levels of the S protein (Jurkat-S) or a fluorescent protein (Jurkat-R expressing m-Cherry, or Jurkat-G, expressing GFP, which serve as an internal negative control). We show that the Jurkat-S&R-flow test has a much broader dynamic range than a commercial ELISA test and performs at least as well in terms of sensitivity and specificity. Also, it is more sensitive and quantitative than the hemagglutination-based test HAT, which we described recently. The Jurkat-flow test requires only a few microliters of blood; thus, it can be used to quantify various Ig isotypes in capillary blood collected from a finger prick. It can be used also to evaluate serological responses in mice, hamsters, cats and dogs. Whilst the Jurkat-flow test is ill-suited and not intended for clinical use, it offers a very attractive solution for laboratories with access to tissue culture and flow cytometry who want to monitor serological responses in humans or in animals, and how these relate to susceptibility to infection, or re-infection, by the virus, and to protection against Covid-19.\n\nNoteThis manuscript has been refereed by Review Commons, and modified thanks to the comments and suggestions from two referees. Those comments, and our replies, are provided at the end of the manuscripts pdf, and can also be accessed by clicking on the box with a little green number found just above the \"Abstract \" tab in the medRXiv window.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Agnes Maurel Ribes", - "author_inst": "Centre Hospitalier Universitaire de Toulouse" - }, - { - "author_name": "Pierre Bessiere", - "author_inst": "Ecole nationale veterinaire de Toulouse" - }, - { - "author_name": "Jean-Charles Guery", - "author_inst": "Institut Toulousain des Maladies Infectieuses et Inflammatoires" - }, - { - "author_name": "Eloise Joly Featherstone", - "author_inst": "York University Hospital" - }, - { - "author_name": "Timothee Bruel", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Remy Robinot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwartz", - "author_inst": "Institut Psateur" - }, - { - "author_name": "Romain Volmer", - "author_inst": "Ecole nationale veterinaire de Toulouse, France" - }, - { - "author_name": "Florence Abravanel", - "author_inst": "Institut Toulousain des Maladies Infectieuses et Inflammatoires" - }, - { - "author_name": "Jacques Izopet", - "author_inst": "Institut Toulousain des Maladies Infectieuses et Inflammatoires" - }, - { - "author_name": "Etienne Joly", - "author_inst": "IPBS, University of Toulouse, CNRS, Toulouse" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.07.21263200", "rel_title": "Distinguishing Incubation and Acute Disease Stages of Mild-to-Moderate COVID-19", @@ -597450,6 +598460,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.07.21263228", + "rel_title": "Analysis of 2.1 million SARS-CoV-2 genomes identifies mutations associated with transmissibility", + "rel_date": "2021-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21263228", + "rel_abs": "Repeated emergence of SARS-CoV-2 variants with increased fitness necessitates rapid detection and characterization of new lineages. To address this need, we developed PyR0, a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR0 to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR0 forecasts growth of new lineages from their mutational profile, identifies viral lineages of concern as they emerge, and prioritizes mutations of biological and public health concern for functional characterization.\n\nOne Sentence summaryA Bayesian hierarchical model of all SARS-CoV-2 viral genomes predicts lineage fitness and identifies associated mutations.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Fritz Heinrich Obermeyer", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Martin Jankowiak", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Nikolaos Barkas", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Stephen F. Schaffner", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Jesse D. Pyle", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Lonya Yurkovetskiy", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Matteo Bosso", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Daniel J. Park", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Mehrtash Babadi", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Bronwyn L. MacInnis", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Jeremy Luban", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Pardis C. Sabeti", + "author_inst": "Harvard University; The Broad Institute or MIT and Harvard; Howard Hughes Medical Institute" + }, + { + "author_name": "Jacob E. Lemieux", + "author_inst": "Broad Institute of MIT and Harvard" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.06.21263160", "rel_title": "Predicting the Effectiveness of the Pfizer-BioNTech BNT162b2 Vaccine from SARS-CoV-2 Variants Neutralisation Data", @@ -598526,45 +599603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.07.21263222", - "rel_title": "Elevated plasma levels of CXCL16 in severe COVID-19 patients", - "rel_date": "2021-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21263222", - "rel_abs": "Genome-wide association studies have recently identified 3p21.31, with lead variant pointing to the CXCR6 gene, as the strongest thus far reported susceptibility risk locus for severe manifestation of COVID-19. In order the determine its role, we measured plasma levels of Chemokine (C{square}X{square}C motif) ligand 16 (CXCL16) in the plasma of COVID-19 hospitalized patients. CXCL16 interacts with CXCR6 promoting chemotaxis or cell adhesion. The CXCR6/CXCL16 axis mediates homing of T cells to the lungs in disease and hyper-expression is associated with localised cellular injury. To characterize the CXCR6/CXCL16 axis in the pathogenesis of severe COVID-19, plasma concentrations of CXCL16 collected at baseline from 115 hospitalized COVID-19 patients participating in ODYSSEY COVID-19 clinical trial were assessed together with a set of controls. We report elevated levels of CXCL16 in a cohort of COVID-19 hospitalized patients. Specifically, we report significant elevation of CXCL16 plasma levels in association with severity of COVID-19 (as defined by WHO scale) (P-value<0.02). Our current study is the largest thus far study reporting CXCL16 levels in COVID-19 hospitalized patients (with whole-genome sequencing data available). The results further support the significant role of the CXCR6/CXCL16 axis in the immunopathogenesis of severe COVID-19 and warrants further studies to understand which patients would benefit most from targeted treatments.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "SANDRA P SMIESZEK", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Vasilios M Polymeropoulos", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Christos M Polymeropulos", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Bartloemiej P Przychodzen", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Gunther Birznieks", - "author_inst": "Vanda Pharmaceuticals Inc." - }, - { - "author_name": "Mihael M Polymeropoulos", - "author_inst": "Vanda Pharmaceuticals Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.07.21263213", "rel_title": "Comprehensive Evaluation of COVID-19 Patient Short- and Long-term Outcomes: Disparities in Healthcare Utilization and Post-Hospitalization Outcomes", @@ -598988,6 +600026,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.06.21263031", + "rel_title": "The efficiency of dynamic regional lockdown approach in controlling the COVID-19 epidemic. Insights from the agent-based epidemiological model for Poland", + "rel_date": "2021-09-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.06.21263031", + "rel_abs": "In this work properties of the dynamic regional lockdown approach to suppress the COVID-19 epidemic spread in Poland were investigated. In particular, an agent based model was used with the aim to indicate an optimal lockdown strategy, defined here as the one which minimizes mean lockdown time over regional unit provided health service is not overwhelmed. With this approach the lockdown extent was also considered by varying restrictions between complete regional school closure and/or significant social distancing in semi-public spaces. In result, a cooperative effect was discovered in the case when closure of schools was accompanied by severe restrictions of social contacts in semi-public spaces. Moreover, the regional lockdown approach implemented here on the level of counties (units of population around 100k) proofed to be successful, that is allowed to identify optimal entrance and release thresholds for lockdown. The authors believe that until significant portion of population is vaccinated such a strategy might be applied.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jakub Zieli\u0144ski", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + }, + { + "author_name": "Magdalena Gruziel-S\u0142omka", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + }, + { + "author_name": "J\u0119drzej M. Nowosielski", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + }, + { + "author_name": "Rafa\u0142 P. Bartczuk", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling & John Paul II Catholic University of Lublin, Institute of Psycholog" + }, + { + "author_name": "Karol Niedzielewski", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + }, + { + "author_name": "Marcin Semeniuk", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + }, + { + "author_name": "\u0141ukasz G\u00f3rski", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + }, + { + "author_name": "Jan Kisielewski", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling & University of Bia\u0142ystok, Faculty of Physics" + }, + { + "author_name": "Antoni Moszy\u0144ski", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + }, + { + "author_name": "Maciej Radwan", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + }, + { + "author_name": "Artur Kaczorek", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + }, + { + "author_name": "Franciszek Rakowski", + "author_inst": "University of Warsaw, Interdisciplinary Centre for Mathematical and Computational Modelling" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.07.21263100", "rel_title": "Incidence of COVID-19 reinfection among Midwestern healthcare employees", @@ -600756,173 +601857,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.03.21262551", - "rel_title": "A Learning Health System Randomized Trial of Monoclonal Antibodies for Covid-19", - "rel_date": "2021-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21262551", - "rel_abs": "BackgroundNeutralizing monoclonal antibodies (mAb) targeting SARS-CoV-2 decrease hospitalization and death in patients with mild to moderate Covid-19. Yet, their clinical use is limited, and comparative effectiveness is unknown.\n\nMethodsWe present the first results of an ongoing, learning health system adaptive platform trial to expand mAb treatment to all eligible patients and evaluate the comparative effectiveness of available mAbs. The trial launched March 10, 2021. Results are reported as of June 25, 2021 due to the U.S. federal decision to pause distribution of bamlanivimab-etesevimab; patient follow-up concluded on July 23, 2021. Patients referred for mAb who met Emergency Use Authorization criteria were provided a random mAb allocation of bamlanivimab, bamlanivimab-etesevimab, or casirivimab-imdevimab with a therapeutic interchange policy. The primary outcome was hospital-free days (days alive and free of hospital) within 28 days, where patients who died were assigned -1 day. The primary analysis was a Bayesian cumulative logistic model of all patients treated at an infusion center or emergency department, adjusting for treatment location, age, sex, and time. Inferiority was defined as a 99% posterior probability of an odds ratio < 1. Equivalence was defined as a 95% posterior probability that the odds ratio is within a given bound.\n\nResultsPrior to trial launch, 3.1% (502) of 16,345 patients who were potentially eligible by an automated electronic health record (EHR) screen received mAb. During the trial period, 23.2% (1,201) of 5,173 EHR-screen eligible patients were treated, a 7.5-fold increase. After including additional referred patients from outside the health system, a total of 1,935 study patients received mAb therapy (128 bamlanivimab, 885 bamlanivimab-etesevimab, 922 casirivimab-imdevimab). Mean age ranged from 55 to 57 years, half were female (range, 53% to 54%), and 17% were Black (range, 12% to 19%). Median hospital-free days were 28 (IQR, 28 to 28) for each mAb group. Hospitalization varied between groups (bamlanivimab, 12.5%; bamlanivimab-etesevimab, 14.7%, casirivimab-imdevimab, 14.3%). Relative to casirivimab-imdevimab, the median adjusted odds ratios were 0.58 (95% credible interval (CI), 0.30 to 1.16) and 0.94 (95% CI, 0.72 to 1.24) for the bamlanivimab and bamlanivimab-etesevimab groups, respectively. These odds ratios yielded 91% and 94% probabilities of inferiority of bamlanivimab versus bamlanivimab-etesevimab and casirivimab-imdevimab respectively, and an 86% probability of equivalence between bamlanivimab-etesevimab and casirivimab-imdevimab, at the prespecified odds ratio bound of 0.25. Twenty-one infusion-related adverse events occurred in 0% (0/128), 1.4% (12/885), and 1.0% (9/922) of patients treated with bamlanivimab, bamlanivimab-etesevimab, and casirivimab-imdevimab, respectively.\n\nConclusionIn non-hospitalized patients with mild to moderate Covid-19, bamlanivimab, compared to bamlanivimab-etesevimab and casirivimab-imdevimab, resulted in 91% and 94% probabilities of inferiority with regards to odds of improvement in hospital-free days within 28 days. There was an 86% probability of equivalence between bamlanivimab-etesevimab and casirivimab-imdevimab at an odds ratio bound of 0.25. However, the trial was unblinded early due to federal distribution decisions, and no mAb met prespecified criteria for statistical inferiority or equivalence. (ClinicalTrials.gov, NCT04790786).", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Erin K McCreary PharmD", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "J Ryan Bariola MD", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Tami Minnier MS", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Richard J Wadas MD", - "author_inst": "Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Judith A Shovel BSN", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Debbie L Albin BS", - "author_inst": "Supply Chain Management/HC Pharmacy, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Oscar C Marroquin MD", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Kevin E Kip PhD", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Kevin Collins MBA", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Mark Schmidhofer MD", - "author_inst": "Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Mary K Wisniewski MA", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "David A Nace MD", - "author_inst": "Division of Geriatric Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA" - }, - { - "author_name": "Colleen Sullivan MHA", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Meredith Axe BS", - "author_inst": "Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Russell Meyer MBA", - "author_inst": "Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Alexandra Weissman MD", - "author_inst": "Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "William Garrard PhD", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Octavia M Peck-Palmer PhD", - "author_inst": "Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Alan Wells MD", - "author_inst": "Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Robert D Bart MD", - "author_inst": "Health Services Division, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Anne Yang MD", - "author_inst": "Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Lindsay Berry PhD", - "author_inst": "Berry Consultants, Austin, TX, USA" - }, - { - "author_name": "Scott Berry PhD", - "author_inst": "Berry Consultants, Austin, TX, USA" - }, - { - "author_name": "Anna McGlothin PhD", - "author_inst": "Berry Consultants, Austin, TX, USA" - }, - { - "author_name": "Amy Crawford PhD", - "author_inst": "Berry Consultants, Austin, TX, USA" - }, - { - "author_name": "Tina Khadem PharmD", - "author_inst": "Health System Office of Healthcare Innovation, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Kelsey Linstrum MS", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Stephanie K Montgomery MS", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Daniel Ricketts MT", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Jason N Kennedy MS", - "author_inst": "Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Caroline J Pidro BS", - "author_inst": "Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of " - }, - { - "author_name": "Ghady Haidar MD", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Graham M Snyder MD", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Bryan J McVerry MD", - "author_inst": "Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA" - }, - { - "author_name": "Christopher W Seymour MD", - "author_inst": "Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Derek C Angus MD", - "author_inst": "Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - }, - { - "author_name": "Paula L Kip PhD", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA" - }, - { - "author_name": "Dave T Huang MD", - "author_inst": "Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.09.08.459502", "rel_title": "Digital Spatial Profiling of Collapsing Glomerulopathy", @@ -601154,6 +602088,81 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.09.09.459577", + "rel_title": "A virus-encoded microRNA contributes to evade innate immune response during SARS-CoV-2 infection", + "rel_date": "2021-09-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.09.459577", + "rel_abs": "SARS-CoV-2 infection results in impaired interferon response in severe COVID-19 patients. However, how SARS-CoV-2 interferes with host immune response is incompletely understood. Here, we sequenced small RNAs from SARS-CoV-2-infected human cells and identified a micro-RNA (miRNA) encoded in a recently evolved region of the viral genome. We show that the virus-encoded miRNA produces two miRNA isoforms in infected cells by the enzyme Dicer and they are loaded into Argonaute proteins. Moreover, the predominant miRNA isoform targets the 3UTR of interferon-stimulated genes and represses their expression in a miRNA-like fashion. Finally, the two viral miRNA isoforms were detected in nasopharyngeal swabs from COVID-19 patients. We propose that SARS-CoV-2 employs a virus-encoded miRNA to hijack the host miRNA machinery and evade the interferon-mediated immune response.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Meetali Singh", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Maxime Chazal", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Piergiuseppe Quarato", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Loan Bourdon", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Christope Malabat", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Thomas Vallet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marco Vignuzzi", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sylvie van der Werf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sylvie Behillil", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Flora Donati", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nathalie Sauvonnet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Giulia Nigro", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Maryline Bourgine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nolwenn Jouvenet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Germano Cecere", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.09.09.459664", "rel_title": "An adjuvanted SARS-CoV-2 RBD nanoparticle elicits neutralizing antibodies and fully protective immunity in aged mice", @@ -602926,77 +603935,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.03.21262874", - "rel_title": "Detection of SARS CoV-2 contamination in the Operating Room and Birthing Room Setting: Risks to attending health care workers", - "rel_date": "2021-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21262874", - "rel_abs": "BackgroundThe exposure risks to front-line health care workers who are in close proximity for prolonged periods of time, caring for COVID-19 patients undergoing surgery or obstetrical delivery is unclear. Understanding of sample types that may harbour virus is important for evaluating risk.\n\nObjectivesTo determine if SARS-CoV-2 viral RNA from patients with COVID-19 undergoing surgery or obstetrical care is present in: 1) the peritoneal cavity of males and females 2) the female reproductive tract, 3) the environment of the surgery or delivery suite (surgical instruments, equipment used, air or floors) and 4) inside the masks of the attending health care workers.\n\nMethodsThe presence of SARS-CoV-2 viral RNA in patient, environmental and air samples was identified by real time reverse transcriptase polymerase chain reaction (RT-PCR). Air samples were collected using both active and passive sampling techniques.\n\nResultsIn this multi-centre observational case series, 32 patients with COVID-19 underwent urgent surgery or obstetrical delivery and 332 patient and environmental samples were collected and analyzed to determine if SARS-CoV-2 RNA was present. SARS-CoV-2 RNA was detected in: 4/24(16.7%) patient samples, 5/60(8.3%) floor, 1/54(1.9%) air, 10/23(43.5%) surgical instruments/equipment, 0/24 cautery filters and 0/143 inner surface of mask samples.\n\nConclusionsWhile there is evidence of SARS-CoV-2 RNA in the surgical and obstetrical operative environment (6% of samples taken), the finding of no detectable virus inside the masks worn by the medical teams would suggest a low risk of infection for our health care workers using appropriate personal protective equipment (PPE).", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Patricia Lee", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Robert Kozak", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Nasrin Alavi", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Hamza Mbareche", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Rose Kung", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Kellie Murphy", - "author_inst": "Sinai Health System" - }, - { - "author_name": "Darian Perruzza", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Stephanie Jarvi", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Elsa Salvant", - "author_inst": "Sunnybrook Research Institute" - }, - { - "author_name": "Noor Niyar Ladhani", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Albert Yee", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Louise-Helene Gagnon", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Richard Jenkinson", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Grace Y. Liu", - "author_inst": "Sunnybrook Health Sciences Centre" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.09.02.21262599", "rel_title": "Severe COVID-19 is associated with sustained biochemical disturbances and prolonged symptomatology; A retrospective single-centre cohort study", @@ -603216,6 +604154,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.02.21263012", + "rel_title": "Infectiousness of places: The impact of human settlement and activity space in the transmission of COVID-19", + "rel_date": "2021-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21263012", + "rel_abs": "Places are fundamental factors in the spread of epidemics, as they are where people agglomerate and interact. This paper explores how different types of places--activity spaces at micro-level and human settlements at macro-level--impact the transmission of infections using evidences from COVID-19. We examine eleven types of activity spaces and find heterogeneous impacts across countries, yet we also find that non-essential activity spaces tend to have larger impacts than essential ones. Contrary to common beliefs, settlement size and density are not positively associated with reproduction numbers. Further, the impacts of closing activity spaces vary with settlement types and are consistently lower in larger settlements in all sample countries, suggesting more complex pattern of virus transmission in large settlements. This work takes first steps in systematically evaluating the epistemological risks of places at multiple scales, which contributes to knowledge in urban resilience, health and livability.\n\nTeaserActivity spaces and human settlement characteristics impact the spread of epidemics in multiple ways and should be considered in policy making.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Lun Liu", + "author_inst": "Peking University" + }, + { + "author_name": "Hui Wang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Zhu Zhang", + "author_inst": "Peking University" + }, + { + "author_name": "Weiyi Zhang", + "author_inst": "Peking University" + }, + { + "author_name": "Shengsheng Zhuang", + "author_inst": "Peking Union Medical College" + }, + { + "author_name": "Tingmiao Lv", + "author_inst": "Peking University" + }, + { + "author_name": "Chi-on Chio", + "author_inst": "Peking University" + }, + { + "author_name": "Yifan Wang", + "author_inst": "Peking University" + }, + { + "author_name": "Rina Dao", + "author_inst": "Peking University" + }, + { + "author_name": "Chuchang Tang", + "author_inst": "Peking University" + }, + { + "author_name": "On-Ieng Ao-Ieong", + "author_inst": "Peking University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.02.21262146", "rel_title": "Immunogenicity of Pfizer mRNA COVID-19 vaccination followed by J&J adenovirus COVID-19 vaccination in two CLL patients", @@ -604532,69 +605529,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.01.21262540", - "rel_title": "Analysis of the Dynamics, Outcome, and Prerequisites of the first German SARS-CoV-2 Superspreading Event", - "rel_date": "2021-09-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.01.21262540", - "rel_abs": "BackgroundThe beginning of the COVID-19 pandemic was shaped by superspreading events including large-scale outbreaks. In Germany the first SARS-CoV-2 outbreak was a superspreading event in a rural area during indoor carnival festivities in February 2020.\n\nMethods51 days after the event all known participants were asked to give blood samples, pharyngeal swabs and answer a self-administered questionnaire. Metric room coordinates for all tables, seats, and ventilation-points were assessed.\n\nFindingsWe analyzed infection rates among all 411 participants, and the risk of infection in relation to various factors including age, alcohol consumption, and ventilation system. Overall, 46% (n=186/404) of the participants had been infected. We demonstrate that the spatial distribution of infected participants was associated with proximity to the ventilation system (represented as inverse distance, with Odds Ratio OR 1.39, 95% KI [0.86; 2.25]). Interestingly, the risk of infection was highly associated with age, whereby children (OR: 0.33 [0.267; 0.414]) and young adults (age 18-25) had a lower risk of infection than older participants resulting in an average infection risk increase of 28% per 10 years age difference. Behavioral differences also impacted the risk of infection including time spent outside (OR: 0.55 [0.33; 0.91]) or smoking (OR: 0.32 [0.124; 0.81]).\n\nInterpretationOur findings underline the importance of proper indoor ventilation for events in the future. The lower susceptibility for children and young adults indicates their limited involvement in superspreading events.\n\nFundingThe government of North Rhine-Westphalia (Germany) supported the study with 65,000 Euro.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe scientific literature was searched for the term \"superspreading event AND Covid-19 OR Sars Cov 2\" and identified published papers from China, South Korea, Europe, and North America. Most researchers analyzed superspreading events within a health care setting e.g. in hospitals or nursing homes, or described the general impact of superspreading events on the global pandemic. Only a few metanalyses of transmission clusters analyzed party occasions (e.g. a nightclub in Berlin, Germany) as superspreading events. These reports describe less than 100 infections and are very limited due to missing data or reporting biases. Therefore, the ability to draw scientific conclusions is also limited. Additionally, to our knowledge, there are no studies, which investigated individual behavior, the location, and role of children during a superspreading event. The research for the study started April 2020 and was concluded in June 2021.\n\nAdded value of this studyOur report analyzes the first COVID-19 superspreading event in Germany in detail, which was not only a unique setting but also included children and adults in the same room. We demonstrate that nearly half of the participants were infected with SARS-CoV-2 and that the proximity of the seating to the ventilation system was an important risk factor for infection. The data showed that low physical distance including singing and duration of attendance at this event increased the risk of infection, while regular smoking and spending the break of the event outside lowered the risk of infection. This underlines the benefit of airing to lower the amount of both droplets and aerosols. Furthermore, we found lower infection in children than adults despite being in the same room suggesting differences in infectability in children. Indeed, we observed that an additional 10 years of age is on average associated with 28% increased risk of infection.\n\nImplications of all the available evidenceTaken together, the results demonstrate the importance of the ventilation system during superspreading events. In particular children and young adults had a lower risk of infection during the event indicating that they have a limited role during this pandemic. Overall, our data demonstrate in detail age-dependent infectability as well as highlights to understand transmission dynamics in order to improve comprehensive public health preparedness measures.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Lukas Wessendorf", - "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany, and German Center for Infection Research (DZIF), partner site Bonn-Cologne" - }, - { - "author_name": "Enrico Richter", - "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany, and German Center for Infection Research (DZIF), partner site Bonn-Cologne" - }, - { - "author_name": "Bianca Schulte", - "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany, and German Center for Infection Research (DZIF), partner site Bonn-Cologne" - }, - { - "author_name": "Ricarda Maria Schmithausen", - "author_inst": "Institute of Hygiene and Public Health, University Hospital, University of Bonn, Germany" - }, - { - "author_name": "Martin Exner", - "author_inst": "Institute of Hygiene and Public Health, University Hospital, University of Bonn, Germany" - }, - { - "author_name": "Nils Lehmann", - "author_inst": "Institute of Medical Informatics, Biometry und Epidemiology (IMIBE), University Hospital Essen, Germany" - }, - { - "author_name": "Martin Coenen", - "author_inst": "Clinical Study Core Unit, Study Center Bonn (SZB), Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Germany" - }, - { - "author_name": "Christine Fuhrmann", - "author_inst": "Clinical Study Core Unit, Study Center Bonn (SZB), Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Germany" - }, - { - "author_name": "Angelika Kellings", - "author_inst": "Clinical Study Core Unit, Study Center Bonn (SZB), Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Germany" - }, - { - "author_name": "Anika Huesing", - "author_inst": "Institute of Medical Informatics, Biometry und Epidemiology (IMIBE), University Hospital Essen, Germany" - }, - { - "author_name": "Karl-Heinz Joeckel", - "author_inst": "Institute of Medical Informatics, Biometry und Epidemiology (IMIBE), University Hospital Essen, Germany" - }, - { - "author_name": "Hendrik Streeck", - "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany, and German Center for Infection Research (DZIF), partner site Bonn-Cologne" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.01.21262990", "rel_title": "Impact and effectiveness of social distancing for COVID-19 mitigation -- A transnational and transregional study", @@ -604798,6 +605732,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.02.21261735", + "rel_title": "A third dose of inactivated vaccine augments the potency, breadth, and duration of anamnestic responses against SARS-CoV-2", + "rel_date": "2021-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21261735", + "rel_abs": "Emergence of variants of concern (VOC) with altered antigenic structures and waning humoral immunity to SARS-CoV-2 are harbingers of a long pandemic. Administration of a third dose of an inactivated virus vaccine can boost the immune response. Here, we have dissected the immunogenic profiles of antibodies from 3-dose vaccinees, 2-dose vaccinees and convalescents. Better neutralization breadth to VOCs, expeditious recall and long-lasting humoral response bolster 3-dose vaccinees in warding off COVID-19. Analysis of 171 complex structures of SARS-CoV-2 neutralizing antibodies identified structure-activity correlates, revealing ultrapotent, VOCs-resistant and broad-spectrum antigenic patches. Construction of immunogenic and mutational heat maps revealed a direct relationship between \"hot\" immunogenic sites and areas with high mutation frequencies. Ongoing antibody somatic mutation, memory B cell clonal turnover and antibody composition changes in B cell repertoire driven by prolonged and repeated antigen stimulation confer development of monoclonal antibodies with enhanced neutralizing potency and breadth. Our findings rationalize the use of 3-dose immunization regimens for inactivated vaccines.\n\nOne sentence summaryA third booster dose of inactivated vaccine produces a highly sifted humoral immune response via a sustained evolution of antibodies capable of effectively neutralizing SARS-CoV-2 variants of concern.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Kang Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Yunlong Richard Cao", + "author_inst": "Peking University" + }, + { + "author_name": "Yunjiao Zhou", + "author_inst": "Shanghai Medical College of Fudan University" + }, + { + "author_name": "Jiajing Wu", + "author_inst": "National Institutes for Food and Drug Control (NIFDC)" + }, + { + "author_name": "Zijing Jia", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Yaling Hu", + "author_inst": "Sinovac Biotech Ltd, Beijing, China" + }, + { + "author_name": "Ayijiang Yisimayi", + "author_inst": "Peking University" + }, + { + "author_name": "Wangjun Fu", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Lei Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Pan Liu", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Kaiyue Fan", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Ruihong Chen", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Lin Wang", + "author_inst": "Sinovac Biotech Ltd, Beijing, China" + }, + { + "author_name": "Li Jing", + "author_inst": "Sinovac Biotech Ltd, Beijing, China" + }, + { + "author_name": "Yao Wang", + "author_inst": "Peking University" + }, + { + "author_name": "Xiaoqi Ge", + "author_inst": "Sinovac Biotech Ltd, Beijing, China" + }, + { + "author_name": "Qianqian Zhang", + "author_inst": "Shanghai Medical College of Fudan University" + }, + { + "author_name": "Jianbo Wu", + "author_inst": "Shanghai Medical College of Fudan University" + }, + { + "author_name": "Nan Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Wei Wu", + "author_inst": "Shanghai Medical College of Fudan University" + }, + { + "author_name": "Yidan Gao", + "author_inst": "Shanghai Medical College of Fudan University" + }, + { + "author_name": "Jingyun Miao", + "author_inst": "Acrobiosystems Inc, Beijing, China" + }, + { + "author_name": "Yinan Jiang", + "author_inst": "Acrobiosystems Inc, Beijing, China" + }, + { + "author_name": "Lili Qin", + "author_inst": "Acrobiosystems Inc, Beijing, China" + }, + { + "author_name": "Ling Zhu", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Weijin Huang", + "author_inst": "Sinovac Biotech Ltd, Beijing, China" + }, + { + "author_name": "Yanjun Zhang", + "author_inst": "Zhejiang Center for Disease Control and Prevention" + }, + { + "author_name": "Huan Zhang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Baisheng Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Qiang Gao", + "author_inst": "Sinovac Biotech Ltd, Beijing, China" + }, + { + "author_name": "Xiaoliang Sunney Xie", + "author_inst": "Peking University" + }, + { + "author_name": "Youchun Wang", + "author_inst": "National Institutes for Food and Drug Control" + }, + { + "author_name": "Qiao Wang", + "author_inst": "Shanghai Medical College of Fudan University" + }, + { + "author_name": "Xiangxi Wang", + "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Bi" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.02.21263010", "rel_title": "Effectiveness of inactive COVID-19 vaccines against severe illness in B.1.617.2 (Delta) variant-infected patients in Jiangsu, China", @@ -605990,89 +607075,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.08.31.21262891", - "rel_title": "Strengthening public COVID-19 response with private facilities in Kisumu, Kenya", - "rel_date": "2021-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262891", - "rel_abs": "INTRODUCTIONIn Africa almost half of healthcare services are delivered through private sector providers. These are often underused in national public health responses. In line with our previous HIV experience and to support and accelerate the public sectors COVID-19 response, we initiated a public-private project (PPP) in Kisumu County, Kenya. In this manuscript we demonstrate this PPPs performance, using COVID-19 testing as an aggregator and with semi-real time digital monitoring tools for rapid scaling of COVID-19 response.\n\nMETHODSCOVID-19 diagnostic testing formed the basis for a PPP between KEMRI, Department of Health Kisumu County, PharmAccess Foundation, and local faith-based and private healthcare facilities: COVID-Dx. COVID-Dx was implemented from June 01, 2020, to March 31, 2021 in Kisumu County, Kenya. Trained laboratory technologists in participating healthcare facilities collected nasopharyngeal and oropharyngeal samples from patients meeting the Kenyan MoH COVID-19 case definition. Samples were rapidly transported by motorbike and tested using RT-PCR at the central reference laboratory in KEMRI. Healthcare workers in participating facilities collected patient clinical data using a digitized MoH COVID-19 Case Identification Form. We shared aggregated results from these data via (semi-) live dashboards with all relevant stakeholders through their mobile phones. Statistical analyses were performed using Stata 16 to inform project processes.\n\nRESULTSNine private facilities participated in the project. A detailed patient trajectory was developed from case identification to result reporting, all steps supported by a semi-real time digital dashboard. A total of 4,324 PCR tests for SARS-CoV-2 (16%) were added to the public response, identifying 425 positives. Geo-mapped and time-tagged information on incident cases was depicted on Google maps dashboards and fed back to policymakers for informed rapid decision making. Preferential COVID-19 testing was performed on health workers at risk, with 1,009 tested (43% of all County health workforce).\n\nCONCLUSIONWe demonstrate feasibility of rapidly increasing the public health sector response to a COVID-19 epidemic outbreak in an African setting. Our PPP intervention in Kisumu, Kenya was based on a joint testing strategy and demonstrated that semi-real time digitalization of patient trajectories in the healthcare system can gain significant efficiencies, linking public and private healthcare efforts, increasing transparency, support better quality health services and informing policy makers to target interventions. This PPP has since scaled to 33 facilities in Kisumu and subsequently to 84 sites in 14 western Kenyan Counties.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Shannen van Duijn", - "author_inst": "PharmAccess Foundation Amsterdam Office, the Netherlands" - }, - { - "author_name": "Hellen C. Barsosio", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Mevis Omollo", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Emmanuel Milimo", - "author_inst": "PharmAccess Foundation Kenya Office, Kisumu, Kenya" - }, - { - "author_name": "Isdorah A. Odero", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Robert Aroka", - "author_inst": "PharmAccess Foundation Kenya Office, Kisumu, Kenya" - }, - { - "author_name": "Teresa de Sanctis", - "author_inst": "PharmAccess Foundation Amsterdam Office, the Netherlands" - }, - { - "author_name": "Alloys K Oloo", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Micah J. June", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Nathalie Houben", - "author_inst": "PharmAccess Foundation Kenya Office, Kisumu, Kenya" - }, - { - "author_name": "Charlotte Wilming", - "author_inst": "PharmAccess Foundation Amsterdam Office, the Netherlands" - }, - { - "author_name": "Kephas Otieno", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Simon Kariuki", - "author_inst": "Kenya Medical Research Institute (KEMRI), Center for Global Health Research (CGHR), Kisumu, Kenya" - }, - { - "author_name": "Simon Onsongo", - "author_inst": "Aga Khan Hospital, Kisumu" - }, - { - "author_name": "Albert Odhiambo", - "author_inst": "County Government of Kisumu, Kisumu, Kenya" - }, - { - "author_name": "Gregory Ganda", - "author_inst": "Department of Health Kisumu" - }, - { - "author_name": "Tobias Rinke de Wit", - "author_inst": "PharmAccess Foundation Amsterdam Office, the Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.03.458829", "rel_title": "Characterization of SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.618 on cell entry, host range, and sensitivity to convalescent plasma and ACE2 decoy receptor", @@ -606468,6 +607470,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.01.21262955", + "rel_title": "Immune response elicited from heterologous SARS-CoV-2 vaccination: Sinovac (CoronaVac) followed by AstraZeneca (Vaxzevria)", + "rel_date": "2021-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.01.21262955", + "rel_abs": "Limited COVID-19 vaccines in many countries have delayed mass-immunization. Although individuals fully vaccinated with Vaxzevria (AstraZeneca) have higher antibody levels than those with CoronaVac (Sinovac), heterologous prime-boost with CoronaVac-Vaxzevria yielded comparable antibody levels to two-dose Vaxzevria. Combination use of different available vaccines may be warranted in Thailand, which faces limited vaccine choice and supply.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ritthideach Yorsaeng", + "author_inst": "Chulalongkorn University" + }, + { + "author_name": "Preeyaporn Vichaiwattana", + "author_inst": "Chulalongkorn University" + }, + { + "author_name": "Sirapa Klinfueng", + "author_inst": "Chulalongkorn University" + }, + { + "author_name": "Lakkhana Wongsrisang", + "author_inst": "Chulalongkorn University" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Chulalongkorn University" + }, + { + "author_name": "Sompong Vongpunsawad", + "author_inst": "Chulalongkorn University" + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Chulalongkorn University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.30.21262446", "rel_title": "Effectiveness of COVID-19 Vaccines Against SARS-CoV-2 Infection During a Delta Variant Epidemic Surge in Multnomah County, Oregon, July 2021", @@ -607944,269 +608989,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.09.02.21262965", - "rel_title": "Whole genome sequencing identifies multiple loci for critical illness caused by COVID-19", - "rel_date": "2021-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21262965", - "rel_abs": "Critical illness in COVID-19 is caused by inflammatory lung injury, mediated by the host immune system. We and others have shown that host genetic variation influences the development of illness requiring critical care1 or hospitalisation2;3;4 following SARS-Co-V2 infection. The GenOMICC (Genetics of Mortality in Critical Care) study recruits critically-ill cases and compares their genomes with population controls in order to find underlying disease mechanisms.\n\nHere, we use whole genome sequencing and statistical fine mapping in 7,491 critically-ill cases compared with 48,400 population controls to discover and replicate 22 independent variants that significantly predispose to life-threatening COVID-19. We identify 15 new independent associations with critical COVID-19, including variants within genes involved in interferon signalling (IL10RB, PLSCR1), leucocyte differentiation (BCL11A), and blood type antigen secretor status (FUT2). Using transcriptome-wide association and colocalisation to infer the effect of gene expression on disease severity, we find evidence implicating expression of multiple genes, including reduced expression of a membrane flippase (ATP11A), and increased mucin expression (MUC1), in critical disease.\n\nWe show that comparison between critically-ill cases and population controls is highly efficient for genetic association analysis and enables detection of therapeutically-relevant mechanisms of disease. Therapeutic predictions arising from these findings require testing in clinical trials.", - "rel_num_authors": 62, - "rel_authors": [ - { - "author_name": "Athanasios Kousathanas", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Erola Pairo-Castineira", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Konrad Rawlik", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Alex Stuckey", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Christopher A Odhams", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Susan Walker", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Clark D Russell", - "author_inst": "Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK" - }, - { - "author_name": "Tomas Malinauskas", - "author_inst": "Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK" - }, - { - "author_name": "Jonathan Millar", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Katherine S Elliott", - "author_inst": "Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK" - }, - { - "author_name": "Fiona Griffiths", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Wilna Oosthuyzen", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Kirstie Morrice", - "author_inst": "Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Sean Keating", - "author_inst": "Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK." - }, - { - "author_name": "Bo Wang", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Daniel Rhodes", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Lucija Klaric", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Marie Zechner", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Nick Parkinson", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Andrew D. Bretherick", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Afshan Siddiq", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Peter Goddard", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Sally Donovan", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "David Maslove", - "author_inst": "Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, ON, Canada." - }, - { - "author_name": "Alistair Nichol", - "author_inst": "Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland." - }, - { - "author_name": "Malcolm G Semple", - "author_inst": "NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, L" - }, - { - "author_name": "Tala Zainy", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Fiona Maleady-Crowe", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Linda Todd", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Shahla Salehi", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Julian Knight", - "author_inst": "Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK" - }, - { - "author_name": "Greg Elgar", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Georgia Chan", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Prabhu Arumugam", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Tom A Fowler", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Augusto Rendon", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Manu Shankar-Hari", - "author_inst": "Department of Intensive Care Medicine, Guy's and St. Thomas NHS Foundation Trust, London, UK." - }, - { - "author_name": "Charlotte Summers", - "author_inst": "Department of Medicine, University of Cambridge, Cambridge, UK." - }, - { - "author_name": "Charles Hinds", - "author_inst": "William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK." - }, - { - "author_name": "Peter Horby", - "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK." - }, - { - "author_name": "Danny McAuley", - "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK" - }, - { - "author_name": "Hugh Montgomery", - "author_inst": "UCL Centre for Human Health and Performance, London, W1T 7HA, UK." - }, - { - "author_name": "Peter J.M. Openshaw", - "author_inst": "National Heart and Lung Institute, Imperial College London, London, UK" - }, - { - "author_name": "Yang Wu", - "author_inst": "Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia" - }, - { - "author_name": "Jian Yang", - "author_inst": "Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China" - }, - { - "author_name": "Paul Elliott", - "author_inst": "Imperial College, London" - }, - { - "author_name": "Timothy Walsh", - "author_inst": "Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK." - }, - { - "author_name": "- GenoMICC Investigators", - "author_inst": "" - }, - { - "author_name": "- 23andMe Investigators", - "author_inst": "" - }, - { - "author_name": "- Covid-19 Human Genetics Initiative", - "author_inst": "" - }, - { - "author_name": "Angie Fawkes", - "author_inst": "Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Lee Murphy", - "author_inst": "Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Kathy Rowan", - "author_inst": "Intensive Care National Audit & Research Centre, London, UK." - }, - { - "author_name": "Chris P Ponting", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "Veronique Vitart", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK." - }, - { - "author_name": "James F Wilson", - "author_inst": "Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK." - }, - { - "author_name": "Richard H Scott", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Sara Clohisey", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Loukas Moutsianas", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "Andy Law", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK." - }, - { - "author_name": "Mark J Caulfield", - "author_inst": "Genomics England, London UK" - }, - { - "author_name": "J. Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.08.29.21262798", "rel_title": "Viral loads of Delta-variant SARS-CoV2 breakthrough infections following vaccination and booster with the BNT162b2 vaccine", @@ -608406,6 +609188,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.31.21262915", + "rel_title": "COVID-19 scenarios for comparing the effectiveness of age-specific vaccination regimes, exemplified for the city of Aschaffenburg (Germany)", + "rel_date": "2021-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262915", + "rel_abs": "Purpose of this reportThe purpose of this rapid communication is to illustrate the effectiveness of different vaccination regimes for controlling the number of severe and critical COVID-19 cases in the city of Aschaffenburg, Germany. Our results show that, despite numerous vaccinations in the past, further vaccinations are necessary to immunize the population and to keep the number of severe and critical cases low in the coming months. Considering that not all people can or want to receive vaccination, we compare different age-specific vaccination approaches.\n\nApplied MethodsWe use the agent-based epidemiological simulator Covasim for discussing the impact of different vaccination strategies. We calibrate it to reproduce the historical course of the COVID-19 pandemic in the city of Aschaffenburg, Germany; for this, we model and integrate numerous public health interventions imposed on the local population. As for some of the political actions rigorous quantification is currently not available, we fit those unknown (free) model parameters to published data on the measured epidemiological dynamics. Then we calculate the state of immunization of the population, gained through infections and vaccinations, at any time in the past, including models for time-dependent immunity decay that have been made available in Covasim. Finally, we define and compare scenarios of different vaccination regimes, especially with regard to vaccinating adolescents and providing booster vaccinations to the elderly.\n\nKey messageWithout further vaccinations, we expect a strong increase in severe and critical cases. In order to restrict their growth our simulations suggest that in all considered cases vaccinations of unvaccinated people is more effective than booster vaccinations for already fully vaccinated people. This applies even to vaccinations of young people who are not themselves at high risk of developing severe or critical illness. We attribute this observation to the fact that immunization of adolescents indirectly protects vulnerable age groups by preventing the spread of the virus more effectively than further immunizing other age groups. This indicates that with the pandemic ongoing, strategies focussed on minimizing individual health risks by vaccinations may no longer coincide with those needed to minimize the number of severe and critical cases.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Tobias Krebs", + "author_inst": "University of Applied Research Aschaffenburg and Center for Scientific Services and Transfer (ZeWiS)" + }, + { + "author_name": "Holger von Jouanne-Diedrich", + "author_inst": "University of Applied Research Aschaffenburg" + }, + { + "author_name": "Michael J Moeckel", + "author_inst": "University of Applied Sciences Aschaffenburg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.26.21262704", "rel_title": "SARS-CoV-2 Variant Tracking and Mitigation: Strategies and Results from In-Person Learning at a Midwestern University in the 2020/2021 School Year", @@ -610066,37 +610875,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.29.21262799", - "rel_title": "The emergence of SARS-CoV-2 variants of concern is driven by acceleration of the evolutionary rate", - "rel_date": "2021-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.29.21262799", - "rel_abs": "The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly generated genome data. These data have revealed the emergence of lineages with mutations associated to transmissibility and antigenicity, known as variants of concern (VOCs). A striking aspect of VOCs is that many of them involve an unusually large number of defining mutations. Current phylogenetic estimates of the evolutionary rate of SARS-CoV-2 suggest that its genome accrues around 2 mutations per month. However, VOCs can have around 15 defining mutations and it is hypothesised that they emerged over the course of a few months, implying that they must have evolved faster for a period of time. We analysed genome sequence data from the GISAID database to assess whether the emergence of VOCs can be attributed to changes in the evolutionary rate of the virus and whether this pattern can be detected at a phylogenetic level using genome data. We fit a range of molecular clock models and assessed their statistical fit. Our analyses indicate that the emergence of VOCs is driven by an episodic increase in the evolutionary rate of around 4-fold the background phylogenetic rate estimate that may have lasted several weeks or months. These results underscore the importance of monitoring the molecular evolution of the virus as a means of understanding the circumstances under which VOCs may emerge.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "John H Tay", - "author_inst": "Peter Doherty Institute, University of Melbourne" - }, - { - "author_name": "Ashleigh F Porter", - "author_inst": "Peter Doherty Institute, University of Melbourne" - }, - { - "author_name": "Wytamma Wirth", - "author_inst": "Peter Doherty Institute University of Melbourne" - }, - { - "author_name": "Sebastian Duchene", - "author_inst": "University of Melbourne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.30.21262821", "rel_title": "The impact of pausing the Oxford-AstraZeneca COVID-19 vaccine on uptake in Europe: a difference-in-differences analysis", @@ -610392,6 +611170,185 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.28.21262763", + "rel_title": "Increasing incidence of parosmia and phantosmia in patients recovering from COVID-19 smell loss", + "rel_date": "2021-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.28.21262763", + "rel_abs": "ImportanceSudden smell loss is a specific early symptom of COVID-19, with an estimated prevalence of ~40% to 75%. Smell impairment affects physical and mental health, and dietary behavior. Thus, it is critical to understand the rate and time course of smell recovery.\n\nObjectiveTo characterize smell function and recovery up to 11 months post COVID-19 infection.\n\nSettings, ParticipantsThis longitudinal survey of individuals suffering COVID-19-related smell loss assessed disease symptoms and gustatory and olfactory function. Participants (n=12,313) who completed an initial respiratory symptoms, chemosensory function and COVID-19 diagnosis survey (S1) between April and September 2020 and completed a follow-up survey (S2) between September 2020 and February 2021; 27.5% participants responded (n=3,386), with 1,468 being diagnosed with COVID-19 and suffering co-occurring smell and taste loss at the beginning of their illness.\n\nMain Outcomes & MeasuresPrimary outcomes are ratings of smell and taste function on a visual analog scale, and self-report of parosmia (smell distortions) and phantosmia (unexplained smells). Secondary outcomes include a checklist of other COVID-19 symptoms.\n\nResultsOn follow-up (median time since COVID-19 onset ~200 days), ~60% of women and ~48% of men reported less than 80% of their pre-illness smell ability. Taste typically recovered faster than smell, and taste loss rarely persisted if smell recovered. Prevalence of parosmia and phantosmia was ~10% of participants in S1 and increased substantially in S2: ~47% for parosmia and ~25% for phantosmia. Persistent smell impairment was associated with more symptoms overall, suggesting it may be a key marker of long-COVID. During COVID-19 illness, the ability to smell was slightly lower among those who did not recover their pre-illness ability to smell at S2.\n\nConclusions and RelevanceWhile smell loss improves for many individuals who lost it due to COVID-19, the prevalence of parosmia and phantosmia increases substantially over time. Olfactory dysfunction is also associated with wider COVID-19 symptoms and may persist for many months after COVID-19 onset. Taste loss in the absence of smell loss is rare. Persistent qualitative smell symptoms are emerging as common long term sequelae; more research into treatment options is strongly warranted given that conservative estimates suggest millions of individuals may experience parosmia following COVID-19. Healthcare providers worldwide need to be prepared to treat post COVID-19 secondary effects on physical and mental health.\n\nTrial registrationThis project was pre-registered at OSF: https://osf.io/3e6zc.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC=\"FIGDIR/small/21262763v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@b2aceforg.highwire.dtl.DTLVardef@77a539org.highwire.dtl.DTLVardef@1004dbborg.highwire.dtl.DTLVardef@ef5c9c_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_ST_ABSQuestionC_ST_ABSWhat are the characteristics of smell and taste recovery of COVID-19 patients?\n\nFindingsIn this preregistered observational study of 1,468 participants, smell loss is associated with a higher number of COVID-19 symptoms, and may persist for at least 11 months following disease onset. While a majority of participants report quantitative improvement in their ability to smell, the prevalence of parosmia and phantosmia increases substantially at follow-up. Taste recovers faster than smell, suggesting taste and smell recover separately and can be distinguished by the respondents.\n\nMeaningOlfactory dysfunction appears to be a component of long-COVID, with parosmia as a prominent symptom in almost half of those with smell loss. More research into treatment is needed, especially given that olfactory dysfunction is associated with depression and loss of appetite. Health professionals should be aware of these common and long lasting effects.", + "rel_num_authors": 41, + "rel_authors": [ + { + "author_name": "Kathrin Ohla", + "author_inst": "Helmut-Schmidt-University / University of the Armed Forces Hamburg" + }, + { + "author_name": "Maria G Veldhuizen", + "author_inst": "Mersin University" + }, + { + "author_name": "Tomer Green", + "author_inst": "The Hebrew University of Jerusalem, Rehovot , Israel" + }, + { + "author_name": "Mackenzie E Hannum", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Alyssa J Bakke", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Shima Moein", + "author_inst": "Institute for Research in Fundamental Sciences (IPM)" + }, + { + "author_name": "Arnaud Tognetti", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Elbrich M Postma", + "author_inst": "Wageningen University" + }, + { + "author_name": "Robert Pellegrino", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Liang-Dar Hwang", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Javier Albayay", + "author_inst": "University of Trento" + }, + { + "author_name": "Sachiko Koyama", + "author_inst": "Indiana University" + }, + { + "author_name": "Alissa Nolden", + "author_inst": "University of Massachusetts, Amherst" + }, + { + "author_name": "Thierry Thomas-Danguin", + "author_inst": "INRAE Centre for Taste, Smell and Feeding Behavior" + }, + { + "author_name": "Carla Mucignat-Caretta", + "author_inst": "University of Padova" + }, + { + "author_name": "Nick S Menger", + "author_inst": "University of Tubingen" + }, + { + "author_name": "Iljia Croijmans", + "author_inst": "Utrecht University" + }, + { + "author_name": "Lina Ozturk", + "author_inst": "Mersin University" + }, + { + "author_name": "Huseyin Yanik", + "author_inst": "Mersin University" + }, + { + "author_name": "Denis Pierron", + "author_inst": "Universite Toulouse III" + }, + { + "author_name": "Veronica Pereda-Loth", + "author_inst": "Universite Toulouse III" + }, + { + "author_name": "Alexia Nunez-Parra", + "author_inst": "University of Chile" + }, + { + "author_name": "Aldair M Martinez Pineda", + "author_inst": "Universite Toulouse III" + }, + { + "author_name": "David Gillespie", + "author_inst": "University College London" + }, + { + "author_name": "Michael C Farruggia", + "author_inst": "Yale University" + }, + { + "author_name": "Cinzia Cecchetto", + "author_inst": "Univeristy of Padova" + }, + { + "author_name": "Marco A Fornazieri", + "author_inst": "Universidade Estadual de Londrina" + }, + { + "author_name": "Carl Philpott", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Vera Voznessenskaya", + "author_inst": "Severtsov Institute of Ecology & Evolution" + }, + { + "author_name": "Keiland Cooper", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Paloma Rohlfs Dominguez", + "author_inst": "Universidad del Pais Vasco/Euskal Herriko Unibertsitatea" + }, + { + "author_name": "Orietta Calcinoni", + "author_inst": "Provate practice" + }, + { + "author_name": "Jasper de Groot", + "author_inst": "Radboud University" + }, + { + "author_name": "Sanne Boesveldt", + "author_inst": "Wageningen University" + }, + { + "author_name": "Surabhi Bhutani", + "author_inst": "San Diego State University" + }, + { + "author_name": "Elisabeth M Weir", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Cara Exten", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Paule V Joseph", + "author_inst": "National Institute on Alcohol Abuse and alcoholism & National Institute of Nursing Research" + }, + { + "author_name": "Valentina Parma", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "John E Hayes", + "author_inst": "Pennsylvania State University" + }, + { + "author_name": "Masha Y Niv", + "author_inst": "The Hebrew University of Jerusalem, Rehovot , Israel" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.31.458325", "rel_title": "Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor", @@ -611788,41 +612745,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.28.458041", - "rel_title": "Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays", - "rel_date": "2021-08-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.28.458041", - "rel_abs": "SARS-CoV-2 main protease (Mpro) is one of the most extensive exploited drug targets for COVID-19. Structurally disparate compounds have been reported as Mpro inhibitors, raising the question of their target specificity. To elucidate the target specificity and the cellular target engagement of the claimed Mpro inhibitors, we systematically characterize their mechanism of action using the cell-free FRET assay, the thermal shift-binding assay, the cell lysate Protease-Glo luciferase assay, and the cell-based Flip-GFP assay. Collectively, our results have shown that majority of the Mpro inhibitors identified from drug repurposing including ebselen, carmofur, disulfiram, and shikonin are promiscuous cysteine inhibitors that are not specific to Mpro, while chloroquine, oxytetracycline, montelukast, candesartan, and dipyridamole do not inhibit Mpro in any of the assays tested. Overall, our study highlights the need of stringent hit validation at the early stage of drug discovery.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC=\"FIGDIR/small/458041v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (41K):\norg.highwire.dtl.DTLVardef@b0c310org.highwire.dtl.DTLVardef@d652deorg.highwire.dtl.DTLVardef@da8d0corg.highwire.dtl.DTLVardef@62449b_HPS_FORMAT_FIGEXP M_FIG C_FIG Flip-GFP and Protease-Glo luciferase assays, coupled with the FRET and thermal shift binding assays, were applied to validate the reported SARS-CoV-2 Mpro inhibitors.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Chunlong Ma", - "author_inst": "University of Arizona" - }, - { - "author_name": "Haozhou Tan", - "author_inst": "University of Arizona" - }, - { - "author_name": "Juliana Choza", - "author_inst": "University of Arizona" - }, - { - "author_name": "Yuying Wang", - "author_inst": "University of Arizona" - }, - { - "author_name": "Jun Wang", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.08.27.21262721", "rel_title": "Short-Term Immune Response After Inactivated SARS-CoV-2 (CoronaVac, Sinovac) And ChAdOx1 nCoV-19 (Vaxzevria, Oxford-AstraZeneca) Vaccinations in Thai Health Care Workers", @@ -612298,6 +613220,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.28.21262733", + "rel_title": "COVID-19 infection among health care workers: Experience in Base Hospital Wathupitiwala,Sri Lanka.", + "rel_date": "2021-08-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.28.21262733", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a serious global health pandemic resulting in high mortality and morbidity. Frontline health care workers (HCWs) are at an increased risk of the acquisition of severe acute respiratory syndrome coronavirus-2 infection (SARS CoV-2) due to their close interaction with infected patients (1, 2). Also, HCWs can serve as reservoirs of SARS CoV-2 cross-transmission both in community and hospital settings (1). However, the extent of COVID-19 infection among HCWs in Sri Lanka is understudied.\n\nObjectivesThis study determined the incidence, demographic characteristics, and risk exposure behavior of HCWs who tested positive for SARS CoV-2 at Base Hospital Wathupitiwala. Furthermore, the rate of acquisition of SARS CoV-2 following COVISHIELD/ChAdOx1 nCoV-19 and Sinopharm /BBIBP-CorV vaccines in HCWs were studied.\n\nMethodsA retrospective cross-sectional descriptive analysis was conducted from May 2021 to August 2021 for a total of 818 HCWs.\n\nResultsHundred and twenty-four HCWs (15.16%) were tested positive for COVID-19. The mean age of infected HCWs was 46.27 years and the majority were females (74.19%). Among all infected persons, 54 (43.55%) were nurses/midwives, 39 (31.45%) were clinical supportive staff and 12(9.68%) were medical officers. The number of infected HCWs rapidly escalated and a total of 64(51.61%) HCWs got an infection during August/2021. No source was identified in most of them (34.68%) followed by community acquisition (33.87%). Thirty-five HCWs (28.23%) had acquired infection during a hospital setting or had a high-risk exposure in recent history. Among hospital-related infections, 37.91% of HCWs had shared meals or shared sleeping rooms with an infected workmate. The majority of the HCWs were tested by the infection control unit as symptomatic screening (70.16%) followed by contact tracing (20.16%). Fifty-six (45.16%) HCWs had a history of single or multiple comorbidities. The vast majority of HCWs (95.97%) presented as mild to asymptomatic disease that followed an uneventful recovery. Body aches, headache, fever, and sore throat were the most commonly reported symptoms among them. Among the five HCWs required therapeutic oxygen supplementation, two unvaccinated HCWs succumbed to the infection. The rate of breakthrough infection among HCWs was 8.93%. The acquisition of disease was significantly higher among unvaccinated HCWs than partially (p<0.0001) or fully vaccinated (p<0.0001) HCWs with either type of vaccine.\n\nConclusionsProtecting HCWs remains a challenge in resource-poor settings. The risk of infection fueled by very contagious circulating variants is continuously high even though vaccination has shown clear benefits in preventing mortality and severe infection. Therefore, all healthcare workers should be vaccinated while ensuring continuous infection control measures in the hospital setting.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "W.A.M.P. Samaranayake", + "author_inst": "Base Hospital Wathupitiwala" + }, + { + "author_name": "G.P.C. Jayawardhana", + "author_inst": "Base Hospital Wathupitiwala" + }, + { + "author_name": "A.L.L. Roshan", + "author_inst": "Base Hospital Wathupitiwala" + }, + { + "author_name": "M.A.M. Wijewardene", + "author_inst": "Base Hospital Wathupitiwala" + }, + { + "author_name": "M.I. Siraj", + "author_inst": "Base Hospital Wathupitiwala" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.27.21262687", "rel_title": "Early immune responses have long-term associations with clinical, virologic, and immunologic outcomes in patients with COVID-19", @@ -613754,73 +614711,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.26.21262697", - "rel_title": "Mental health and substance use associated with hospitalization among people with laboratory confirmed diagnosis of COVID-19 in British Columbia: a population-based cohort study", - "rel_date": "2021-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262697", - "rel_abs": "BackgroundThis study identified factors associated with hospital admission among people with laboratory-diagnosed COVID-19 cases in British Columbia.\n\nMethodsThis study was performed using the BC COVID-19 Cohort, which integrates data on all COVID-19 cases, hospitalizations, medical visits, emergency room visits, prescription drugs, chronic conditions and deaths. The analysis included all laboratory-diagnosed COVID-19 cases in British Columbia as of January 15th, 2021. We evaluated factors associated with hospital admission using multivariable Poisson regression analysis with robust error variance.\n\nFindingsFrom 56,874 COVID-19 cases included in the analyses, 2,298 were hospitalized. Models showed significant association of the following factors with increased hospitalization risk: male sex (adjusted risk ratio (aRR)=1.27; 95%CI=1.17-1.37), older age (p-trend <0.0001 across age groups with a graded increase in hospitalization risk with increasing age [aRR 30-39 years=3.06; 95%CI=2.32-4.03, to aRR 80+years=43.68; 95%CI=33.41-57.10 compared to 20-29 years-old]), asthma (aRR=1.15; 95%CI=1.04-1.26), cancer (aRR=1.19; 95%CI=1.09-1.29), chronic kidney disease (aRR=1.32; 95%CI=1.19-1.47), diabetes (treated without insulin aRR=1.13; 95%CI=1.03-1.25, requiring insulin aRR=5.05; 95%CI=4.43-5.76), hypertension (aRR=1.19; 95%CI=1.08-1.31), injection drug use (aRR=2.51; 95%CI=2.14-2.95), intellectual and developmental disabilities (aRR=1.67; 95%CI=1.05-2.66), problematic alcohol use (aRR=1.63; 95%CI=1.43-1.85), immunosuppression (aRR=1.29; 95%CI=1.09-1.53), and schizophrenia and psychotic disorders (aRR=1.49; 95%CI=1.23-1.82). Among women of reproductive age, in addition to age and comorbidities, pregnancy (aRR=2.69; 95%CI=1.42-5.07) was associated with increased risk of hospital admission.\n\nInterpretationOlder age, male sex, substance use, intellectual and developmental disability, chronic comorbidities, and pregnancy increase the risk of COVID-19-related hospitalization.\n\nFundingBC Centre for Disease Control, Canadian Institutes of Health Research.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSFactors such as older age, social inequities and chronic health conditions have been associated to severe COVID-19 illness. Most of the evidence comes from studies that dont include all COVID-19 diagnoses in a jurisdiction), focusing on in-hospital mortality. In addition, mental illness and substance use were not evaluated in these studies. This study assessed factors associated with hospital admission among people with laboratory-diagnosed COVID-19 cases in British Columbia.\n\nAdded value of this studyIn this population-based cohort study that included 56,874 laboratory-confirmed COVID-19 cases, older age, male sex, injection drug use, problematic alcohol use, intellectual and developmental disability, schizophrenia and psychotic disorders, chronic comorbidities and pregnancy were associated with the risk of hospitalization. Insulin-dependent diabetes was associated with higher risk of hospitalization, especially in the subpopulation younger than 40 years. To the best of our knowledge this is the first study reporting this finding, (insulin use and increased risk of COVID-19-related death has been described previously).\n\nImplications of all the available evidencePrioritization of vaccination in population groups with the above mentioned risk factors could reduce COVID-19 serious outcomes. The findings indicate the presence of the syndemic of substance use, mental illness and COVID-19, which deserve special public health considerations.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "H\u00e9ctor Alexander Vel\u00e1squez Garc\u00eda", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "James Wilton", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Kate Smolina", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Mei Chong", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Drona Rasali", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Michael Otterstatter", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Caren Rose", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Natalie Prystajecky", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Samara David", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Eleni Galanis", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Geoffrey McKee", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Mel Krajden", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Naveed Zafar Janjua", - "author_inst": "BC Centre for Disease Control" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.25.21262627", "rel_title": "History of suicide attempts and COVID-19 infection in Veterans with schizophrenia or schizoaffective disorder: effect modification by age and obesity", @@ -614324,6 +615214,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.26.21262523", + "rel_title": "Association between tocilizumab, sarilumab and all-cause mortality at 28 days in hospitalized patients with COVID-19: A network meta-analysis", + "rel_date": "2021-08-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262523", + "rel_abs": "ObjectiveTo estimate pairwise associations between administration of tocilizumab, sarilumab and usual care or placebo with 28-day mortality, in COVID-19 patients receiving concomitant corticosteroids and non-invasive or mechanical ventilation, based on all available direct and indirect evidence.\n\nMethodsEligible trials randomized hospitalized patients with COVID-19 that compared either interleukin-6 receptor antagonist with usual care or placebo in a recent prospective meta-analysis (27 trials, 10930 patients) or that directly compared tocilizumab with sarilumab. Data were restricted to patients receiving corticosteroids and either non-invasive or invasive ventilation at randomization.\n\nPairwise associations between tocilizumab, sarilumab and usual care or placebo for all-cause mortality 28 days after randomization were estimated using a frequentist contrast-based network meta-analysis of odds ratios (ORs), implementing multivariate fixed-effects models that assume consistency between the direct and indirect evidence.\n\nResultsOne trial (REMAP-CAP) was identified that directly compared tocilizumab with sarilumab and supplied results on all-cause mortality at 28-days. This network meta-analysis was based on 898 eligible patients (278 deaths) from REMAP-CAP and 3710 eligible patients from 18 trials (1278 deaths) from the prospective meta-analysis. Summary ORs were similar for tocilizumab [0.82 [0.71-0.95, P=0.008]] and sarilumab [0.80 [0.61-1.04, P=0.09]] compared with usual care or placebo. The summary OR for 28-day mortality comparing tocilizumab with sarilumab was 1.03 [95%CI 0.81-1.32, P=0.80]. The P value for the global test for inconsistency was 0.28.\n\nConclusionAdministration of either tocilizumab or sarilumab was associated with lower 28-day all-cause mortality compared with usual care or placebo. The association is not dependent on the choice of interleukin-6 receptor antagonist.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Peter J Godolphin", + "author_inst": "University College London" + }, + { + "author_name": "David J Fisher", + "author_inst": "University College London" + }, + { + "author_name": "Lindsay R Berry", + "author_inst": "Berry Consultants" + }, + { + "author_name": "Lennie PG Derde", + "author_inst": "University Medical Center Utrecht" + }, + { + "author_name": "Janet V Diaz", + "author_inst": "World Health Organization" + }, + { + "author_name": "Anthony C Gordon", + "author_inst": "Imperial College London" + }, + { + "author_name": "Elizabeth Lorenzi", + "author_inst": "Berry Consultants" + }, + { + "author_name": "John C Marshall", + "author_inst": "University of Toronto" + }, + { + "author_name": "Srinivas Murthy", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Manu Shankar-Hari", + "author_inst": "King's College London" + }, + { + "author_name": "Jonathan AC Sterne", + "author_inst": "University of Bristol" + }, + { + "author_name": "Jayne F Tierney", + "author_inst": "University College London" + }, + { + "author_name": "Claire L Vale", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.08.26.21262649", "rel_title": "Behavioural barriers to COVID-19 testing in Australia: Two national surveys to identify barriers and estimate prevalence by health literacy level", @@ -615948,45 +616905,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.24.21262580", - "rel_title": "The efficacy and safety of bamlanivimab treatment against COVID-19: A meta-analysis", - "rel_date": "2021-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262580", - "rel_abs": "BackgroundBamlanivimab is routinely used in the treatment of coronavirus disease 2019 (COVID-19) in worldwide. We performed a meta-analysis to investigate the efficacy and safety of bamlanivimab treatment in patients with COVID-19.\n\nMethodsWe searched articles from Web of Science, PubMed, Embase, the Cochrane Library and MedRxiv between 30 January 2020 and August 5, 2021. We selected randomized clinical trials (RCTs) and observational studies with a control group to assess the efficiency of bamlanivimab in treating patients with COVID-19.\n\nResultsOur meta-analysis retrieved 3 RCTs and 7 cohort studies including 14461 patients. Bmlanivimab may help outpatients to prevent hospitalization or emergency department visit (RR 0.41 95%CI 0.29 to 0.58), reduce ICU admission (RR 0.47 95%CI 0.23 to 0.92) and mortality (RR 0.32 95%CI 0.13 to 0.77) from the disease. The combination of bamlanivimab and etesevimab may had a greater potential for positive treatment outcome.\n\nConclusionBamlanivimab has demonstrated clinical efficacy on mild or moderate ill patients with COVID-19 to prevent hospitalization, reduce severity and mortality from the disease. Combinations of two or more monoclonal antibody increase the effect. Well-designed clinical trials to identify the clinical and biochemical characteristics in COVID-19 patients population that could benefit from bamlanivimab are warranted in the future.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSCan bamlanivimab treat COVID-19 patients? What are the factors that have great impact on the treatment outcome?\n\nFindingsIn this meta-analysis that retrieved 3 RCTs and 7 cohort studies and included 14461 adults, Bmlanivimab may help outpatients to prevent hospitalization or emergency department visit (RR 0.41 95%CI 0.29 to 0.58), reduce ICU admission (RR 0.47 95%CI 0.23 to 0.92) and mortality (RR 0.32 95%CI 0.13 to 0.77) from the disease.\n\nMeaningIn COVID-19 pandemic, the use of bamlanivimab may be warranted. Combinations of two or more monoclonal antibody increase the effect.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Huairong Xiang", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Bei He", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Yun Li", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Xuan Cheng", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Qizhi Zhang", - "author_inst": "second xiangya hospital central south university" - }, - { - "author_name": "Wenxing Peng", - "author_inst": "second xiangya hospital central south university" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.08.24.21262554", "rel_title": "Impact of the early stages of the COVID-19 pandemic on coverage of RMNH interventions in Ethiopia", @@ -616218,6 +617136,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.25.21262632", + "rel_title": "Longevity of SARS-CoV-2 Antibody in Health Care Workers: 6-Months Follow Up", + "rel_date": "2021-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262632", + "rel_abs": "The prevalence and longevity of acquired immunity to coronavirus disease 2019 (COVID-19) in health care workers (HCWs) is of great interest, especially with the roll-out of vaccines for SARS-CoV-2. Determining such immunity may enhance knowledge about susceptibility of HCWs to COVID-19, frequency of vaccine administration, and degree of workplace risk, and may also support enactment of better workplace policies and procedures.\n\nThe present study reports on 6-months follow-up serosurveillance to determine the longevity of SARS-CoV-2 antibodies in HCWs.\n\nSub-sample (n=35) of the original serosurveillance in HCWs (n = 3,458) with baseline, 8-week, and 6-month blood sampling were analyzed. Information on job duties, location, COVID-19 symptoms, polymerase chain reaction test history, travel since January 2020, and household contacts with COVID-19 was collected.\n\nOf 35 subjects, 13 were seropositive at baseline and maintained positivity at 8-week follow-up, with 3 losing positivity at 6-month follow-up. Among 22 subjects who were seronegative at baseline and seropositive at 8-week follow-up, all but one maintained positivity at 6-month follow-up. There was no significant effect of all factors (e.g., age, gender, job duties) examined at the .05 level on seropositivity at 6-month follow-up. The observed antibody longevity was 7.0+/-0.6 months for seropositive subjects (n=13), and 4.5+/-0.8 months for those seronegative subjects (n=22), at baseline. The longest duration of seropositivity observed in this cohort was 7.9 months (236 days).\n\nWith reported COVID-19-related symptoms up to 4.7 months prior to baseline blood sampling, possibly longer antibody presence is suggested. Similarly, seropositivity at 6-month follow-up further suggests greater antibody longevity than observed in this study.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Michael Brant-Zawadzki", + "author_inst": "Hoag Center for Research and Education, Hoag Memorial Hospital Presbyterian" + }, + { + "author_name": "Deborah Fridman", + "author_inst": "Hoag Center for Research and Education, Hoag Memorial Hospital Presbyterian" + }, + { + "author_name": "Philip A. Robinson", + "author_inst": "Infection Prevention, Hoag Memorial Hospital Presbyterian" + }, + { + "author_name": "Randy German", + "author_inst": "Laboratory Administrative Services, Hoag Memorial Hospital Presbyterian" + }, + { + "author_name": "Arell Shapiro", + "author_inst": "Transfusion & Laboratory Medicine, Hoag Memorial Hospital Presbyterian" + }, + { + "author_name": "Marcus Breit", + "author_inst": "Hoag Family Cancer Institute, Hoag Memorial Hospital Presbyterian" + }, + { + "author_name": "Stacy Wilton", + "author_inst": "Hoag Center for Research and Education, Hoag Memorial Hospital Presbyterian" + }, + { + "author_name": "Elmira Burke", + "author_inst": "Quality Management, Hoag Memorial Hospital Presbyterian" + }, + { + "author_name": "Jason Bock", + "author_inst": "Embic Corporation" + }, + { + "author_name": "Junko Hara", + "author_inst": "Hoag Center for Research and Education, Hoag Memorial Hospital Presbyterian; Embic Corporation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.23.21256078", "rel_title": "Survivors of SARS-CoV-2 Infection Show Neuropsychiatric Sequelae Measured by Surveys, Neurocognitive Testing, and Magnetic Resonance Imaging: Preliminary Results", @@ -617962,45 +618935,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.08.24.457397", - "rel_title": "Direct RNA sequencing reveals SARS-CoV-2 m6A sites and possible differential DRACH motif methylation among variants", - "rel_date": "2021-08-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.24.457397", - "rel_abs": "The causative agent of COVID-19 pandemic, the SARS-CoV-2 coronavirus, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 100 modified bases that are essential for proper function. Among internal modified bases, the N6-methyladenosine, or m6A, is the most frequent, and is implicated in SARS-CoV-2 immune response evasion. Although the SARS-CoV-2 genome is RNA, almost all genomes sequenced so far are in fact, reverse transcribed complementary DNAs. This process reduces the true complexity of these viral genomes because incorporation of dNTPs hides RNA base modifications. Here, in this perspective paper, we present an initial exploration of the Nanopore direct RNA sequencing to assess the m6A residues in the SARS-CoV-2 sequences of ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N, ORF10 and the 3-untranslated region. We identified 15 m6A methylated positions, of which, 6 are in ORF N. Also, because m6A is associated with the DRACH motif, we compared its distribution in major SARS-CoV-2 variants. Although DRACH is highly conserved among variants we show that variants Beta and Eta have a fourth position C>U change in DRACH at 28,884b that could affect methylation. The Nanopore technology offers a unique opportunity for the study of viral epitranscriptomics. This technique is PCR-free and is not sequencing-by-synthesis, therefore, no PCR bias and synthesis errors are introduced. The modified bases are preserved and assessed directly with no need for chemical treatments or antibodies. This is the first report of direct RNA sequencing of a Brazilian SARS-CoV-2 sample coupled with the identification of modified bases.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Joao H. Campos", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Juliana T. Maricato", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Carla T. Braconi", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Fernando Antoneli", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Luiz Mario R. Janini", - "author_inst": "Federal University of Sao Paulo, Brazil" - }, - { - "author_name": "Marcelo RS Briones", - "author_inst": "Federal University of Sao Paulo, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.08.23.457411", "rel_title": "Woodsmoke particulates alter expression of antiviral host response genes in human nasal epithelial cells infected with SARS-CoV-2 in a sex-dependent manner", @@ -618348,6 +619282,20 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.20.21262349", + "rel_title": "COVID-19 mitigation measures in primary schools and association with infection and school staff wellbeing: an observational survey linked with routine data in Wales, UK", + "rel_date": "2021-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.20.21262349", + "rel_abs": "IntroductionSchool-based COVID-19 mitigation strategies have greatly impacted the primary school day (children aged 3-11) including: wearing face coverings, 2-metre distancing, no mixing of children, and no breakfast clubs or extra-curricular activities. This study examines these mitigation methods and association with COVID-19 infection, respiratory infection, and school staff wellbeing between October to December 2020 in Wales, UK.\n\nMethodsA school staff survey captured self-reported COVID-19 mitigation measures in the school, participant anxiety and depression, and open-text responses regarding experiences of teaching and implementing measures. These survey responses were linked to national-scale COVID-19 test results data to examine association of measures in the school and the likelihood of a positive (staff or pupil) COVID-19 case in the school (clustered by school, adjusted for school size and free school meals using logistic regression). Linkage was conducted through the SAIL (Secure Anonymised Information Linkage) Databank.\n\nResultsResponses were obtained from 353 participants from 59 primary schools within 15 of 22 local authorities. Having more direct non-household contacts was associated with a higher likelihood of COVID-19 positive case in the school (1-5 contacts compared to none, OR 2.89 (1.01, 8.31)) and a trend to more self-reported cold symptoms. Staff face covering was not associated with a lower odds of school COVID-19 cases (mask vs. no covering OR 2.82 (1.11, 7.14)) and was associated with higher self-reported cold symptoms. School staff reported the impacts of wearing face coverings on teaching, including having to stand closer to pupils and raise their voices to be heard. 67.1% were not able to implement 2-metre social distancing from pupils. We did not find evidence that maintaining a 2-metre distance was associated with lower rates of COVID-19 in the school.\n\nConclusionsImplementing, adhering to and evaluating COVID-19 mitigation guidelines is challenging in primary school settings. Our findings suggest that reducing non-household direct contacts lowers infection rates. There was no evidence that face coverings, 2-metre social distancing or stopping children mixing was associated with lower odds of COVID-19 or cold infection rates in the school. Primary school staff found teaching challenging during COVID-19 restrictions, especially for younger learners and those with additional learning needs.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.17.21262188", "rel_title": "Fall 2021 Resurgence and COVID-19 Seroprevalence in Canada: Modelling waning and boosting COVID-19 immunity in Canada, A Canadian Immunization Research Network Study", @@ -619892,41 +620840,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.24.457457", - "rel_title": "Defective ORF8 dimerization in delta variant of SARS CoV2 leads to abrogation of ORF8 MHC-I interaction and overcome suppression of adaptive immune response", - "rel_date": "2021-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.24.457457", - "rel_abs": "In India, the breakthrough infections during second wave of COVID-19 pandemic was due to SARS-COV-2 delta variant (B.1.617.2). It was reported that majority of the infections were caused by the delta variant and only 9.8% percent cases required hospitalization whereas, only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections was observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Down regulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant results in structural instability of ORF8 dimer caused by disruption of hydrogen bonding and salt bridges as revealed by structural analysis and MD simulation studies of ORF8 dimer. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 may not hindering the MHC-I expression thereby resulting in better immune response against SARS-CoV-2 delta variant, which partly explains the sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC=\"FIGDIR/small/457457v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (40K):\norg.highwire.dtl.DTLVardef@751eeaorg.highwire.dtl.DTLVardef@140b5b5org.highwire.dtl.DTLVardef@159a3a5org.highwire.dtl.DTLVardef@6c206_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Armi Chaudhari", - "author_inst": "gujarat biotechnology research center" - }, - { - "author_name": "Dr. Indira Singh", - "author_inst": "Gujarat Biotechnology Research center" - }, - { - "author_name": "Dr. Madhvi Joshi", - "author_inst": "Gujarat Biotechnology Research Centre" - }, - { - "author_name": "Dr. AMRUTLAL PATEL", - "author_inst": "Gujarat Biotechnology research center" - }, - { - "author_name": "Proff. Chaitanya Joshi", - "author_inst": "Gujarat Biotechnology research center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.08.19.21262310", "rel_title": "Predicting SARS-CoV-2 infections for children and youth with single symptom screening", @@ -620226,6 +621139,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.17.21262138", + "rel_title": "Anti-PF4 levels of patients with VITT do not reduce 4 months following AZD1222 vaccination", + "rel_date": "2021-08-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.17.21262138", + "rel_abs": "BackgroundAnti-Platelet Factor 4 (PF4) IgG antibodies that activate platelets via Fc{gamma}RIIa have been shown to be an important part of the pathophysiology of vaccine-induced immune thrombocytopenia and thrombosis (VITT). There is now extensive literature on its presentation and initial management. There is no literature however on what happens to these patients following discharge.\n\nMethodsWe collected clinical data and samples from seven patients presenting with VITT and followed them up for 82-145 days. We also collected clinical samples from them at last follow-up. Testing for anti-PF4/heparin antibodies was done using an anti-PF4/heparin enzymatic immunoassay. Flow Cytometry was used to look at Fc{gamma}RIIa levels on patient platelets. Light Transmission Aggregometry with patient serum and healthy donor / patient platelets was used to analyse platelet responsiveness, in the presence and absence of PF4.\n\nFindingsAll patients were discharged on direct oral anticoagulants. Two patients remain completely symptom free, three have ongoing headaches, two have residual neurological deficits. Two patients developed mild thrombocytopenia and worsening headache (but without cerebral venous sinus thrombosis) and were retreated, one of these with rituximab. All patients, except the one treated with rituximab, had similar anti-PF4 antibody titres at 80-120 days to their levels at diagnosis. Platelets from patients at follow-up had normal levels of Fc{gamma}RIIa and had normal responses to thrombin and collagen-related-peptide. Patient serum from diagnosis strongly activated healthy donor platelets in the presence of PF4. Serum from follow-up was much weaker at stimulating platelets, even in the presence of PF4.\n\nInterpretationThis study shows that despite similar PF4 antibody titres at diagnosis and during follow-up, there are further differences in patient serum, that are not apparent from currently used testing, that result in lower levels of platelet activation during the follow-up period. Further understanding of these factors are important in order to assess duration of anticoagulation for these patients.\n\nFundingThis work was supported by an Accelerator Grant (AA/18/2/34218) from the British Heart Foundation (BHF) and by a National Institute for Health Research (NIHR) grant.\n\nKey pointsO_LIPF4 antibody titres do not reduce up to 4-months post ChAdOx1 nCoV-19 in patients with VITT\nC_LIO_LIDespite similar PF4 antibody titres, diagnostic serum is more potent at activating platelets in the presence of PF4 than follow-up serum.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Phillip LR Nicolson", + "author_inst": "Institute of Cardiovascular Sciences, University of Birmingham" + }, + { + "author_name": "Samantha J Montague", + "author_inst": "Institute of Cardiovascular Sciences, University of Birmingham" + }, + { + "author_name": "Christopher W Smith", + "author_inst": "nstitute of Cardiovascular Sciences, University of Birmingham" + }, + { + "author_name": "Clare S Lodwick", + "author_inst": "Worcester Acute Hospitals NHS Trust" + }, + { + "author_name": "Charlotte Stoneley", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust" + }, + { + "author_name": "Matthew Roberts", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust" + }, + { + "author_name": "Steve P Watson", + "author_inst": "Institute of Cardiovascular Sciences, University of Birmingham" + }, + { + "author_name": "Gillian C Lowe", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust" + }, + { + "author_name": "William A Lester", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2021.08.21.21262399", "rel_title": "Integrated immune networks in SARS-CoV-2 infected pregnant women reveal differential NK cell and unconventional T cell activation", @@ -622074,69 +623038,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.19.21262296", - "rel_title": "Assessment of inter-laboratory differences in SARS-CoV-2 consensus genome assemblies between public health laboratories in Australia", - "rel_date": "2021-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262296", - "rel_abs": "Whole-genome sequencing of viral isolates is critical for informing transmission patterns and ongoing evolution of pathogens, especially during a pandemic. However, when genomes have low variability in the early stages of a pandemic, the impact of technical and/or sequencing errors increases. We quantitatively assessed inter-laboratory differences in consensus genome assemblies of 72 matched SARS-CoV-2-positive specimens sequenced at different laboratories in Sydney, Australia. Raw sequence data were assembled using two different bioinformatics pipelines in parallel, and resulting consensus genomes were compared to detect laboratory-specific differences. Matched genome sequences were predominantly concordant, with a median pairwise identity of 99.997%. Identified differences were predominantly driven by ambiguous site content. Ignoring these produced differences in only 2.3% (5/216) of pairwise comparisons, each differing by a single nucleotide. Matched samples were assigned the same Pango lineage in 98.2% (212/216) of pairwise comparisons, and were mostly assigned to the same phylogenetic clade. However, epidemiological inference based only on single nucleotide variant distances may lead to significant differences in the number of defined clusters if variant allele frequency thresholds for consensus genome generation differ between laboratories. These results underscore the need for a unified, best-practices approach to bioinformatics between laboratories working on a common outbreak problem.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Charles S.P. Foster", - "author_inst": "School of Medical Sciences, Faculty of Medicine & Health, University of New South Wales" - }, - { - "author_name": "Sacha Stelzer-Braid", - "author_inst": "School of Medical Sciences, Faculty of Medicine & Health, University of New South Wales" - }, - { - "author_name": "Ira W. Deveson", - "author_inst": "Garvan Institute of Medical Research," - }, - { - "author_name": "Rowena A. Bull", - "author_inst": "The Kirby Institute for Infection and Immunity, University of New South Wales" - }, - { - "author_name": "Malinna Yeang", - "author_inst": "Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital" - }, - { - "author_name": "Jane Phan-Au", - "author_inst": "School of Medical Sciences, Faculty of Medicine & Health, University of New South Wales" - }, - { - "author_name": "Mariana Ruiz Silva", - "author_inst": "School of Medical Sciences, Faculty of Medicine & Health, University of New South Wales" - }, - { - "author_name": "Sebastiaan J. van Hal", - "author_inst": "NSW Health Pathology, Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital" - }, - { - "author_name": "Rebecca J. Rockett", - "author_inst": "Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital" - }, - { - "author_name": "Vitali Sintchenko", - "author_inst": "Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital" - }, - { - "author_name": "Ki Wook Kim", - "author_inst": "School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales" - }, - { - "author_name": "William D. Rawlinson", - "author_inst": "Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.17.21262165", "rel_title": "Interpreting Wastewater SARS-CoV-2 Results using Bayesian Analysis", @@ -622440,6 +623341,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.16.21262100", + "rel_title": "CORONAVIRUS DISEASE 2019 IN A TERTIARY PEDIATRIC CENTER IN PORTUGAL", + "rel_date": "2021-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262100", + "rel_abs": "ObjectivesDescribe the demographic, clinical, laboratory, and imaging features of SARS-CoV-2 infected children at a tertiary pediatric center in Portugal during the first 6 months of the COVID-19 pandemic.\n\nDesignSingle center, descriptive study of pediatric patients, who had a confirmed SARS-CoV-2 infection from March 7 to September 20, 2020.\n\nSettingTertiary Pediatric referral center.\n\nPatients18 years or younger.\n\nMain outcome measuresIncidence, mortality, age of infection, clinical characteristics, treatment prescribed and outcome.\n\nResultsA total of 300 patients were included with a median age of 5 years (IQR 1-11) and in 67% a contact was identified (co-habitant in 52.7%). 56 (18.7%) had pre-existing medical conditions. A mode of three days mediated symptom appearance to diagnose. The most common symptoms were fever (55.7%), cough (38.3%), and nasal congestion (24%). 23% of the patients were admitted due to complications related to COVID-19 and 2% required intensive care. We used drugs with antiviral activity in 9% of the patients, immunomodulatory medication with corticosteroids in 3.3%, and intravenous immunoglobulin in 1.7%. Two (0.6%) children died and 2.3% reported short-term sequelae.\n\nConclusionsCOVID-19 is usually a mild disease in children, but a small proportion of patients develop severe and critical disease. Fatal outcomes were rare overall and exclusive of severe previous medical conditions. Suspecting and diagnosing COVID-19 in children based on their symptoms without epidemiologic information and virus testing is very challenging. Our data also reflect the uncertainties regarding specific treatment options, highlighting that additional data on antiviral and immunomodulatory drugs are urgently needed.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tiago Milheiro Silva", + "author_inst": "Hospital Dona Estefania" + }, + { + "author_name": "Ana Margarida Garcia", + "author_inst": "Hospital Dona Estefania" + }, + { + "author_name": "Catarina Gouveia", + "author_inst": "Hospital Dona Estefania" + }, + { + "author_name": "Flora Candeias", + "author_inst": "Hospital Dona Estefania" + }, + { + "author_name": "Maria Joao Brito", + "author_inst": "Hospital Dona Estefania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.19.21262280", "rel_title": "Anticipating the hospital burden of future COVID-19 epidemic waves", @@ -623652,41 +624588,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.08.18.21262166", - "rel_title": "Changes in the serial interval and transmission dynamics associated with the SARS-CoV-2 Delta variant in South Korea", - "rel_date": "2021-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.18.21262166", - "rel_abs": "We estimated mean serial interval and superspreading potential for the predominant Delta variant of SARS-CoV-2. Mean serial intervals were similar with 3.7 and 3.5 days during early and latter periods, respectively. Furthermore, the risk of superspreading events was similar with 23% and 25% of cases seeded 80% of all transmissions.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sukhyun Ryu", - "author_inst": "Konyang University College of Medicine, South Korea" - }, - { - "author_name": "Dasom Kim", - "author_inst": "Konyang University College of Medicine, South Korea" - }, - { - "author_name": "Jun-Sik Lim", - "author_inst": "Seoul National University, South Korea" - }, - { - "author_name": "Sheikh Taslim Ali", - "author_inst": "The University of Hong Kong, China" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.17.21262183", "rel_title": "The association between immunosuppressants use and COVID-19 adverse outcome: National COVID-19 cohort in South Korea", @@ -623990,6 +624891,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.20.457146", + "rel_title": "SARS-CoV-2 hijacks p38\u03b2/MAPK11 to promote viral protein translation", + "rel_date": "2021-08-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.20.457146", + "rel_abs": "SARS-CoV-2, the causative agent of the COVID-19 pandemic, drastically modifies infected cells in an effort to optimize virus replication. Included is the activation of the host p38 mitogen-activated protein kinase (MAPK) pathway, which plays a major role in inflammation and is a central driver of COVID-19 clinical presentations. Inhibition of p38/MAPK activity in SARS-CoV-2-infected cells reduces both cytokine production and viral replication. Here, we combined genetic screening with quantitative phosphoproteomics to better understand interactions between the p38/MAPK pathway and SARS-CoV-2. We found that several components of the p38/MAPK pathway impacted SARS-CoV-2 replication and that p38{beta} is a critical host factor for virus replication, and it prevents activation of the type-I interferon pathway. Quantitative phosphoproteomics uncovered several SARS-CoV-2 nucleocapsid phosphorylation sites near the N-terminus that were sensitive to p38 inhibition. Similar to p38{beta} depletion, mutation of these nucleocapsid residues was associated with reduced virus replication and increased activation of type-I interferon signaling. Taken together, this study reveals a unique proviral function for p38{beta} that is not shared with p38 and supports exploring p38{beta} inhibitor development as a strategy towards developing a new class of COVID-19 therapies.\n\nImportanceSARS-CoV-2 is the causative agent of the COVID-19 pandemic that has claimed millions of lives since its emergence in 2019. SARS-CoV-2 infection of human cells requires the activity of several cellular pathways for successful replication. One such pathway, the p38 mitogen-activated protein kinase (MAPK) pathway, is required for virus replication and disease pathogenesis. Here, we applied systems biology approaches to understand how MAPK pathways benefit SARS-CoV-2 replication to inform the development of novel COVID-19 drug therapies.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Christina A Higgins", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Benjamin E Nilsson-Payant", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Andrew Kurland", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Tomer M Yaron", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jared L Johnson", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Boris Bonaventure", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Prithy Adhikary", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ilona Golynker", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Brad R Rosenberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Oded Danziger", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Maryline Panis", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Lewis C Cantley", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Benjamin R tenOever", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jeffrey R Johnson", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.08.18.456891", "rel_title": "Neutralising antibodies against the SARS-CoV-2 Delta variant induced by Alhydroxyquim-II-adjuvanted trimeric spike antigens", @@ -625522,33 +626502,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.14.21257136", - "rel_title": "Worldwide association of lifestyle related factors and COVID-19 mortality", - "rel_date": "2021-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.14.21257136", - "rel_abs": "BackgroundSeveral lifestyle related factors such as obesity and diabetes have been identified as risk factors for Coronavirus disease 2019 (COVID-19) mortality. The objective of this study was to examine the global association between lifestyle related factors and COVID-19 mortality using data from each individual country.\n\nMethodsThe association between prevalence of seven lifestyle related factors (overweight, insufficient physical activity, smoking, type 2 diabetes, hypertension, hyperlipidemia, and age over 65) and COVID-19 mortality was assessed by linear and multivariable regression among 186 countries. The cumulative effect of lifestyle related factors on COVID-19 mortality was assessed by dividing countries into four categories according to the number of lifestyle related factors in the upper half range and comparing the mean mortality between groups.\n\nResultsIn linear regression, COVID-19 mortality was significantly associated with overweight, insufficient physical activity, hyperlipidemia, and age [≥]65. In multivariable regression, overweight and age [≥]65 demonstrated significant association with COVID-19 mortality (P = 0.0039, 0.0094). Countries with more risk factors demonstrated greater COVID-19 mortality (P for trend <0.001).\n\nConclusionLifestyle related factors, especially overweight and elderly population, were associated with increased COVID-19 mortality on a global scale. Global effort to reduce burden of lifestyle related factors along with protection and vaccination of these susceptible groups may help reduce COVID-19 mortality.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jingzhou Wang", - "author_inst": "University of Chicago" - }, - { - "author_name": "Toshiro Sato", - "author_inst": "Keio University" - }, - { - "author_name": "Atsushi NA Sakuraba", - "author_inst": "Univ of Chicago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.16.21262036", "rel_title": "Comparison of Antibody Levels in Response to SARS-CoV-2 Infection and Vaccination Type in a Midwestern Cohort", @@ -625820,6 +626773,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.15.21262007", + "rel_title": "Dynamics of seroconversion of anti-SARS-CoV-2 IgG antibodies in the Czech unvaccinated population: nationwide prospective seroconversion (PROSECO) study", + "rel_date": "2021-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.15.21262007", + "rel_abs": "BackgroundAlthough the Czech Republic weathered the first wave of the COVID-19 epidemic with relatively low incidence, the second wave of the global pandemic saw it rank among countries bearing the greatest COVID-19 burden, both in Europe and on a worldwide scale. The aim of the nationwide prospective seroconversion (PROSECO) study was to investigate the dynamics of seroconversion of anti-SARS-CoV-2 IgG antibodies in the Czech population.\n\nMethodsAll clients of the second largest health insurance company in the Czech Republic were sent a written invitation to participate in this longitudinal study. The study includes the first 30,054 persons who provided a blood sample between October 2020 and March 2021. Seroprevalence was compared between calendar periods of blood sample collection, RT-PCR test results, sociodemographic factors, and other characteristics.\n\nFindingsThe data show a dramatic increase in seropositivity over time, from 28% in October/November 2020 to 43% in December 2020/January 2021 to 51% in February/March 2021. These trends were consistent with government data on cumulative viral antigenic prevalence in the population captured by PCR testing - although the seroprevalence rates established in this study were considerably higher than those listed in government data. Data pooled across the entire study period exhibited minor differences in seropositivity between sexes, age groups and body mass index categories; results were similar between test providing laboratories. Seropositivity was substantially higher among symptomatic vs. asymptomatic persons (76% vs. 34%). At least one third of all seropositive participants were asymptomatic, and 28% participants who developed antibodies against SARS-CoV-2 never underwent PCR testing.\n\nInterpretationAntibody response provides a better marker of past SARS-CoV-2 infection than PCR testing data. Our data on seroconversion confirm the rapidly increasing prevalence in the Czech population during the dramatically rising pandemic wave prior to the beginning of massive vaccination. The planned second and third assessment of the study participants (April 2021 - September 2021, October 2021 - March 2022) will provide valuable evidence on the seroprevalence changes following vaccination and persistence of antibodies resulting from natural infection and vaccination.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSSimilarly to most European countries, the first COVID-19 epidemic wave in the Czech Republic produced a relatively low incidence (86.9 confirmed cases per 100,000 persons over three months). At the peaks of the second wave, however, over 100 confirmed cases per 100,000 persons were diagnosed daily and the Czech Republic ranked among the countries with the greatest burden of COVID-19 in Europe and in the world. Only a few nationwide population-based studies have been published covering the second wave of the epidemic in Europe, and none of them from the Central and Eastern European region.\n\nAdded value of this studyThe PROSECO study will provide key data from the heavily affected Central European region and contribute to the epidemiological and serological characteristics of the SARS-CoV-2 infection. All 30,054 study participants were recruited between October 2020 and March 2021, thus covering all three epidemic peaks (November 2020, January and March 2021) of the second COVID-19 epidemic wave. This allows us to follow the dynamics of seroconversion of anti-SARS-CoV-2 IgG antibodies in the immunologically naive and unvaccinated population during the COVID-19 pandemic. The study participants will be re-assessed in the second (April 2021 - September 2021) and third (October 2021 - March 2022) PROSECO phases to further study the post-infection/post-vaccination dynamics of seroconversion in/after a period of massive vaccination.\n\nImplications of all the available evidenceData from the first phase of the PROSECO study indicate that the percentage of the population that has been exposed to the SARS-CoV-2 may be substantially higher than estimates based on official data on cumulative viral positivity incidence as at least one third of seropositive participants were asymptomatic, and 28% of participants who developed antibodies against SARS-CoV-2 never underwent PCR testing. Regional seroprevalence data provide key information to inform, in combination with other surveillance data, public health policies and will be instrumental for the successful management of the subsequent phases of the global pandemic.\n\nThe number of seropositive participants who never underwent RT-PCR testing demonstrates the importance of serological population-based studies describing the spread and exposure to the virus in the population over time.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Pavel Piler", + "author_inst": "RECETOX Centre, Masaryk University" + }, + { + "author_name": "Vojtech Thon", + "author_inst": "RECETOX Centre, Masaryk University" + }, + { + "author_name": "Lenka Andryskova", + "author_inst": "RECETOX Centre, Masaryk University" + }, + { + "author_name": "Kamil Dolezel", + "author_inst": "QualityLab Association" + }, + { + "author_name": "David Kostka", + "author_inst": "Health Insurance Company of the Ministry of the Interior of the Czech Republic" + }, + { + "author_name": "Tomas Pavlik", + "author_inst": "Institute of Biostatistics and Analyses, Masaryk University" + }, + { + "author_name": "Ladislav Dusek", + "author_inst": "Institute of Health Information and Statistics of the Czech Republic" + }, + { + "author_name": "Hynek Pikhart", + "author_inst": "Department of Epidemiology & Public Health, University College London" + }, + { + "author_name": "Martin Bobak", + "author_inst": "Department of Epidemiology & Public Health, University College London" + }, + { + "author_name": "Jana Klanova", + "author_inst": "RECETOX Centre, Masaryk University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.15.21261584", "rel_title": "A second dramatic rise in seroprevalence rates of SARS-CoV-2 antibodies among adult healthy blood donors in Jordan; have we achieved herd immunity?", @@ -627236,145 +628244,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.13.454991", - "rel_title": "A screening pipeline identifies a broad-spectrum inhibitor of bacterial AB toxins with cross protection against influenza A virus H1N1 and SARS-CoV-2", - "rel_date": "2021-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.13.454991", - "rel_abs": "A challenge for the development of host-targeted anti-infectives against a large spectrum of AB-like toxin-producing bacteria encompasses the identification of chemical compounds corrupting toxin transport through both endolysosomal and retrograde pathways. Here, we performed a high-throughput screening of small chemical compounds blocking active Rac1 proteasomal degradation triggered by the Cytotoxic Necrotizing Factor-1 (CNF1) toxin, followed by orthogonal screens against two AB toxins hijacking defined endolysosomal (Diphtheria toxin) or retrograde (Shiga-like toxin 1) pathways to intoxicate cells. This led to the identification of the molecule N-(3,3-diphenylpropyl)-1-propyl-4-piperidinamine, referred to as C910. This compound induces the swelling of EEA1-positive early endosomes, in absence of PIKfyve kinase inhibition, and disturbs the trafficking of CNF1 and the B-subunit of Shiga toxin along the endolysosomal or retrograde pathways, respectively. Together, we show that C910 protects cells against 8 bacterial AB toxins including large clostridial glucosylating toxins from Clostridium difficile. Of interest, C910 also reduced viral infection in vitro including influenza A virus subtype H1N1 and SARS-CoV-2. Moreover, parenteral administration of C910 to the mice resulted in its accumulation in lung tissues and reduced lethal influenza infection.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Yu Wu", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Nassim Mahtal", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Lea Swistak", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sara Sagadiev", - "author_inst": "Seattle Childrens Research Institute" - }, - { - "author_name": "Mridu Acharya", - "author_inst": "Seattle Childrens Research Institute" - }, - { - "author_name": "Caroline Demeret", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sylvie Van der Werf", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Florence Guivel-Benhassine", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwartz", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Serena Petracchini", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Amel Mettouchi", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Elea Paillares", - "author_inst": "Insitut Pasteur" - }, - { - "author_name": "Lucie Caramelle", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Pierre Couvineau", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Robert Thai", - "author_inst": "Univeristy Paris Saclay, CEA" - }, - { - "author_name": "Peggy Barbe", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Mathilde Keck", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Arnaud Machelart", - "author_inst": "University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille" - }, - { - "author_name": "Valentin Sencio", - "author_inst": "University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille" - }, - { - "author_name": "Francois Trottein", - "author_inst": "University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille" - }, - { - "author_name": "Martin Sachse", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Gaetan Chicanne", - "author_inst": "University Toulouse III Paul Sabatier" - }, - { - "author_name": "Bernard Payrastre", - "author_inst": "University Toulouse III Paul Sabatier" - }, - { - "author_name": "Florian Ville", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Victor Kreis", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Michel-Robert Popoff", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ludger Johannes", - "author_inst": "Institut Curie" - }, - { - "author_name": "Jean-Christophe Cintrat", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Julien Barbier", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Daniel Gillet", - "author_inst": "University Paris-Saclay, CEA" - }, - { - "author_name": "Emmanuel Lemichez", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.15.456341", "rel_title": "Infection and transmission of SARS-CoV-2 and its alpha variant in pregnant white-tailed deer", @@ -627606,6 +628475,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.08.14.456353", + "rel_title": "Cutting epitopes to survive: the case of lambda variant", + "rel_date": "2021-08-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.14.456353", + "rel_abs": "This manuscript concisely reports an in-silico study on the potential impact of the Spike protein mutations on immuno-escape ability of SARS-CoV-2 lambda variant. Biophysical and bioinformatics data suggest that a combination of shortening immunogenic epitope loops and generation of potential N-glycosylation sites may be a viable adaptation strategy potentially allowing this emerging viral variant escaping host immunity.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Stefano Pascarella", + "author_inst": "Sapienza University of Rome, Italy" + }, + { + "author_name": "Massimo Ciccozzi", + "author_inst": "University Campus Bio-Medico of Rome" + }, + { + "author_name": "Martina Bianchi", + "author_inst": "University of Rome \"La Sapienza\"" + }, + { + "author_name": "Domenico Benvenuto", + "author_inst": "Faculty of Medicine - Campus Bio-Medico University of Rome, Italy." + }, + { + "author_name": "Roberto Cauda", + "author_inst": "Fondazione Policlinico Universitario \"A.Gemelli\" IRCCS" + }, + { + "author_name": "Antonio Cassone", + "author_inst": "Center of Genomics, Genetics and Biology, Siena, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.08.13.456305", "rel_title": "ImputeCoVNet: 2D ResNet Autoencoder for Imputation of SARS-CoV-2 Sequences", @@ -628910,61 +629818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.11.21261876", - "rel_title": "SARS-CoV-2 variants: levels of neutralisation required for protective immunity", - "rel_date": "2021-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261876", - "rel_abs": "A number of SARS-CoV-2 variants of concern (VOC) have been identified that partially escape serum neutralisation activity elicited by current vaccines. Recent studies have also shown that vaccines demonstrate reduced protection against symptomatic infection with SARS-CoV-2 variants. Here we integrate published data on in vitro neutralisation and clinical protection to understand and predict vaccine efficacy against existing SARS-CoV-2 variants. We find that neutralising activity against the ancestral SARS-CoV-2 is highly predictive of neutralisation of the VOC, with all vaccines showing a similar drop in neutralisation to the variants. Neutralisation levels remain strongly correlated with protection from infection with SARS-CoV-2 VOC (r=0.81, p=0.0005). We apply an existing model relating in vitro neutralisation to protection (parameterised on data from ancestral virus infection) and find this remains predictive of vaccine efficacy against VOC once drops in neutralisation to the VOC are taken into account. Modelling of predicted vaccine efficacy against variants over time suggests that protection against symptomatic infection may drop below 50% within the first year after vaccination for some current vaccines. Boosting of previously infected individuals with existing vaccines (which target ancestral virus) has been shown to significantly increase neutralising antibodies. Our modelling suggests that booster vaccination should enable high levels of immunity that prevent severe infection outcomes with the current SARS-CoV-2 VOC, at least in the medium term.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Deborah Cromer", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Megan Steain", - "author_inst": "School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia." - }, - { - "author_name": "Arnold Reynaldi", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Timothy E Schlub", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Adam K Wheatley", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Jennifer A Juno", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Stephen J Kent", - "author_inst": "University of Melbourne" - }, - { - "author_name": "James A Triccas", - "author_inst": "School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia." - }, - { - "author_name": "David S Khoury", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Miles Philip Davenport", - "author_inst": "Kirby Institute, University of New South Wales, Sydney, Australia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.11.21261732", "rel_title": "COVID-19 in Connecticut institutions of higher education during the 2020-2021 academic year", @@ -629304,6 +630157,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.11.21261845", + "rel_title": "Changing Dynamics of COVID-19 in the U.S. with the Emergence of the Delta Variant: Projections of the COVID-19 Simulator", + "rel_date": "2021-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261845", + "rel_abs": "With the recent emergence of the B.1.617.2 (Delta) variant of SARS-CoV-2 in the U.S., many states are seeing rising cases and hospitalizations after a period of steady decline. As We used the COVID-19 Simulator, an interactive online tool that utilizes a validated mathematical model, to simulate the trajectory of COVID-19 at the state level in the U.S. COVID-19 Simulators forecasts are updated weekly and included in the Centers for Disease Control and Prevention (CDC) ensemble model. We employed our model to analyze scenarios where the Delta variant becomes dominant in every state.\n\nThe combination of high transmissibility of the Delta variant, low vaccination coverage in several regions, and more relaxed attitude towards social distancing is expected to result in as surge in COVID-19 deaths in at least 40 states. In several states - including Idaho, Maine, Montana, Nebraska, North Carolina, Oregon, Puerto Rico, Washington, and West Virginia - the projected daily deaths in 2021 could exceed the prior peak daily deaths under current social distancing behavior and vaccination rate. The number of COVID-19 deaths across the U.S. could exceed 1600 per day.\n\nBetween August 1, 2021, and December 31, 2021, there could be additional 157,000 COVID-19 deaths across the U.S. Of note, our model projected approximately 20,700 COVID-19 deaths in Texas, 16,000 in California, 12,400 in Florida, 12,000 in North Carolina, and 9,300 in Georgia during this period. In contrast, the projected number of COVID-19 deaths would remain below 200 in New Jersey, Massachusetts, Connecticut, Vermont, and Rhode Island.\n\nWe project COVID-19 deaths based on the current vaccination rates and social distancing behavior. Our hope is that the findings of this report serve a warning sign and people revert to wearing masks and maintain social distancing to reduce COVID-19 associated deaths in the U.S. Our projections are updated weekly by incorporating vaccination rates and social distancing measures in each state; the latest results can be found at the COVID-19 Simulator website.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jagpreet Chhatwal", + "author_inst": "Massachusetts General Hospital, Harvard Medical School" + }, + { + "author_name": "Yingying (Jade) Xiao", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Peter Carl Powell Mueller", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Turgay Ayer", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Madeline Grace Adee", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Ozden Dalgic", + "author_inst": "Value Analytics Labs" + }, + { + "author_name": "Mary Ann Ladd", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Benjamin Linas", + "author_inst": "Boston Medical Center, Boston University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.12.21261825", "rel_title": "Pandemic excess mortality in Spain, Sweden, and Switzerland during the COVID-19 pandemic in 2020 was at its highest since 1918", @@ -630908,77 +631808,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.12.21261951", - "rel_title": "Neutralization of VOCs including Delta one year post COVID-19 or vaccine", - "rel_date": "2021-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261951", - "rel_abs": "BackgroundSARS-CoV-2 variants, such as Alpha, Beta, Gamma and Delta, are raising concern about the efficiency of neutralizing antibodies (NAb) induced by wild-type infection or vaccines based on the wild-type spike.\n\nMethodsWe determined IgG and NAb against SARS-CoV-2 variants one year following mild wild-type infection (n=104) and two-dose regimens with BNT162b2 (BNT/BNT) (n=67), ChAdOx1 (ChAd/ChAd) (n=82), or heterologous ChAdOx1 followed by BNT162b2 (ChAd/BNT) (n=116).\n\nFindingsWild type spike IgG and NAb remained detectable in 80% (83/104) of unvaccinated participants one year post mild infection. The neutralizing capacity was similar against wild type (reference), Alpha (0.95 (0.92-0.98) and Delta 1.03 (0.95-1.11) but significantly reduced against Beta (0.54 (0.48-0.60)) and Gamma 0.51 (0.44-0.61). Similarly, BNT/BNT and ChAd/ChAd elicited sustained capacity against Alpha and Delta (1.01 (0.78-1.31) and 0.85 (0.64-1.14)) and (0.96 (0.84-1.09) and 0.82 (0.61-1.10) respectively), with reduced capacity against Beta (0.67 (0.50-0.88) and 0.53 (0.40-0.71)) and Gamma (0.12 (0.06-0.27) and 0.54 (0.37-0.80)). A similar trend was found following ChAd/BNT (0.74 (0.66-0.83) and 0.70 (0.50-0.97) against Alpha and Delta and 0.29 (0.20-0.42) and 0.13 (0.08-0.20) against Beta and Gamma).\n\nInterpretationPersistent neutralization of the wide-spread Alpha and Delta variants one year after wild-type infection may aid vaccine policy makers in low-resource settings when prioritizing vaccine supply. The reduced capacity of neutralizing Beta and Gamma strains, but not the Alpha and Delta strains following both infection and three different vaccine regimens argues for caution against Beta and Gamma-exclusive mutations in the efforts to optimize next generation SARS-CoV-2 vaccines.\n\nFundingA full list of funding bodies that contributed to this study can be found in the Acknowledgements section", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Sebastian Havervall", - "author_inst": "Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" - }, - { - "author_name": "Ulrika Marking", - "author_inst": "Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" - }, - { - "author_name": "Max Gordon", - "author_inst": "Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" - }, - { - "author_name": "Henry Ng", - "author_inst": "Department of Medical Cell Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden" - }, - { - "author_name": "Nina Greilert-Norin", - "author_inst": "Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" - }, - { - "author_name": "Sarah Lindbo", - "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" - }, - { - "author_name": "Kim Blom", - "author_inst": "Public Health Agency of Sweden, Solna, Sweden" - }, - { - "author_name": "Peter Nilsson", - "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" - }, - { - "author_name": "Mia Phillipson", - "author_inst": "Department of Medical Cell Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden" - }, - { - "author_name": "Jonas Klingstrom", - "author_inst": "Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden" - }, - { - "author_name": "Sara Mangsbo", - "author_inst": "Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden" - }, - { - "author_name": "Mikael Aberg", - "author_inst": "Department of Medical Sciences, Clinical Chemistry and Science for Life Laboratory, Uppsala University, Uppsala, Sweden" - }, - { - "author_name": "Sophia Hober", - "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" - }, - { - "author_name": "Charlotte Thalin", - "author_inst": "Danderyd Hospital, Karolinska Institute, Stockholm, Sweden" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.12.21261970", "rel_title": "A highly efficient T-cell immunoassay provides assessment of B cell help function of SARS-CoV-2 specific memory CD4+ T cells", @@ -631298,6 +632127,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.12.21261966", + "rel_title": "B and T cell responses after a third dose of SARS-CoV-2 vaccine in Kidney Transplant Recipients", + "rel_date": "2021-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261966", + "rel_abs": "BackgroundAccumulating evidence suggests that solid organ transplant recipients, as opposed to the general population, show strongly impaired responsiveness towards standard SARS-CoV-2 mRNA-based vaccination, demanding alternative strategies for protection of this vulnerable group.\n\nMethodsIn line with recent recommendations, a third dose of either heterologous ChAdOx1 (AstraZeneca) or homologous BNT162b2 (BioNTech) was administered to 25 kidney transplant recipients (KTR) without humoral response after 2 doses of BNT162b2, followed by analysis of serological responses and vaccine-specific B- and T-cell immunity.\n\nResults9/25 (36%) KTR under standard immunosuppressive treatment seroconverted until day 27 after the third vaccination, while one patient developed severe COVID-19 infection immediately after vaccination. Cellular analysis seven days after the third dose showed significantly elevated frequencies of viral spike protein receptor binding domain specific B cells in humoral responders as compared to non-responders. Likewise, portions of spike-reactive CD4+ T helper cells were significantly elevated in seroconverting patients. Furthermore, overall frequencies of IL-2+, IL-4+ and polyfunctional CD4+ T cells significantly increased after the third dose, whereas memory/effector differentiation remained unaffected.\n\nConclusionsOur data suggest that a fraction of transplant recipients benefits from triple vaccination, where seroconversion is associated with quantitative and qualitative changes of cellular immunity. At the same time, the study highlights that modified vaccination approaches for immunosuppressed patients still remain an urgent medical need.\n\nSignificance statementProtection of solid organ transplant recipients against SARS-Cov-2 by vaccination remains an unmet need given the low immunogenicity of available vaccines in the presence of immunosuppression. Administration of a third dose to 25 kidney transplant recipients (KTR) resulted in seroconversion in 36% of patients, associated with significant quantitative and functional changes within the spike-antigen-specific B-cell- and CD4+ T-helper cell compartment. Our data support the need for individual humoral monitoring of immunosuppressed individuals after vaccination as well as continued efforts to adapt vaccination protocols for this at-risk group.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Eva Schrezenmeier", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Hector Rincon-Arevalo", + "author_inst": "Charite- Universitaetsmedizin Berlin" + }, + { + "author_name": "Ana-Luisa Stefanski", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Alexander Potekhin", + "author_inst": "MVZ Diaverum Neubrandenburg" + }, + { + "author_name": "Henriette Staub-Hohenbleicher", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Mira Choi", + "author_inst": "Charite- Universitaetsmedizin Berlin" + }, + { + "author_name": "Friederike Bachmann", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Vanessa Pross", + "author_inst": "Charite- Universitaetsmedizin Berlin" + }, + { + "author_name": "Charlotte Hammett", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Hubert Schrezenmeier", + "author_inst": "Institute of Transfusion Medicine, Ulm University" + }, + { + "author_name": "Carolin Ludwig", + "author_inst": "Institute of Transfusion Medicine, Ulm University" + }, + { + "author_name": "Bernd Jahrsdoerfer", + "author_inst": "Institute of Transfusion Medicine, Ulm University" + }, + { + "author_name": "Andreia C Lino", + "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin" + }, + { + "author_name": "Kai-Uwe Eckardt", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Katja Kotsch", + "author_inst": "Charite- Universitaetsmedizin Berlin" + }, + { + "author_name": "Thomas Doerner", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Klemens Budde", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Arne Sattler", + "author_inst": "Charite-Universitaetsmedizin Berlin" + }, + { + "author_name": "Fabian Halleck", + "author_inst": "Charite-Universitaetsmedizin Berlin" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.08.11.21261934", "rel_title": "The D614G virus mutation enhances anosmia in COVID-19 patients: Evidence from a systematic review and meta-analysis of studies from South Asia", @@ -633206,77 +634126,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.11.455959", - "rel_title": "Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using in situ hybridization", - "rel_date": "2021-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.11.455959", - "rel_abs": "The widespread Coronavirus Disease 2019 (COVID-19) is caused by infection with the novel coronavirus SARS-CoV-2. Currently, we have a limited toolset available for visualizing SARS-CoV-2 in cells and tissues, particularly in tissues from patients who died from COVID-19. Generally, single-molecule RNA FISH techniques have shown mixed results in formalin fixed paraffin embedded tissues such as those preserved from human autopsies. Here, we present a platform for preparing autopsy tissue for visualizing SARS-CoV-2 RNA using RNA FISH with amplification by hybridization chain reaction (HCR). We developed probe sets that target different regions of SARS-CoV-2 (including ORF1a and N) as well as probe sets that specifically target SARS-CoV-2 subgenomic mRNAs. We validated these probe sets in cell culture and tissues (lung, lymph node, and placenta) from infected patients. Using this technology, we observe distinct subcellular localization patterns of the ORF1a and N regions, with the ORF1a concentrated around the nucleus and the N showing a diffuse distribution across the cytoplasm. In human lung tissue, we performed multiplexed RNA FISH HCR for SARS-CoV-2 and cell-type specific marker genes. We found viral RNA in cells containing the alveolar type 2 (AT2) cell marker gene (SFTPC) and the alveolar macrophage marker gene (MARCO), but did not identify viral RNA in cells containing the alveolar type 1 (AT1) cell marker gene (AGER). Moreover, we observed distinct subcellular localization patterns of viral RNA in AT2 cells and alveolar macrophages, consistent with phagocytosis of infected cells. In sum, we demonstrate the use of RNA FISH HCR for visualizing different RNA species from SARS-CoV-2 in cell lines and FFPE autopsy specimens. Furthermore, we multiplex this assay with probes for cellular genes to determine what cell-types are infected within the lung. We anticipate that this platform could be broadly useful for studying SARS-CoV-2 pathology in tissues as well as extended for other applications including investigating the viral life cycle, viral diagnostics, and drug screening.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kofi K Acheampong", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Dylan L Schaff", - "author_inst": "Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Benjamin L Emert", - "author_inst": "Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Jonathan Lake", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Sam Reffsin", - "author_inst": "Department of Bioengineering, School of Engineering Arts and Sciences, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Emily K Shea", - "author_inst": "Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Courtney E Comar", - "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia PA, Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia PA" - }, - { - "author_name": "Leslie A Litzky", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Nigar A Khurram", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, Department of Pathology, Northwestern" - }, - { - "author_name": "Michael Feldman", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Susan R Weiss", - "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia PA Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Philadelphia PA" - }, - { - "author_name": "Kathleen T Montone", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA" - }, - { - "author_name": "Sara Cherry", - "author_inst": "Department of Pathology and Laboratory Medicine, Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Department of Biochemistry and Biophysi" - }, - { - "author_name": "Sydney M Shaffer", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, Department of Bioengineering, School " - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.10.455737", "rel_title": "Molecular mimicry between Spike and human thrombopoietin may induce thrombocytopenia in COVID-19", @@ -633439,6 +634288,145 @@ "type": "confirmatory results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.08.11.455984", + "rel_title": "Durability of SARS-CoV-2-specific T cell responses at 12-months post-infection", + "rel_date": "2021-08-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.11.455984", + "rel_abs": "BackgroundCharacterizing the longevity and quality of cellular immune responses to SARS-CoV-2 is critical to understanding immunologic approaches to protection against COVID-19. Prior studies suggest SARS-CoV-2-specific T cells are present in peripheral blood 10 months after infection. Further analysis of the function, durability, and diversity of the cellular response long after natural infection, over a wider range of ages and disease phenotypes, is needed to further identify preventative and therapeutic interventions.\n\nMethodsWe identified participants in our multi-site longitudinal, prospective cohort study 12-months post SARS-CoV-2 infection representing a range of disease severity. We investigated the function, phenotypes, and frequency of T cells specific for SARS-CoV-2 using intracellular cytokine staining and spectral flow cytometry. In parallel, the magnitude of SARS-CoV-2-specific antibodies was compared.\n\nResultsSARS-CoV-2-specific antibodies and T cells were detected at 12-months post-infection. Severity of acute illness was associated with higher frequencies of SARS-CoV-2-specific CD4 T cells and antibodies at 12-months. In contrast, polyfunctional and cytotoxic T cells responsive to SARS-CoV-2 were identified in participants over a wide spectrum of disease severity.\n\nConclusionsOur data show that SARS-CoV-2 infection induces polyfunctional memory T cells detectable at 12-months post-infection, with higher frequency noted in those who originally experienced severe disease.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Zhongyan Lu", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Eric D Laing", + "author_inst": "Uniformed Services University of the Health" + }, + { + "author_name": "Jarina Pena-Damata", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Katherine Pohida", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Marana S Tso", + "author_inst": "Uniformed Services University of the Health" + }, + { + "author_name": "Emily C Samuels", + "author_inst": "Uniformed Services University of the Health" + }, + { + "author_name": "Nusrat J Epsi", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Batsukh Dorjbal", + "author_inst": "Uniformed Services University of the Health Sciences," + }, + { + "author_name": "Camille Lake", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Stephanie A Richard", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Ryan C Maves", + "author_inst": "Naval Medical Center San Diego" + }, + { + "author_name": "David A Lindholm", + "author_inst": "Brooke Army Medical Center" + }, + { + "author_name": "Julia Rozman", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Caroline English", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Nikhil Huprikar", + "author_inst": "Walter Reed National Military Medical Center" + }, + { + "author_name": "Katrin Mende", + "author_inst": "Uniformed Services University of the Health Sciences; Brooke Army Medical Center" + }, + { + "author_name": "Rhonda E Colombo", + "author_inst": "Uniformed Services University of the Health Sciences; Madigan Army Medical Center" + }, + { + "author_name": "Christopher J Colombo", + "author_inst": "Madigan Army Medical Center" + }, + { + "author_name": "Christopher C Broder", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Anuradha Ganesan", + "author_inst": "Uniformed Services University of the Health Sciences; Walter Reed National Military Medical Center" + }, + { + "author_name": "Charlotte A Lanteri", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Brian K Agan", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "David Tribble", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Mark P Simons", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Clifton L Dalgard", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Paul W Blair", + "author_inst": "Henry M. Jackson Foundation" + }, + { + "author_name": "Josh Chenoweth", + "author_inst": "Henry M. Jackson Foundation" + }, + { + "author_name": "Simon D Pollett", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Andrew L Snow", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Timothy H Burgess", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Allison MW Malloy", + "author_inst": "Uniformed Services University of the Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.03.21261482", "rel_title": "Reducing false reassurance following negative results from asymptomatic coronavirus (Covid-19) testing: an online experiment", @@ -634691,37 +635679,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.10.455799", - "rel_title": "Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences", - "rel_date": "2021-08-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.10.455799", - "rel_abs": "More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status. Although many lineages, including the main variants of concern, can be identified clearly using spike-only sequences, some spike-only sequences are shared among tens or hundreds of Pango lineages. To facilitate the classification of SARS-CoV-2 lineages using subgenomic sequences we introduce the notion of designating such sequences to a \"lineage set\", which represents the range of Pango lineages that are consistent with the observed mutations in a given spike sequence. These data provide a foundation for the development of software tools that can assign newly-generated spike nucleotide sequences to Pango lineage sets.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Oliver Pybus", - "author_inst": "Department of Zoology, University of Oxford" - }, - { - "author_name": "Michael E Abram", - "author_inst": "Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA." - }, - { - "author_name": "Elizabeth J Kelly", - "author_inst": "Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA." - }, - { - "author_name": "Andrew Rambaut", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.08.10.455627", "rel_title": "An ultrapotent neutralizing bispecific antibody with broad spectrum against SARS-CoV-2 variants", @@ -635109,6 +636066,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.07.21261578", + "rel_title": "SARS-CoV-2 vaccine effectiveness in immunosuppressed kidney transplant recipients", + "rel_date": "2021-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.07.21261578", + "rel_abs": "COVID-19 vaccine protection against infection in immunosuppressed solid organ transplant recipients is unknown but possibly weak with the low proportion of these patients mounting a robust humoral and cellular immune response after vaccination. Using a retrospective cohort study design with cross-over, we assessed vaccine effectiveness among 782 kidney transplant recipients registered at Hamad Medical Corporation, the national public healthcare provider in Qatar, where the BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines have been used in the national immunization campaign. Vaccine effectiveness against any SARS-CoV-2 infection was estimated at 46.6% (95% CI: 0.0-73.7%) [≥]14 days after the second dose, 66.0% (95% CI: 21.3-85.3%) [≥]42 days after the second dose, and 73.9% (95% CI: 33.0-89.9%) [≥]56 days after the second dose. Vaccine effectiveness against any severe, critical, or fatal COVID-19 disease was estimated at 72.3% (95% CI: 0.0-90.9%) [≥]14 days after the second dose, 85.0% (95% CI: 35.7-96.5%) [≥]42 days after the second dose, and 83.8% (95% CI: 31.3-96.2%) [≥]56 days after the second dose. Most vaccine breakthrough infections occurred in the first few weeks after receiving the first and/or second dose. Vaccine effectiveness reached considerable levels in kidney transplant recipients, but vaccine protection mounted slowly and did not reach a high level until several weeks after the second dose.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Sawsan AlMukdad", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Jobin Paravila Joy", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Houssein H. Ayoub", + "author_inst": ", Qatar University" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + }, + { + "author_name": "Fatiha Benslimane", + "author_inst": "Qatar University" + }, + { + "author_name": "Hebah A. Al Khatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Patrick Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Mohammad Rubayet Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Gheyath Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed Ghaith Al Kuwari", + "author_inst": "Primary Health Care Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamad M. Alkadi", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Omar Ali", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Muna Al-Maslamani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Hassan Al Malki", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Yousuf Almaslamani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.06.21261709", "rel_title": "The impact of the COVID-19 pandemic on diagnoses of common mental health disorders in adults in Catalonia, Spain", @@ -636701,61 +637793,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.08.06.455494", - "rel_title": "Broad-spectrum in vitro antiviral activity of ODBG-P-RVn: an orally-available, lipid-modified monophosphate prodrug of remdesivir parent nucleoside (GS-441524)", - "rel_date": "2021-08-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455494", - "rel_abs": "The intravenous administration of remdesivir for COVID-19 confines its utility to hospitalized patients. We evaluated the broad-spectrum antiviral activity of ODBG-P-RVn, an orally available, lipid-modified monophosphate prodrug of the remdesivir parent nucleoside (GS-441524) against viruses that cause diseases of human public health concern, including SARS-CoV-2. ODBG-P-RVn showed 20-fold greater antiviral activity than GS-441524 and had near-equivalent activity to remdesivir in primary-like human small airway epithelial cells. Our results warrant investigation of ODBG-P-RVn efficacy in vivo.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael K Lo", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Punya Shrivastava-Ranjan", - "author_inst": "CDC" - }, - { - "author_name": "Payel Chatterjee", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Mike Flint", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "James R Beadle", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Nadejda Valiaeva", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Robert Schooley", - "author_inst": "UCSD" - }, - { - "author_name": "Karl Y. Hostetler", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Joel Montgomery", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Christina F Spiropoulou", - "author_inst": "U.S. Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.08.06.455491", "rel_title": "High genetic barrier to escape from human polyclonal SARS-CoV-2 neutralizing antibodies", @@ -637267,6 +638304,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.06.21261710", + "rel_title": "Antibody Attributes that Predict the Neutralization and Effector Function of Polyclonal Responses to SARS-CoV-2", + "rel_date": "2021-08-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.06.21261710", + "rel_abs": "While antibodies provide significant protection from SARS-CoV-2 infection and disease sequelae, the specific attributes of the humoral response that contribute to immunity are incompletely defined. In this study, we employ machine learning to relate characteristics of the polyclonal antibody response raised by natural infection to diverse antibody effector functions and neutralization potency with the goal of generating both accurate predictions of each activity based on antibody response profiles as well as insights into antibody mechanisms of action. To this end, antibody-mediated phagocytosis, cytotoxicity, complement deposition, and neutralization were accurately predicted from biophysical antibody profiles in both discovery and validation cohorts. These predictive models identified SARS-CoV-2-specific IgM as a key predictor of neutralization activity whose mechanistic relevance was supported experimentally by depletion. Validated models of how different aspects of the humoral response relate to antiviral antibody activities suggest desirable attributes to recapitulate by vaccination or other antibody-based interventions.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Harini Natarajan", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Shiwei Xu", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Andrew R. Crowley", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Ssavannah E. Butler", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Joshua A. Weiner", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Evan M Bloch", + "author_inst": "Johns Hopkins Medicine" + }, + { + "author_name": "Kirsten Littlefield", + "author_inst": "Johns Hopkins Bloomberg School of Public Health," + }, + { + "author_name": "Sarah E. Benner", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Ruchee Shrestha", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Olivia Ajayi", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Wendy F. Weiland-Alter", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "David J Sullivan", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Shmuel Shoham", + "author_inst": "The Johns Hopkins Hospital, , MD" + }, + { + "author_name": "Thomas Quinn", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Arturo Casadevall", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Andrew Redd", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Aaron AR Tobian", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Ruth I. Connor", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Peter F. Wright", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Margaret E Ackerman", + "author_inst": "Dartmouth College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.08.07.21261587", "rel_title": "SARS-CoV-2 Breakthrough Infections among the Healthcare Workers Post-Vaccination with ChAdOx1 nCoV-19 Vaccine in the South Indian State of Kerala.", @@ -638499,45 +639635,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.05.21261660", - "rel_title": "Rapid antigen testing for SARS-CoV-2 infection in a university setting in Ireland: learning from a 6-week pilot study.", - "rel_date": "2021-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261660", - "rel_abs": "ObjectivesWith the ongoing circulation of SARS-CoV-2 in countries across the world it is essential to identify effective ways to reduce the risk of infection while allowing society to function as close to normal as possible. Serial testing using rapid lateral flow antigen tests is a possible way to do this by screening populations in a targeted way, identifying infectious (both symptomatic and asymptomatic) people and removing them from circulation while infectious. To make rapid antigen testing effective, high levels of participation are important. This study was designed to evaluate the establishment of a testing programme in a university setting and assess some of the factors that impact participation in such a study among both staff and students.\n\nStudy DesignObservational, survey\n\nMethodsA trial period of SARS-CoV-2 rapid testing using the Abbott Panbio rapid antigen test was set up and staff and students based in the University College Dublin Veterinary Hospital were asked to take part voluntarily for 6 weeks. Following the trial period, we used a questionnaire to evaluate satisfaction and to understand some reasons behind participation or lack thereof.\n\nResultsOverall, almost all respondents to the survey stated that they were happy with having a testing programme present in the workplace and it helped to reduce anxiety associated with COVID-19. Findings indicated that staff and students did not participate equally in the voluntary testing programme. The findings also highlighted that intrinsic motivations and extrinsic motivations for participation differ. For example, participation among staff was much higher than among students, motivational messaging focused on protecting others did not resonate with students as much as staff, convenience was a key factor driving participation in both cohorts and the pressure of being forced to miss class (if positive) close to exam time provided motivation to students to avoid testing.\n\nConclusionsIntroducing antigen testing into a workplace helped to reduce overall anxiety associated with the potential impact of COVID-19, but achieving good participation was challenging. Participation is key to a successful, campus wide antigen testing programme but reaching high levels of participation is not straightforward and can not be taken for granted. Different motivations drive participation in different cohorts and different messaging/incentivisation is needed to encourage participation in those different cohorts. The findings reported here should inform any SARS-CoV-2 testing programme that will run in these types of settings in the future.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Gerald Barry", - "author_inst": "University College Dublin" - }, - { - "author_name": "Catherine McCarney", - "author_inst": "University College Dublin" - }, - { - "author_name": "Marc Farrelly", - "author_inst": "University College Dublin" - }, - { - "author_name": "Carmel Mooney", - "author_inst": "University College Dublin" - }, - { - "author_name": "Rory Breathnach", - "author_inst": "University College Dublin" - }, - { - "author_name": "Simon More", - "author_inst": "University College Dublin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.05.21261642", "rel_title": "The unique evolutionary dynamics of the SARS-CoV-2 Delta variant", @@ -638901,6 +639998,189 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.05.21259863", + "rel_title": "Recording of 'COVID-19 vaccine declined' among vaccination priority groups: a cohort study on 57.9 million NHS patients' primary care records in situ using OpenSAFELY", + "rel_date": "2021-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21259863", + "rel_abs": "BackgroundAll patients in England within vaccine priority groups were offered a COVID-19 vaccine by mid-April 2021. Clinical record systems contain codes to denote when such an offer has been declined by a patient (although these can in some cases be entered for a variety of other reasons including vaccination delay, or other administrative issues). We set out to describe the patterns of usage of codes for COVID-19 vaccines being declined.\n\nMethodsWith the approval of NHS England and using the full pseudonymised primary care records for 57.9 million NHS patients, we identified all patients in key vaccine priority groups: aged over 50, or over 16 and at increased risk from COVID-19 (Clinically Extremely Vulnerable [CEV] or otherwise \"at risk\"). We describe the proportion of patients recorded as declining a COVID-19 vaccination for each priority group, and by other clinical and demographic factors; whether patients recorded as \"declined\" subsequently went on to receive a vaccination; and the distribution of code usage across GP practices.\n\nResultsOf 24.5 million patients in priority groups as of May 25th 2021, 89.2% had received a vaccine, 8.8% had neither a vaccination nor a decline recorded, and 663,033 (2.7%) had a decline code recorded. Of patients with a recorded decline, 125,587 (18.9%) were subsequently vaccinated. Subsequent vaccination was slightly more common in the South Asian population than other ethnicities (e.g. 32.3% vs 22.8%, over 65s). The proportion of declining-unvaccinated patients varied strongly with ethnicity (Black 15.3%, South Asian 5.6%, White 1.5% in over 80s); and was higher in patients from more deprived areas. COVID-19 vaccine decline codes were present in almost all practices (98.8%), but with wide variation between practices in rates of usage. Among all priority groups, declining-unvaccinated status was most common in CEV (3.3%).\n\nConclusionsClinical codes indicative of COVID-19 vaccinations being declined are widely used in English general practice. They are substantially more common among Black and South Asian patients, and patients from more deprived areas. There is a need for more detailed survey and/or qualitative research with patients and clinicians to determine the most common reasons for these recorded declines.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Helen J Curtis", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Inglesby", + "author_inst": "University of Oxford" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "University of Oxford" + }, + { + "author_name": "Richard Croker", + "author_inst": "University of Oxford" + }, + { + "author_name": "William J Hulme", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christopher T Rentsch", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Krishnan Bhaskaran", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Alex J Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Caroline E Morton", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Evans", + "author_inst": "University of Oxford" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sebastian CJ Bacon", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christopher Bates", + "author_inst": "TPP" + }, + { + "author_name": "George Hickman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tom Ward", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jessica Morley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jonathan Cockburn", + "author_inst": "TPP" + }, + { + "author_name": "Simon Davy", + "author_inst": "University of Oxford" + }, + { + "author_name": "Anna Schultze", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Elizabeth J Williamson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Helen I McDonald", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Laurie Tomlinson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Rohini Mathur", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Kevin Wing", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Angel YS Wong", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Harriet Forbes", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "John Tazare", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "John Parry", + "author_inst": "TPP" + }, + { + "author_name": "Frank Hester", + "author_inst": "TPP" + }, + { + "author_name": "Sam Harper", + "author_inst": "TPP" + }, + { + "author_name": "Shaun O'Hanlon", + "author_inst": "EMIS" + }, + { + "author_name": "Alex Eavis", + "author_inst": "EMIS" + }, + { + "author_name": "Richard Jarvis", + "author_inst": "EMIS" + }, + { + "author_name": "Dima Avramov", + "author_inst": "EMIS" + }, + { + "author_name": "Paul Griffiths", + "author_inst": "EMIS" + }, + { + "author_name": "Aaron Fowles", + "author_inst": "EMIS" + }, + { + "author_name": "Nasreen Parkes", + "author_inst": "EMIS" + }, + { + "author_name": "Stephen JW Evans", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ian J Douglas", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Liam Smeeth", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.04.21261596", "rel_title": "Epidemiological characteristics of the B.1.526 SARS-CoV-2 variant", @@ -640445,37 +641725,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.04.21261332", - "rel_title": "Temporal considerations in the 2021 COVID-19 lockdown of Ho Chi Minh City", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261332", - "rel_abs": "The success of Vietnam in controlling the spread of COVID-19 hinges on a timely implementation of its coherent strategy of containment and rapid tracing and testing efforts. The Vietnamese living in Mekong Delta are currently being besieged by the SARS-Cov-2 Delta variant as they undergo several and extended levels of lockdown. In this work we examine the temporal aspects of the lockdown in Ho Chi Minh City and predict the progress of the outbreak in terms of the total number of confirmed cases.\n\nA compartmental model with containment is fit to data to estimate the rate of transmission in Ho Chi Minh City. The severity of the lockdown is estimated from publicly-available data on mobility and coupled to the rate of infection. Various scenarios on when to begin a lockdown and its duration are assessed. This report, dated 27 July 2021, supports a lockdown of at least 3 weeks and predicts that there could be half as many cases had the inevitable lockdown started a week earlier.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Emmanuel Lance Christopher VI M Plan", - "author_inst": "Duy Tan University" - }, - { - "author_name": "Huong Thi Le", - "author_inst": "Thang Long University" - }, - { - "author_name": "Manh Duy Le", - "author_inst": "Duy Tan University" - }, - { - "author_name": "Haidang Phan", - "author_inst": "Duy Tan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.03.21261365", "rel_title": "Population normalisation in wastewater-based epidemiology for improved understanding of SARS-CoV-2 prevalence: A multi-site study", @@ -640687,6 +641936,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.02.21261480", + "rel_title": "A qualitative exploration of the perspectives of international medical students residing in university hostels amid COVID-19 pandemic lockdown", + "rel_date": "2021-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261480", + "rel_abs": "BackgroundCOVID-19 pandemic has portentously frightened the existence of life all over the world. The lockdown approach was adopted as a containment strategy as the disease itself has manifested severe social, economic, and psychiatric implications.\n\nObjectivesTo explore the perception and preparedness of international medical students residing in university hostels amid the COVID-19 pandemic lockdown.\n\nDesignA semi-structured interview guide was developed in this qualitative study design. All the interviews were audio-taped, transcribed verbatim, and then analyzed for thematic contents by standard content analysis framework.\n\nSettingInterviews were conducted in university hostels in Punjab, Pakistan.\n\nParticipantsA total of 11 international medical students were interviewed face-to-face through the purposive sampling technique to obtain in-depth individual viewpoints.\n\nResultsThe thematic content analysis yielded five major themes: Familiarity with COVID-19, Perceptions and attitudes towards COVID-19, Preparedness for safety against COVID-19, Barriers to lifestyle, and Psychological perspectives. A better general perception and preparedness among international medical students regarding COVID-19 was found. Good knowledge regarding the overview of COVID-19; adequate preventive approaches such as social distancing, use of masks, gloves, and sanitizers; and compliance with the lockdown measures were reported by the respondents. The pertinent issue raised by the respondents is the disturbance in normal routine due to distortion in social life and isolation that may cause psychological stress.\n\nConclusionsThe findings from this study lighten the peoples perspectives that help the government to prepare public health strategies based on population-focused approaches. The present study demonstrates the respondents opinion on COVID-19 management by personal hygiene, social distancing, and complying with the lockdown measures. Furthermore, it demands that timely and evidence-based teaching-learning techniques should be adopted for students engagement which ensures mental health and self-motivation as well. Therefore, they can utilize their time productively which could have a long-term effect on their careers and healthcare services.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sitaram Khadka", + "author_inst": "Shree Birendra Hospital, Nepalese Army Institute of Health Sciences" + }, + { + "author_name": "Muhammad Usman", + "author_inst": "University of Veterinary and Animal Sciences" + }, + { + "author_name": "Mohammad Saleem", + "author_inst": "University of the Punjab" + }, + { + "author_name": "Moshin Ali", + "author_inst": "Govt. College University, Faisalabad, Pakistan" + }, + { + "author_name": "Huma Rasheed", + "author_inst": "University of Veterinary and Animal Sciences" + }, + { + "author_name": "Santoshi Giri", + "author_inst": "Nepal Public Health Research and Development Center" + }, + { + "author_name": "Hafiz Asad Saeed", + "author_inst": "Pak Emirates Military Hospital, Rawalpindi, Pakistan" + }, + { + "author_name": "Ravi Prasad Gupta", + "author_inst": "University of the Punjab" + }, + { + "author_name": "Yogesh Bajgain", + "author_inst": "University of the Punjab" + }, + { + "author_name": "Janak Shahi", + "author_inst": "University of the Punjab" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.03.21261442", "rel_title": "Estimating the number of symptomatic SARS-CoV-2 infections among vaccinated individuals in the United States-January-April, 2021", @@ -642731,49 +644035,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.02.21261500", - "rel_title": "Temporal Geospatial Analysis of COVID-19 Pre-infection Determinants of Risk in South Carolina", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261500", - "rel_abs": "IntroductionDisparities and their geospatial patterns exist in coronavirus disease 2019 (COVID-19) morbidity and mortality for people who are engaged with clinical care. However, studies centered on viral infection cases are scarce. It remains unclear with respect to the disparity structure, its geospatial characteristics, and the pre-infection determinants of risk (PIDRs) for people with the infection. This work aimed to assess the geospatial associations between PIDRs and COVID-19 infection at the county level in South Carolina by different timepoints during the pandemic.\n\nMethodWe used global models including spatial error model (SEM), spatial lag model (SLM), and conditional autoregressive model (CAR), as well as geographically weighted regression model (GWR) as a local model to examine the associations between COVID-19 infection rate and PIDRs. The data were retrieved from multiple sources including USAFacts, US Census Bureau, and Population Estimates Program.\n\nResultsThe percentage of males and the percentage of the unemployed population were statistically significant (p values < 0.05) with positive coefficients in the three global models (SEM, SLM, CAR) throughout the time. The percentage of white population and obesity rate showed divergent spatial correlations at different times of the pandemic. GWR models consistently have a better model fit than global models, suggesting non-stationary correlations between a region and its neighbors.\n\nConclusionCharacterized by temporal-geospatial patterns, disparities and their PIDRs exist in COVID-19 incidence at the county level in South Carolina. The temporal-geospatial structure of disparities and their PIDRs found in COVID-19 incidence are different from mortality and morbidity for patients who are connected with clinical care. Our findings provided important evidence for prioritizing different populations and developing tailored interventions at different times of the pandemic. These findings provided implications on containing early viral transmission and mitigating consequences of infectious disease outbreaks for possible future pandemics.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tianchu Lyu", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Nicole Hair", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Nicholas Yell", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Zhenlong Li", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Chen Liang", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Xiaoming Li", - "author_inst": "University of South Carolina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.03.21261438", "rel_title": "COVID-19 impact on stroke admissions during France's first epidemic peak: an exhaustive, nationwide, observational study", @@ -643017,6 +644278,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.04.455181", + "rel_title": "Limited variation between SARS-CoV-2-infected individuals in domain specificity and relative potency of the antibody response against the spike glycoprotein", + "rel_date": "2021-08-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.04.455181", + "rel_abs": "The spike protein of SARS-CoV-2 is arranged as a trimer on the virus surface, composed of three S1 and three S2 subunits. Infected and vaccinated individuals generate antibodies against spike, which can neutralize the virus. Most antibodies target the receptor-binding domain (RBD) and N-terminal domain (NTD) of S1; however, antibodies against other regions of spike have also been isolated. The variation between infected individuals in domain specificity of the antibodies and in their relative neutralization efficacy is still poorly characterized. To this end, we tested serum and plasma samples from 85 COVID-19 convalescent subjects using 7 immunoassays that employ different domains, subunits and oligomeric forms of spike to capture the antibodies. Samples were also tested for their neutralization of pseudovirus containing SARS-CoV-2 spike and of replication-competent SARS-CoV-2. We observed strong correlations between the levels of NTD- and RBD-specific antibodies, with a fixed ratio of each type to all anti-spike antibodies. The relative potency of the response (defined as the measured neutralization efficacy relative to the total level of spike-targeting antibodies) also exhibited limited variation between subjects, and was not associated with the overall amount of anti-spike antibodies produced. Accordingly, the ability of immunoassays that use RBD, NTD and different forms of S1 or S1/S2 as capture antigens to estimate the neutralizing efficacy of convalescent samples was largely similar. These studies suggest that host-to-host variation in the polyclonal response elicited against SARS-CoV-2 spike is primarily limited to the quantity of antibodies generated rather than their domain specificity or relative neutralization potency.\n\nIMPORTANCEInfection by SARS-CoV-2 elicits antibodies against various domains of the spike protein, including the RBD, NTD and S2. Different infected individuals generate vastly different amounts of anti-spike antibodies. By contrast, as we show here, there is a remarkable similarity in the properties of the antibodies produced. Different individuals generate the same proportions of antibodies against each domain of the spike protein. Furthermore, the relationship between the amount of anti-spike antibodies produced and their neutralization efficacy of SARS-CoV-2 is highly conserved. Therefore, the observed variation in the neutralizing activity of the antibody response in COVID-19 convalescent subjects is caused by differences in the amounts of antibodies rather than their recognition properties or relative antiviral activity. These findings suggest that COVID-19 vaccine strategies that focus on enhancing the overall level of the antibodies will likely elicit a more uniformly efficacious protective response.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Hanora A Van Ert", + "author_inst": "The University of Iowa" + }, + { + "author_name": "Dana W Bohan", + "author_inst": "The University of Iowa" + }, + { + "author_name": "Kai J Rogers", + "author_inst": "University of Iowa" + }, + { + "author_name": "Mohammad Fili", + "author_inst": "Iowa State University" + }, + { + "author_name": "Anthony Roberth Rojas Chavez", + "author_inst": "The University of Iowa" + }, + { + "author_name": "Enya Qing", + "author_inst": "Loyola University" + }, + { + "author_name": "Changze Han", + "author_inst": "University of Iowa" + }, + { + "author_name": "Spencer M Dempewolf", + "author_inst": "The University of Iowa" + }, + { + "author_name": "Guiping Hu", + "author_inst": "Iowa State University" + }, + { + "author_name": "Nathan Schwery", + "author_inst": "The University of Iowa" + }, + { + "author_name": "Kristina M Sevcik", + "author_inst": "The University of Iowa" + }, + { + "author_name": "Natalie Ruggio", + "author_inst": "The University of Iowa" + }, + { + "author_name": "Devlin Boyt", + "author_inst": "The University of Iowa" + }, + { + "author_name": "Michael Pentella", + "author_inst": "University of Iowa" + }, + { + "author_name": "Tom Gallagher", + "author_inst": "Loyola University Chicago" + }, + { + "author_name": "J Brooks Jackson", + "author_inst": "University of Iowa Hospitals and Clinics" + }, + { + "author_name": "Anna E. Merrill", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "C Michael Knudson", + "author_inst": "University of Iowa Hospitals and Clinics" + }, + { + "author_name": "Grant Brown", + "author_inst": "University of Iowa" + }, + { + "author_name": "Wendy Maury", + "author_inst": "University of Iowa" + }, + { + "author_name": "Hillel Haim", + "author_inst": "The University of Iowa" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.08.02.21261486", "rel_title": "Estimating infection-related human mobility networks based on time series data of COVID-19 infection in Japan", @@ -644493,65 +645853,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.02.21261479", - "rel_title": "Tear antibodies to SARS-CoV-2: implications for transmission", - "rel_date": "2021-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261479", - "rel_abs": "ObjectivesSARS-CoV-2 can be transmitted by aerosols and the ocular surface may be an important route of transmission. Little is known about protective antibody responses to SARS-CoV-2 in tears after infection or vaccination. We analysed SARS-CoV-2 specific IgG and IgA responses in human tears after either COVID-19 infection or vaccination.\n\nMethodsWe recruited 16 subjects with COVID-19 infection an average of 7 months previously and 15 subjects before and 2 weeks after Comirnaty (Pfizer-BioNtech) vaccination. Plasma, saliva and basal tears were collected. Pre-pandemic plasma, saliva and basal tears from 11 individuals were included as healthy controls. Antibody responses to 5 SARS-CoV-2 antigens were measured via multiplex.\n\nResultsIgG antibodies to Spike and Nucleoprotein were detected in tears, saliva and plasma from subjects with prior SARS-CoV-2 infection in comparison to uninfected controls. While RBD-specific antibodies were detected in plasma, minimal RBD-specific antibodies were detected in tears and saliva. In contrast, high levels of IgG antibodies to Spike and RBD, but not Nucleoprotein, were induced in tears, saliva and plasma of subjects receiving 2 doses of the Comirnaty vaccine. Increased levels of IgA1 and IgA2 antibodies to SARS-CoV-2 antigens were detected in plasma following infection or vaccination, but were unchanged in tears and saliva.\n\nConclusionBoth infection and vaccination induce SARS-CoV-2-specific IgG antibodies in tears. RBD-specific IgG antibodies in tears were induced by vaccination but were not present 7 months post-infection. This suggests neutralising antibodies may be low in the tears late following infection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kevin John Selva", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Samantha K Davis", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Ebene R Haycroft", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Wen Shi Lee", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Ester Lopez", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Arnold Reynaldi", - "author_inst": "Kirby Institute, University of New South Wales, Kensington, NSW, Australia" - }, - { - "author_name": "Miles Philip Davenport", - "author_inst": "Kirby Institute, University of New South Wales, Kensington, NSW, Australia" - }, - { - "author_name": "Helen E Kent", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Jennifer A Juno", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Amy W Chung", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - }, - { - "author_name": "Stephen J Kent", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.02.21260750", "rel_title": "Hydroxychloroquine Prophylaxis against Coronavirus Disease-19: Practice Outcomes among Health-Care Workers", @@ -644887,6 +646188,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.02.454829", + "rel_title": "Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit.", + "rel_date": "2021-08-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.02.454829", + "rel_abs": "Three highly pathogenic betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread of these is SARS-CoV-2. The identification of CoVs with zoonotic potential in animal reservoirs suggests that additional outbreaks are likely to occur. Evidence suggests that neutralizing antibodies are important for protection against infection with CoVs. Monoclonal antibodies targeting conserved neutralizing epitopes on diverse CoVs can form the basis for prophylaxis and therapeutic treatments and enable the design of vaccines aimed at providing pan-coronavirus protection. To this end, we previously identified a neutralizing monoclonal antibody, CV3-25 that binds to the SARS-CoV-2 fusion machinery, neutralizes the SARS-CoV-2 Beta variant comparably to the ancestral Wuhan Hu-1 strain, cross neutralizes SARS-CoV-1 and displays cross reactive binding to recombinant proteins derived from the spike-ectodomains of HCoV-OC43 and HCoV-HKU1. Here, we show that the neutralizing activity of CV3-25 is also maintained against the Alpha, Delta and Gamma variants of concern as well as a SARS-CoV-like bat coronavirus with zoonotic potential by binding to a conserved linear peptide in the stem-helix region on sarbecovirus spikes. A 1.74[A] crystal structure of a CV3-25/peptide complex demonstrates that CV3-25 binds to the base of the stem helix at the HR2 boundary to an epitope that is distinct from other stem-helix directed neutralizing mAbs. Thus, CV3-25 defines a novel site of sarbecovirus vulnerability that will inform pan-CoV vaccine development.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Nicholas Hurlburt", + "author_inst": "Fred Hutch" + }, + { + "author_name": "Leah Homad", + "author_inst": "Fred Hutch" + }, + { + "author_name": "Irika Siha", + "author_inst": "Fred Hutch" + }, + { + "author_name": "Madeleine F Jenewein", + "author_inst": "Fred Hutch" + }, + { + "author_name": "Anna MacCamy", + "author_inst": "Fred Hutch" + }, + { + "author_name": "Yu-Hsin Wan", + "author_inst": "Fred Hutch" + }, + { + "author_name": "Jim Boonyaratanakornkit", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Anton M Sholukh", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Panpan Zhou", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Dennis Burton", + "author_inst": "Scripps Institute" + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Leonidas Stamatatos", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Marie Pancera", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Andrew McGuire", + "author_inst": "Fred Hutch" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.03.454910", "rel_title": "Vaccinia virus-based vaccines confer protective immunity against SARS-CoV-2 virus in Syrian hamsters", @@ -646487,89 +647859,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.29.21261006", - "rel_title": "Association of E484K and L452R spike protein mutations with SARS-CoV-2 infection in vaccinated persons---Maryland, January - May 2021", - "rel_date": "2021-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261006", - "rel_abs": "BackgroundThe E484K and L452R amino acid substitutions on the spike protein of SARS-CoV-2 are associated with reduced neutralization by antibodies from acquired immunity. This study examines the respective association of these mutations with infection in persons who had previously received a COVID-19 vaccine.\n\nMethodsGenetic sequences from SARS-CoV-2 specimens collected from Maryland residents and reported to Maryland Department of Health were linked to vaccination history. The prevalence of infections in fully vaccinated persons -- defined as being at least two weeks past receiving the final scheduled dose of a COVID-19 vaccine series -- was compared between infections caused by viruses carrying E484K to those not carrying E484K, and between infections caused by viruses carrying L452R to those not carrying L452R, using logistic regression to adjust for confounding.\n\nResultsOf 9,048 sequenced SARS-CoV-2 specimens examined, 265 (2.9%) were collected from fully vaccinated persons. In adjusted analysis, the E484K substitution was associated with an increase in the odds of the sequenced specimen being collected from a fully vaccinated person (OR 1.96, 95% CI, 1.36 to 2.83). The L452R mutation was not significantly associated with infections in vaccinated persons (OR 1.07, 95% CI, 0.69 to 1.68).\n\nConclusionThough more than 97% of SARS-CoV-2 infections were in persons who were not fully vaccinated, the E484K mutation was associated with increased odds of SARS-CoV-2 infection in vaccinated persons. Linking vaccination and sequencing data can help identify and estimate the impact SARS-CoV-2 mutations may have on vaccine effectiveness.\n\nSummaryIn viruses sequenced for Marylands routine SARS-CoV-2 genomic surveillance, the spike protein amino acid substitution E484K was more prevalent in viruses that infected vaccinated people than in viruses that infected people who were not vaccinated.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Kenneth Aaron Feder", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Ami Patel", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Venkata R Vepachedu", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Catherine Dominguez", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Eric N Keller", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Liore Klein", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Curi Kim", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Tim Blood", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Judie Hyun", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Theo Williams", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Katherine Anne Feldman", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Heba H Mostafa", - "author_inst": "Johns Hopkins University, School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "Christopher Paul Morris", - "author_inst": "Johns Hopkins University, School of Medicine, Department of Pathology, Division of Medical Microbiology" - }, - { - "author_name": "Jacques Ravel", - "author_inst": "University of Maryland School of Medicine, Institute for Genomic Sciences" - }, - { - "author_name": "Monique Duwell", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "David Blythe", - "author_inst": "Maryland Department of Health" - }, - { - "author_name": "Robert Myers", - "author_inst": "Maryland Department of Health" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.29.21261314", "rel_title": "Rapid comparative evaluation of SARS-CoV-2 rapid point-of-care antigen tests", @@ -646953,6 +648242,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.07.30.454520", + "rel_title": "Spike protein multiorgan tropism suppressed by antibodies targeting SARS-CoV-2", + "rel_date": "2021-08-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.30.454520", + "rel_abs": "While there is clinical evidence of severe acute respiratory syndrome coronavirus 2 multiorgan tropism in severely infected coronavirus 19 patients, its unclear if there is differential multiorgan biodistribution and organ uptake in healthy young individuals, a group that usually has asymptomatic to moderate coronavirus 19 symptoms. In addition, for antibody therapies and vaccines that target the spike protein, its unclear if these reduce severe acute respiratory syndrome coronavirus 2 or spike protein multiorgan tropism equally. We used fluorescently labeled spike protein near infrared fluorescence to study viral behavior, using an in vivo dynamic imaging system, in young mice. We found a spike protein body-wide biodistribution followed by a slow regional elimination, except for the liver, which showed an accumulation. Spike protein uptake was highest for the lungs, and this was followed by kidney, heart and liver, but, unlike the choroid plexus, it was not detected in the brain parenchyma or cerebrospinal fluid. Thus, the brain vascular barriers were effective in restricting the entry of spike protein into brain parenchyma in young healthy mice. While both anti-angiotensin converting enzyme 2 and anti-spike protein antibodies suppressed spike protein biodistribution and organ uptake, anti-spike protein antibody was more effective. By extension, our data support the efficacy of these antibodies on severe acute respiratory syndrome coronavirus 2 biodistribution kinetics and multiorgan tropism that could determine coronavirus 19 organ-specific outcomes.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Molly Brady", + "author_inst": "University of Rochester" + }, + { + "author_name": "Abigail Combs", + "author_inst": "University of Rochester" + }, + { + "author_name": "Chethana Venkatraman", + "author_inst": "University of Rochester" + }, + { + "author_name": "Alexander Solorzano", + "author_inst": "University of Rochester" + }, + { + "author_name": "Angelique Johnson", + "author_inst": "University of Rochester" + }, + { + "author_name": "Conor McQuaid", + "author_inst": "University of Rochester" + }, + { + "author_name": "Akib Rahman", + "author_inst": "University of Rochester" + }, + { + "author_name": "Hannah Leyva", + "author_inst": "University of Rochester" + }, + { + "author_name": "Wing-Chi Edmund Kwok", + "author_inst": "University of Rochester" + }, + { + "author_name": "Ronald W Wood", + "author_inst": "University of Rochester" + }, + { + "author_name": "Rashid Deane", + "author_inst": "University of Rochester" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2021.07.30.454529", "rel_title": "Multi-layered transcriptomic analyses reveal an immunological overlap between COVID-19 and hemophagocytic lymphohistiocytosis associated with disease severity", @@ -648689,57 +650037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.29.21261317", - "rel_title": "Correlation of SARS-CoV-2 Breakthrough Infections to Time-from-vaccine; Preliminary Study", - "rel_date": "2021-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261317", - "rel_abs": "The short-term effectiveness of a two-dose regimen of the BioNTech/Pfizer mRNA BNT162b2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine was widely demonstrated. However, long term effectiveness is still unknown. A nationwide vaccination campaign was initiated early in Israel, allowing for a real-world evaluation of the interaction between protection and time-from-vaccine. The Delta (B.1.617.2) variant became the dominant strain in Israel in June 2021, as Israel is currently experiencing a new surge of cases. Leveraging the centralized computerized database of Maccabi Healthcare Services (MHS), we assessed the correlation between time-from-vaccine and incidence of breakthrough infection. We found that the risk for infection was significantly higher for early vaccinees compared to those vaccinated later. This preliminary finding should prompt further investigagions into long-term protection against different strains, and prospective clinical trials to examine the effect of a booster vaccine against breakthrough infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Roni Lotan", - "author_inst": "Maccabi health care services" - }, - { - "author_name": "Sivan Gazit", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Gabriel Chodik", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Tal Patalon", - "author_inst": "Maccabi health care services" - }, - { - "author_name": "Galit Perez", - "author_inst": "Maccabi health care servises" - }, - { - "author_name": "Amir Ben Tov", - "author_inst": "Maccabi health care services" - }, - { - "author_name": "barak mizrahi", - "author_inst": "ki" - }, - { - "author_name": "Nir Kalkstein", - "author_inst": "KI" - }, - { - "author_name": "Asaf Peretz", - "author_inst": "Assuta medical center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.29.21261156", "rel_title": "Performance of Immunoglobulin G Serology on Finger Prick Capillary Dried Blood Spot Samples to Measure SARS-CoV-2 Humoral Immunogenicity", @@ -649039,6 +650336,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.07.30.21261361", + "rel_title": "Increased Autotaxin levels in severe COVID-19, correlating with IL-6 levels, endothelial dysfunction biomarkers, and impaired functions of dendritic cells", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.30.21261361", + "rel_abs": "Autotaxin (ATX; ENPP2) is a secreted lysophospholipase D catalysing the extracellular production of lysophosphatidic acid (LPA), a pleiotropic signalling phospholipid. Genetic and pharmacologic studies have previously established a pathologic role for ATX and LPA signalling in pulmonary injury, inflammation, and fibrosis. Here, increased ENPP2 mRNA levels were detected in immune cells from nasopharyngeal swab samples of COVID-19 patients, and increased ATX serum levels were found in severe COVID-19 patients. ATX serum levels correlated with the corresponding increased serum levels of IL-6 and endothelial damage biomarkers, suggesting an interplay of the ATX/LPA axis with hyperinflammation and the associated vascular dysfunction in COVID-19. Accordingly, dexamethasone (Dex) treatment of mechanically ventilated patients reduced ATX levels, as shown in two independent cohorts, indicating that the therapeutic benefits of Dex include the suppression of ATX. Moreover, large scale analysis of multiple single cell RNAseq datasets revealed the expression landscape of ENPP2 in COVID-19 and further suggested a role for ATX in the homeostasis of dendritic cells, that exhibit both numerical and functional deficits in COVID-19. Therefore, ATX has likely a multifunctional role in COVID-19 pathogenesis, worth of suggesting that its pharmacological targeting might represent an additional therapeutic option.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Ioanna Nikitopoulou", + "author_inst": "National & Kapodistrian University of Athens, Medical School" + }, + { + "author_name": "Dionysios Fanidis", + "author_inst": "Biomedical Sciences Research Center Alexander Fleming" + }, + { + "author_name": "Konstantinos Ntatsoulis", + "author_inst": "Biomedical Sciences Research Center Alexander Fleming" + }, + { + "author_name": "Panagiotis Moulos", + "author_inst": "Biomedical Sciences Research Center Alexander Fleming" + }, + { + "author_name": "George Mpekoulis", + "author_inst": "Hellenic Pasteur Institute" + }, + { + "author_name": "Maria Evangelidou", + "author_inst": "Hellenic Pasteur Institute" + }, + { + "author_name": "Vasiliki Dimakopoulou", + "author_inst": "University Hospital of Patras" + }, + { + "author_name": "Alice G Vassiliou", + "author_inst": "National & Kapodistrian University of Athens Medical School" + }, + { + "author_name": "Edison Jahaj", + "author_inst": "National & Kapodistrian University of Athens Medical School" + }, + { + "author_name": "Stamatios Tsipilis", + "author_inst": "National & Kapodistrian University of Athens Medical School" + }, + { + "author_name": "Stylianos E Orfanos", + "author_inst": "National & Kapodistrian University of Athens Medical School" + }, + { + "author_name": "Ioanna Dimopoulou", + "author_inst": "National & Kapodistrian University of Athens Medical School" + }, + { + "author_name": "Emmanouil Angelakis", + "author_inst": "Hellenic Pasteur Institute" + }, + { + "author_name": "Karolina Akinosoglou", + "author_inst": "University Hospital of Patras" + }, + { + "author_name": "Niki Vassilaki", + "author_inst": "Hellenic Pasteur Institute" + }, + { + "author_name": "Argyris Tzouvelekis", + "author_inst": "University Hospital of Patras" + }, + { + "author_name": "Anastasia Kotanidou", + "author_inst": "National & Kapodistrian University of Athens Medical School" + }, + { + "author_name": "Vassilis Aidinis", + "author_inst": "Biomedical Sciences Research Center Alexander Fleming" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.07.29.21261282", "rel_title": "Age-specific rate of severe and critical SARS-CoV-2 infections estimated with multi-country seroprevalence studies", @@ -650247,69 +651631,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.07.27.21261210", - "rel_title": "Can Vaccine Prioritization Reduce Disparities in Covid-19 Burden for Historically Marginalized Populations?", - "rel_date": "2021-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261210", - "rel_abs": "1.ImportanceNationally stated goals for distributing SARS-CoV-2 vaccines included to reduce COVID-19 mortality, morbidity, and inequity using prioritization groups. However, the impact of these prioritization strategies is not well understood, particularly their effect on health inequity in COVID-19 burden for historically marginalized racial and ethnic populations.\n\nObjectiveTo assess the impact of vaccination prioritization and operational strategies on disparities in COVID-19 burden among historically marginalized populations, and on mortality and morbidity by race and ethnicity.\n\nDesignWe use an agent-based simulation model of North Carolina to project SARS-CoV-2 infections and COVID-19-associated deaths (mortality), hospitalizations (morbidity), and cases over 18 months (7/1/2020-12/31/2021) with vaccine distribution beginning 12/13/2020 to frontline medical and people 75+, assuming initial uptake similar to influenza vaccine. We study two-stage subsequent prioritization including essential workers (\"essential\"), adults 65+ (\"age\"), adults with high-risk health conditions, HMPs, or people in low income tracts, with eligibility for the general population in the third stage. For age-essential and essential-age strategies, we also simulated maximal uptake (100% for HMP or 100% for everyone), and we allowed for distribution to susceptible-only people.\n\nResultsPrioritizing Age then Essential had the largest impact on mortality (2.5% reduction from no prioritization); Essential then Age had the lowest morbidity and reduced infections (4.2% further than Age-Essential) without significantly impacting mortality. Under each prioritization scenario, the age-adjusted mortality burden for HMPs is higher (e.g., 33.3-34.1% higher for the Black population, 13.3%-17.0% for the Hispanic population) compared to the White population, and the gap grew under some prioritizations. In the Age-Essential strategy, the burden on HMPs decreases only when uptake is increased to 100% in HMPs. However, the Black population still had the highest mortality rate even with the Susceptible-Only distribution.\n\nConclusions and RelevanceSimulation results show that prioritization strategies have differential impact on mortality, morbidity, and disparities overall and by race and ethnicity. If prioritization schemes were not paired with increased uptake in HMPs, disparities did not improve and could worsen. Although equity was one of the tenets of vaccine distribution, the vaccination strategies publicly outlined are insufficient to remove and may exacerbate disparities between racial and ethnic groups, thus targeted strategies are needed for the future.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Erik Rosenstrom", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Jessica A. Mele", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Julie Ivy", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Maria Mayorga", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Mehul Patel", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Kristen Hassmiller Lich", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Karl D Johnson", - "author_inst": "University of North Carolina Gillings School of Global Public Health" - }, - { - "author_name": "Paul Delamater", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Pinar Keskinocak", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Ross Boyce", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Raymond Smith", - "author_inst": "East Carolina University" - }, - { - "author_name": "Julie L Swann", - "author_inst": "North Carolina State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.07.26.21261162", "rel_title": "Diagnostic performance of a novel digital immunoassay (RapidTesta SARS-CoV-2): a prospective observational study with 1,127 nasopharyngeal samples", @@ -650625,6 +651946,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.28.21260814", + "rel_title": "Influence of social determinants of health and county vaccination rates on machine learning models to predict COVID-19 case growth in Tennessee", + "rel_date": "2021-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21260814", + "rel_abs": "The SARS-CoV-2 (COVID-19) pandemic has exposed health disparities throughout the United States, particularly among racial and ethnic minorities. As a result, there is a need for data-driven approaches to pinpoint the unique constellation of clinical and social determinants of health (SDOH) risk factors that give rise to poor patient outcomes following infection in US communities.\n\nWe combined county-level COVID-19 testing data, COVID-19 vaccination rates, and SDOH information in Tennessee. Between February-May 2021, we trained machine learning models on a semi-monthly basis using these datasets to predict COVID-19 incidence in Tennessee counties. We then analyzed SDOH data features at each time point to rank the impact of each feature on model performance.\n\nOur results indicate that COVID-19 vaccination rates play a crucial role in determining future COVID-19 disease risk. Beginning in mid-March 2021, higher vaccination rates significantly correlated with lower COVID-19 case growth predictions. Further, as the relative importance of COVID-19 vaccination data features grew, demographic SDOH features such as age, race, and ethnicity decreased while the impact of socioeconomic and environmental factors, including access to healthcare and transportation, increased.\n\nIncorporating a data framework to track the evolving patterns of community-level SDOH risk factors could provide policymakers with additional data resources to improve health equity and resilience to future public health emergencies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Lukasz S Wylezinski", + "author_inst": "Decode Health, Inc., IQuity Labs, Inc., and Vanderbilt University School of Medicine" + }, + { + "author_name": "Coleman R Harris", + "author_inst": "Decode Health, Inc., IQuity Labs, Inc., and Vanderbilt University School of Medicine" + }, + { + "author_name": "Cody N Heiser", + "author_inst": "Decode Health, Inc., IQuity Labs, Inc., and Vanderbilt University School of Medicine" + }, + { + "author_name": "Jamieson D Gray", + "author_inst": "Decode Health, Inc. and IQuity Labs, Inc." + }, + { + "author_name": "Charles F Spurlock III", + "author_inst": "Decode Health, Inc., IQuity Labs, Inc., New York University Wagner School of Public Health, and Vanderbilt University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.07.30.454437", "rel_title": "Highly efficient SARS-CoV-2 infection of human cardiomyocytes: spike protein-mediated cell fusion and its inhibition", @@ -652341,153 +653697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.07.28.21261159", - "rel_title": "Six Month Safety and Efficacy of the BNT162b2 mRNA COVID-19 Vaccine", - "rel_date": "2021-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261159", - "rel_abs": "BackgroundBNT162b2 is a lipid nanoparticle-formulated, nucleoside-modified RNA vaccine encoding a prefusion-stabilized, membrane-anchored SARS-CoV-2 full-length spike protein. BNT162b2 is highly efficacious against COVID-19 and is currently authorized for emergency use or conditional approval worldwide. At the time of authorization, data beyond 2 months post-vaccination were unavailable.\n\nMethodsIn an ongoing, placebo-controlled, observer-blinded, multinational, pivotal efficacy study, 44,165 [≥]16-year-old participants and 2,264 12-15-year-old participants were randomized to receive 2 doses, 21 days apart, of 30 {micro}g BNT162b2 or placebo. Study endpoints reported here are vaccine efficacy (VE) against laboratory-confirmed COVID-19 and safety data, both up to 6 months post-vaccination.\n\nResultsBNT162b2 continued to be safe and well tolerated. Few participants had adverse events leading to study withdrawal. VE against COVID-19 was 91% (95% CI 89.0-93.2) through up to 6 months of follow-up, among evaluable participants and irrespective of previous SARS-CoV-2 infection. VE of 86%-100% was seen across countries and in populations with diverse characteristics of age, sex, race/ethnicity, and COVID-19 risk factors in participants without evidence of previous SARS-CoV-2 infection. VE against severe disease was 97% (95% CI 80.3-99.9). In South Africa, where the SARS-CoV-2 variant of concern, B.1.351 (beta), was predominant, 100% (95% CI 53.5, 100.0) VE was observed.\n\nConclusionWith up to 6 months of follow-up and despite a gradually declining trend in vaccine efficacy, BNT162b2 had a favorable safety profile and was highly efficacious in preventing COVID-19. (ClinicalTrials.gov number, NCT04368728)", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Stephen J Thomas", - "author_inst": "State University of New York, Upstate Medical University, Syracuse , NY" - }, - { - "author_name": "Edson D Moreira Jr.", - "author_inst": "Associa\u00e7\u00e3o Obras Sociais Irm\u00e3 Dulce and Oswaldo Cruz Foundation, Bahia, Brazil" - }, - { - "author_name": "Nicholas Kitchin", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Hurley, UK" - }, - { - "author_name": "Judith Absalon", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Alejandra Gurtman", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Stephen Lockhart", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Hurley, UK" - }, - { - "author_name": "John L Perez", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Collegeville, PA" - }, - { - "author_name": "Gonzalo P\u00e9rez Marc", - "author_inst": "iTrials-Hospital Militar Central, Buenos Aires, Argentina" - }, - { - "author_name": "Fernando P Polack", - "author_inst": "Fundacion INFANT, Buenos Aires, Argentina" - }, - { - "author_name": "Cristiano Zerbini", - "author_inst": "Centro Paulista de Investiga\u00e7\u00e3o Clinica, S\u00e3o Paulo, Brazil" - }, - { - "author_name": "Ruth Bailey", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Hurley, UK" - }, - { - "author_name": "Kena A Swanson", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Xia Xu", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Collegeville, PA" - }, - { - "author_name": "Satrajit Roychoudhury", - "author_inst": "Global Product Development, Pfizer Inc, Peapack, NJ" - }, - { - "author_name": "Kenneth Koury", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Salim Bouguermouh", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Warren V Kalina", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "David Cooper", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Robert W Frenck Jr.", - "author_inst": "Cincinnati Children's Hospital, Cincinnati, OH" - }, - { - "author_name": "Laura L Hammitt", - "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, MD" - }, - { - "author_name": "\u00d6zlem T\u00fcreci", - "author_inst": "BioNTech, Mainz, Germany" - }, - { - "author_name": "Haylene Nell", - "author_inst": "Tiervlei Trial Centre, Karl Bremer Hospital, Cape Town, South Africa" - }, - { - "author_name": "Axel Schaefer", - "author_inst": "Medizentrum Essen Borbeck, Essen, Germany" - }, - { - "author_name": "Serhat \u00dcnal", - "author_inst": "Hacettepe University, Ankara, Turkey" - }, - { - "author_name": "Qi Yang", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Paul Liberator", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Dina B Tresnan", - "author_inst": "Worldwide Safety, Safety Surveillance and Risk Management, Pfizer, Inc, Groton, CT" - }, - { - "author_name": "Susan Mather", - "author_inst": "Worldwide Safety, Safety Surveillance and Risk Management, Pfizer, Inc, Collegeville, PA" - }, - { - "author_name": "Philip R Dormitzer", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "U\u011fur \u015eahin", - "author_inst": "BioNTech, Mainz, Germany" - }, - { - "author_name": "William C Gruber", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "Kathrin U Jansen", - "author_inst": "Vaccine Research and Development, Pfizer Inc, Pearl River, NY" - }, - { - "author_name": "- C4591001 Clinical Trial Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.26.21261130", "rel_title": "Vaccine effectiveness when combining the ChAdOx1 vaccine as the first dose with an mRNA COVID-19 vaccine as the second dose", @@ -652883,6 +654092,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.28.453981", + "rel_title": "Single-Cell Profiling of the Antigen-Specific Response to BNT162b2 SARS-CoV-2 RNA Vaccine", + "rel_date": "2021-07-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.28.453981", + "rel_abs": "RNA-based vaccines against SARS-CoV-2 are critical to limiting COVID-19 severity and spread. Cellular mechanisms driving antigen-specific responses to these vaccines, however, remain uncertain. We used single-cell technologies to identify and characterized antigen-specific cells and antibody responses to the RNA vaccine BNT162b2 in longitudinal samples from a cohort of healthy donors. Mass cytometry and machine learning pinpointed a novel expanding, population of antigen-specific non-canonical memory CD4+ and CD8+ T cells. B cell sequencing suggested progression from IgM, with apparent cross-reactivity to endemic coronaviruses, to SARS-CoV-2-specific IgA and IgG memory B cells and plasmablasts. Responding lymphocyte populations correlated with eventual SARS-CoV-2 IgG and a donor lacking these cell populations failed to sustain SARS-CoV-2-specific antibodies and experienced breakthrough infection. These integrated proteomic and genomic platforms reveal an antigen-specific cellular basis of RNA vaccine-based immunity.\n\nONE SENTENCE SUMMARYSingle-cell profiling reveals the cellular basis of the antigen-specific response to the BNT162b2 SARS-CoV-2 RNA vaccine.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Kevin J Kramer", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Erin M Wilfong", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Kelsey Voss", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Sierra Barone", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Andrea R Shiakolas", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Nagarajan Raju", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Caroline E Roe", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Naveenchandra Suryadevara", + "author_inst": "Vanderbilt University Vaccine Center" + }, + { + "author_name": "Lauren M Walker", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Steven C Wall", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Ariana Paulo", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Samuel Schaefer", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Debolanle Dahunsi", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Camille S. Westlake", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "James E. Crowe", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Robert H Carnahan Jr.", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Jeffrey C Rathmell", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Rachel H Bonami", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Ivelin S Georgiev", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Jonathan Michael Irish", + "author_inst": "Vanderbilt University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.07.28.454098", "rel_title": "SARS-CoV-2 in the Republic of Guinea: Fragment and Whole-Genome Sequencing, Phylogenetic Analysis", @@ -654235,77 +655539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.24.21261046", - "rel_title": "High throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses.", - "rel_date": "2021-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.24.21261046", - "rel_abs": "BackgroundIn the current phase of COVID-19 pandemic, we are facing two serious public health challenges that include deficits in SARS-CoV-2 variant monitoring, and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent and dynamics of the outbreak are required to understand the transmission of the virus amongst seemingly unrelated cases and provide critical epidemiological information. To address these challenges, we evaluated a new high-throughput next-generation sequencing (NGS), respiratory viral panel (RVP) that includes 40 viral pathogens with the aim of analyzing viral subtypes, mutational variants of SARS-CoV-2, model to understand the spread of the virus in the state of Georgia, USA, and to assess other circulating viruses in the same population.\n\nMethodsThis study evaluated a total of 522 samples that included 483 patient samples and 42 synthetic positive control material. The performance metrics were calculated for both clinical and reference control samples by comparing detection results with the RT-PCR assay. The limit of detection (LoD) studies were conducted as per the FDA guidelines. Inference and visualization of the phylogeny of the SARS-CoV-2 sequences were performed through the Nextstrain Command-Line Interface (CLI) tool, utilizing the associated augur and auspice toolkits.\n\nResultsThe performance metrics calculated using both the clinical samples and the reference controls revealed a PPA, NPA and accuracy of 95.98%, 85.96% and 94.4%, respectively. The LoD was determined to be 10 copies/ml with all 25 replicates detected across two different runs. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF 3a and, S84L in ORF8 covarying with the D614G spike protein mutation were the most prevalent, early in the pandemic, in Georgia, USA. In our analysis, isolates from the same county formed paraphyletic groups, which indicated virus transmission between counties.\n\nConclusionThe study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats, models that provide insights into viral transmission patterns and predict transmission/ resurgence of regional outbreaks and provide critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nikhil Shri Sahajpal", - "author_inst": "Augusta University" - }, - { - "author_name": "Ashis K Mondal", - "author_inst": "Augusta University" - }, - { - "author_name": "Allan Njau", - "author_inst": "Aga Khan University Hospital" - }, - { - "author_name": "Zachary Petty", - "author_inst": "University of Georgia" - }, - { - "author_name": "Jiani Chen", - "author_inst": "University of Georgia" - }, - { - "author_name": "Sudha Ananth", - "author_inst": "Augusta University" - }, - { - "author_name": "Pankaj Ahluwalia", - "author_inst": "Augusta University" - }, - { - "author_name": "Colin Williams", - "author_inst": "Augusta University" - }, - { - "author_name": "Ted M Ross", - "author_inst": "University System of Georgia" - }, - { - "author_name": "Alka Chaubey", - "author_inst": "Augusta University" - }, - { - "author_name": "Grace DeSantis", - "author_inst": "Illumina Inc." - }, - { - "author_name": "Gary P. Schroth", - "author_inst": "Illumina Inc." - }, - { - "author_name": "Justin Bahl", - "author_inst": "University of Georgia" - }, - { - "author_name": "Ravindra Kolhe", - "author_inst": "Augusta University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.24.21261065", "rel_title": "COVID-Q: validation of the first COVID-19 questionnaire based on patient-rated symptom gravity", @@ -654729,6 +655962,81 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.07.26.453787", + "rel_title": "N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry", + "rel_date": "2021-07-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.26.453787", + "rel_abs": "N-glycosylation plays an important role in the structure and function of membrane and secreted proteins. The spike protein on the surface of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is heavily glycosylated and the major target for developing vaccines, therapeutic drugs and diagnostic tests. The first major SARS-CoV-2 variant carries a D614G substitution in the spike (S-D614G) that has been associated with altered conformation, enhanced ACE2 binding, and increased infectivity and transmission. In this report, we used mass spectrometry techniques to characterize and compare the N-glycosylation of the wild type (S-614D) or variant (S-614G) SARS-CoV-2 spike glycoproteins prepared under identical conditions. The data showed that half of the N-glycosylation sequons changed their distribution of glycans in the S-614G variant. The S-614G variant showed a decrease in the relative abundance of complex-type glycans (up to 45%) and an increase in oligomannose glycans (up to 33%) on all altered sequons. These changes led to a reduction in the overall complexity of the total N-glycosylation profile. All the glycosylation sites with altered patterns were in the spike head while the glycosylation of three sites in the stalk remained unchanged between S-614G and S-614D proteins.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Dongxia Wang", + "author_inst": "Centers for Disease Control and Prevention (CDC)" + }, + { + "author_name": "Bin Zhou", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Theodore Keppel", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Maria Solano", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jakub Baudys", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jason Goldstein", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "M.G. Finn", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Xiaoyu Fan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Asheley P Chapman", + "author_inst": "Georgia Institute of Technology. Atlanta" + }, + { + "author_name": "Jonathan Bundy", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Adrian R. Woolfitt", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Sarah Osman", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "James L. Pirkle", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "David E. Wentworth", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "John R. Barr", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.07.23.453327", "rel_title": "Mutations in two SARS-CoV-2 variants of concern reflect two distinct strategies of antibody escape", @@ -656445,37 +657753,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.24.21261047", - "rel_title": "Proxalutamide Improves Inflammatory, Immunologic, and Thrombogenic Markers in Mild-to-Moderate COVID-19 Males and Females: an Exploratory Analysis of a Randomized, Double-Blinded, Placebo-Controlled Trial Early Antiandrogen Therapy (EAT) with Proxalutamide (The EAT-Proxa Biochemical AndroCoV-Trial)", - "rel_date": "2021-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.24.21261047", - "rel_abs": "BackgroundThe androgen theory on COVID-19 is based on the fact that males, in particular when affected by androgenetic alopecia, and females with hyperandrogenic states are more severely affected by COVID-19, while chronic users of antiandrogens experiment lower rates of COVID-19 complications. The theory finds plausibility on the androgen-mediated transmembrane protease serine 2 (TMPRSS-2), a key protein for SARS-CoV-2 cell entry. We demonstrated reduction of hospitalization rate using a potent non-steroidal antiandrogen (NSAA), proxalutamide, in both females and males COVID-19 outpatients. In this joint exploratory analysis, we aimed to demonstrate whether the efficacy of proxalutamide on mild-to-moderate COVID-19 could be justified by improvements in inflammatory, immunologic, and thrombogenic responses.\n\nMethodsThis is a joint post-hoc analysis of two double-blind, placebo-controlled two-arm randomized clinical trials (RCTs) on proxalutamide 200mg/day for seven days for female and male COVID-19 outpatients, respectively, compared to standard of care (SOC), of hematocrit, neutrophils lymphocytes, eosinophils, platelets, neutrophil-to-lymphocyte (N/L) ratio, ferritin, fibrinogen, D-dimer, ultrasensitive C-reactive protein (usCRP) lactate 1-hour erythrocyte sedimentation rate (1hESR), total testosterone, estradiol, sex hormone binding globulin (SHBG), oxygen saturation and heart rate measured on days 0, 1 and 7.\n\nResultsA total of 445 subjects were enrolled (268 males and 177 females) between October 21th 2020 and February 28th 2021, with similar baseline characteristics. Neutrophils were lower in proxalutamide group in Day 1 (p = 0.005) and Day 7 (p < 0.0001). Lymphocytes were higher in the proxalutamide group in Day 7 (p = 0.0001). Eosinophils were higher in the proxalutamide arm in Day 1 (p = 0.04) and Day 7 (p < 0.00010. In Day 7, platelets were higher in proxalutamide arm (p = 0.03). Ferritin levels were lower in proxalutamide arm in Day 7 (p = 0.03) Fibrinogen levels were lower in proxalutamide group in Days 1 and 7 (p < 0.0001 for both days). D-dimer levels were lower in proxalutamide group in Days 1 and 7 (p < 0.0001 for both days). UsCRP levels were reduced in proxalutamide group in Day 7 (p < 0.0001). 1hESR) was reduced in proxalutamide arm in Day 1 (p = 0.0009) and Day 7 (p < 0.0001). In males, testosterone levels were higher in proxalutamide group in Day 1 (p = 0.048) and Day 7 (p = 0.0001). In females, testosterone levels were higher in proxalutamide group in Day 7 (p = 0.018), and estradiol levels were higher in proxalutamide arm in Day 1 (p = 0.044). Oxygen saturation was higher in proxalutamide in Day 1 (p = 0.0006) and Day 7 (p < 0.0001).\n\nConclusionsThe substantial improvements observed in immunologic, inflammatory, thrombotic and oxygen markers with proxalutamide may support the reduction of hospitalization rate observed in both females and males with COVID-19 using proxalutamide, compared to standard of care.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Flavio A Cadegiani", - "author_inst": "Applied Biology, Inc. Irvine, CA, USA, and Corpometria Institute, Brasilia, Brazil." - }, - { - "author_name": "Andy Goren", - "author_inst": "Applied Biology, Inc. Irvine, CA, USA." - }, - { - "author_name": "Carlos Gustavo Wambier", - "author_inst": "Warren Alpert Medical School of Brown University" - }, - { - "author_name": "Ricardo Zimerman", - "author_inst": "Hospital da Brigada Militar, Porto Alegre, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.24.21261007", "rel_title": "Use of Indomethacin for mild and moderate Covid -19 patients. A Randomized Control Trial", @@ -656747,6 +658024,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.21.21260956", + "rel_title": "Ethnic disparities in incident SARS-CoV-2 infections became wider during the second wave of SARS-CoV-2 in Amsterdam, the Netherlands: a population-based longitudinal study", + "rel_date": "2021-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260956", + "rel_abs": "BackgroundSurveillance data in high-income countries have reported more frequent SARS-CoV-2 diagnoses in ethnic minority groups. We examined the cumulative incidence of SARS-CoV-2 and its determinants in six ethnic groups in Amsterdam, the Netherlands.\n\nMethodsWe analyzed participants enrolled in the population-based HELIUS cohort, who were tested for SARS-CoV-2-specific antibodies and answered COVID-19-related questions between June 24-October 9, 2020 (after the first wave) and November 23, 2020-March 31, 2021 (during the second wave). We modeled SARS-CoV-2 incidence from January 1, 2020-March 31, 2021 using Markov models adjusted for age and sex. We compared incidence between ethnic groups over time and identified determinants of incident infection within ethnic groups.\n\nFindings2,497 participants were tested after the first wave; 2,083 (83{middle dot}4%) were tested during the second wave. Median age at first visit was 54 years (interquartile range=44-61); 56{middle dot}6% were female. Compared to Dutch-origin participants (15{middle dot}9%), cumulative SARS-CoV-2 incidence was higher in participants of South-Asian Surinamese (25{middle dot}0%; adjusted hazard ratio [aHR]=1{middle dot}66;95%CI=1{middle dot}16-2{middle dot}40), African Surinamese (28{middle dot}9%;aHR=1{middle dot}97;95%CI=1{middle dot}37-2{middle dot}83), Turkish (37{middle dot}0%;aHR=2{middle dot}67;95%CI=1{middle dot}89-3{middle dot}78), Moroccan (41{middle dot}9%;aHR=3{middle dot}13;95%CI=2{middle dot}22-4{middle dot}42), and Ghanaian (64{middle dot}6%;aHR=6{middle dot}00;95%CI=4{middle dot}33-8{middle dot}30) origin. Compared to those of Dutch origin, differences in incidence became wider during the second versus first wave for all ethnic minority groups (all p for interaction<0.05), except Ghanaians. Having household members with suspected SARS-CoV-2 infection, larger household size, and low health literacy were common determinants of SARS-CoV-2 incidence across groups.\n\nInterpretationSARS-CoV-2 incidence was higher in the largest ethnic minority groups of Amsterdam, particularly during the second wave. Prevention measures, including vaccination, should be encouraged in these groups.\n\nFundingZonMw, Public Health Service of Amsterdam, Dutch Heart Foundation, European Union, European Fund for the Integration of non-EU immigrants.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Liza Coyer", + "author_inst": "Public Health Service of Amsterdam; Amsterdam UMC" + }, + { + "author_name": "Anders Boyd", + "author_inst": "Public Health Service of Amsterdam; Stichting HIV Monitoring" + }, + { + "author_name": "Janke Schinkel", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Charles Agyemang", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Henrike Galenkamp", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Anitra D.M. Koopman", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Tjalling Leenstra", + "author_inst": "Public Health Service of Amsterdam" + }, + { + "author_name": "Yvonne T.H.P. van Duijnhoven", + "author_inst": "Public Health Service of Amsterdam" + }, + { + "author_name": "Eric P. Moll van Charante", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Bert-Jan H. van den Born", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Anja Lok", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Arnoud Verhoeff", + "author_inst": "Public Health Service of Amsterdam; University of Amsterdam" + }, + { + "author_name": "Aeilko H. Zwinderman", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Suzanne Jurriaans", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Karien Stronks", + "author_inst": "Amsterdam UMC" + }, + { + "author_name": "Maria Prins", + "author_inst": "Public Health Service of Amsterdam; Amsterdam UMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.21.21260959", "rel_title": "Proteomic and metabolomic signatures associated with the immune response in healthy individuals immunized with an inactivated SARS-CoV-2 vaccine", @@ -659375,89 +660731,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.22.21260854", - "rel_title": "Air travel-related outbreak of multiple SARS-CoV-2 variants", - "rel_date": "2021-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21260854", - "rel_abs": "BackgroundA large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of >400,000 newly confirmed cases on 7 May 2021.\n\nMethodsEpidemiological information including date of symptom onset, date of positive-sample detection, and travel and contact history for individual cases from this flight were collected. Whole genome sequencing was performed, and sequences were classified based on the dynamic Pango nomenclature system. Maximum-likelihood phylogenetic analysis compared sequences from this flight alongside other cases imported from India to Hong Kong on 26 flights between June 2020 and April 2021, as well as sequences from India or associated with India-related travel from February to April 2021, and 1,217 reference sequences.\n\nResultsSequence analysis identified six lineages of SARS-CoV-2 belonging to two variants of concern (Alpha and Delta) and one variant of public health interest (Kappa) involved in this outbreak. Phylogenetic analysis confirmed at least three independent sub-lineages of Alpha with limited onward transmission, a superspreading event comprising 37 cases of Kappa, and transmission of Delta to only one passenger. Additional analysis of another 26 flights from India to Hong Kong confirmed widespread circulation of all three variants in India since early March 2021.\n\nConclusionsThe broad spectrum of disease severity and long incubation period of SARS-CoV-2 pose a challenge for surveillance and control. As illustrated by this particular outbreak, opportunistic infections of SARS-CoV-2 can occur irrespective of variant lineage, and requiring a nucleic acid test within 72 hours of departure may be insufficient to prevent importation or in-flight transmission.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Vijaykrishna Dhanasekaran", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kimberly M Edwards", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ruopeng Xie", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Haogao Gu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Dillon C Adam", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Lydia DJ Chang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Sammi SY Cheuk", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Shreya Gurung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Pavithra Krishnan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Daisy YM Ng", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Gigi YZ Liu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Carrie KC Wan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Samuel SM Cheng", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Dominic NC Tsang", - "author_inst": "Centre for Health Protection" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Malik Peiris", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Leo LM Poon", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.21.21260964", "rel_title": "Phase 1 safety and pharmacokinetics studies of BRII-196 and BRII-198, SARS-CoV-2 spike-targeting monoclonal antibodies", @@ -659741,6 +661014,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.22.21261008", + "rel_title": "A collaborative maternity dashboard (CoMaND) for the COVID-19 pandemic: a protocol for timely, adaptive monitoring of perinatal outcomes in Melbourne, Australia", + "rel_date": "2021-07-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21261008", + "rel_abs": "BackgroundThe COVID-19 pandemic has resulted in a range of unprecedented disruptions to the delivery of maternity care globally and has been associated with regional changes in perinatal outcomes such as stillbirth and preterm birth. Metropolitan Melbourne endured one of the longest and most stringent lockdowns in 2020. This paper presents the protocol for a collaborative maternity dashboard project to monitor perinatal outcomes in Melbourne, Australia, during the COVID-19 pandemic.\n\nMethodsDe-identified maternal and newborn outcomes will be collected monthly from all public maternity services in Melbourne, allowing rapid analysis of a multitude of perinatal indicators. Weekly outcomes will be displayed as run charts according to established methods for detecting non-random signals in health care. A pre-pandemic median for all indicators will be calculated for the period of January 2018 to March 2020. A significant shift is defined as [≤] six consecutive weeks, all above or below the pre-pandemic median. Additional statistical analyses such as regression, time-series, and survival analyses will be performed for an in-depth examination of maternal and perinatal outcomes of interests.\n\nEthics and DisseminationThis study has been registered as an observational study with the Australian and New Zealand Clinical Trials Registry (ACTRN12620000878976).\n\nStrengths and weaknesses of this study This project is the first clinician-led, multi-centre perinatal data collection system for metropolitan Melbourne.\n It complements the state government data collection, with the significant benefits of more timely and flexible reporting of outcomes, and granular detail on emerging areas of concern.\n The study relies on primary source coding of exposure and outcomes from each hospital that have not been internally validated during the study period.\n Data from private maternity hospitals, containing 25% of Melbourne births, are not available.\n This resource will support data-informed hospital pandemic responses through to the end of 2022.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Lisa Hui", + "author_inst": "Department of Obstetrics and Gynaecology, Melbourne Medical School, The University of Melbourne" + }, + { + "author_name": "Melvin B Marzan", + "author_inst": "Department of Obstetrics and Gynaecology, Melbourne Medical School, The University of Melbourne" + }, + { + "author_name": "Stephanie Potenza", + "author_inst": "Department of Obstetrics and Gynaecology, Mercy Hospital for Women, Mercy Health" + }, + { + "author_name": "Daniel L Rolnik", + "author_inst": "Department of Obstetrics and Gynaecology, Monash University" + }, + { + "author_name": "Joanne M Said", + "author_inst": "Department of Obstetrics and Gynaecology, Melbourne Medical School, The University of Melbourne" + }, + { + "author_name": "Kirsten R Palmer", + "author_inst": "Department of Obstetrics and Gynaecology, Monash University" + }, + { + "author_name": "Clare L Whitehead", + "author_inst": "Department of Obstetrics and Gynaecology, Melbourne Medical School, The University of Melbourne" + }, + { + "author_name": "Penelope M Sheehan", + "author_inst": "Department of Obstetrics and Gynaecology, Eastern Health" + }, + { + "author_name": "Jolyon Ford", + "author_inst": "Department of Obstetrics and Gynaecology, Peninsula Health" + }, + { + "author_name": "Natasha Pritchard", + "author_inst": "Department of Obstetrics and Gynaecology, Melbourne Medical School, The University of Melbourne" + }, + { + "author_name": "Ben W Mol", + "author_inst": "Department of Obstetrics and Gynaecology, Monash University" + }, + { + "author_name": "Susan Walker", + "author_inst": "Department of Obstetrics and Gynaecology, Melbourne Medical School, The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.07.21.21260963", "rel_title": "Blockade of Interleukin Seventeen (IL-17A) with Secukinumab in Hospitalized COVID-19 patients - the BISHOP study.", @@ -661285,69 +662621,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.20.21260754", - "rel_title": "Increase in ventilatory ratio indicates progressive alveolar damage and suggests poor prognosis in severe COVID-19: A single-center retrospective observational study.", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260754", - "rel_abs": "BackgroundThe symptoms of severe COVID-19 are complex and wide-ranging even in intensive care unit (ICU) patients, who may successfully discontinue respiratory support in a short period or conversely require prolonged respiratory support. Damage in the lungs of COVID-19 patients is characterized pathologically as diffuse alveolar damage, the degree of which correlates with the severity of the disease. We hypothesized that the ventilatory ratio (VR), a surrogate parameter for the dead space fraction, might stratify the severity of COVID-19 and predict the successful discontinuation of respiratory support.\n\nMethodsForty COVID-19 patients in our ICU were enrolled in this study. Respiratory variables were collected from 2 hours (day 0) after the initiation of respiratory support. We monitored the longitudinal values of VR and other respiratory parameters for 28 days. Patients successfully discontinued from respiratory support by day 28 of ICU stay were defined as the successfully discontinued group, while those who died or failed to discontinue were defined as the failed to discontinue group. VR and other respiratory parameters were compared between these groups.\n\nResultsExcept for advanced age, prolonged ventilation period, and higher mortality in the failed to discontinue group, there were no significant differences between the groups in terms of any other background or respiratory parameter at 2 hours (day 0) after initiation of respiratory support. Longitudinal VR monitoring revealed significantly higher VR values in the failed to discontinue group than the successfully discontinued group on day 4 of respiratory support. Upon predicting the failure to discontinue respiratory support, the area under the receiver operating characteristic curve of VR values on day 4 of respiratory support was 0.748. A threshold of 1.56 achieved the highest predictive performance with a sensitivity of 0.667 and a specificity of 0.762. This threshold enabled the prediction of the successfully discontinued outcome at 0.810 of the negative predictive value.\n\nConclusionsElevated VR values on day 4 of respiratory support were predictive of successful discontinuation of respiratory support in patients with severe COVID-19. Longitudinal VR values after initiation of respiratory support can be used as a practical index to stratify severe COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Natsuko Kaku", - "author_inst": "Osaka City University" - }, - { - "author_name": "Yu Nakagama", - "author_inst": "Osaka City University" - }, - { - "author_name": "Michinori Shirano", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Sari Shinomiya", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Kazuhiro Shimazu", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Katsuaki Yamazaki", - "author_inst": "National Cerebral and Cardiovascular Center Hospital" - }, - { - "author_name": "Yoshito Maehata", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Ryo Morita", - "author_inst": "Osaka City General Hospital, Osaka City Hospital Organization" - }, - { - "author_name": "Yuko Nitahara", - "author_inst": "Osaka City University" - }, - { - "author_name": "Hiromasa Yamamoto", - "author_inst": "Osaka City University" - }, - { - "author_name": "Yasumitsu Mizobata", - "author_inst": "Osaka City University" - }, - { - "author_name": "Yasutoshi Kido", - "author_inst": "Osaka City University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.07.18.21260718", "rel_title": "Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in Qatar", @@ -661683,6 +662956,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.16.21260509", + "rel_title": "Access to COVID-19 Vaccines in High-, Middle-, and Low-Income Countries Hosting Clinical Trials", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260509", + "rel_abs": "The COVID-19 pandemic has led to the rapid development of multiple vaccines, vaccines that were tested in clinical trials located in several countries around the world. Because prior research has shown that pharmaceuticals do not receive consistent and timely authorization for use in lower-income countries where they are tested, we conducted a cross-sectional study examining the authorization or approval and delivery for COVID-19 vaccines recommended by the World Health Organization (WHO) in the countries where they were tested. While countries of varying incomes have largely authorized the COVID-19 vaccines tested within their populations for use, high-income countries have received proportionately more doses, enabling them to more fully vaccinate their populations. As many lower-income countries continue to experience inequitable shortfalls in COVID-19 vaccine supply amid the ongoing pandemic, efforts must be undertaken to ensure timely access in countries across all income groups, including those hosting clinical trials.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Reshma Ramachandran", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Joseph S. Ross", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Jennifer E Miller", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.18.21259553", "rel_title": "Deep Optical Blood Analysis: COVID-19 Detection as a Case Study in Next Generation Blood Screening", @@ -663547,53 +664847,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.19.21260792", - "rel_title": "Prevalence of SARS CoV-2 infection among Health Care Workers of a hybrid tertiary COVID 19 hospital in Kerala", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260792", - "rel_abs": "Back ground and objectivesThis study was undertaken to estimate the prevalence of SARS-CoV-2 infection among Health care workers [HCWs] of a hybrid COVID treatment hospital in Kerala.\n\nMethodsThe study was conducted during 3rd week of January 2021. Among 3550 HCWs, 979 subjects were selected by stratified random sampling and grouped into high risk and low risk category based on job setting. Demographic details and clinical information regarding previous history of COVID 19 were collected at the time of SARS-CoV-2 IgG testing.\n\nResultsFrom 979 subjects, the data with respect to 940 health care workers were analysed. SARS-CoV-2 IgG was detected in 19.1% of HCWs. Seroprevalence among high risk group was 20.3% and that in low risk group was 7.4% [p=0.005]. In high-risk group, seropositivity was noted in 30.54 % of nurses, 19% hospital attenders, 18.9% resident doctors and 6.4% consultant doctors. In those with past history of SARS-CoV-2 infection, seropositivity was 75.4%. In those who were COVID positive during July2020, 33.3% were still IgG reactive.\n\nInterpretation and conclusionThe study reported 19.1% SARS CoV-2 IgG reactivity among health care workers in our hospital. Seropositivity was significantly higher in high risk group compared to low risk group. Antibody decay kinetics in our study is comparable to that in published literature. Infection control challenges in hybrid hospitals account for higher seropositivity in this study compared to overall seroprevalence among HCWs in Kerala.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jessy S J", - "author_inst": "Dept of Biochemistry, Government Medical College Hospital, Thiruvananthapuram, Kerala India" - }, - { - "author_name": "Shamha Beegum", - "author_inst": "Dept of Biochemistry, Goverment Medical College, Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Genga Gopakumar", - "author_inst": "Dept of Biochemistry, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Bindu G", - "author_inst": "Dept of Biochemistry, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Chntha S", - "author_inst": "Deot of Community Medicine, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Sukshma Sasidharan", - "author_inst": "Dept of Biochemistry, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "Ansu Tonio", - "author_inst": "Dept of Biochemistry, Government Medical College Thiruvananthapuram, Kerala, India" - }, - { - "author_name": "ARAVIND REGHUKUMAR", - "author_inst": "Dept of Infectious Diseases, Government Medical College Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.20.21260855", "rel_title": "SARS-CoV-2 incidence, transmission and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-2021", @@ -663817,6 +665070,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.20.21260577", + "rel_title": "All-cause mortality during SARS-CoV-2 Pandemic in India: Nationally-representative estimates independent of official death registry", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260577", + "rel_abs": "We estimate excess deaths in India during the COVID pandemic using monthly deaths in the sample of a privately-conducted, nationally-representative, large, panel data set. The data set includes roughly 174,000 households (1.2 million members) and spans January 2015 - June 2021. We estimate COVID is associated with 3.36 million (95% CI: 2.08-4.63 million) excess deaths, a 17.3% increase in the all-cause death rate, until April 2021. Excess deaths spike during the peaks of the 2 infection waves in India. The second wave is associated with significantly more excess deaths than the first. The age-pattern of deaths is skewed towards the elderly relative to baseline.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sabareesh Ramachandran", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Anup Malani", + "author_inst": "University of Chicago" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.19.21260746", "rel_title": "Global predictions of short- to medium-term COVID-19 transmission trends : a retrospective assessment", @@ -665221,33 +666497,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.18.21260733", - "rel_title": "Spanish Version of the Attitude Towards COVID-19 Vaccines Scale: Reliability and Validity Assessment", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.18.21260733", - "rel_abs": "Background and purpose: The negative attitude to vaccines for coronavirus disease (COVID-19) has motivated the adaptation of instruments for this specific purpose. However, details of the reliability and validity of these scales are unknown. The study aimed to evaluate some indicators of the reliability and validity of the Spanish version of the Attitude towards COVID-19 Vaccines Scale. Methods: A validation study was carried out with 1,136 students of emerging age (18 and 29 years) from a Colombian university; 65.5% were female. Cronbach's alpha and McDonald's omega were calculated for reliability, and exploratory and confirmatory factor analyzes for validity. Additionally, the gender differential item functioning (DIF) was estimated with Kendall's tau b. Results: The Spanish version of Attitude towards COVID-19 Vaccines Scale showed high internal consistency (Cronbach's alpha of 0.94 and McDonald's omega of 0.95), a one-dimensional structure with acceptable goodness-of-fit indicators (CFI=0.94, TLI=0.91, and SRMR=0.04), and non-gender DIF (Kendall's tau b between 0.02 and 0.06). Conclusions: The Spanish version of the Attitude towards COVID-19 Vaccines Scale presents some appropriate reliability and validity indicators among university emerging adults. These findings should be explored in samples with other characteristics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Adalberto Campo-Arias", - "author_inst": "Universidad del Magdalena, Santa Marta, Colombia" - }, - { - "author_name": "Leynin Esther Caamano-Rocha", - "author_inst": "Universidad del Magdalena, Santa Marta, Colombia" - }, - { - "author_name": "John Carlos Pedrozo-Pupo", - "author_inst": "Universidad del Magdalena, Santa Marta, Colombia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.18.21260567", "rel_title": "Predicting Managers' Mental Health Across Countries Using Country-Level COVID-19 Statistics", @@ -665507,6 +666756,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.07.16.21260675", + "rel_title": "Estimation of COVID-19 recovery and decease periods in Canada using machine learning algorithms", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260675", + "rel_abs": "We derive a novel model escorted by large scale compartments, based on a set of coupled delay differential equations with extensive delays, in order to estimate the incubation, recovery and decease periods of COVID-19, and more generally any infectious disease. This is possible thanks to machine learning algorithms applied to publicly available database of confirmed corona cases, recovered cases and death toll. In this purpose, we separate i) the total cases into 14 groups corresponding to 14 incubation periods, ii) the recovered cases into 406 groups corresponding to a combination of incubation and recovery periods, and iii) the death toll into 406 groups corresponding to a combination of incubation and decease periods. In this paper, we focus on recovery and decease periods and their correlation with the incubation period. The estimated mean recovery period we obtain is 22.14 days (95% Confidence Interval(CI): 22.00 to 22.27), and the 90th percentile is 28.91 days (95% CI: 28.71 to 29.13), which is in agreement with statistical supported studies. The bimodal gamma distribution reveals that there are two groups of recovered individuals with a short recovery period, mean 21.02 days (95% CI: 20.92 to 21.12), and a long recovery period, mean 38.88 days (95% CI 38.61 to 39.15). Our study shows that the characteristic of the decease period and the recovery period are alike. From the bivariate analysis, we observe a high probability domain for recovered individuals with respect to incubation and recovery periods. A similar domain is obtained for deaths analyzing bivariate distribution of incubation and decease periods.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Subhendu Paul", + "author_inst": "Carleton University" + }, + { + "author_name": "Emmanuel Lorin", + "author_inst": "Carleton University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.21.21260926", "rel_title": "Increasing SARS-CoV-2 antibody prevalence in England at the start of the second wave: REACT-2 Round 4 cross-sectional study in 160,000 adults", @@ -667039,105 +668311,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2021.07.21.451321", - "rel_title": "Unlike Chloroquine, mefloquine inhibits SARS-CoV-2 infection in physiologically relevant cells and does not induce viral variants.", - "rel_date": "2021-07-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.21.451321", - "rel_abs": "Repositioning of clinical approved drugs could represent the fastest way to identify therapeutic options during public health emergencies, the majority of drugs explored for repurposing as antivirals for 2019 coronavirus disease (COVID-19) have failed to demonstrate clinical benefit. Without specific antivirals, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to cause major global mortality. Antimalarial drugs, such as chloroquine (CQ)/hydroxychloroquine (HCQ) and mefloquine have emerged as potential anti-SARS-CoV-2 antivirals. CQ/HCQ entered the Solidarity and RECOVERY clinical trials against COVID-19 and showed lack of efficacy. Importantly, mefloquine is not a 4-aminoquinoline like CQ and HCQ and has been previously repurposed for other respiratory diseases. Unlike the 4-aminoquinolines that accumulate in the high pH of intracellular lysosomes of the lung, the high respiratory tract penetration of mefloquine is driven by its high lipophilicity. While CQ and HCQ exhibit activity in Vero E6 cells, their activity is obviated in TMPRSS2-expressing cells, such as Calu-3 cells, which more accurately recapitulate in vivo entry mechanisms for SARS-CoV-2. Accordingly, here we report the anti-SARS-CoV-2 activity of mefloquine in Calu-3 type II pneumocytes and primary human monocytes. Mefloquine inhibited SARS-CoV-2 replication in Calu-3 cells with low cytotoxicity and EC50 and EC90 values of 1.2 and 5.3 {micro}M, respectively. In addition, mefloquine reduced up to 68% the SARS-CoV-2 RNA levels in infected monocytes, reducing viral-induced inflammation. Mefloquine blocked early steps of the SARS-CoV-2 replicative cycle and was less prone than CQ to induce drug-associated viral mutations and synergized with RNA polymerase inhibitor. The pharmacological parameters of mefloquine are consistent with its plasma exposure in humans and its tissue-to-plasma predicted coefficient points that this drug may accumulate in the lungs. These data indicate that mefloquine could represent an orally available clinically approved drug option against COVID-19 and should not be neglected on the basis of the failure of CQ and HCQ.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Carolina Q. Sacramento", - "author_inst": "Fiocruz" - }, - { - "author_name": "Natalia Fintelman-Rodrigues", - "author_inst": "Fiocruz" - }, - { - "author_name": "Suelen S. G. Dias", - "author_inst": "Fiocruz" - }, - { - "author_name": "Jairo R Temerozo", - "author_inst": "Oswaldo Cruz Institute" - }, - { - "author_name": "Aline de Paula D. Da Silva", - "author_inst": "Fiocruz" - }, - { - "author_name": "Carine S. da Silva", - "author_inst": "Fiocruz" - }, - { - "author_name": "Andre C. Ferreira", - "author_inst": "FIOCRUZ" - }, - { - "author_name": "Mayara Mattos", - "author_inst": "Fiocruz" - }, - { - "author_name": "Vinicius C. Soares", - "author_inst": "Fiocruz" - }, - { - "author_name": "Filipe Pereira-Dutra", - "author_inst": "Fiocruz" - }, - { - "author_name": "Milene D. Miranda", - "author_inst": "Fiocruz" - }, - { - "author_name": "Debora F. Barreto-Vieira", - "author_inst": "Fiocruz" - }, - { - "author_name": "Marcos Alexandre N. da Silva", - "author_inst": "Fiocruz" - }, - { - "author_name": "Suzana de Siqueira Santos", - "author_inst": "Fundacao Getulio Vargas" - }, - { - "author_name": "Mateo Torres", - "author_inst": "Fundacao Getulio Vargas" - }, - { - "author_name": "Rajith K. R. Rajoli", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Alberto Paccanaro", - "author_inst": "Fundacao Getulio Vargas" - }, - { - "author_name": "Andrew Owen", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Dumith C. Bou-Habib", - "author_inst": "Fiocruz" - }, - { - "author_name": "Patricia T. Bozza", - "author_inst": "Fiocruz" - }, - { - "author_name": "Thiago Moreno L. Souza", - "author_inst": "Fiocruz" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.16.452756", "rel_title": "Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence", @@ -667561,6 +668734,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.19.452809", + "rel_title": "CRISPR screens for host factors critical for infection by SARS-CoV-2 variants of concern identify GATA6 as a central modulator of ACE2.", + "rel_date": "2021-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.19.452809", + "rel_abs": "The global spread of SARS-CoV-2 led to the most challenging pandemic in this century, posing major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SASR-CoV-2 can provide insights into the virus pathogenesis, and facilitates the development of novel broad-spectrum host-directed therapeutics. Here, employing genome-scale CRISPR screens, we provide a comprehensive data-set of cellular factors that are exploited by WT-SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. These screens identified known and novel host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination and Heparan sulfate biogenesis. In addition, the host phosphatidylglycerol biosynthesis processes appeared to have major anti-viral functions. Comparative analysis of the different VOCs revealed the host factors KREMEN2 and SETDB1 as potential unique candidates required only to the Alpha variant, providing a possible explanation for the increased infectivity of this variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential pro-viral gene for all variants inspected. We revealed that GATA6 directly regulates ACE2 transcription and accordingly, is critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals showed an elevated level of GATA6, indicating the important role GATA6 may be playing in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 resulted in down-modulation of ACE2 and consequently to inhibition of the viral infectivity. Overall, we show GATA6 represents a target for the development of anti-SARS-CoV-2 therapeutic strategies and reaffirm the value of the CRISPR loss-of-function screens in providing a list of potential new targets for therapeutic interventions.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Yaara Finkel", + "author_inst": "Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel" + }, + { + "author_name": "Yfat Yahalom-Rone", + "author_inst": "Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Nir Paran", + "author_inst": "Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Theodor Chitlaru", + "author_inst": "Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Ofir Israeli", + "author_inst": "Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Inbar Cohen-Gihon", + "author_inst": "Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Moshe Aftalion", + "author_inst": "Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Reut Falach", + "author_inst": "Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Uri Elia", + "author_inst": "Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Ital Nemet", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel Hashomer, Israel" + }, + { + "author_name": "Limor Kliker", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel Hashomer, Israel" + }, + { + "author_name": "Michal Mandelboim", + "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Tel Hashomer, Israel" + }, + { + "author_name": "Adi Beth-Din", + "author_inst": "Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Tomer Israely", + "author_inst": "Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Ofer Cohen", + "author_inst": "Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel" + }, + { + "author_name": "Noam Stern-Ginossar", + "author_inst": "Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel" + }, + { + "author_name": "Adi Bercovich-Kinori", + "author_inst": "Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.20.453027", "rel_title": "The SARS-CoV-2 reproduction number R0 in cats", @@ -668817,129 +670073,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.15.21260213", - "rel_title": "Temporal Variations in Seroprevalence of SARS-CoV-2 Infections by Race and Ethnicity in Arkansas.", - "rel_date": "2021-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260213", - "rel_abs": "ObjectiveOur objective is to estimate CoV-2 infection rates in a rural state using seroprevalence of antibodies to CoV-2 as an indicator of infection.\n\nStudy Design and SettingThis is a single-site study within an academic center and regional programs within the state of Arkansas. We obtained residual serum samples from a convenience sample of adults who were outpatients and came to the hospital or regional clinic for non-COVID-related reasons. We collected remnant in three time periods (August 15 to September 5, September 12 to October 24, and November 7 to December 19).\n\nResultsIn 2020, the overall age, gender, and race standardized prevalence of CoV-2 antibodies was 2.6% (August to September), 4.1% (September to October), and 7.4% (November to December). There was no difference in seroprevalence between urban compared to rural areas. Positive tests were not uniformly distributed across racial and ethnic minorities. Higher seroprevalence rates were found in Hispanics and Blacks or African Americans compared to whites across all time periods.\n\nConclusionsIn a state with a large rural population, 2.6-7.4% of people experienced CoV-2 infection by December 2020. Blacks and Hispanics had disproportionately higher rates of CoV-2 infections than whites.\n\nWhat is new?O_ST_ABSKey findingsC_ST_ABSIn this prospective convenience sampling of remnant sera, we found increasing seroprevalence from 2.6% to 7.4% (August 2020 to December 2020). Higher seroprevalence rates were found in Hispanics and Blacks or African Americans compared to whites across all time periods, and no difference was determined between those individuals from rural or urban areas.\n\nWhat this adds to what is knownIn a largely rural population, Blacks and Hispanics had disproportionately higher rates of CoV-2 infections than whites, and these populations need to be studied further regarding outcomes.\n\nWhat is the implication?There are health disparities that exist regarding CoV-2 infections, and we should target vaccination information and education to these groups.\n\nHighlights- SARS-CoV-2 infections increased from 2.6% to 7.4% from August to December 2020.\n- Higher seroprevalence was found in Hispanics and Blacks as compared to whites.\n- There was no difference in the seroprevalence in rural compared to urban areas.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Joshua L Kennedy", - "author_inst": "University of Arkansas for Medical Sciences/ Arkansas Children's Research Institute" - }, - { - "author_name": "J Craig Forrest", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Sean G Young", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Benjamin Amick", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Mark Williams", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Laura James", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Jessica Snowden", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Victor Cardenas", - "author_inst": "UAMS Fay W. Boozman College of Public Health" - }, - { - "author_name": "Danielle Boothe", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Catherine Kirkpatrick", - "author_inst": "Arkansas Children's Research Institute" - }, - { - "author_name": "Zeel Modi", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Katherine Caid", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Shana Owens", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Marianne Kouassi", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ryan Mann", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Claire Putt", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Katherine Irish-Clardy", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Michael Macechko", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ronald K Brimberry", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Wendy N Nembhard", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ruofei Du", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Jing Jin", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Namvar Zohoori", - "author_inst": "Arkansas Department of Health" - }, - { - "author_name": "Atul Kothari", - "author_inst": "Arkansas Department of Health" - }, - { - "author_name": "Hoda Hagrass", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ericka Olgaard", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Karl W Boehme", - "author_inst": "University of Arkansas for Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.15.21260561", "rel_title": "Viral Load of SARS-CoV-2 in Respiratory Aerosols Emitted by COVID-19 Patients while Breathing, Talking, and Singing", @@ -669391,6 +670524,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.07.15.21260234", + "rel_title": "Post-COVID-19 symptoms are not uncommon among recovered patients-A cross-sectional online survey among the Indian population.", + "rel_date": "2021-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260234", + "rel_abs": "BackgroundCoronavirus disease-2019 (COVID-19) can have a myriad of symptoms. However, it is now known that most patients recovered from COVID-19 have symptoms related to COVID-19. There is a paucity of literature on post-COVID-19 symptoms from India. Hence we aimed to assess the incidence of post-COVID-19 symptoms in patients recovered from COVID-19. Methods: An online Microsoft forms survey was conducted through multiple social media platforms.\n\nResultsOf the 5,347 individuals who received and clicked the link, a total of 2038 infected patients responded (Supplementary figure). Approximately 48% (967/2038) had recovered from COVID-19 within 1-3 months (short-term recovered), 34.2% (375/2038) had recovered from COVID-19 >3 months ago (long recovered), and 18.4% (375) were recovered within the last one month (recently recovered). Nearly 38% (770/2038) had a history of hospitalization for COVID-19. Of them, 34.28% (264/770) required oxygen therapy during the hospital stay. Most patients were discharged within 5-10 days of hospital stay (54%, 415/770). Only 5.58% (43/770) required a stay of more than 20 days. Seventy-five percent (575/770) of the hospitalized patients received steroid therapy. Of those who received steroid therapy, 56.5% (325/575) had not required oxygen therapy. Forty percent (233/575) of patients received steroid therapy for two weeks, 24% (138/575) for one week, 33.73% received steroids only during the hospital stay, and 1.73% were still on steroid therapy during the survey.\n\nMost importantly, of the 2038 respondents, 41.8% (851/2038) still had persistent symptoms related to COVID-Most common symptom was fatigue (64.15%), followed by body pain (31%) and gastrointestinal symptoms (25%) (Figure). Six percent (49/851) of them required hospitalization for post-COVID-19 symptoms. Forty-six percent (449/967) in the short term recovered group (1-3 months), 40.1% (279/696) in the long-recovered group, and 32.8% (123/375) in the recently recovered group had persistent symptoms related to COVID-19 (P=0.001). Forty-eight percent (374/770) of the hospitalized patients developed post-COVID-19 symptoms, while only 37.6% (477/1268) developed post-COVID-19 symptoms among the non-hospitalized patients (P<0.001). Fifty-three percent (303/575) of those who received steroids developed post-COVID-19 symptoms, while only 36.41% (71/195) of those who did not receive steroids developed post-COVID-19 symptoms (P<0.001). 49% (159/325) of patients who received steroids despite being not requiring oxygen developed post-COVID-19 symptoms compared to only 37.5% (543/1449) who did not receive steroids and were not on oxygen therapy (P<0.001). Nearly 40% (336/851) of respondents felt that post-COVID-19 symptoms are not being appropriately treated or taken care of seriously.\n\nConclusionsPost-COVID-19 symptoms are common in patients who recovered from COVID-19. These symptoms are more often noted in patients who received steroid therapy. Post-COVID-19 symptomatology is present in a significant number of patients and requires to be addressed seriously.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Venkat Guduru Rao", + "author_inst": "Asian Institute of Gastroenterology Hospitals, Hyderabad, India" + }, + { + "author_name": "Vishwanath Gella", + "author_inst": "Asian Institute of Gastroenterology Hospitals, Hyderabad, India" + }, + { + "author_name": "Madhuri Radhakrishnan", + "author_inst": "Asian Institute of Gastroenterology Hospitals, Hyderabad, India" + }, + { + "author_name": "Jagadeesh V Kumar", + "author_inst": "Asian Institute of Gastroenterology Hospitals, Hyderabad, India" + }, + { + "author_name": "Robin Chatterjee", + "author_inst": "Asian Institute of Gastroenterology Hospitals, Hyderabad, India" + }, + { + "author_name": "Anand V Kulkarni", + "author_inst": "Asian Institute of Gastroenterology" + }, + { + "author_name": "Nageshwar D Reddy", + "author_inst": "Asian Institute of Gastroenterology Hospitals, Hyderabad, India" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.15.21260605", "rel_title": "COVID-19 Chest X-Ray Image Classification Using Deep Learning", @@ -670907,37 +672083,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.19.452918", - "rel_title": "Rosin Soap Exhibits Virucidal Activity", - "rel_date": "2021-07-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.19.452918", - "rel_abs": "Chemical methods of virus inactivation are used routinely to prevent viral transmission in both a personal hygiene capacity but also in at-risk environments like hospitals. Several virucidal products exist, including hand soaps, gels and surface disinfectants. Resin acids, which can be derived from Tall oil produced from trees, have been shown to exhibit anti-bacterial activity. However, whether these products or their derivatives have virucidal activity is unknown. Here, we assessed the capacity of Rosin soap to inactivate a panel of pathogenic mammalian viruses in vitro. We show that Rosin soap can inactivate the human enveloped viruses: influenza A virus (IAV), respiratory syncytial virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For IAV, rosin soap could provide a 100,000-fold reduction in infectivity. However, Rosin soap failed to affect the non-enveloped encephalomyocarditis virus (EMCV). The inhibitory effect of Rosin soap against IAV infectivity was dependent on its concentration but not dependent on incubation time nor temperature. Together, we demonstrate a novel chemical inactivation method against enveloped viruses, which could be of use in preventing virus infections in certain settings.\n\nImportanceViruses remain a significant cause of human disease and death, most notably illustrated through the current Covid-19 pandemic. Control of virus infection continues to pose a significant global health challenge to the human population. Viruses can spread through multiple routes, including via environmental and surface contamination where viruses can remain infectious for days. Methods to inactivate viruses on such surfaces may help mitigate infection. Here we present evidence identifying a novel virucidal product in Rosin soap, which is produced from Tall oil from coniferous trees. Rosin soap was able to rapidly and potently inactivate influenza virus and other enveloped viruses.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Derek J Fairley", - "author_inst": "Belfast Health and Social Care Trust" - }, - { - "author_name": "Hannele Kettunen", - "author_inst": "Hankkija Oy" - }, - { - "author_name": "Juhani Vuorenmaa", - "author_inst": "Hankkija Oy" - }, - { - "author_name": "Juha Orte", - "author_inst": "Forchem Oy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.16.452748", "rel_title": "Key substitutions in the spike protein of SARS-CoV-2 variants can predict resistance to monoclonal antibodies, but other substitutions can modify the effects", @@ -671193,6 +672338,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.14.21260291", + "rel_title": "Sequencing SARS-CoV-2 from Antigen Tests", + "rel_date": "2021-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.14.21260291", + "rel_abs": "Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-based SARS-CoV-2 detection tests, which use anterior nasal swabs for SARS-CoV-2 antigen detection. Despite this shift in testing methods, the need for whole-genome sequence surveillance remains. Thus, we developed a workflow for whole-genome sequencing with antigen test-derived swabs as an input rather than nasopharyngeal swabs. In this study, we use excess clinical specimens processed using the BinaxNOW COVID-19 Ag Card. We demonstrate that whole-genome sequencing from antigen tests is feasible and yields similar results from RT-PCR-based assays utilizing a swab in viral transport media.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ashley E Nazario-Toole", + "author_inst": "59th Medical Wing, Clinical Investigations and Research Support Laboratory, Joint Base San Antonio-Lackland, TX, USA" + }, + { + "author_name": "Holly M Nguyen", + "author_inst": "59th Medical Wing, Clinical Investigations and Research Support Laboratory, Joint Base San Antonio-Lackland, TX, USA" + }, + { + "author_name": "Hui Xia", + "author_inst": "59th Medical Wing, Clinical Investigations and Research Support Laboratory, Joint Base San Antonio-Lackland, TX, USA" + }, + { + "author_name": "Dianne N Frankel", + "author_inst": "Trainee Health Surveillance, 559th Medical Group, THLS, Joint Base San Antonio-Lackland, TX, USA" + }, + { + "author_name": "John W Kieffer", + "author_inst": "Trainee Health Surveillance, 559th Medical Group, THLS, Joint Base San Antonio-Lackland, TX, USA" + }, + { + "author_name": "Thomas F Gibbons", + "author_inst": "59th Medical Wing, Clinical Investigations and Research Support Laboratory, Joint Base San Antonio-Lackland, TX, USA" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.14.21260307", "rel_title": "Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity in uninfected and previously infected individuals", @@ -672861,77 +674045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.07.13.21260417", - "rel_title": "Clinical outcomes in vaccinated individuals hospitalized with Delta variant of SARS-CoV-2", - "rel_date": "2021-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260417", - "rel_abs": "Emerging variants of SARS-CoV-2 with increased transmissibility or immune escape have been causing large outbreaks of COVID-19 infections across the world. As most of the vaccines currently in use have been derived from viral strains circulating in the early part of the pandemic, it becomes imperative to constantly assess the efficacy of these vaccines against emerging variants. In this hospital-based cohort study, we analysed clinical profiles and outcomes of 1161 COVID-19 hospitalized patients (vaccinated with COVISHIELD (ChAdOx1) or COVAXIN (BBV-152), n = 495 and unvaccinated n = 666) in Hyderabad, India between April 24th and May 31st 2021. Viral genome sequencing revealed that >90% of patients in both groups were harbouring the Delta variant (Pango lineage B.1.617.2) of SARS-CoV-2. Vaccinated individuals showed higher neutralizing antibodies (545{+/-}1256 AU/ml Vs 51.1{+/-}296 AU/ml; p<0.001) and significantly decreased Ferritin (392.26 {+/-} 448.4 ng/mL Vs 544.82 {+/-} 641.41 ng/mL; p<0.001) and LDH (559.45 {+/-} 324.05 U/L Vs 644.99 {+/-} 294.03 U/L; p<0.001), when compared to the unvaccinated group. Severity of the disease (3.2% Vs 7.2%; p=0.0039) and requirement of ventilatory support (2.8% Vs 5.9%; p=0.0154) were significantly low in the vaccinated group despite the fact that these individuals had significantly higher age and risk factors. The rate of mortality was about 50% lower (2/132=1.51%) in the completely vaccinated breakthrough infections although mortality in individuals who had received a single dose was similar to the unvaccinated group (9/269=3.35% vs 23/666= 3.45%). Our results demonstrate that both COVISHIELD and COVAXIN are effective in preventing disease severity and mortality against the Delta variant in completely vaccinated hospitalized patients.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jagadeesh Kumar V", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Divya Tej Sowpati", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Apoorva Munigela", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Sofia Banu", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Archana Bharadwaj Siva", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Mitnala Sasikala", - "author_inst": "Asian Healthcare Foundation, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Chandrasekhar Nutalapati", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Anand Kulkarni", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - }, - { - "author_name": "Payel Mukherjee", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Lamuk Zaveri", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "- CCMB COVID-19 Team", - "author_inst": "" - }, - { - "author_name": "- AIG Hospitals COVID-19 Vaccine study Team", - "author_inst": "" - }, - { - "author_name": "Karthik Bharadwaj Tallapaka", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007" - }, - { - "author_name": "Nageshwar Reddy D", - "author_inst": "AIG Hospitals, Internal Medicine, Mindspace Rd, Gachibowli, Hyderabad, Telangana 500032" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.13.21260442", "rel_title": "Rapid and Quantitative Detection of Human Antibodies Against the 2019 Novel Coronavirus SARS CoV2 and its Variants as a Result of Vaccination and Infection", @@ -673147,6 +674260,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.13.21260482", + "rel_title": "Acute phase clinical manifestation of COVID-19 is linked to long-COVID symptoms; A 9-month follow-up study", + "rel_date": "2021-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260482", + "rel_abs": "BackgroundThe number of long-COVID is rising but it is not still clear which patients will develop long-covid and what will be the symptoms if they do.We followed up 95 patientswith confirmed COVID-19 after 9 months of the original study to delineate possible long COVID symptoms.\n\nMethodsThe original study included 201 patients who were treated in a large referral center from March to May 2020. Ninty percent of the patients reported physical or psychological symptoms within 9 months post-COVID.\n\nFindingsEasy fatigability was the most common 51.04 % long-COVID symptoms followed by anxiety 38.54 %, dyspnea 38.54 %, and new headache 38.54%. There was no association between COVID-19 severity in the acute phase (admission status) and the number of long-COVID symptoms (F(1, 93) = 0.75, p = 0.45 (n.s.)), chronic fatigue syndrome (CFS) (F(1,93) = -0.49, p = 0.62 (n.s.), MOCA scores (F(1, 90) = 0.073, p = 0.787 (n.s.)) in the future. Being female (F(1, 92) = -2.27, p = 0.02), having a higher number of symptoms in the acute phase(F(1,93) = 2.76, p = 0.0068),and experiencing constitutional neuropsychiatric symptoms(F(1, 93)= 2.529, p = 0.01) in the acute phase were associated with higher occurance of CFS in follow up. Moreover, constitutional neuropsychiatric symptoms in acute phase were associated with cognitive dificits (lower MOCA score) (F(1, 93) = 10.84, p= 0.001) in the follow up.\n\nConclusionsSeverity of the acute disease does not seem to be related to long-COVID symptoms. However, specific clinical presentations might be predictors of distinct long-COVID symptoms. Constitutional neuropsychiatric symptoms in the acute phase are associated with important and debilitating chronic symptoms including chronic fatigue syndrome, and cognitive deficits. These results might pave the way for findingthe underlying mechanisms of long-COVID and provide additional insight into possible candidate treatments for COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "FatemehSadat Mirfazeli", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Atiye Sarabi-Jamab", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Alireza kordi", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Behnam Shariati", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Seyed Vahid Shariat", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Salar Bahrami", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Shabnam Nohesara", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Mostafa Almasi-Dooghaee", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Seyed Hamid Reza Faiz", + "author_inst": "Iran University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.07.13.21260444", "rel_title": "Adoption and continued use of mobile contact tracing technology: Multilevel explanations from a three-wave panel survey and linked data", @@ -674427,29 +675591,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.14.452401", - "rel_title": "Improving comparability of studies using HCoV-OC43 as a surrogate for SARS-CoV-2", - "rel_date": "2021-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.14.452401", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has renewed interest in human coronaviruses that cause the common cold, particularly as research with them at biosafety level (BSL)-2 avoids the added costs and biosafety concerns that accompany work with SARS-COV-2, BSL-3 research. One of these, human coronavirus OC43 (HCoV-OC43), is a well-matched surrogate for SARS-CoV-2 because it is also a Betacoronavirus, targets the human respiratory system, is transmitted via respiratory aerosols and droplets and is relatively resistant to disinfectants. Unfortunately, growth of HCoV-OC43 in the recommended human colon cancer (HRT-18) cells does not produce obvious cytopathic effect (CPE) and its titration in these cells requires expensive antibody-based detection. Consequently, multiple quantification approaches for HCoV-OC43 using alternative cell lines exist, which complicates comparison of research results. Hence, we investigated the basic growth parameters of HCoV-OC43 infection in three of these cell lines (HRT-18, human lung fibroblasts (MRC-5) and African green monkey kidney (Vero E6) cells) including the differential development of cytopathic effect (CPE) and explored reducing the cost, time and complexity of antibody-based detection assay. Multi-step growth curves were conducted in each cell type in triplicate at a multiplicity of infection of 0.1 with daily sampling for seven days. Samples were quantified by tissue culture infectious dose50(TCID50)/ml or plaque assay (cell line dependent) and additionally analyzed on the Sartorius Virus Counter 3100 (VC), which uses flow virometry to count the total number of intact virus particles in a sample. We improved the reproducibility of a previously described antibody-based detection based TCID50 assay by identifying commercial sources for antibodies, decreasing antibody concentrations and simplifying the detection process. The growth curves demonstrated that HCoV-O43 grown in MRC-5 cells reached a peak titer of [~]107 plaque forming units/ml at two days post infection (dpi). In contrast, HCoV-OC43 grown on HRT-18 cells required six days to reach a peak titer of [~]106.5 TCID50/ml. HCoV-OC43 produced CPE in Vero E6 cells but these growth curve samples failed to produce CPE in a plaque assay after four days. Analysis of the VC data in combination with plaque and TCID50 assays together revealed that the defective:infectious virion ratio of MRC-5 propagated HCoV-OC43 was less than 3:1 for 1-6 dpi while HCoV-OC43 propagated in HRT-18 cells varied from 41:1 at 1 dpi, to 329:4 at 4 dpi to 94:1 at 7 dpi. These results should enable better comparison of extant HCoV-OC43 study results and prompt further standardization efforts.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Erin E. Schirtzinger", - "author_inst": "Kansas State University" - }, - { - "author_name": "A. Sally Davis", - "author_inst": "Kansas State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.12.21260360", "rel_title": "The impact of hypoxia on B cells in COVID-19", @@ -674817,6 +675958,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.14.21260494", + "rel_title": "Variation in COVID-19 excess mortality by age, sex, and province within Italy", + "rel_date": "2021-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.14.21260494", + "rel_abs": "1Although previous evidence suggests that the infection fatality rate from COVID-19 varies by age and sex, and that transmission intensity varies geographically within countries, no study has yet explored the age-sex-space distribution of excess mortality associated with the COVID pandemic. By applying the principles of small-area estimation to existing models formulations for excess mortality, this study develops a method for assessing excess mortality across small populations and assesses the pattern of COVID excess mortality by province, year, week, age group, and sex in Italy from March through May 2020. We estimate that 53,200 excess deaths occurred across Italy during this time period, compared to just 35,500 deaths where COVID-19 was registered as the underlying cause of death. Out of the total excess mortality burden, 97% of excess deaths occurred among adults over age 60, and 68% of excess deaths were concentrated among adults over age 80. The burden of excess mortality was unevenly distributed across the country, with just three of Italys 107 provinces accounting for 32% of all excess mortality. This method for estimating excess mortality can be adapted to other countries where COVID-19 diagnostic capacity is still insufficient, and could be incorporated into public health rapid response systems.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nathaniel J Henry", + "author_inst": "Big Data Institute, Li Ka Shing Centre for Information Discovery, University of Oxford, Oxford, UK" + }, + { + "author_name": "Ahmed Elagali", + "author_inst": "Kids Institute, Perth Children Hospital, Perth, Western Australia, Australia" + }, + { + "author_name": "Michele Nguyen", + "author_inst": "Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore" + }, + { + "author_name": "Michael Chipeta", + "author_inst": "Big Data Institute, Li Ka Shing Centre for Information Discovery, University of Oxford, Oxford, UK" + }, + { + "author_name": "Catrin Moore", + "author_inst": "Big Data Institute, Li Ka Shing Centre for Information Discovery, University of Oxford, Oxford, UK" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.13.21260408", "rel_title": "Adding a reaction-restoration type transmission rate dynamic law to the basic SEIR COVID-19 model", @@ -676456,33 +677632,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.14.21259081", - "rel_title": "Use of 1-MNA to Improve Exercise Tolerance and Fatigue in Patients After COVID-19", - "rel_date": "2021-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.14.21259081", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is a serious respiratory disease that results from infection with a newly discovered coronavirus (SARS-COV-2). Unfortunately, COVID-19 is not only a short-term infection but that patients (pts) recovering from SARS-CoV2 infection complain of persisting symptoms including: fatigue, diffuse myalgia and weakness, which may lead to chronic fatigue syndrome. There is currently no evidence that nutritional supplements and/or physical exercise can assist in the recovery of pts with chronic fatigue syndrome. 1-Methylnicotinamide (1-MNA) is an endogenic substance that is produced in the liver when nicotinic acid is metabolized. 1-MNA demonstrates anti-inflammatory and anti-thrombotic properties. Therefore, we investigated whether 1-MNA supplements could improve exercise tolerance and decrease fatigue among patients recovering from SARS-CoV-2.\n\nMethodsThe study population was composed of pts after COVID-19, expressing subjective feelings of limited tolerance to exercise. The selected pts were randomized into two groups: GrM0 - without supplementation; GrM1 - with 1-MNA supplementation. At the beginning of the study (Phase 0), in both groups, a 6-minute walk test (6MWT) was carried out and fatigue assessment with Fatigue Severity Scale (FSS) was performed. After 1 month (Phase 1), a follow up FSS and 6MWT once more were performed in both groups.\n\nResultsA significant improvement in the mean distance covered in the 6MWT was noted among the pts in GrM1, compared to those in GrM0. We also noted that in GrM1 the 6MWT distance was significantly higher after 1 month of supplementation with 1-MNA, compared to the beginning of the study (515.18 m in Phase 0 vs 557.8m in Phase 1; p = 0.000034). In GrM1, significantly more pts improved their distance in the 6MWT (23 out of 25 pts, equal to 92%), by a mean of 47 meters, compared to GrM0 (15 of 25 pts, equal to 60%) (p = 0.0061). After one month, significantly more patients in the group without 1-MNA had severe fatigue (FSS [≥] 4) compared to the group with supplementation (GrM1 = 5 pts (20%) vs GrM0 = 14pts (56%); p = 0.008).\n\nConclusions1-MNA supplementation significantly improved physical performance in a 6-minute walk test and reduced the percentage of patients with severe fatigue after COVID-19. The comprehensive action of 1-MNA, including anti-inflammatory and anticoagulant effects, as well as activation of the SIRT1 enzyme, may be beneficial for the recovery of patients with persistent symptoms of fatigue and low tolerance to exercise after COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Michal Chudzik", - "author_inst": "Cardiology Ambulatory Centre, Saint Family Hospital, Lodz, Poland" - }, - { - "author_name": "Joanna Kapusta", - "author_inst": "Department of Internal Medicine and Cardiac Rehabilitation, Medical University of Lodz, Poland" - }, - { - "author_name": "Monika Burzynska", - "author_inst": "Department of Epidemiology and Biostatistics, the Chair of Social and Preventive Medi-cine of the Medical University of Lodz, Poland." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.07.13.452256", "rel_title": "Tissue Specific Age Dependence of the Cell Receptors Involved in the SARS-CoV-2 Infection", @@ -676866,6 +678015,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.14.452343", + "rel_title": "Repurposing screen highlights broad-spectrum coronavirus antivirals and their host targets", + "rel_date": "2021-07-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.14.452343", + "rel_abs": "Libraries composed of licensed drugs represent a vast repertoire of molecules modulating physiologic processes in humans, thus providing unique opportunities for discovery of host targeting antivirals. We interrogated the ReFRAME repurposing library with 12,993 molecules for broad-spectrum coronavirus antivirals and discovered 134 compounds inhibiting an alphacoronavirus, mapping to 59 molecular target categories. Dominant targets included the 5-hydroxytryptamine receptor and dopamine receptor and cyclin-dependent kinase inhibitors. Counter-screening with SARS-CoV-2 and validation in primary cells identified Phortress, an aryl hydrocarbon receptor (AHR) ligand, Bardoxolone and Omaveloxolone, two nuclear factor, erythroid 2 like 2 (NFE2L2) activators as inhibitors of both alpha- and betacoronaviruses. The landscape of coronavirus targeting molecules provides important information for the development of broad-spectrum antivirals reinforcing pandemic preparedness.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Sibylle Haid", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + }, + { + "author_name": "Alina Matthaei", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + }, + { + "author_name": "Melina Winkler", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + }, + { + "author_name": "Svenja M Sake", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + }, + { + "author_name": "Antonia P Gunesch", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + }, + { + "author_name": "Jessica Rueckert", + "author_inst": "Hanover Medical School" + }, + { + "author_name": "Gabrielle Vieyres", + "author_inst": "Heinrich Pette Institute, Leibniz Institute for Experimental Virology" + }, + { + "author_name": "David Kuehl", + "author_inst": "Heinrich Pette Institute, Leibniz Institute for Experimental Virology" + }, + { + "author_name": "Tu-Trinh Nguyen", + "author_inst": "Scripps Research Institute" + }, + { + "author_name": "Lisa Lasswitz", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + }, + { + "author_name": "Francisco Zapatero", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + }, + { + "author_name": "Graham Brogden", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + }, + { + "author_name": "Gisa Gerold", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + }, + { + "author_name": "Bettina Wiegmann", + "author_inst": "Hanover Medical School" + }, + { + "author_name": "Ursula Bilitewski", + "author_inst": "HZI" + }, + { + "author_name": "Mark Broenstrup", + "author_inst": "HZI" + }, + { + "author_name": "Thomas Schulz", + "author_inst": "Hanover Medical School" + }, + { + "author_name": "Thomas Pietschmann", + "author_inst": "TWINCORE - Centre for Experimental and Clinical Infection Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.13.449251", "rel_title": "Water-soluble tocopherol derivatives inhibit SARS-CoV-2 RNA-dependent RNA polymerase", @@ -678286,45 +679522,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.09.21260253", - "rel_title": "Transmission of SARS-CoV-2 into and within immigrant households. Nation-wide registry-study from Norway", - "rel_date": "2021-07-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260253", - "rel_abs": "BackgroundMinority ethnic groups and immigrants have been hit disproportionally hard by COVID-19 in many developed countries, including Norway. Most transmissions of SARS-CoV-2 occur in households.\n\nMethodsUsing individual-level registry data of all Norwegian residents we compared infections across all multi-person households. A household with at least one member born abroad was defined as an immigrant household. For the subset of households where at least one person tested positive for SARS-CoV-2 from August 1st 2020 to May 1st 2021, we calculated secondary attack rates (SARs) as the percent of other household members testing positive within 14 days after the first household member tested positive. Logistic regression model was used to adjust for sex, age, household composition and geography.\n\nResultsAmong all multi-person households in Norway (n=1 421 642), immigrant households (n=341 604) comprised more members on average (3.2) than households with only Norwegian-born members (2.8). The share of immigrant households where at least one member had been tested, was 56% (vs 49% in the households with only Norwegian-born members), and the share where at least one member was infected was 3.7% (vs 1.4% in households with only Norwegian-born members). Secondary attack rates were higher in immigrant (32%) than Norwegian-born households (20%). Results differed considerably by country of birth, with secondary attack rates particularly high in households from Syria, Iraq, Turkey, and Pakistan, also after adjustment for sex, age, household composition and geography.\n\nConclusionSARS-CoV-2 is more frequently introduced into multi-person immigrant households than into households with only Norwegian-born members, and transmission within the household occurs more frequently in immigrant households. The results are likely related to living conditions, family composition or differences in social interaction, emphasizing the need to prevent introduction of SARS-CoV-2 into these vulnerable households.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Fredrik Methi", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Rannveig Kaldager Hart", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Anna Aasen Godoy", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Silje Bakken Jorgensen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Oliver Kacelnik", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kjetil Elias Telle", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.07.21260167", "rel_title": "Indications that Stockholm has reached herd immunity, given limited restrictions, against several variants of SARS-CoV-2", @@ -678644,6 +679841,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.07.13.452194", + "rel_title": "A drug candidate for treating adverse reactions caused by pathogenic antibodies inducible by COVID-19 virus and vaccines", + "rel_date": "2021-07-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.13.452194", + "rel_abs": "In a recent study, we reported that certain anti-spike antibodies of COVID-19 and SARS-CoV viruses can have a pathogenic effect through binding to sick lung epithelium cells and misleading immune responses to attack self-cells. We termed this new pathogenic mechanism \"Antibody Dependent Auto-Attack\" (ADAA). This study explores a drug candidate for prevention and treatment of such ADAA-based diseases. The drug candidate is a formulation comprising N-acetylneuraminic acid methyl ester (NANA-Me), an analog of N-acetylneuraminic acid. NANA-Me acts through a unique mechanism of action (MOA) which is repairment of the missing sialic acid on sick lung epithelium cells. This MOA can block the antibodies binding to sick cells, which are vulnerable to pathogenic antibodies. Our in vivo data showed that the formulation significantly reduced the sickness and deaths caused by pathogenic anti-spike antibodies. Therefore, the formulation has the potential to prevent and treat the serious conditions caused by pathogenic antibodies during a COVID-19 infection. In addition, the formulation has potential to prevent and treat the adverse reactions of COVID-19 vaccines because the vaccines can induce similar antibodies, including pathogenic antibodies. The formulation will be helpful in increasing the safety of the vaccines without reducing the vaccines efficacy. Compared to existing antiviral drugs, the formulation has a unique MOA of targeting receptors, broad spectrum of indications, excellent safety profile, resistance to mutations, and can be easily produced.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Huiru Wang", + "author_inst": "Huirui Biopharma" + }, + { + "author_name": "Xiancong Wu", + "author_inst": "HuaAn McAb Biotechnology" + }, + { + "author_name": "Yuekai Zhang", + "author_inst": "Biolynx Technology" + }, + { + "author_name": "Qiuchi Chen", + "author_inst": "HuaAn McAb Biotechnology" + }, + { + "author_name": "Lin Dai", + "author_inst": "HuaAn McAb Biotechnology" + }, + { + "author_name": "Yuxing Chen", + "author_inst": "HuaAn McAb Biotechnology" + }, + { + "author_name": "Xiaoling Liu", + "author_inst": "HuaAn McAb Biotechnology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.12.452076", "rel_title": "Analysis of amino acid change dynamics reveals SARS-CoV-2 variant emergence", @@ -680068,65 +681308,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.10.451880", - "rel_title": "A mouse-adapted SARS-CoV-2 strain replicating in standard laboratory mice.", - "rel_date": "2021-07-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.10.451880", - "rel_abs": "SARS-CoV-2 has infected almost 200 million humans and caused over 4 million deaths worldwide. Evaluating countermeasures and improving our understanding of COVID-19 pathophysiology require access to animal models that replicate the hallmarks of human disease. Mouse infection with SARS-CoV-2 is limited by poor affinity between the virus spike protein and its cellular receptor ACE2. We have developed by serial passages the MACo3 virus strain which efficiently replicates in the lungs of standard mouse strains and induces age-dependent lung lesions. Compared to other mouse-adapted strains and severe mouse models, infection with MACo3 results in mild to moderate disease and will be useful to investigate the role of host genetics and other factors modulating COVID-19 severity.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Xavier Montagutelli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Matthieu Prot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Gregory Jouvion", - "author_inst": "Ecole Nationale Veterinaire" - }, - { - "author_name": "Laurine Levillayer", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laurine Conquet", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Eduard Reyes-Gomez", - "author_inst": "Ecole Nationale Veterinaire" - }, - { - "author_name": "Flora Donati", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Melanie Albert", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sylvie van der Werf", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean Jaubert", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.07.21260153", "rel_title": "Transient infection with SARS-CoV-2 without induction of systemic immunity", @@ -680434,6 +681615,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.09.21260249", + "rel_title": "Pandemic trends in health care use: From the hospital bed to the general practitioner with COVID-19", + "rel_date": "2021-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260249", + "rel_abs": "AimTo explore whether the acute 30-day burden of COVID-19 on health care use has changed from the beginning to the end of the pandemic.\n\nMethodsIn all Norwegians (N=122 699) who tested positive for SARS-CoV-2 in three pandemic waves (March 1st-July 31st 2020 (1st wave), August 1st-December 31st 2020 (2nd wave), and January 1st-May 31st 2021 (3rd wave)), we studied the age- and sex-specific share of patients (by age groups 1-19, 20-67, and 68 or more) who had: 1) Relied on self-care, 2) used primary care, and 3) used specialist care.\n\nResultsWe find that a remarkably high and stable share (70-80%) of patients with COVID-19 exclusively had contact with primary care in the acute phase, both in the 1st, 2nd and 3rd wave. The mean number of primary care visits ranged between 2 and 4. We also show that the use of specialist care in the acute 30-day phase of COVID-19 has decreased, from 14% being hospitalized at least once during spring 2020, to 4% during spring 2021. The mean number of hospital bed-days decreased significantly for men from the 1st to the 2nd wave (from 13 days, 95% CI=11.5-14.5 to 10 days (9-11) for men aged [≥]68 years, and from 11 days (10-12) to 9 days (8-10) for men aged 20-67 years), but not for women.\n\nConclusionCOVID-19 places a continued high demand on the primary care services, and a decreasing demand on the specialist care services.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Fredrik Methi", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Kjersti Helene Hernaes", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Katrine Damgaard Skyrud", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Karin Magnusson", + "author_inst": "Norwegian Institute of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.09.21260228", "rel_title": "WHY SOME HESITATE MORE: CROSS-CULTURAL VARIATION IN CONSPIRACY BELIEFS, BELIEF IN SCIENCE, AND VACCINE ATTITUDES", @@ -682018,97 +683230,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.07.21260124", - "rel_title": "BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in Systemic Lupus Erythematosus", - "rel_date": "2021-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21260124", - "rel_abs": "ObjectivesOur aims were to evaluate Systemic Lupus Erythematosus (SLE) disease activity and SARS-CoV-2 specific immune responses after BNT162b2 vaccination.\n\nMethodsIn this prospective study, disease activity and clinical assessments were recorded from the first dose of vaccine, until day 15 after the second dose in 126 SLE patients. SARS-CoV-2 antibody responses were measured against wild-type spike antigen while serum-neutralizing activity was assessed against the SARS-CoV-2 historical strain and variants of concerns (VOCs). Vaccine-specific T-cell responses were quantified by Interferon (IFN)-{gamma} release assay after the second dose.\n\nResultsBNT162b2 was well tolerated and no statistically significant variations of BILAG and SLEDAI scores were observed throughout the study in SLE patients with active and inactive disease at baseline. Mycophenolate Mofetil (MMF) and Methotrexate (MTX) treatments were associated with drastically reduced BNT162b2 antibody-response ({beta}=-78; p=0.007, {beta}=-122; p<0.001, respectively). Anti-spike antibody response was positively associated with baseline total IgG serum levels, naive B cell frequencies ({beta}=2; p=0.018, {beta}=2.5; p=0.003) and SARS-CoV-2-specific T cell response (r=0.462; p=0.003). In responders, serum neutralization activity decreased against VOCs bearing the E484K mutation but remained detectable in a majority of patients.\n\nConclusionMMF, MTX and poor baseline humoral immune status, particularly: low naive B cell frequencies, are independently associated with impaired BNT162b2 mRNA antibody response, delineating SLE patients who might need adapted vaccine regimens and follow-up.\n\nKEY MESSAGESO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIBNT162b2 efficacy and safety has been described in studies mixing different RMDs\nC_LI\n\nWhat does this study add?O_LINo serious adverse effects, nor SLE flares have been documented after BNT162b2 in SLE patients.\nC_LIO_LINot only MMF and MTX, but also a poor humoral immune status at baseline impair vaccine antibody response\nC_LIO_LIAlbeit decreased, serum neutralizing activity against VOCs is conferred to vaccine-responders.\nC_LI\n\nHow might this impact on clinical practice or future developments?O_LIThese parameters could be helpful for physicians to delineate which patients should have antibody measurement after full BNT162b2 vaccination and should be proposed a third injection of BNT162b2 vaccine.\nC_LI", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Quentin Moyon", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Delphine Sterlin", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Makoto Miyara", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Francois Anna", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Alexis Mathian", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Raphael Lhote", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Pascale Ghillani-Dalbin", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Paul Breillat", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Sasi Mudumba", - "author_inst": "Genalyte" - }, - { - "author_name": "Sophia de Alba", - "author_inst": "Genalyte" - }, - { - "author_name": "Fleur Cohen-Aubart", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Julien Haroche", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Micheline Pha", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Thi Huong Du Boutin", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Hedi Chaieb", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Pedro Flores", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Pierre Charneau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Guy Gorochov", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Zahir Amoura", - "author_inst": "Sorbonne Universite" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.08.451640", "rel_title": "Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica", @@ -682328,6 +683449,93 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.07.08.451654", + "rel_title": "Evaluation of intranasal nafamostat or camostat for SARS-CoV-2 chemoprophylaxis in Syrian golden hamsters", + "rel_date": "2021-07-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.08.451654", + "rel_abs": "Successful development of a chemoprophylaxis against SARS-CoV-2 could provide a tool for infection prevention implementable alongside vaccination programmes. Camostat and nafamostat are serine protease inhibitors that inhibit SARS-CoV-2 viral entry in vitro but have not been characterised for chemoprophylaxis in animal models. Clinically, nafamostat is limited to intravenous delivery and while camostat is orally available, both drugs have extremely short plasma half-lives. This study sought to determine whether intranasal dosing at 5 mg/kg twice daily was able to prevent airborne transmission of SARS-CoV-2 from infected to uninfected Syrian golden hamsters. SARS-CoV-2 viral RNA was above the limits of quantification in both saline- and camostat-treated hamsters 5 days after cohabitation with a SARS-CoV-2 inoculated hamster. However, intranasal nafamostat-treated hamsters remained RNA negative for the full 7 days of cohabitation. Changes in body weight over the course of the experiment were supportive of a lack of clinical symptomology in nafamostat-treated but not saline- or camostat-treated animals. These data are strongly supportive of the utility of intranasally delivered nafamostat for prevention of SARS-CoV-2 infection and further studies are underway to confirm absence of pulmonary infection and pathological changes.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Megan Neary", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Helen Box", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Joanne Sharp", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Lee Tatham", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Paul Curley", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Joanne Herriott", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Edyta Kijak", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Usman Arshad", + "author_inst": "University of Liverpool" + }, + { + "author_name": "James J Hobson", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Rajith KR Rajoli", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Henry Pertinez", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Anthony Valentijn", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Kevin Dhaliwal", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Frank McCaughan", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Steve P Rannard", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Anja Kipar", + "author_inst": "University of Zurich" + }, + { + "author_name": "James P Stewart", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Andrew Owen", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.07.08.451607", "rel_title": "Ultrastructural analysis of nasopharyngeal epithelial cells from patients with SARS-CoV-2 infection", @@ -683820,37 +685028,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.07.06.451227", - "rel_title": "T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations", - "rel_date": "2021-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.06.451227", - "rel_abs": "Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which can help the virus to evade either CD8 or CD4 T-cell responses. We developed T-cell COVID-19 Atlas (T-CoV, https://t-cov.hse.ru) - the comprehensive web portal, which allows one to analyze how SARS-CoV-2 mutations alter the presentation of viral peptides by HLA molecules. The data are presented for common virus variants and the most frequent HLA class I and class II alleles. Binding affinities of HLA molecules and viral peptides were assessed with accurate in silico methods. The obtained results highlight the importance of taking HLA alleles diversity into account: mutation-mediated alterations in HLA-peptide interactions were highly dependent on HLA alleles. For example, we found that the essential number of peptides tightly bound to HLA-B*07:02 in the reference Wuhan variant ceased to be tight binders for the Indian (Delta) and the UK (Alpha) variants. In summary, we believe that T-CoV will help researchers and clinicians to predict the susceptibility of individuals with different HLA genotypes to infection with variants of SARS-CoV-2 and/or forecast its severity.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Stepan Nersisyan", - "author_inst": "HSE University" - }, - { - "author_name": "Anton Zhiyanov", - "author_inst": "HSE University" - }, - { - "author_name": "Maxim Shkurnikov", - "author_inst": "HSE University" - }, - { - "author_name": "Alexander Tonevitsky", - "author_inst": "HSE University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.07.06.451119", "rel_title": "Nonclinical Safety and Immunogenicity of an rVSV-\u0394G-SARS-CoV-2-S vaccine in mice, hamsters, rabbits and pigs", @@ -684262,6 +685439,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.07.05.451199", + "rel_title": "An Autoantigen Profile from Jurkat T-Lymphoblasts Provides a Molecular Guide for Investigating Autoimmune Sequelae of COVID-19", + "rel_date": "2021-07-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.05.451199", + "rel_abs": "In order to understand autoimmune phenomena contributing to the pathophysiology of COVID-19 and post-COVID syndrome, we have been profiling autoantigens (autoAgs) from various cell types. Although cells share numerous autoAgs, each cell type gives rise to unique COVID-altered autoAg candidates, which may explain the wide range of symptoms experienced by patients with autoimmune sequelae of SARS-CoV-2 infection. Based on the unifying property of affinity between autoantigens (autoAgs) and the glycosaminoglycan dermatan sulfate (DS), this paper reports 140 candidate autoAgs identified from proteome extracts of human Jurkat T-cells, of which at least 105 (75%) are known targets of autoantibodies. Comparison with currently available multi-omic COVID-19 data shows that 125 (89%) of DS-affinity proteins are altered at protein and/or RNA levels in SARS-CoV-2-infected cells or patients, with at least 94 being known autoAgs in a wide spectrum of autoimmune diseases and cancer. Protein alterations by ubiquitination and phosphorylation in the viral infection are major contributors of autoAgs. The autoAg protein network is significantly associated with cellular response to stress, apoptosis, RNA metabolism, mRNA processing and translation, protein folding and processing, chromosome organization, cell cycle, and muscle contraction. The autoAgs include clusters of histones, CCT/TriC chaperonin, DNA replication licensing factors, proteasome and ribosome proteins, heat shock proteins, serine/arginine-rich splicing factors, 14-3-3 proteins, and cytoskeletal proteins. AutoAgs such as LCP1 and NACA that are altered in the T cells of COVID patients may provide insight into T-cell responses in the viral infection and merit further study. The autoantigen-ome from this study contributes to a comprehensive molecular map for investigating acute, subacute, and chronic autoimmune disorders caused by SARS-CoV-2.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Julia Y. Wang", + "author_inst": "Curandis" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Guizhou Medical University" + }, + { + "author_name": "Michael W. Roehrl", + "author_inst": "Curandis" + }, + { + "author_name": "Victor B. Roehrl", + "author_inst": "Curandis" + }, + { + "author_name": "Michael H. Roehrl", + "author_inst": "Memorial Sloan Kettering Cancer Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.07.02.21259902", "rel_title": "Neurological, neuropsychiatric and psychiatric symptoms during COVID-19 infection and after recovery: a systematic review of observational studies", @@ -685698,49 +686910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.05.21250138", - "rel_title": "Peritraumatic Distress of COVID-19 on Physicians in Bangladesh: Implications and Policy Recommendations", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21250138", - "rel_abs": "COVID-19 pandemic has been an ultimate test of resource management for any governance, especially in the healthcare system. Bangladesh, being a developing country and with very limited resources, is fighting the COVID-19 pandemic. The frontline workers, especially the physicians and nurses are going through immense physical and psychological stress during the pandemic. Social unawareness, the absence of strict preventive policies, increasing workload, and the lack of resource management are making the frontline healthcare workers extremely vulnerable to COVID-19. In this paper, we present the outcome of our study on peritraumatic distress of COVID-19 among physicians in Bangladesh. Based on the user study, we have identified a number of key factors behind the peritraumatic distress and psychological stress caused by COVID-19. Our study shows, more than 78% respondents are suffering from peritraumatic psychological distress. We also recommended some very important and yet easy to implement policies to reduce the peritraumatic stress of the physicians of Bangladesh. These policy recommendations were a result of the survey analysis and the suggestions from the COVID-19 designated physicians.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Zafar Ahmad", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Abdullah al Kium", - "author_inst": "Sir Salimullah Medical College" - }, - { - "author_name": "Md Ripon Ahammed", - "author_inst": "National Institute of Cardiovascular Diseases" - }, - { - "author_name": "Md Montaser Hamid", - "author_inst": "Shahjalal University of Science and Technology" - }, - { - "author_name": "Sarmina Tarannum", - "author_inst": "Sir Salimullah Medical College" - }, - { - "author_name": "Mohammad Ruhul Amin", - "author_inst": "Fordham University" - }, - { - "author_name": "Md. Daharul Islam", - "author_inst": "Sir Salimullah Medical College" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.07.05.21259790", "rel_title": "What We Learned From COVID 19? Trying to find best approach from pathophysiology to treatment.", @@ -686048,6 +687217,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.06.21259528", + "rel_title": "Pre-vaccination and early B cell signatures predict antibody response to SARS-CoV-2 mRNA vaccine", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21259528", + "rel_abs": "SARS-CoV-2 mRNA vaccines are highly effective, although weak antibody responses are seen in some individuals with correlates of immunity that remain poorly understood. Here we longitudinally dissected antibody, plasmablast, and memory B cell (MBC) responses to the two-dose Moderna mRNA vaccine in SARS-CoV-2-uninfected adults. Robust, coordinated IgA and IgG antibody responses were preceded by bursts of spike-specific plasmablasts after both doses, but earlier and more intensely after dose two. Distinct antigen-specific MBC populations also emerged post-vaccination with varying kinetics. We identified antigen non-specific pre-vaccination MBC and post-vaccination plasmablasts after dose one and their spike-specific counterparts early after dose two that correlated with subsequent antibody levels. These baseline and response signatures can thus provide early indicators of serological efficacy and explain response variability in the population.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Lela Kardava", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Nicholas Rachmaninoff", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "William Lau", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Clarisa Buckner", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Krittin Trihemasava", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Felipe Lopes de Assis", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Wei Wang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Xiaozhen Zhang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Yimeng Wang", + "author_inst": "Institute for Bioscience and Biotechnology Research" + }, + { + "author_name": "Chi-I Chiang", + "author_inst": "Institute for Bioscience and Biotechnology Research" + }, + { + "author_name": "Sandeep Narpala", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Robert Reger", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Genevieve McCormack", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Catherine Seamon", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Richard Childs", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Anthony Suffredini", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Jeffrey Strich", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Daniel Chertow", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Richard Davey", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Michael Sneller", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Yuxing Li", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Adrian McDermott", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Tae-Wook Chun", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Anthony Fauci", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "John Tsang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Susan Moir", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.06.21260074", "rel_title": "A case-control study of autoimmune AEFIs following COVID-19 vaccination reported to VAERS", @@ -687448,49 +688736,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.07.451505", - "rel_title": "Immunogenicity of low dose prime-boost vaccination of mRNA vaccine CV07050101 in non-human primates", - "rel_date": "2021-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.07.451505", - "rel_abs": "Many different vaccine candidates against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent of COVID-19, are currently approved and under development. Vaccine platforms vary from mRNA vaccines to viral-vectored vaccines, and several candidates have been shown to produce humoral and cellular responses in small animal models, non-human primates and human volunteers. In this study, six non-human primates received a prime-boost intramuscular vaccination with 4 {micro}g of mRNA vaccine candidate CV07050101, which encodes a pre-fusion stabilized spike (S) protein of SARS-CoV-2. Boost vaccination was performed 28 days post prime vaccination. As a control, six animals were similarly injected with PBS. Humoral and cellular immune responses were investigated at time of vaccination, and two weeks afterwards. No antibodies could be detected two and four weeks after prime vaccination. Two weeks after boost vaccination, binding but no neutralizing antibodies were detected in 4 out of 6 non-human primates. SARS-CoV-2 S protein specific T cell responses were detected in these 4 animals. In conclusion, prime-boost vaccination with 4 {micro}g of vaccine candidate CV07050101 resulted in limited immune responses in 4 out of 6 non-human primates.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Neeltje van Doremalen", - "author_inst": "NIH" - }, - { - "author_name": "Robert Fischer", - "author_inst": "NIH" - }, - { - "author_name": "Jonathan Schulz", - "author_inst": "NIH" - }, - { - "author_name": "Myndi Holbrook", - "author_inst": "NIH" - }, - { - "author_name": "Jamie Lovaglio", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Benjamin Petsch", - "author_inst": "CureVac AG, Tuebingen, Germany" - }, - { - "author_name": "Vincent Munster", - "author_inst": "NIAID" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.06.451353", "rel_title": "Receptor-binding domain recombinant protein RBD219-N1C1 on alum-CpG induces broad protection against SARS-CoV-2 variants of concern", @@ -687930,6 +689175,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.30.21259820", + "rel_title": "SARS-CoV-2 B.1.1.7 lineage rapidly spreads and overwhelms R.1 lineage in Japan: serial and stationary observation in a community", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259820", + "rel_abs": "BackgroundThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan.\n\nMethodsWe performed the whole genome sequencing using SARS-CoV-2 positive samples (n=325) collected from February 2020 to the end of June 2021. The number of analyzed samples accounted for 15.4% of the total 2,109 samples identified in our community. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages.\n\nResultsWe identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta) These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April, 2021.\n\nConclusionWe clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yosuke Hirotsu", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Masao Omata", + "author_inst": "Yamanashi Central Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.30.21259757", "rel_title": "Sex- and Gender-specific Risk Factors of Post-COVID-19 Syndrome: A Population-based Cohort Study in Switzerland", @@ -689302,85 +690570,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.04.21259903", - "rel_title": "Relating SARS-CoV-2 shedding rate in wastewater to daily positive tests data: A consistent model based approach", - "rel_date": "2021-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.04.21259903", - "rel_abs": "During the COVID-19 pandemic, wastewater-based epidemiology (WBE) has been engaged to complement medical surveillance and in some cases to also act as an early diagnosis indicator of viral spreading in the community. Most efforts worldwide by the scientific community and commercial companies focus on the formulation of protocols for SARS CoV-2 analysis in wastewater and approaches addressing the quantitative relationship between WBE and medical surveillance are lacking. In the present study, a mathematical model is developed which uses as input the number of daily positive medical tests together with the highly non-linear shedding rate curve of individuals to estimate the evolution of virus shedding rate in wastewater along calendar days. A comprehensive parametric study by the model using as input actual medical surveillance and WBE data for the city of Thessaloniki ([~]700,000 inhabitants, North Greece) during the outbreak of November 2020 reveals the conditions under which WBE can be used as an early warning tool for predicting pandemic outbreaks. It is shown that early warning capacity is different along the days of an outbreak and depends strongly on the number of days apart between the day of maximum shedding rate of infected individuals in their disease cycle and the day of their medical testing. The present data indicate for Thessaloniki an average early warning capacity of around 2 days. Moreover, the data imply that there exists a proportion between unreported cases (asymptomatic persons with mild symptoms that do not seek medical advice) and reported cases. The proportion increases with the number of reported cases. The early detection capacity of WBE improves substantially in the presence of an increasing number of unreported cases. For Thessaloniki at the peak of the pandemic in mid-November 2020, the number of unreported cases reached a maximum around 4 times the number of reported cases.\n\nHIGHLIGHTSO_LIModel estimates viral load evolution in wastewater from infected people dynamics\nC_LIO_LIIdentifying actual conditions for which WBE can be used as an early warning tool\nC_LIO_LIEarly warning capacity increases with an increasing number of unreported cases\nC_LIO_LIIn Thessaloniki Nov20 outbreak, the early warning capacity of WBE was about 2 days\nC_LIO_LIIn Thessaloniki Nov20 outbreak, unreported cases were up to 4 times reported cases\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Maria Petala", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Margaritis Kostoglou", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Thodoris Karapantsios", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Chrysostomos Dovas", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Theodoros Lytras", - "author_inst": "National Public Health Organization, Athens, Greece & European University Cyprus, Nicosia, Cyprus" - }, - { - "author_name": "Dimitrios Paraskevis", - "author_inst": "National and Kapodistrian University of Athens, Athens, Greece" - }, - { - "author_name": "Emmanouel Roilides", - "author_inst": "Infectious Diseases Unit and 3rd Department of Pediatrics, Aristotle University School of Health Sciences, Hippokration Hospital" - }, - { - "author_name": "Anastasia Koutsolioutsou-Benaki", - "author_inst": "National Public Health Organization" - }, - { - "author_name": "Georgios Panagiotakopoulos", - "author_inst": "National Public Health Organization" - }, - { - "author_name": "Vana Sypsa", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Symeon Metallidis", - "author_inst": "Faculty of Medicine, AHEPA General Hospital, Aristotle University of Thessaloniki" - }, - { - "author_name": "Anna Papa", - "author_inst": "Medical School, Aristotle University of Thessaloniki, Thessaloniki" - }, - { - "author_name": "Efstratios Stylianidis", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Agis Papadopoulos", - "author_inst": "Thessaloniki Water Supply and Sewerage Company S.A." - }, - { - "author_name": "Sotirios Tsiodras", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Nikolaos Papaioannou", - "author_inst": "Aristotle University of Thessaloniki" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.04.21259992", "rel_title": "Late surges in COVID-19 cases and varying transmission potential partially due to public health policy changes in 5 Western states, March 10, 2020-January 10, 2021", @@ -689636,6 +690825,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.04.21259490", + "rel_title": "Generation of false positive SARS-CoV-2 antigen results with testing conditions outside manufacturer recommendations: A scientific approach to pandemic misinformation", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.04.21259490", + "rel_abs": "ObjectivesAntigen-based rapid diagnostics tests (Ag-RDTs) are useful tools for SARS-CoV-2 detection. However, misleading demonstrations of the Abbott Panbio COVID-19 Ag-RDT on social media claimed that SARS-CoV-2 antigen could be detected in municipal water and food products. To offer a scientific rebuttal to pandemic misinformation and disinformation, this study explored the impact of using the Panbio SARS-CoV-2 assay with conditions falling outside of manufacturer recommendations.\n\nMethodsUsing Panbio, various water and food products, laboratory buffers, and SARS-CoV-2-negative clinical specimens were tested, with and without manufacturer buffer. Additional experiments were conducted to assess the role of each Panbio buffer component (tricine, NaCl, pH, and tween-20), as well as the impact of temperatures (4{degrees}C, 20{degrees}C, and 45{degrees}C) and humidity (90%) on assay performance.\n\nResultsDirect sample testing (without the kit buffer), resulted in false positive signals resembling those obtained with SARS-CoV-2-positive controls tested under proper conditions. The likely explanation of these artifacts is non-specific interactions between the SARS-CoV-2-specific conjugated and capture antibodies, as proteinase K treatment abrogated this phenomenon, and thermal shift assays showed pH-induced conformational changes under conditions promoting artifact formation. Omitting, altering, and reverse engineering the kit buffer all supported the importance of maintaining buffering capacity, ionic strength, and pH for accurate kit function. Interestingly, the Panbio assay could tolerate some extremes of temperature and humidity outside of manufacturer claims.\n\nConclusionsOur data support strict adherence to manufacturer instructions to avoid false positive SARS-CoV-2 Ag-RDT reactions, otherwise resulting in anxiety, overuse of public health resources, and dissemination of misinformation.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Glenn Patriquin", + "author_inst": "Nova Scotia Health" + }, + { + "author_name": "Ross Davidson", + "author_inst": "Queen Elizabeth II HSC" + }, + { + "author_name": "Todd F Hatchette", + "author_inst": "Nova Scotia Health Authority" + }, + { + "author_name": "Breanne M Head", + "author_inst": "National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC)" + }, + { + "author_name": "Edgard Mejia", + "author_inst": "National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC)" + }, + { + "author_name": "Michael G. Becker", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Adrienne F.A. Meyers", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Paul A. Sandstrom", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Jacob Hatchette", + "author_inst": "Praxes Medical Group" + }, + { + "author_name": "Ava Block", + "author_inst": "Praxes Medical Group" + }, + { + "author_name": "Nicole Smith", + "author_inst": "Praxes Medical Group" + }, + { + "author_name": "John Ross", + "author_inst": "Praxes Medical Group" + }, + { + "author_name": "Jason J LeBlanc", + "author_inst": "Nova Scotia Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.03.21258887", "rel_title": "Heterologous prime-boost vaccination with ChAdOx1 nCoV-19 and BNT162b2 mRNA", @@ -691116,33 +692372,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.30.21259794", - "rel_title": "Examining the Relationship between COVID-19 Vaccinations and Reported Incidence", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259794", - "rel_abs": "As COVID-19 has caused significant morbidity and mortality throughout the world, the development and distribution of an effective vaccine have been swift but not without challenges. Earlier demand and access barriers have seemingly been addressed with more free and accessible vaccines now available for a wide variety of ages. While rates of COVID-19 have decreased overall, some geographic areas continue to experience rapid outbreaks. The purpose of this study was to examine the relationship between vaccination uptake and weekly COVID-19 cases throughout locations in the state of Missouri.\n\nMethodsAmong all Missouri counties and two cities (n=117), weekly COVID-19 incidence and cumulative proportion of residents fully vaccinated were abstracted from the Missouri Department of Health and Senior Services during a 25-week period from January 4 to Jun 26, 2021. Additional ecological variables known to be associated with COVID-19 incidence and prevalence were collected from the U.S. Census Bureau and integrated into data: total population, proportion of nonwhite residents, annual median household income, proportion of residents working in public facing occupations. Descriptive and inferential statistics were completed which included the calculation of both linear and nonlinear models using repeated measure data to determine the quantitative association between vaccination uptake and reported COVID-19 cases in the presence of location characteristics.\n\nResultsThroughout the 25 weeks of observations, the average weekly number of COVID-19 cases reported was 66.1 (SD=260.8) while the average cumulative proportion vaccinated individuals at the end of the 25 weeks was 25.8% (SD=6.8%) among study locations. While graphing seemed to suggest a more nonlinear relationship between COVID-19 incidence and proportion vaccinated, comparison of crude linear and nonlinear models pointed to the relationship likely being linear during study period. The final adjusted linear model exhibited a significant relationship between COVID-19 cases and proportion vaccinated, specifically every percent increase in population vaccinated resulted in 3 less weekly COVID-19 cases being reported ({beta} -3.74, p<0.001. Additionally, when controlling for other factors, the adjusted model revealed locations with higher proportions of nonwhite residents were likely to experience less weekly COVID-19 cases ({beta} -1.48, p=0.037).\n\nDiscussionOverall, this study determined that increasing the proportion of residents vaccinated decreases COIVD-19 cases by a substantial amount over time. These findings provide insights into possible messaging strategies that can be leveraged to develop more effective implementation and uptake. As the COVID-19 pandemic persists and vaccination numbers begin to plateau, diverse communication strategies become a critical necessity to reach a wider population.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Enbal Shacham", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Stephen Scroggins", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Alexander Garza", - "author_inst": "SSM Health St. Louis" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.30.21259491", "rel_title": "Reduced COVID-19 Hospitalizations among New York City Residents Following Age-Based SARS-CoV-2 Vaccine Eligibility: Evidence from a Regression Discontinuity Design", @@ -691490,6 +692719,61 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2021.07.03.450938", + "rel_title": "A SARS-CoV-2 nucleocapsid protein TR-FRET assay amenable to high-throughput screening", + "rel_date": "2021-07-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.03.450938", + "rel_abs": "Drug development for specific antiviral agents against coronavirus disease 2019 (COVID-19) is still an unmet medical need as the pandemic continues to spread globally. Although huge efforts for drug repurposing and compound screens have put forth, only few compounds remain in late stage clinical trials. New approaches and assays are needed to accelerate COVID-19 drug discovery and development. Here we report a time-resolved fluorescence resonance energy transfer-based assay that detects the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (NP) produced in infected cells. It uses two specific anti-NP monoclonal antibodies (MAbs) conjugated to donor and acceptor fluorophores that produces a robust ratiometric signal for high throughput screening of large compound collections. Using this assay, we measured a half maximal inhibitory concentration (IC50) for Remdesivir of 9.3 M against infection with SARS-CoV-2 USA/WA1/2020 (WA-1). The assay also detected SARS-CoV-2 South African (Beta, {beta}), Brazilian/Japanese variant P.1 (Gamma, {gamma}), and Californian (Epsilon, {varepsilon}), variants of concern or interest (VoC). Therefore, this homogeneous SARS-CoV-2 NP detection assay can be used for accelerating lead compound discovery for drug development and for evaluating drug efficacy against emerging SARS-CoV-2 VoC.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Kirill Gorshkov", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Desarey Morales Vasquez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Bruce Nguyen Tran", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Juan Carlos de la Torre", + "author_inst": "Scripps Research Institute" + }, + { + "author_name": "Thomas Moran", + "author_inst": "Icahn School of Medicine at Mt. Sinai" + }, + { + "author_name": "Catherine Z. Chen", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Wei Zheng", + "author_inst": "National Center for Advancing Translational Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.07.04.450986", "rel_title": "Dynamics of SARS-CoV-2 host cell interactions inferred from transcriptome analyses", @@ -692702,77 +693986,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.28.21258780", - "rel_title": "Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections", - "rel_date": "2021-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21258780", - "rel_abs": "ImportanceVaccine breakthrough by an emergent SARS-CoV-2 variant poses a great risk to global public health.\n\nObjectiveTo determine the SARS-CoV-2 variant responsible for 6 cases of vaccine breakthrough.\n\nDesignNasopharyngeal swabs from suspected vaccine breakthrough cases were tested for SARS-CoV-2 by qPCR for Wuhan-Hu1 and Alpha variant. Positive samples were then sequenced by Swift Normalase Amplicon Panels to determine the causal variant.\n\nSettingTransmission event occurred at events surrounding a wedding outside of Houston, TX. Two patients from India, likely transmitted the Delta variant to other guests.\n\nParticipantsFollowing a positive SARS-CoV-2 qPCR test at a third-party site, six fully vaccinated patients were investigated. Three males and three females ranged from 53 to 69 years old. One patient suffered from diabetes while three others were classified as overweight. No significant other comorbidities were identified. None of the patients had a history of failed vaccination.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhich SARS-CoV-2 variant is responsible for 6 cases of vaccine breakthrough, one interventional monoclonal antibody treatment, and one death?\n\nFindingsViral sequencing revealed 6 vaccinated patients were infected with the Delta SARS-CoV-2 variant. With no histories of vaccine breakthrough, this suggests Delta variant may possess immune evasion in patients that received the Pfizer BNT162b2, Moderna mRNA-1273, and Covaxin BBV152.\n\nMeaningDelta variant may pose the highest risk out of any currently circulating SARS-CoV-2 variants, with increased transmissibility over Alpha variant and possible vaccine breakthrough.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Timothy Farinholt", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Harshavardhan Doddapaneni", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Xiang Qin", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Vipin Menon", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Qingchang Meng", - "author_inst": "Baylor College Medicine" - }, - { - "author_name": "Ginger Metcalf", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Hsu Chao", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Marie-Claude Gingras", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Paige Farinholt", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Charu Agrawal", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Donna Muzny", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Pedro A. Piedra", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Richard A. Gibbs", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Joseph Petrosino", - "author_inst": "Baylor College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.02.450964", "rel_title": "SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome", @@ -693012,6 +694225,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.02.450959", + "rel_title": "SARS-CoV-2 Lambda Variant Remains Susceptible to Neutralization by mRNA Vaccine-elicited Antibodies and Convalescent Serum", + "rel_date": "2021-07-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.02.450959", + "rel_abs": "The SARS-CoV-2 lambda variant (lineage C.37) was designated by the World Health Organization as a variant of interest and is currently increasing in prevalence in South American and other countries. The lambda spike protein contains novel mutations within the receptor binding domain (L452Q and F490S) that may contribute to its increased transmissibility and could result in susceptibility to re-infection or a reduction in protection provided by current vaccines. In this study, the infectivity and susceptibility of viruses with the lambda variant spike protein to neutralization by convalescent sera and vaccine-elicited antibodies was tested. Virus with the lambda spike had higher infectivity and was neutralized by convalescent sera and vaccine-elicited antibodies with a relatively minor 2.3-3.3-fold decrease in titer on average. The virus was neutralized by the Regeneron therapeutic monoclonal antibody cocktail with no loss of titer. The results suggest that vaccines in current use will remain protective against the lambda variant and that monoclonal antibody therapy will remain effective.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Takuya Tada", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Hao Zhou", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Belinda M Dcosta", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Marie I Samanovic", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Mark J Mulligan", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Nathaniel R Landau", + "author_inst": "NYU Grossman School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.06.29.21259686", "rel_title": "Prospective sero surveillance among healthcare workers vaccinated with ChAdOx1 nCoV-19 Corona vaccine in a tertiary hospital of Kerala, India", @@ -694620,49 +695872,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.06.23.21259415", - "rel_title": "Use of recently vaccinated individuals to detect bias in test-negative case-control studies of COVID-19 vaccine effectiveness", - "rel_date": "2021-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259415", - "rel_abs": "Post-authorization observational studies play a key role in understanding COVID-19 vaccine effectiveness following the demonstration of efficacy in clinical trials. While bias due to confounding, selection bias, and misclassification can be mitigated through careful study design, unmeasured confounding is likely to remain in these observational studies. Phase III trials of COVID-19 vaccines have shown that protection from vaccination does not occur immediately, meaning that COVID-19 risk should be similar in recently vaccinated and unvaccinated individuals, in the absence of confounding or other bias. Several studies have used the estimated effectiveness among recently vaccinated individuals as a negative control exposure to detect bias in vaccine effectiveness estimates. In this paper we introduce a theoretical framework to describe the interpretation of such a bias-indicator in test-negative studies, and outline assumptions that would allow the use of recently vaccinated individuals to correct bias due to unmeasured confounding.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Matt D.T. Hitchings", - "author_inst": "University of Florida" - }, - { - "author_name": "Joseph A. Lewnard", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Natalie E. Dean", - "author_inst": "University of Florida" - }, - { - "author_name": "Albert I. Ko", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Otavio T. Ranzani", - "author_inst": "Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain" - }, - { - "author_name": "Jason R. Andrews", - "author_inst": "Stanford University" - }, - { - "author_name": "Derek A.T. Cummings", - "author_inst": "University of Florida" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.23.21259414", "rel_title": "The COVID-related mental health load of neonatal healthcare professionals: a multicentre study in Italy.", @@ -694970,6 +696179,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.28.21259644", + "rel_title": "The Role of CRP, Interleukin-6 and Their Derived Immune-Inflammatory Indices in Early Prediction of Severity and Mortality of COVID-19 Patients", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259644", + "rel_abs": "BackgroundIn coronavirus disease 2019 (COVID-19), finding sensitive biomarkers is critical for detecting severe cases early and intervening effectively.\n\nObjectivesTo compare and evaluate the predictive value of C-reactive protein (CRP), interleukin-6 (IL-6), and their derived immune-inflammatory indices (CRP/albumin (CRP/alb), lymphocyte/CRP (L/CRP), and lymphocyte/IL-6 (L/IL-6)) in COVID-19 patients.\n\nMethodsOn admission, 85 confirmed COVID-19 patients, their measured and collected laboratory data were obtained and compared.\n\nResultsLevels of CRP, IL-6, and CRP/alb were significantly higher (P=0.001) in severe patients and non-survivors, but L/CRP and L/IL-6 were significantly lower (P=0.001). We observed the best predictive performance for COVID-19 severity at 1.65 for CRP/alb and 260.86 for L/CRP with 84.7% diagnostic accuracy for both. The best diagnostic accuracy for COVID-19 in-hospital mortality was 87.1% by IL-6 at 120 pg/ml and 85.9% by L/IL-6 at 5.40. The multi-marker prediction surpassed the performance of a single biomarker prediction. IL-6 was an independent risk factor associated with severe disease development (odds ratio (OR): 1.033; 95% confidence interval (CI): 1.002-1.066).\n\nConclusionsPretreatment values of CRP, IL-6, and their derived indices could be included in the diagnostic work-up of COVID-19 to determine the severity and predict the outcome.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sara I. Taha", + "author_inst": "Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt." + }, + { + "author_name": "Aalaa K. Shata", + "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Ain Shams university, Cairo, Egypt." + }, + { + "author_name": "Eman M. El-Sehsah", + "author_inst": "Department of Medical Microbiology and Immunology, Mansoura Faculty of Medicine, Mansoura, Egypt" + }, + { + "author_name": "Shaimaa H. Fouad", + "author_inst": "Department of Internal Medicine / Allergy and Clinical Immunology, Ain Shams University, Cairo, Egypt." + }, + { + "author_name": "Aya H. Moussa", + "author_inst": "Department of Anesthesia, Intensive Care and Pain Management, Faculty of Medicine, Ain Shams University, Cairo, Egypt." + }, + { + "author_name": "Shaimaa A. Abdalgeleel", + "author_inst": "Department of Biostatistics and Epidemiology, National Cancer Institute, Cairo University, Cairo, Egypt." + }, + { + "author_name": "Nouran M. Moustafa", + "author_inst": "Department of Basic Medical Science, Faculty of Medicine, Dar Al Uloom University, Riyadh, Saudi Arabia & Department of Microbiology and Immunology, Faculty of " + }, + { + "author_name": "Mariam K. Youssef", + "author_inst": "Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.27.21259432", "rel_title": "SARS-CoV-2 Seroprevalence among First Responders in Northeastern Ohio", @@ -696626,69 +697882,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.02.450920", - "rel_title": "Betacoronavirus-specific alternate splicing", - "rel_date": "2021-07-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.02.450920", - "rel_abs": "Viruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection as well as datasets from the betacoronaviruses SARS-CoV and MERS as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification and a smaller number of exons than differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by DAS and DGE in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS, potentially modifying a broad range of cellular functions and affecting a diverse set of genes and biological functions.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Guy Karlebach", - "author_inst": "The Jackson Laboratory for Genomic Medicine" - }, - { - "author_name": "Stephen J Baylin", - "author_inst": "Johns Hopkins University, School of Medicine" - }, - { - "author_name": "Daniel Butler", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA" - }, - { - "author_name": "Jonathan Foox", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Shawn Levy", - "author_inst": "HudsonAlpha Institute for Biotechnology" - }, - { - "author_name": "Cem Meydan", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA" - }, - { - "author_name": "Christopher Mozsary", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA" - }, - { - "author_name": "Amanda M Saravia-Butler", - "author_inst": "Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA" - }, - { - "author_name": "Eve Wurtele", - "author_inst": "Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, 50011, USA" - }, - { - "author_name": "Christopher Mason", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Afshin Beheshti", - "author_inst": "KBR, NASA Ames Research Center" - }, - { - "author_name": "Peter N. Robinson", - "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.07.02.450896", "rel_title": "Implications of Spike-glycoprotein processing at S1/S2 by Furin, at S2' by Furin and/or TMPRSS2 and shedding of ACE2: cell-to-cell fusion, cell entry and infectivity of SARS-CoV-2", @@ -696996,6 +698189,209 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.01.21259859", + "rel_title": "Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259859", + "rel_abs": "Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting response efforts when community transmission is detected. However, this assessment requires that a true comparison can be made between the new variant and its predecessors because factors other than the virus genotype may influence spread and transmission. In this study, we develop a framework that integrates genomic surveillance data to estimate the relative effective reproduction number (Rt) of co-circulating lineages. We use Connecticut, a state in the northeastern United States in which the SARS-CoV-2 variants B.1.1.7 and B.1.526 co-circulated in early 2021, as a case study for implementing this framework. We find that the Rt of B.1.1.7 was 6-10% larger than that of B.1.526 in Connecticut in the midst of a COVID-19 vaccination campaign. To assess the generalizability of this framework, we apply it to genomic surveillance data from New York City and observe the same trend. Finally, we use discrete phylogeography to demonstrate that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of B.1.1.7 were larger than those resulting from B.1.526 introductions. Our framework, which uses open-source methods requiring minimal computational resources, may be used to monitor near real-time variant dynamics in a myriad of settings.", + "rel_num_authors": 47, + "rel_authors": [ + { + "author_name": "Mary E. Petrone", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Jessica E. Rothman", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Mallery I. Breban", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Isabel M. Ott", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Alexis Russell", + "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA" + }, + { + "author_name": "Erica Lasek-Nesselquist", + "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, U" + }, + { + "author_name": "Kevin Kelly", + "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA" + }, + { + "author_name": "Greg Omerza", + "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA" + }, + { + "author_name": "Nicholas Renzette", + "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA" + }, + { + "author_name": "Anne E. Watkins", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Chaney C. Kalinich", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Tara Alpert", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Anderson F. Brito", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Rebecca Earnest", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Irina R. Tikhonova", + "author_inst": "Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA" + }, + { + "author_name": "Christopher Castaldi", + "author_inst": "Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA" + }, + { + "author_name": "John P. Kelly", + "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA" + }, + { + "author_name": "Matthew Shudt", + "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA" + }, + { + "author_name": "Jonathan Plitnick", + "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, U" + }, + { + "author_name": "Erasmus Schneider", + "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, U" + }, + { + "author_name": "Steven Murphy", + "author_inst": "Murphy Medical Associates, Greenwich, CT 06830, USA" + }, + { + "author_name": "Caleb Neal", + "author_inst": "Murphy Medical Associates, Greenwich, CT 06830, USA" + }, + { + "author_name": "Eva Laszlo", + "author_inst": "Murphy Medical Associates, Greenwich, CT 06830, USA" + }, + { + "author_name": "Ahmad Altajar", + "author_inst": "Murphy Medical Associates, Greenwich, CT 06830, USA" + }, + { + "author_name": "Claire Pearson", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA" + }, + { + "author_name": "Anthony Muyombwe", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA" + }, + { + "author_name": "Randy Downing", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA" + }, + { + "author_name": "Jafar Razeq", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA" + }, + { + "author_name": "Linda Niccolai", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Madeline S. Wilson", + "author_inst": "Yale Health Center, Yale University, New Haven, CT 06510, USA" + }, + { + "author_name": "Margaret L. Anderson", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Jianhui Wang", + "author_inst": "Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA" + }, + { + "author_name": "Chen Liu", + "author_inst": "Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA" + }, + { + "author_name": "Pei Hui", + "author_inst": "Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA" + }, + { + "author_name": "Shrikant Mane", + "author_inst": "Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA" + }, + { + "author_name": "Bradford P. Taylor", + "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA" + }, + { + "author_name": "William P. Hanage", + "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA" + }, + { + "author_name": "Marie L. Landry", + "author_inst": "Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA" + }, + { + "author_name": "David R. Peaper", + "author_inst": "Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA" + }, + { + "author_name": "Kaya Bilguvar", + "author_inst": "Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, US" + }, + { + "author_name": "Joseph R. Fauver", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Lauren M. Gardner", + "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore 21218, MD, USA" + }, + { + "author_name": "Virginia E. Pitzer", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Kirsten St. George", + "author_inst": "Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, U" + }, + { + "author_name": "Mark D. Adams", + "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA" + }, + { + "author_name": "Nathan D. Grubaugh", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Ecology and Evolutionary Biology, Yale U" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.27.21259602", "rel_title": "Airborne PM2.5 and the Emergence of 10 SARS-CoV-2 Variants: The Multifaceted Influence of an Airborne Pollutant on Viral Natural Selection determining SARS-CoV-2 Evolution - An Environmental Wake-up Call or an Ecological Fallacy?", @@ -698780,149 +700176,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2021.06.28.21259576", - "rel_title": "Immunogenicity of COVID-19 Vaccination in Immunocompromised Patients: An Observational, Prospective Cohort Study Interim Analysis", - "rel_date": "2021-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259576", - "rel_abs": "ObjectivesImmunocompromised patients were excluded from COVID-19 vaccine clinical trials. The objectives of the study were to measure antibody responses, levels, and neutralization capability after COVID-19 vaccination among immunocompromised patients and compare these variables to those of immunocompetent healthcare workers.\n\nMethodsThis is an interim analysis of an ongoing observational, prospective cohort study which launched on April 14, 2021 across Western Pennsylvania. Participants were healthy healthcare workers (HCW) and immunocompromised patients who had completed their COVID-19 vaccination series. Individuals with a history of COVID-19 were not eligible. Serum was collected to measure for the presence of IgG against the SARS-CoV-2 Spike protein using a semi-quantitative assay; antibody levels were available for comparisons. A quasi-random subset of patients was selected for pseudovirus neutralization assays. Seropositivity with 95% Clopper-Pearson exact confidence intervals and distribution of antibody levels were measured. To identify risk factors for seronegativity, clinical characteristics were univariately compared between antibody reactive and non-reactive individuals within the immunocompromised group.\n\nResults107 HCW and 489 immunocompromised patients were enrolled. Compared to HCWs, seropositivity was significantly lower (p<.001) among immunocompromised patients with Solid organ transplant (SOT), autoimmune, hematological malignancies, and solid tumors (HCW=98.1%; SOT=37.2%; autoimmune=83.8%; hematological malignancies=54.7%; and solid tumor=82.4%, p < 0.05). Over 94% of patients with Human Immunodeficiency Virus were seropositive. Among seropositive patients, antibody levels were much lower among SOT (4.5 [2.1,13.1], p=.020). Neutralization titers tightly correlated with antibody levels (Spearman r = 0.91, p < 0.0001).\n\nConclusionOur findings demonstrate the heterogeneity of the humoral immune response to COVID-19 vaccines based on underlying immunosuppressive condition and highlight an urgent need to optimize and individualize COVID-19 prevention in these patients. These findings also have implications on public health guidance, particularly given revised Centers for Disease Control and Prevention recommendations permitting vaccinated individuals to abandon masking and social distancing in most settings. Future studies are warranted to determine assessment of cellular immunity, longitudinal measurement of immune responses, and the safety and efficacy of revaccination.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Ghady Haidar", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Mounzer Agha", - "author_inst": "UPMC Hillman Cancer Center" - }, - { - "author_name": "Amy Lukanski", - "author_inst": "UPMC Wolff Center" - }, - { - "author_name": "Kelsey Linstrum", - "author_inst": "UPMC Health Care Innovation" - }, - { - "author_name": "Rachel Troyan", - "author_inst": "UPMC Wolff Center" - }, - { - "author_name": "Andrew Bilderback", - "author_inst": "UPMC Wolff Center" - }, - { - "author_name": "Scott Rothenberger", - "author_inst": "Division of General Internal Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Deborah K McMahon", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Melissa Crandall", - "author_inst": "Clinical Laboratory, University of Pittsburgh Medical Center" - }, - { - "author_name": "P Nathan Enick", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Michelle Sobolewksi", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Kevin Collins", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center" - }, - { - "author_name": "Marc B Schwartz", - "author_inst": "Department of Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Jeffrey M Dueker", - "author_inst": "Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Fernanda P Silveira", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Mary E Keebler", - "author_inst": "Department of Cardiology, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Abhinav Humar", - "author_inst": "Division of Transplantation, Department of Surgery, University of Pittsburgh School of Medicine" - }, - { - "author_name": "James D Luketich", - "author_inst": "Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Matthew R Morrell", - "author_inst": "Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Joseph M Pilewski", - "author_inst": "Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "John F McDyer", - "author_inst": "Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Bhanu Pappu", - "author_inst": "Hillman Cancer Center, University of Pittsburgh Medical Center" - }, - { - "author_name": "Robert L Ferris", - "author_inst": "Hillman Cancer Center, University of Pittsburgh Medical Center" - }, - { - "author_name": "Stanley M Marks", - "author_inst": "Hillman Cancer Center, University of Pittsburgh Medical Center" - }, - { - "author_name": "Cynthia Klamar-Blain", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Urvi M Parikh", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Amy Heaps", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Paula L Kip", - "author_inst": "University of Pittsburgh Medical Center" - }, - { - "author_name": "Alan Wells", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Tami Minnier", - "author_inst": "UPMC Wolff Center" - }, - { - "author_name": "Derek Angus", - "author_inst": "UPMC Health Care Innovation" - }, - { - "author_name": "John W Mellors", - "author_inst": "Division of Infectious Diseases, University of Pittsburgh School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.21.21258023", "rel_title": "ASSESSMENT OF POTENTIAL SARS-CoV-2 VIRUS N GENE INTEGRATION INTO HUMAN GENOME REVEALS NO SIGNIFICANT IMPACT ON RT-qPCR COVID-19 DIAGNOSTIC TESTING", @@ -699210,6 +700463,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2021.06.26.21259568", + "rel_title": "A Systematic Review: The Dimensions and Indicators utilized in the Performance Evaluation of Health Care Organizations- An Implication during COVID-19 Pandemic", + "rel_date": "2021-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.26.21259568", + "rel_abs": "BackgroundThe balanced scorecard (BSC) has been implemented to evaluate the performance of health care organizations (HCOs). BSC proved to be effective in improving financial performance and patient satisfaction.\n\nAimThis systematic review aims to identify key performance indicators (KPIs) and dimensions that are vital and most frequently used by health care managers in BSC implementations. Additionally, it attempts to analyze the resulting dimensions during the COVID-19 era.\n\nMethodsThis systematic review adheres to PRISMA guidelines. The PubMed, Embase, Cochrane, and Google Scholar databases and Google search engine were inspected to find all implementations of BSC at HCO. The risk of bias was assessed using the nonrandomized intervention studies (ROBINS-I) tool to evaluate the quality of observational and quasi- experimental studies and the Cochrane (RoB 2) tool for randomized controlled trials (RCTs).\n\nResultsThere were 33 eligible studies, of which we identified 36 BSC implementations. The categorization and regrouping of the 797 KPIs resulted in 46 subdimensions. The reassembly of these subdimensions resulted in 13 major dimensions: financial, efficiency and effectiveness, availability and quality of supplies and services, managerial tasks, health care workers (HCW) scientific development error-free and safety, time, HCW-centeredness, patient-centeredness, technology, and information systems, community care and reputation, HCO building, and communication. On the other hand, this review detected that BSC design modification to include external and managerial perspectives was necessary for many BSC implementations.\n\nConclusionThis review solves the KPI categorization dilemma. It also guides researchers and health care managers in choosing dimensions for future BSC implementations and performance evaluations in general. Consequently, dimension uniformity will improve the data sharing and comparability among studies. Additionally, despite the pandemic negatively influencing many dimensions, the researchers observed a lack of comprehensive HCO performance evaluations. In the same vein, although some resulting dimensions were assessed separately during the pandemic, other dimensions still lack investigation. Lastly, BSC dimensions may play an essential role in tackling the COVID-19 pandemic. However, further research is required to investigate the BSC implementation effect in mitigating the pandemic consequences on HCO.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Faten Amer", + "author_inst": "Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pecs, Pecs, Hungary/ Institute for Health Insurance, Faculty of Health Sciences, U" + }, + { + "author_name": "Sahar Hammoud", + "author_inst": "Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Haitham Khatatbeh", + "author_inst": "Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Szimonetta Lohner", + "author_inst": "Cochrane Hungary, Clinical Center of the University of Pecs, Medical School, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Imre Boncz", + "author_inst": "Institute for Health Insurance, Faculty of Health Sciences, University of Pecs, Hungary" + }, + { + "author_name": "Dora Endrei", + "author_inst": "Institute for Health Insurance, Faculty of Health Sciences, University of Pecs, Hungary" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.06.23.21259405", "rel_title": "Resurgence of SARS-CoV-2 in India: Potential role of the B.1.617.2 (Delta) variant and delayed interventions", @@ -700634,41 +701926,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.06.24.21259505", - "rel_title": "Assessment of COVID-19 vaccine hesitancy among Zimbabweans: A rapid national survey", - "rel_date": "2021-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259505", - "rel_abs": "BackgroundTo minimise the devastating effects of the coronavirus disease 2019 (COVID-19) pandemic, scientists hastily developed a vaccine. However, the scale-up of the vaccine is likely to be hindered by the widespread social media misinformation. We, therefore, conducted a study to assess the COVID-19 vaccine hesitancy among Zimbabweans.\n\nMethodsWe conducted a descriptive online cross-sectional survey using a self-administered questionnaire among adults. The questionnaire assessed willingness to be vaccinated; socio-demographic characteristics, individual attitudes and perceptions, effectiveness, and safety of the vaccine. Multivariable logistic regression analysis was utilized to examine the independent factors associated with vaccine uptake.\n\nResultsWe analysed data for 1168 participants, age range of 19-89 years with the majority being females (57.5%). Half (49.9%) of the participants reported that they would accept the COVID-19 vaccine. The majority were uncertain about the effectiveness of the vaccine (76.0%) and its safety (55.0%). About half lacked trust in the governments ability to ensure the availability of an effective vaccine and 61.0% mentioned that they would seek advice from a healthcare worker to vaccinate. Age 55 years and above [vs 18-25 years - Adjusted Odds Ratio (AOR): 2.04, 95% Confidence Interval (CI): 1.07-3.87], chronic disease [vs no chronic disease - AOR: 1.72, 95%CI: 1.32-2.25], males [vs females - AOR: 1.84, 95%CI: 1.44-2.36] and being a healthcare worker [vs not being a health worker - AOR: 1.73, 95%CI: 1.34-2.24] were associated with increased likelihood to vaccinate. History of COVID-19 infection [vs no history - AOR: 0.45, 95%CI: 0.25-0.81) and rural residence [vs urban - AOR: 0.64, 95%CI: 0.40-1.01] were associated with reduced likelihood to vaccinate.\n\nConclusionWe found half of the participants willing to vaccinate against COVID-19. The majority lacked trust in the government and were uncertain about vaccine effectiveness and safety. The policymakers should consider targeting geographical and demographic groups which were unlikely to vaccinate with vaccine information, education, and communication to improve uptake.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Paddington T Mundagowa", - "author_inst": "Africa University" - }, - { - "author_name": "Samantha N Tozivepi", - "author_inst": "Africa University" - }, - { - "author_name": "Edward T Chiyaka", - "author_inst": "Kent State University" - }, - { - "author_name": "Fadzai Mukora-Mutseyekwa", - "author_inst": "Africa University" - }, - { - "author_name": "Richard Makurumidze", - "author_inst": "University of Zimbabwe College of Health Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.28.450244", "rel_title": "Systematic genome-scale identification of host factors for SARS-CoV-2 infection across models yields a core single gene dependency; ACE2", @@ -701076,6 +702333,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.06.29.450330", + "rel_title": "Genetic diversity and evolution of SARS-CoV-2 in Belgium during the first wave outbreak", + "rel_date": "2021-06-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.29.450330", + "rel_abs": "SARS-CoV-2, the causative agent of COVID-19 was first detected in Belgium on 3rd February 2020, albeit the first epidemiological wave started in March and ended in June 2020. One year after the first epidemiological wave hit the country data analyses reveled the temporal and variant distribution of SARS-CoV-2 and its implication with Belgian epidemiological measures. In this study, 766 complete SARS-CoV-2 genomes of samples originating from the first epidemiological were sequenced to characterize the temporal and geographic distribution of the COVID-19 pandemic in Belgium through phylogenetic and variant analysis. Our analysis reveals the presence of the major circulating SARS-CoV-2 clades (G, GH and GR) and lineages circulating in Belgium at that time. Moreover, it contextualizes the density of SARS-CoV-2 cases over time with non-intervention measures taken to prevent the spread of SARS-CoV-2 in Belgium, specific international case imports and the functional implications of the most representative non-synonymous mutations present in Belgium between February to June 2020.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Tony Wawina-Bokalanga", + "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Clinical and Epidemiological Virology, Zoonotic Infectious Diseases Unit," + }, + { + "author_name": "Joan Marti-Carreras", + "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Clinical and Epidemiological Virology, Zoonotic Infectious Diseases Unit," + }, + { + "author_name": "Bert Vanmechelen", + "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Clinical and Epidemiological Virology, Zoonotic Infectious Diseases Unit," + }, + { + "author_name": "Mandy Bloemen", + "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Clinical and Epidemiological Virology, Zoonotic Infectious Diseases Unit," + }, + { + "author_name": "Elke Wollants", + "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Clinical and Epidemiological Virology, Zoonotic Infectious Diseases Unit," + }, + { + "author_name": "Lies Laenen", + "author_inst": "Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium" + }, + { + "author_name": "Lize Cuypers", + "author_inst": "Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium" + }, + { + "author_name": "Kurt Beuselinck", + "author_inst": "Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium" + }, + { + "author_name": "Katrien Lagrou", + "author_inst": "Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium" + }, + { + "author_name": "Emmanuel Andre", + "author_inst": "Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium" + }, + { + "author_name": "Marc Van Ranst", + "author_inst": "Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium" + }, + { + "author_name": "Piet Maes", + "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Clinical and Epidemiological Virology, Zoonotic Infectious Diseases Unit," + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.06.29.450356", "rel_title": "Thrombocytopenia and splenic platelet directed immune responses after intravenous ChAdOx1 nCov-19 administration", @@ -703168,69 +704488,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.28.449914", - "rel_title": "Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants", - "rel_date": "2021-06-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.28.449914", - "rel_abs": "The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has led to growing concerns over increased transmissibility and the ability of some variants to partially escape immunity. Sera from participants immunized on a prime-boost schedule with the mRNA-1273 COVID-19 vaccine were tested for neutralizing activity against several SARS-CoV-2 variants, including variants of concern (VOCs) and variants of interest (VOIs), compared to neutralization of the wild-type SARS-CoV-2 virus (designated as D614G). Results showed minimal effects on neutralization titers against the B.1.1.7 (Alpha) variant (1.2-fold reduction compared with D614G); other VOCs such as B.1.351 (Beta, including B.1.351-v1, B.1.351-v2, and B.1.351-v3), B.1.617.2 (Delta), and P.1 (Gamma) showed decreased neutralization titers ranging from 2.1-fold to 8.4-fold reductions compared with D614G, although all remained susceptible to mRNA-1273-elicited serum neutralization.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Angela Choi", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Matthew Koch", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Kai Wu", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Groves Dixon", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Judith Oestreicher", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Holly Legault", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Guillaume B.E. Stewart-Jones", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Tonya Colpitts", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Rolando Pajon", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Hamilton Bennett", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Andrea Carfi", - "author_inst": "Moderna Inc" - }, - { - "author_name": "Darin K Edwards", - "author_inst": "Moderna Inc" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.25.449831", "rel_title": "Solar simulated ultraviolet radiation inactivates HCoV-NL63 and SARS-CoV-2 coronaviruses at environmentally relevant doses", @@ -703630,6 +704887,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.06.24.21259453", + "rel_title": "Conditionality of COVID-19 vaccine acceptance in European countries", + "rel_date": "2021-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259453", + "rel_abs": "The COVID-19 vaccine rollout in recent months offers a powerful preventive measure that may help control SARS-CoV-2 transmission. Nevertheless, long-standing public hesitation around vaccines has heightened public health concerns that vaccine coverage may not achieve desired public health impacts.This cross-sectional survey was conducted online in December 2020 among 7000 respondents (aged 18 to 65) in Belgium, France, Germany, Italy, Spain, Sweden, and Ukraine. The survey included open text boxes for fuller explanation of responses. Projected COVID-19 vaccine coverage varied and may not be sufficiently high among certain populations to achieve herd immunity. Overall, 56.9% would accept a COVID-19 vaccine, 19.0% would not, and 24.1% did not know or preferred not to say. By country, between 44% (France) and 66% (Italy) of respondents would accept a COVID-19 vaccine. Respondents expressed conditionality in open responses, voicing concerns about vaccine safety and mistrust of authorities. Public health campaigns must tackle these safety concerns.\n\nHighlightsO_LIMixed-method survey studied expected COVID vaccine uptake in 7 European countries.\nC_LIO_LIProjected COVID vaccine acceptance by country ranged from 44% to 66%.\nC_LIO_LIExplicit COVID vaccine acceptance or rejection was conditional.\nC_LIO_LIStudy finds concerns about vaccine safety and authorities competence and honesty.\nC_LIO_LIVaccine communications should address safety anxieties and target specific groups.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Leonardo w Heyerdahl", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Muriel Vray", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Benedetta Lana", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nastassia Tvardik", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nina Gobat", + "author_inst": "University of Oxford" + }, + { + "author_name": "Marta Wanat", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah Tonkin-Crine", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sibyl Anthierens", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Herman Goossens", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Tamara Giles-vernick", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.25.21259523", "rel_title": "A spectrum of HRCT chest findings in RT-PCR positive asymptomatic COVID-19 patients at a COVID designated hospital in Nepal", @@ -705398,33 +706710,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.22.21258971", - "rel_title": "Temporal Analysis of Social Determinants Associated with COVID-19 Mortality", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21258971", - "rel_abs": "This study examines how social determinants associated with COVID-19 mortality change over time. Using US county-level data from July 5 and December 28, 2020, the effect of 19 high-risk factors on COVID-19 mortality rate was quantified at each time point with negative binomial mixed models. Then, these high-risk factors were used as controls in two association studies between 40 social determinants and COVID-19 mortality rates using data from the same time points. The results indicate that counties with certain ethnic minorities and age groups, immigrants, prevalence of diseases like pediatric asthma and diabetes and cardiovascular disease, socioeconomic inequalities, and higher social association are associated with increased COVID-19 mortality rates. Meanwhile, more mental health providers, access to exercise, higher income, chronic lung disease in adults, suicide, and excessive drinking are associated with decreased mortality. Our temporal analysis also reveals a possible decreasing impact of socioeconomic disadvantage and air quality, and an increasing effect of factors like age, which suggests that public health policies may have been effective in protecting disadvantaged populations over time or that analysis utilizing earlier data may have exaggerated certain effects. Overall, we continue to recognize that social inequality still places disadvantaged groups at risk, and we identify possible relationships between lung disease, mental health, and COVID-19 that need to be explored on a clinical level.\n\nCCS CONCEPTSO_LIApplied computing [->] Health informatics.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shayom Debopadhaya", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "John S Erickson", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Kristin P Bennett", - "author_inst": "Rensselaer Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.22.21259345", "rel_title": "Multi-centre post-implementation evaluation of SARS-CoV-2 antigen-based point of care tests used for asymptomatic screening of continuing care healthcare workers", @@ -705692,6 +706977,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.22.21259346", + "rel_title": "Can Auxiliary Indicators Improve COVID-19 Forecasting and Hotspot Prediction?", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21259346", + "rel_abs": "Short-term forecasts of traditional streams from public health reporting (such as cases, hospitalizations, and deaths) are a key input to public health decision-making during a pandemic. Since early 2020, our research group has worked with data partners to collect, curate, and make publicly available numerous real-time COVID-19 indicators, providing multiple views of pandemic activity in the U.S. This paper studies the utility of five such indicators--derived from de-identified medical insurance claims, self-reported symptoms from online surveys, and COVID-related Google search activity--from a forecasting perspective. For each indicator, we ask whether its inclusion in an autoregressive (AR) model leads to improved predictive accuracy relative to the same model excluding it. Such an AR model, without external features, is already competitive with many top COVID-19 forecasting models in use today. Our analysis reveals that (a) inclusion of each of these five indicators improves on the overall predictive accuracy of the AR model; (b) predictive gains are in general most pronounced during times in which COVID cases are trending in \"flat\" or \"down\" directions; (c) one indicator, based on Google searches, seems to be particularly helpful during \"up\" trends.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Daniel J McDonald", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Jacob Bien", + "author_inst": "University of Southern California" + }, + { + "author_name": "Alden Green", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Addison J Hu", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Nat DeFries", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Sangwon Hyun", + "author_inst": "University of Southern California" + }, + { + "author_name": "Natalia L Oliveira", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "James Sharpnack", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Jingjing Tang", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Robert Tibshirani", + "author_inst": "Stanford University" + }, + { + "author_name": "Val\u00e9rie Ventura", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Larry Wasserman", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Ryan J Tibshirani", + "author_inst": "Carnegie Mellon University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.21.21259254", "rel_title": "Acceptability, usability and performance of lateral flow immunoassay tests for SARS-CoV-2 antibodies: REACT-2 study of self-testing in non-healthcare key workers", @@ -707100,37 +708452,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.24.449840", - "rel_title": "Phylogenetic network analysis revealed the recombinant origin of the SARS-CoV-2 VOC202012/01 (B.1.1.7) variant first discovered in U.K.", - "rel_date": "2021-06-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.24.449840", - "rel_abs": "The emergence of new variants of the SARS-CoV-2 virus poses serious problems to the control of the current COVID-19 pandemic. Understanding how the variants originate is critical for effective control of the spread of the virus and the global pandemic. The study of the virus evolution so far has been dominated by phylogenetic tree analysis, which however is inappropriate for a few important reasons. Here we used phylogenetic network approach to study the origin of the VOC202012/01 (Alpha) or so-called UK variant (PANGO Lineage B.1.1.7). The multiple network analyses using different methods consistently revealed that the VOC202012/01 variant was a result of recombination, in contrast to the common assumption that the variant evolved from step-wise mutations in a linear order. The study provides an example for the power and application of phylogenetic network analysis in studying virus evolution, which can be applied to study the evolutionary processes leading to the emergence of other variants of the SARS-CoV-2 virus as well as many other viruses.\n\nSignificanceThe emergence of new variants of the SARS-CoV-2 virus, including the Alpha variant first found in U.K., poses serious challenges to the control of the current COVID-19 pandemic. Understanding how new variant originated is paramount to end the pandemic as effectively and quickly as possible. The dominant phylogenetic tree approach to study virus evolution has been inadequate and even misleading. Here we used a phylogenetic network approach to study the origin of the VOC202012/01 (Alpha) variant which was first reported in U.K. last year but has soon spread into many other countries, leading to dramatic increase in infection and death. Multiple analyses consistently revealed that the variant originated through recombination of pre-existing virus strains, highlighting an important but largely ignored mechanism in the evolution of the SARS-CoV-2 virus so far.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Xianfa Xie", - "author_inst": "Virginia State University" - }, - { - "author_name": "Teash-Juan Lewis", - "author_inst": "Virginia State University" - }, - { - "author_name": "Nikoli Green", - "author_inst": "Virginia State University" - }, - { - "author_name": "Zhenping Wang", - "author_inst": "Virginia State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.25.449750", "rel_title": "A random priming amplification method for whole genome sequencing of SARS-CoV-2 and H1N1 influenza A virus.", @@ -707322,6 +708643,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.21.21259259", + "rel_title": "Clinical profile and immediate outcome of Multisystem Inflammatory Syndrome in Children (MIS-C) associated with Covid-19: a multicentric study", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21259259", + "rel_abs": "STRUCTURED ABSTRACTO_ST_ABSINTRODUCTIONC_ST_ABSFollowing an asymptomatic or mildly symptomatic Corona virus disease (COVID 19), otherwise healthy children, may develop serious manifestations in form of cardiac, neurological, respiratory, gastrointestinal and dermatologic dysfunction. Many such cases were being observed in Odisha, an eastern state of India and reported from different health care facilities. We related these unexplained serious manifestations to Multisystem Inflammatory Syndrome associated with COVID 19 (MIS-C) and planned this study.\n\nMETHODSThis retrospective observational study was carried out in three tertiary care centres: Kalinga Institute of Medical Sciences, Bhubaneswar, MKCG Medical college Berhampur and Jagannath Hospital, Bhubaneswar between July to September of year 2020. Study population include all children from 1 month to 15 years admitted to hospital with MIS-C according to WHO Diagnostic Criteria. All the data were analyzed by SPSS.\n\nRESULTSA total of 21 children were included in our study. Maximum number of cases were male (76.2%), predominate age group was 6-10 yrs (47.6%). Predominate symptoms /signs in our observation were fever, pain abdomen, seizure and hypotension. Most of these cases were positive for SARS CoV antibody (80.95%). Response to immunotherapy was dramatic. Mortality (9%) of our study is higher to 1.8-3% from western literature. None of our patient had coronary abnormality while 2 had mild cardiac dysfunction at discharge comparable to other studies.\n\nCONCLUSIONMIS-C following exposure to COVID 19 infection in children is a clinical syndrome which needs early suspicion and appropriate intervention to prevent mortality.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Geetanjali Sethy", + "author_inst": "PRN Medical College, Baripada, Odisha" + }, + { + "author_name": "Bibhudatta Mishra", + "author_inst": "Jagannath Hospital, Bhubaneswar, Odisha" + }, + { + "author_name": "Mukesh Kumar Jain", + "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar" + }, + { + "author_name": "Sibabratta Patnaik", + "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar" + }, + { + "author_name": "Reshmi Mishra", + "author_inst": "Kalinga Institute of Medical Sciences,Bhubaneswar" + }, + { + "author_name": "Jyoti Ranjan Behera", + "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar" + }, + { + "author_name": "Bandya Sahoo", + "author_inst": "Kalinga Institute of Medical Sciences, Bhubaneswar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.06.21.21259268", "rel_title": "COVID-19 pandemic dynamics in India and impact of the SARS-CoV-2 Delta (B.1.617.2) variant", @@ -708790,73 +710154,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.21.449211", - "rel_title": "Anti-prothrombin autoantibodies enriched after infection with SARS-CoV-2 and influenced by strength of antibody response against SARS-CoV-2 proteins", - "rel_date": "2021-06-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.21.449211", - "rel_abs": "Antiphospholipid antibodies (aPL), assumed to cause antiphospholipid syndrome (APS), are notorious for their heterogeneity and detect phospholipids and phospholipid-binding proteins. The persistent presence of Lupus anticoagulant and/or aPL against cardiolipin and/or {beta}2 glycoprotein I have been shown to be independent risk factors for vascular thrombosis and pregnancy morbidity in APS. aPL production is thought to be triggered by - among other factors - viral infections, though infection-associated aPL have mostly been considered non-pathogenic. Recently, the potential pathogenicity of infection-associated aPL has gained momentum since an increasing number of patients infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been described with coagulation abnormalities and hyperinflammation, together with the presence of aPL. Here, we present data from a multicentric, mixed-severity study including three cohorts of individuals who contracted SARS-CoV-2 as well as non-infected blood donors. We simultaneously measured 10 different criteria and non-criteria aPL (IgM and IgG) by using a line immunoassay. Further, IgG antibody response against three SARS-CoV-2 proteins was investigated using tripartite automated blood immunoassay technology. Our analyses revealed that selected non-criteria aPL were enriched concomitant to or after an infection with SARS-CoV-2. Linear mixed-effects models suggest an association of aPL to prothrombin (PT) with the strength of the antibody response against SARS-CoV-2 and that it is further influenced by SARS-CoV-2 disease severity and sex of the individuals. In conclusion, our study is the first to report an association between disease severity, anti-SARS-CoV-2 immunoreactivity and aPL against PT in patients with SARS-CoV-2.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Marc Emmenegger", - "author_inst": "University of Zurich" - }, - { - "author_name": "Sreedhar Saseendran Kumar", - "author_inst": "ETH Zurich, Basel" - }, - { - "author_name": "Vishalini Emmenegger", - "author_inst": "ETH Zurich, Basel" - }, - { - "author_name": "Tomas Malinauskas", - "author_inst": "Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK" - }, - { - "author_name": "Thomas Buettner", - "author_inst": "GA Generic Assays GmbH" - }, - { - "author_name": "Laura Rose", - "author_inst": "GA Generic Assays GmbH" - }, - { - "author_name": "Peter Schierack", - "author_inst": "Institute of Biotechnology, Faculty Environment and Natural Sciences and Faculty of Health Sciences Brandenburg, University of Technology Cottbus-Senftenberg" - }, - { - "author_name": "Martin F Sprinzl", - "author_inst": "Johannes Gutenberg University Medical Center Mainz" - }, - { - "author_name": "Clemens J Sommer", - "author_inst": "Johannes Gutenberg University Medical Center Mainz" - }, - { - "author_name": "Karl J Lackner", - "author_inst": "Johannes Gutenberg University Medical Center Mainz" - }, - { - "author_name": "Adriano Aguzzi", - "author_inst": "University Hospital Zurich" - }, - { - "author_name": "Dirk Roggenbuck", - "author_inst": "GA Generic Assays GmbH, Institute of Biotechnology, Faculty Environment and Natural Sciences and Faculty of Health Sciences Brandenburg, University of Technolog" - }, - { - "author_name": "Katrin B M Frauenknecht", - "author_inst": "Johannes Gutenberg University Medical Center Mainz and University Hospital Zurich" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.14.21258907", "rel_title": "Hybrid-Quantum approach for the optimal lockdown to stop the SARS-CoV-2 community spread subject to maximizing nation economy globally", @@ -709104,6 +710401,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.18.21259150", + "rel_title": "Small-molecule metabolome identifies potential therapeutic targets against COVID-19", + "rel_date": "2021-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21259150", + "rel_abs": "BackgroundRespiratory viruses are transmitted and acquired via the nasal mucosa, and thereby may influence the nasal metabolome composed of biochemical products produced by both host cells and microbes. Studies of the nasal metabolome demonstrate virus-specific changes that sometimes correlate with viral load and disease severity. Here, we evaluate the nasopharyngeal metabolome of COVID-19 infected individuals and report several small molecules that may be used as potential therapeutic targets. Specimens were tested by qRT-PCR with target primers for three viruses: Influenza A (INFA), respiratory syncytial virus (RSV), and SARS-CoV-2, along with asymptomatic controls. The nasopharyngeal metabolome was characterized using an LC-MS/MS-based small-molecule screening kit capable of quantifying 141 analytes. A machine learning model identified 28 discriminating analytes and correctly categorized patients with a viral infection with an accuracy of 96% (R2=0.771, Q2=0.72). A second model identified 5 analytes to differentiate COVID19-infected patients from those with INFA or RSV with an accuracy of 85% (R2=0.442, Q2=0.301). Specifically, LysoPCaC18:2 concentration was significantly increased in COVID19 patients (P< 0.0001), whereas beta-hydroxybutyric acid, Met SO, succinic acid, and carnosine concentrations were significantly decreased (P< 0.0001). This study demonstrates that COVID19 infection results in a unique NP metabolomic signature with carnosine and LysoPCaC18:2 as potential therapeutic targets.\n\nSignificance StatementEfforts to elucidate how SARS-CoV-2 interacts with the host has become a global priority. To identify biomarkers for potential therapeutic interventions, we used a targeted metabolomics approach evaluating metabolite profiles in the nasal mucosa of COVID-19 patients and compared metabolite profiles to those of other respiratory viruses (influenza A, RSV). We identified a COVID-19-specific signature characterized by changes to LysoPCaC18:2, beta-hydroxybutyric acid, Met SO, succinic acid, and carnosine. Carnosine is a promising potential target against SARS-CoV-2 as it has been shown to interfere with binding of SARS-CoV-2 to the ACE2 receptor. This study provides compelling evidence for the use of metabolomics as an avenue for the identification of novel drug targets for viral respiratory infections in the nasopharynx.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Sean M.P. Bennet", + "author_inst": "Kingston Health Sciences Centre" + }, + { + "author_name": "Martin Kaufmann", + "author_inst": "Kingston Health Sciences Centre" + }, + { + "author_name": "Kaede Takami", + "author_inst": "Kingston Health Sciences Centre" + }, + { + "author_name": "Calvin Sjaarda", + "author_inst": "Queens University" + }, + { + "author_name": "Katya Douchant", + "author_inst": "Kingston Health Sciences Centre" + }, + { + "author_name": "Emily Moslinger", + "author_inst": "Kingston Health Sciences Centre" + }, + { + "author_name": "Henry Wong", + "author_inst": "Kingston Health Sciences Centre" + }, + { + "author_name": "David E Reed", + "author_inst": "Kingston Health Sciences Centre" + }, + { + "author_name": "Anne K Ellis", + "author_inst": "Queens University" + }, + { + "author_name": "Stephen Vanner", + "author_inst": "Kingston Health Sciences Centre" + }, + { + "author_name": "Robert I Colautti", + "author_inst": "Queens University" + }, + { + "author_name": "Prameet M Sheth", + "author_inst": "Kingston Health Sciences Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.19.21259169", "rel_title": "SARS-CoV-2 under an elimination strategy in Hong Kong", @@ -710640,25 +712000,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.15.21258969", - "rel_title": "Modeling the waves of Covid-19", - "rel_date": "2021-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258969", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe challenges with modeling the spread of Covid-19 are its power-type growth during the middle stages with the exponents depending on time, and the saturations mainly due to the protective measures, though weakening and partial destruction of the virus due to mutations is a consideration too. The two-phase solution we propose for the total number of detected cases of Covid-19 describes the actual curves in many countries almost with the accuracy of physics laws. Bessel functions play the key role in our approach. The differential equations we obtain are of universal type; they describe momentum risk-management in behavioral psychology, transient processes in invasion ecology, etc. Due to a very small number of parameters, namely, the initial transmission rate and the intensity of the hard and soft measures, we obtain a convincing explanation of the surprising uniformity of the spread in many different areas. This theory can be used for forecasting the epidemic spread, evaluating the efficiency of the protective measures and the vaccinations. For instance, the early projection for the 3rd wave in the USA was very exact. The data until summer 2021 for India, South Africa and UK are discussed.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ivan Cherednik", - "author_inst": "UNC at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.18.21259156", "rel_title": "Factors affecting the transmission of SARS-CoV-2 in school settings", @@ -710790,6 +712131,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.06.17.21258837", + "rel_title": "An Extended Susceptible-Exposed-Infected-Recovered (SEIR) Model with Vaccination for Forecasting the COVID-19 Pandemic in Sri Lanka", + "rel_date": "2021-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21258837", + "rel_abs": "The role of modelling in predicting the spread of an epidemic is important for health planning and policies. This study aimed to apply a compartmental model for predicting the variations of epidemiological parameters in Sri Lanka. We used a dynamic Susceptible-Exposed-Infected-Recovered-Vaccinated (SEIRV) model and simulated potential vaccine strategies under a range of epidemic conditions. The predictions were based on different vaccination coverages (5% to 90%), vaccination-rates (1%, 2%, 5%) and vaccine-efficacies (40%, 60%, 80%) under different R0 (2,4,6). We estimated the duration, exposed, and infected populations. When the R0 was increased, the days of reduction of susceptibility and the days to reach the peak of the infection were reduced gradually. At least 45% vaccine coverage is required for reducing the infected population to mitigate a disastrous situation in Sri Lanka. The results revealed that when R0 is increased in the SEIRV model along with the increase of vaccination efficacy and vaccination rate, the population to be vaccinated is reducing. Thus, the vaccination offers greater benefits to the local population by reducing the time to reach the peak, exposed and infected population through flattening the curves.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "R.M. Nayani Umesha Rajapaksha", + "author_inst": "Health Promotion Bureau, Ministry of Health, Sri Lanka" + }, + { + "author_name": "Millawage Supun Dilara Wijesinghe", + "author_inst": "Health Promotion Bureau, Ministry of Health, Sri Lanka" + }, + { + "author_name": "Toms K Thomas", + "author_inst": "SRM University, Sikkim, India." + }, + { + "author_name": "Sujith P. Jayasooriya", + "author_inst": "Innovation for Development Consultants" + }, + { + "author_name": "W. M. Prasad Chathuranga Weerasinghe", + "author_inst": "Health Promotion Bureau, Ministry of Health, Sri Lanka" + }, + { + "author_name": "B. M. Indika Gunawardana", + "author_inst": "Health Promotion Bureau, Ministry of Health, Sri Lanka" + }, + { + "author_name": "Shalini Bhakta", + "author_inst": "SRM University Sikkim, India" + }, + { + "author_name": "Yibeltal Assefa", + "author_inst": "The University of Queensland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.14.21258904", "rel_title": "Association between overcrowded households, multigenerational households, and COVID-19: a cohort study", @@ -711710,117 +713098,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.16.21258673", - "rel_title": "Antibody neutralization to SARS-CoV-2 and variants after one year in Wuhan", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21258673", - "rel_abs": "Most COVID-19 patients can build effective humoral immunity against SARS-CoV-2 after recovery(1, 2). However, it remains unknown how long the protection can maintain and how efficiently it can protect people from the reinfection of the emerging SARS-CoV-2 variants. Here we evaluated the sera from 248 COVID-19 convalescents around one year post-infection in Wuhan, the earliest epicenter of SARS-CoV-2. We demonstrated that the SARS-CoV-2 immunoglobulin G (IgG) maintains at a high level and potently neutralizes the infection of the original strain (WT) and the B.1.1.7 variant in most patients. However, they showed varying degrees of efficacy reduction against the other variants of concern (P.1, B.1.525, and especially B.1.351) in a patient-specific manner. Mutations in RBD including K417N, E484K, and E484Q/L452R (B.1.617) remarkably impair the neutralizing activity of the convalescents sera. Encouragingly, we found that a small fraction of patients sera showed broad neutralization potency to multiple variants and mutants, suggesting the existence of broadly neutralizing antibodies recognizing the epitopes beyond the mutation sites. Our results suggest that the SARS-CoV-2 vaccination effectiveness relies more on the timely re-administration of the epitope-updated vaccine than the durability of the neutralizing antibodies.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Qianyun Liu", - "author_inst": "Wuhan University" - }, - { - "author_name": "Qing Xiong", - "author_inst": "Wuhan University" - }, - { - "author_name": "Fanghua Mei", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Chengbao Ma", - "author_inst": "Wuhan University" - }, - { - "author_name": "Zhen Zhang", - "author_inst": "Wuhan University" - }, - { - "author_name": "Bing Hu", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Junqiang Xu", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Yongzhong Jiang", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Faxian Zhan", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Xianying Chen", - "author_inst": "Wuhan University" - }, - { - "author_name": "Ming Guo", - "author_inst": "Wuhan University" - }, - { - "author_name": "Xin Wang", - "author_inst": "Wuhan University" - }, - { - "author_name": "Yaohui Fang", - "author_inst": "National Virus Resource Center, Wuhan Institute of Virology" - }, - { - "author_name": "Shu Shen", - "author_inst": "National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences" - }, - { - "author_name": "Yingle Liu", - "author_inst": "Wuhan University" - }, - { - "author_name": "Fang Liu", - "author_inst": "Wuhan University" - }, - { - "author_name": "Li Zhou", - "author_inst": "Wuhan University" - }, - { - "author_name": "Ke Xu", - "author_inst": "Wuhan University" - }, - { - "author_name": "Changwen Ke", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Fei Deng", - "author_inst": "National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences" - }, - { - "author_name": "Kun Cai", - "author_inst": "Hubei Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Huan Yan", - "author_inst": "Wuhan University" - }, - { - "author_name": "Yu Chen", - "author_inst": "Wuhan University" - }, - { - "author_name": "Ke Lan", - "author_inst": "Wuhan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.18.21259072", "rel_title": "Evaluation of the effectiveness of remdesivir in treating severe COVID-19 using data from the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, national cohort study.", @@ -712048,6 +713325,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.15.21258935", + "rel_title": "The relative strength and timing of innate immune and CD8 T-cell responses underlie the heterogeneous outcomes of SARS-CoV-2 infection", + "rel_date": "2021-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258935", + "rel_abs": "SARS-CoV-2 infection results in highly heterogeneous outcomes, from cure without symptoms to acute respiratory distress and death. While immunological correlates of disease severity have been identified, how they act together to determine the outcomes is unknown. Here, using a new mathematical model of within-host SARS-CoV-2 infection, we analyze diverse clinical datasets and predict that a subtle interplay between innate and CD8 T-cell responses underlies disease heterogeneity. Our model considers essential features of these immune arms and immunopathology from cytokines and effector cells. Model predictions provided excellent fits to patient data and, by varying the strength and timing of the immune arms, quantitatively recapitulated viral load changes in mild, moderate, and severe disease, and death. Additionally, they explained several confounding observations, including viral recrudescence after symptom loss, prolonged viral positivity before cure, and mortality despite declining viral loads. Together, a robust conceptual understanding of COVID-19 outcomes emerges, bearing implications for interventions.\n\nTeaserModeling explains how a subtle interplay between innate immune and CD8 T-cell responses determines the severity of COVID-19.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Budhaditya Chatterjee", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Harshbir Singh Sandhu", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Narendra M Dixit", + "author_inst": "Indian Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.15.21258669", "rel_title": "COMPARATIVE IMMUNOGENICITY OF BNT162b2 mRNA VACCINE WITH NATURAL COVID-19 INFECTION", @@ -713608,125 +714912,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.19.21259125", - "rel_title": "Plasma gradient of soluble urokinase-type plasminogen activator receptor is linked to pathogenic plasma proteome and immune transcriptome and stratifies outcomes in severe COVID-19", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.19.21259125", - "rel_abs": "Disease caused by SARS-CoV-2 coronavirus (COVID-19) has resulted in significant morbidity and mortality world-wide. A systemic hyper-inflammation characterizes the severe COVID-19 disease often associated with acute respiratory distress syndrome (ARDS). Blood biomarkers capable of risk stratification are of great importance in effective triage and critical care of severe COVID-19 patients. In the present study we report higher plasma abundance of soluble urokinase-type plasminogen activator receptor (sUPAR), expressed by an abnormally expanded circulating myeloid cell population, in severe COVID-19 patients with ARDS. Plasma sUPAR level was found to be linked to a characteristic proteomic signature of plasma, linked to coagulation disorders and complement activation. Receiver operator characteristics curve analysis identified a cut-off value of sUPAR at 1996.809 pg/ml that could predict survival in our cohort (Odds ratio: 2.9286, 95% confidence interval 1.0427-8.2257). Lower sUPAR level than this threshold concentration was associated with a differential expression of the immune transcriptome as well as favourable clinical outcomes, both in terms of survival benefit (Hazard ratio: 0.3615, 95% confidence interval 0.1433-0.912) and faster disease remission in our patient cohort. Thus we identified sUPAR as a key pathogenic circulating molecule linking systemic hyperinflammation to the hypercoagulable state and stratifying clinical outcomes in severe COVID-19 patients with ARDS.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Jafar Sarif", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Deblina Raychaudhuri", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Ranit D'Rozario", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Purbita Bandopadhyay", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Praveen Singh", - "author_inst": "Cardiorespiratory Disease Biology, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Priyanka Mehta", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Md. Asmaul Hoque", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Bishnu Prasad Sinha", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Manoj Kushwaha", - "author_inst": "Cardiorespiratory Disease Biology, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Shweta Sahni", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Priti Devi", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Partha Chattopadhyay", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Shekhar Ranjan Paul", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Yogiraj Ray", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Kausik Chaudhuri", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Sayantan Banerjee", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Debajyoti Majumdar", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Bibhuti Saha", - "author_inst": "School of Tropical Medicine, Kolkata, India" - }, - { - "author_name": "Biswanath Sharma Sarkar", - "author_inst": "Department of Medicine, ID & BG Hospital, Kolkata, India" - }, - { - "author_name": "Prasun Bhattacharya", - "author_inst": "Medical College, Kolkata, India" - }, - { - "author_name": "Shilpak Chatterjee", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Sandip Paul", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Pramit Ghosh", - "author_inst": "Deben Mahata Government Medical College & Hospital. Purulia, India" - }, - { - "author_name": "Rajesh Pandey", - "author_inst": "INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Shantanu Sengupta", - "author_inst": "Cardiorespiratory Disease Biology, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India" - }, - { - "author_name": "Dipyaman Ganguly", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.20.21258949", "rel_title": "Role of physiotherapy team in critically ill COVID-19 patients pronation: can a multidisciplinary management reduce the complications rate?", @@ -713993,6 +715178,85 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.06.21.449178", + "rel_title": "Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune pathways related to tissue injury", + "rel_date": "2021-06-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.21.449178", + "rel_abs": "Severe lung damage in COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways and genes present across the spectrum of histopathological damage in COVID-19 lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from areas of interest within well preserved post-mortem lung samples from three patients. Despite substantial inter-patient heterogeneity we discovered evidence for a common immune cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines including CXCL9, CXCL10 and CXCL11 which are known to promote the recruitment of CXCR3+ immune cells. The tumour necrosis factor (TNF) superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were found to be consistently upregulated in the areas with severe tissue damage. We used published spatial and single cell SARS-CoV-2 datasets to confirm our findings in the lung tissue from additional cohorts of COVID-19 patients. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies.\n\nOne Sentence SummarySpatial analysis identifies IFN{gamma} response signatures as focal to severe alveolar damage in COVID-19 pneumonitis.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Amy R Cross", + "author_inst": "University of Oxford" + }, + { + "author_name": "Carlos de Andrea", + "author_inst": "Universidad de Navarra" + }, + { + "author_name": "Maria Villalba-Esparza", + "author_inst": "Department of Pathology, Clinica de la Universidad de Navarra, Pamplona, Spain" + }, + { + "author_name": "Manuel Landecho Acha", + "author_inst": "Clinica Universidad de Navarra" + }, + { + "author_name": "Lucia Cerundolo", + "author_inst": "University of Oxford" + }, + { + "author_name": "Praveen Weeratunga", + "author_inst": "Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit" + }, + { + "author_name": "Rachel Etherington", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laura Denney", + "author_inst": "University of Oxford" + }, + { + "author_name": "Graham Ogg", + "author_inst": "Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit" + }, + { + "author_name": "Ling-Pei Ho", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ian Roberts", + "author_inst": "Oxford University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Joanna Hester", + "author_inst": "University of Oxford" + }, + { + "author_name": "Paul Klenerman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ignacio Melero", + "author_inst": "Universidad de Navarra" + }, + { + "author_name": "Stephen Sansom", + "author_inst": "University of Oxford" + }, + { + "author_name": "Fadi Issa", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.06.20.449191", "rel_title": "The challenge of structural heterogeneity in the native mass spectrometry studies of the SARS-CoV-2 spike protein interactions with its host cell-surface receptor", @@ -715729,89 +716993,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.06.14.21258910", - "rel_title": "A Multi-center, Prospective, Observational-cohort controlled study of Clinical Outcomes following COVID-19 Convalescent plasma therapy in hospitalized COVID-19 patients", - "rel_date": "2021-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.14.21258910", - "rel_abs": "BackgroundThe SARS-CoV2 pandemic has caused high inpatient mortality and morbidity throughout the world. COVID19 convalescent plasma has been utilized as a potential therapy for patients hospitalized with COVID19 pneumonia. This study evaluated the outcomes of hospitalized COVID19 patients treated with COVID19 convalescent plasma in a prospective, observational multicenter trial.\n\nMethodsFrom April 2020 through August 2020, hospitalized COVID19 patients at 16 participating hospitals in Colorado were enrolled and treated with COVID19 convalescent plasma (CCP) and compared to hospitalized patients with COVID19 who were not treated with convalescent plasma. Plasma antibody levels were determined following the trial given that antibody tests were not approved at the initiation of the trial. CCP-treated and untreated COVID19 hospitalized patients were matched using propensity scores followed by analysis for length of hospitalization and inpatient mortality.\n\nResults542 total hospitalized COVID19 patients were enrolled at 16 hospitals across the region. A total of 468 hospitalized COVID19 patients were entered into propensity score matching with 188 patients matched for analysis in the CCP-treatment and control arms. Fine-Gray models revealed increased length of hospital stay in CCP-treated patients and no change in inpatient mortality compared to controls. In subgroup analysis of CCP-treated patients within 7 days of admission, there was no difference in length of hospitalization and inpatient mortality.\n\nConclusionsThese data show that treatment of hospitalized COVID19 patients with CCP did not significantly improve patient hospitalization length of stay or inpatient mortality.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Lakshmi Chauhan", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Jack Pattee", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Joshay Ford", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Chris Thomas", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Kelsey Lesteberg", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Eric Richards", - "author_inst": "University of Colorado Health System" - }, - { - "author_name": "Michele Loi", - "author_inst": "Children's Hospital Colorado" - }, - { - "author_name": "Larry J Dumont", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Kyle Annen", - "author_inst": "Children's Hospital Colorado" - }, - { - "author_name": "Mary Berg", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Mercedes Zirbes", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Amanda Miller", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Timothy C Jenkins", - "author_inst": "Denver Health Medical Center" - }, - { - "author_name": "Tellen D Bennett", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Daniel Monkowski", - "author_inst": "University of Colorado Health System" - }, - { - "author_name": "Rebecca S Boxer", - "author_inst": "Institute for Health Research, Kaiser Permanente of Colorado" - }, - { - "author_name": "J. David Beckham", - "author_inst": "University of Colorado Anschutz Medical Campus" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.14.21258855", "rel_title": "The Clinical Utility of Serial Procalcitonin and Procalcitonin Clearance in Predicting the Outcome of COVID-19 Patients", @@ -716067,6 +717248,57 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.06.18.448921", + "rel_title": "Identification of SGLT2 inhibitor Ertugliflozin as a treatment for COVID-19 using computational and experimental paradigm", + "rel_date": "2021-06-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.18.448921", + "rel_abs": "Drug repurposing can expedite the process of drug development by identifying known drugs which are effective against SARS-CoV-2. The RBD domain of SARS-CoV-2 Spike protein is a promising drug target due to its pivotal role in viral-host attachment. These specific structural domains can be targeted with small molecules or drug to disrupt the viral attachment to the host proteins. In this study, FDA approved Drugbank database were screened using a virtual screening approach and computational chemistry methods. Five drugs were short listed for further profiling based on docking score and binding energies. Further these selected drugs were tested for their in vitro biological activity. There was significant correlation between the prediction from computational studies and the actual RBD-ACE2 binding inhibition by the drugs. Then, we performed a series of studies that mimic some of the biological events seen in COVID-19 patients such as secretion of IL1{beta}, presentation of a more thrombogenic endothelium by production of thrombomodulin and accumulation of inflammatory cells such as monocytes in the lungs. Of all the drugs, most promising drug was Ertugliflozin which is used for type-2 diabetes. This drug possesses several desired properties and may be a good candidate for immediate repurposing for treatment of COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shalini Saxena", + "author_inst": "In Silico Discovery Research Academic Services (INDRAS) Pvt Ltd Tirumalanagar Moula Ali Hyderabad 500040 TS India" + }, + { + "author_name": "Kranti Meher", + "author_inst": "Reagene Innovations Pvt Ltd" + }, + { + "author_name": "Madhuri Rotella", + "author_inst": "Reagene Innovations Pvt Ltd" + }, + { + "author_name": "Subhramanayam Vangala", + "author_inst": "Reagene Innovations Pvt Ltd" + }, + { + "author_name": "Satish Chandran", + "author_inst": "Reagene Innovations Pvt Ltd" + }, + { + "author_name": "Nikhil Malhotra", + "author_inst": "TechMahindra Ltd" + }, + { + "author_name": "Ratnakar Palakodeti", + "author_inst": "Tech Mahindra Gateway Building, Apollo Bunder, Mumbai-400001, Maharashtra, India" + }, + { + "author_name": "Sreedhara Voleti", + "author_inst": "INDRAS Pvt. Ltd." + }, + { + "author_name": "Uday Saxena", + "author_inst": "Reagene" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.06.18.448939", "rel_title": "Probing Affinity, Avidity, Anti-Cooperativity, and Competition in Antibody and Receptor Binding to the SARS-CoV-2 Spike by Single Particle Mass Analyses", @@ -717487,25 +718719,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.17.448882", - "rel_title": "Post-Infection Entry Mechanism of Ricin A Chain-Pokeweed Antiviral Proteins (RTA-PAPs) Chimeras is Mediated by Viroporins", - "rel_date": "2021-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.17.448882", - "rel_abs": "The limitations of virus-specific antiviral drugs became apparent during the current COVID-19 pandemic. The search for broad range antiviral proteins of a new kind to answer current and future pandemics has become an even more pressing matter. Here, the author further describes the expected anti-SARS-CoV-2 mechanisms of a novel broad range antiviral chimeric protein constructed between ricin A chain and pokeweed antiviral proteins. The latest in protein-ligand docking software were used to determine binding affinity of RTA-PAPs to SARS-CoV-2 frameshift stimulation element and elucidate the preferential post-infection entry mechanisms of RTA-PAPs into virus infected cells over non-infected ones, by doing a comparative analysis between in vitro and in silico results on numerous viruses. The results obtained strongly suggest that the post-infection preferential entry of RTA-PAPs into infected cells is mediated by the presence of viroporins integrated into the host cell membrane. The discovery of this mechanism revealed RTA-PAPs, and proteins like them, to be a new class of broad range antivirals that target with high specificity viroporin producing viruses, and with gain of functions in antiviral activities, post-infection.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Yasser Hassan", - "author_inst": "Ophiuchus Medicine Inc." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "synthetic biology" - }, { "rel_doi": "10.1101/2021.06.17.448459", "rel_title": "Memory B cells control SARS-CoV-2 variants upon mRNA vaccination of naive and COVID-19 recovered individuals.", @@ -717957,6 +719170,169 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.14.21258567", + "rel_title": "Subcutaneous REGEN-COV Antibody Combination for Covid-19 Prevention", + "rel_date": "2021-06-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.14.21258567", + "rel_abs": "BackgroundCasirivimab and imdevimab (REGEN-COV) markedly reduces risk of hospitalization or death in high-risk individuals with Covid-19. Here we explore the possibility that subcutaneous REGEN-COV prevents SARS-CoV-2 infection and subsequent Covid-19 in individuals at high risk of contracting SARS-CoV-2 by close exposure in a household with a documented SARS-CoV-2-infected individual.\n\nMethodsIndividuals [≥]12 years were enrolled within 96 hours of a household contact being diagnosed with SARS-CoV-2 and randomized 1:1 to receive 1200 mg REGEN-COV or placebo via subcutaneous injection. The primary efficacy endpoint was the proportion of participants without evidence of infection (SARS-CoV-2 RT-qPCR- negative) or prior immunity (seronegative) who subsequently developed symptomatic SARS-CoV-2 infection during a 28-day efficacy assessment period.\n\nResultsSubcutaneous REGEN-COV significantly prevented symptomatic SARS-CoV-2 infection compared with placebo (81.4% risk reduction; 11/753 [1.5%] vs. 59/752 [7.8%], respectively; P<0.0001), with 92.6% risk reduction after the first week (2/753 [0.3%] vs. 27/752 [3.6%], respectively). REGEN-COV also prevented overall infections, either symptomatic or asymptomatic (66.4% risk reduction). Among infected participants, the median time to resolution of symptoms was 2 weeks shorter with REGEN-COV vs. placebo (1.2 vs. 3.2 weeks, respectively), and the duration of time with high viral load (>104 copies/mL) was lower (0.4 vs. 1.3 weeks, respectively). REGEN-COV was generally well tolerated.\n\nConclusionsAdministration of subcutaneous REGEN-COV prevented symptomatic Covid-19 and asymptomatic SARS-CoV-2 infection in uninfected household contacts of infected individuals. Among individuals who became infected, REGEN-COV reduced the duration of symptomatic disease, decreased maximal viral load, and reduced the duration of detectable virus.\n\n(ClinicalTrials.gov number, NCT04452318.)", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Meagan P O'Brien", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Eduardo Forleo Neto", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Bret J Musser", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Flonza Isa", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Kuo-Chen Chan", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Neena Sarkar", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Katharine J Bar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ruanne V Barnabas", + "author_inst": "University of Washington; Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Dan H Barouch", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School" + }, + { + "author_name": "Myron S Cohen", + "author_inst": "Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill" + }, + { + "author_name": "Christopher B Hurt", + "author_inst": "Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill" + }, + { + "author_name": "Dale R Burwen", + "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Mary A Marovich", + "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health" + }, + { + "author_name": "Peijie Hou", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Ingeborg Heirman", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "John D Davis", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Kenneth C Turner", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Divya Ramesh", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Adnan Mahmood", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Andrea T Hooper", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Jennifer D Hamilton", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Yunji Kim", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Lisa A Purcell", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Alina Baum", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Christos A Kyratsous", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "James Krainson", + "author_inst": "Clinical Trials of Florida, LLC" + }, + { + "author_name": "Richard Perez-Perez", + "author_inst": "Medical Research of Westchester" + }, + { + "author_name": "Rizwana Mohseni", + "author_inst": "Catalina Research Institute, LLC" + }, + { + "author_name": "Bari Kowal", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "A Thomas DiCioccio", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Neil Stahl", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Leah Lipsch", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Ned Braunstein", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "Gary Herman", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "George D Yancopoulos", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "David M Weinreich", + "author_inst": "Regeneron Pharmaceuticals, Inc." + }, + { + "author_name": "- the Covid-19 Phase 3 Prevention Trial Team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.12.448196", "rel_title": "Exposure route, sex, and age influence disease outcome in a golden Syrian hamster model of SARS-CoV-2 infection", @@ -720097,69 +721473,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2021.06.14.447967", - "rel_title": "Interferon-stimulated and metallothionein-expressing macrophages are associated with acute and chronic allograft dysfunction after lung transplantation", - "rel_date": "2021-06-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.14.447967", - "rel_abs": "Lung transplant (LT) recipients experience episodes of immune-mediated acute lung allograft dysfunction (ALAD). ALAD episodes are a risk factor for chronic lung allograft dysfunction (CLAD), the major cause of death after LT. We have applied single-cell RNA sequencing (scRNAseq) to bronchoalveolar lavage (BAL) cells from stable and ALAD patients and to cells from explanted CLAD lung tissue to determine key cellular elements in dysfunctional lung allografts, with a focus on macrophages. We identified two alveolar macrophage (AM) subsets uniquely represented in ALAD. Using pathway analysis and differentially expressed genes, we annotated these as pro-inflammatory interferon-stimulated gene (ISG) and metallothionein-mediated inflammatory (MT) AMs. Functional analysis of an independent set of AMs in vitro revealed that ALAD AMs exhibited a higher expression of CXCL10, a marker of ISG AMs, and increased secretion of pro-inflammatory cytokines compared to AMs from stable patients. Using publicly available BAL scRNAseq datasets, we found that ISG and MT AMs are associated with more severe inflammation in COVID-19 patients. Analysis of cells from four explanted CLAD lungs revealed similar macrophage populations. Using a single nucleotide variation calling algorithm, we also demonstrated contributions of donor and recipient cells to all AM subsets early post-transplant, with loss of donor-derived cells over time. Our data reveals extensive heterogeneity among lung macrophages after LT and indicates that specific sub-populations may be associated with allograft dysfunction, raising the possibility that these cells may represent important therapeutic targets.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sajad Moshkelgosha", - "author_inst": "UHN" - }, - { - "author_name": "Allen Duong", - "author_inst": "UHN" - }, - { - "author_name": "Gavin Wilson", - "author_inst": "UHN" - }, - { - "author_name": "Tallulah Andrews", - "author_inst": "UHN" - }, - { - "author_name": "Gregory Berra", - "author_inst": "UHN" - }, - { - "author_name": "Benjamin Renaud-Picard", - "author_inst": "UHN" - }, - { - "author_name": "Mingyao Liu", - "author_inst": "UHN" - }, - { - "author_name": "Shaf Keshavjee", - "author_inst": "UHN" - }, - { - "author_name": "Sonya MacParland", - "author_inst": "UHN" - }, - { - "author_name": "Jonathan Yeung", - "author_inst": "UHN" - }, - { - "author_name": "Tereza Martinu", - "author_inst": "UHN" - }, - { - "author_name": "Stephen C Juvet", - "author_inst": "University Health Network" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.14.448461", "rel_title": "Protective efficacy of rhesus adenovirus COVID-19 vaccines against mouse-adapted SARS-CoV-2", @@ -720386,6 +721699,77 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.06.14.448358", + "rel_title": "Multi-Dimensional Reduction Clustering of Complex Carbohydrates Reveal Tissue Metabolism, Heterogeneity and Histopathology", + "rel_date": "2021-06-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.14.448358", + "rel_abs": "Formalin-fixed paraffin-embedded (FFPE) human tissues represent the world's largest collection of accessible clinical specimens with matched, well-annotated clinical course for disease progression. Currently, FFPE sections are limited to low throughput histo- and immunological assessments. Extracting largescale molecular information remains a major technological barrier to uncover the vast potential within FFPE specimens for translation and clinical research. Two critical but understudied facets of glucose metabolism are anabolic pathways for glycogen and N-linked glycan biosynthesis. Together, these complex carbohydrates represent bioenergetics, protein-structure function, and tissue architecture in human biology. Herein, we report the high-dimensional Metabolomics-Assisted Digital pathology Imaging (Madi) workflow that combines matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) with machine learning for the comprehensive assessment of tissue heterogeneity, histopathology, and metabolism in human FFPE sections. In normal human tissue sections, Madi accurately identifies anatomical regions within liver and the brain. In human lung diseases, Madi accurately predicts major lung pathologies such as honeycomb change, late-stage fibrosis, diffuse alveolar damage (DAD), and acute fibrinous and organizing pneumonia (AFOP) from idiopathic pulmonary fibrosis (IPF) and COVID-19 pneumonia specimens with precision. In depth pathway enrichment analyses reveal unique metabolic pathways are associated with distinct pathological regions, which highlight aberrant complex carbohydrate metabolism as a previously unknown molecular event associated with disease progression that could hold key to future therapeutic interventions.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Lindsey R Conroy", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Derek B Allison", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Qi Sun", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Lyndsay EA Young", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Tara R Hawkinson", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Harrison A Clarke", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Juanita E Ferreira", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Autumn V Hammonds", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Robert J McDonald", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Kimberly J Absher", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Warren J Alilain", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Christopher M Waters", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Jinze Liu", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Ramon C Sun", + "author_inst": "University of Kentucky" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2021.06.14.448426", "rel_title": "Proinflammatory responses in SARS-CoV-2 infected and soluble spike glycoprotein S1 subunit activated human macrophages", @@ -721542,29 +722926,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.11.21258661", - "rel_title": "Grouping theory of epidemiology", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258661", - "rel_abs": "Background (traditional theory)there are general and principle models and calculation formulas for epidemics, mainly the basic reproduction number R0 of a certain epidemic disease such as COVID-19, the newly confirmed number Cn=Rn-1Cn-1, The threshold of herd immunity is (R0-1)/R0.\n\nInnovation theoryBased on the fact that there are groups of different tends (that is, different R0 or Rk), a grouping model of epidemiology is proposed, and a complete and detailed calculation formula is given. The basic relationship is that the overall infection numbers of is equal to the sum of the infection number of groups, namely: Rt={sum}(fkRk), where fk is the population proportion of each group, and Rk is the basic reproduction number of each groups. Its important application is the grouping strategy in which prevention and control measures are inclined to high-risk groups. The basic relationship is that the basic reproduction number of each group is equal to the product of the control coefficient of its measures and the original basic reproduction number, namely: Rk={zeta}kR0k. Compared with the traditional strategy of equal treatment, the grouping strategy has the characteristics of high efficiency, low consumption, and low threshold of herd immunity.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Chaohui Zhang", - "author_inst": "(Unaffiliated)" - }, - { - "author_name": "Wenyu Ling", - "author_inst": "(Unaffiliated)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.14.21258236", "rel_title": "Survey of COVID-19 associated symptoms and reported deaths in an urban community in Kano, Nigeria.", @@ -721724,6 +723085,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2021.06.11.21258778", + "rel_title": "Poor Readability of COVID-19 Vaccine Information for the General Public: A Lost Opportunity", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258778", + "rel_abs": "BackgroundAll adults in the Unites States now have access to COVID-19 vaccines. During the vaccination process, Emergency Use Authorization (EUA) fact sheets are provided.\n\nObjectiveTo analyze the ease of reading (i.e., readability) of the EUA-approved fact sheets for the vaccines currently available in the United States, the V-Safe adverse event survey script, and the Centers for Disease Control and Prevention (CDC) website on COVID-19 vaccines.\n\nDesignWe analyzed the readability of Pfizer, Moderna, and Janssen EUA fact sheets, as well as the V-Safe survey script and the vaccine-related information on the CDC website.\n\nMeasurementsReadability factors include the following: average length of paragraphs, sentences, and words; font size and style; use of passive voice; the Gunning-Fog index; the Flesch Reading Ease index; and the Flesch-Kincaid Grade Level index.\n\nResultsOnly the V-Safe adverse event survey script met readability standards for adequate comprehension. The mean readability scores of the EUA fact sheets and the CDC website were as follows: Flesch Reading Ease score (mean 44.35); Flesch-Kincaid Grade Level (mean 10.48); and Gunning-Fog index (mean 11.8). These scores indicate that a 10th-12th grade-level education is necessary to comprehend these documents.\n\nConclusionThe average person in the United States would have difficulty understanding the information provided in the EUA fact sheets and CDC COVID-19 vaccine website; however, the V-Safe survey was written at an appropriate reading level. To ensure that the public fully understands information regarding COVID-19 vaccines, simplified information material should be developed.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Luke S Buthun", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Scott Feeder", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Gregory A Poland", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.06.11.21258734", "rel_title": "Investigating the intention to receive the COVID-19 vaccination in Macao: implications for vaccination strategies", @@ -722905,89 +724293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.11.21258575", - "rel_title": "Support needs and barriers to accessing support: Baseline results of a mixed-methods national survey of people bereaved during the COVID-19 pandemic", - "rel_date": "2021-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258575", - "rel_abs": "BackgroundThe COVID-19 pandemic is a mass bereavement event which has profoundly disrupted grief experiences. Understanding support needs and access to support among people bereaved at this time is crucial to ensuring appropriate bereavement support infrastructure.\n\nAimTo investigate grief experiences, support needs and use of formal and informal bereavement support among people bereaved during the pandemic.\n\nDesignBaseline results from a longitudinal survey. Support needs and experiences of accessing support are reported using descriptive statistics and thematic analysis of free-text data.\n\nSetting/Participants711 adults bereaved in the UK between March-December 2020, recruited via media, social media, national associations and community/charitable organisations.\n\nResultsHigh-level needs for emotional support were identified. Most participants had not sought support from bereavement services (59%, n=422) or their GP (60%, n=428). Of participants who had sought such support, over half experienced difficulties accessing bereavement services (56%, n=149)/GP support (52%, n=135). 51% reported high/severe vulnerability in grief; among these, 74% were not accessing bereavement or mental-health services. Barriers included limited availability, lack of appropriate support, discomfort asking for help, and not knowing how to access services. 39% (n=279) experienced difficulties getting support from family/friends, including relational challenges, little face-to-face contact, and disrupted collective mourning. The perceived uniqueness of pandemic bereavement and wider societal strains exacerbated their isolation.\n\nConclusionsPeople bereaved during the pandemic have high levels of support needs alongside difficulties accessing support. We recommend increased provision and tailoring of bereavement services, improved information on support options, and social/educational initiatives to bolster informal support and ameliorate isolation.\n\nKey statementsO_ST_ABSWhat is already known about the topic?C_ST_ABS- Features of pandemic bereavement, such as traumatic death experiences, exacerbate family distress and add to the complexity of grief.\n- In pre-pandemic times most people mainly relied on the informal support of friends and family to cope with their bereavement, but an estimated 40% required more formal therapeutic support from bereavement or mental health services.\n- Bereaved people experience difficulties getting the support that they need from bereavement services and their social networks.\n\n\nWhat this paper adds- Participants had high level needs for emotional support, especially dealing with/expressing feelings, with 51% experiencing high or severe vulnerability in grief; however, 74% of this group were not accessing formal bereavement service or mental health support.\n- Most participants had not tried to access bereavement services, for reasons such as lack of appropriate support, discomfort in asking for help and uncertainty of how to access services; of the 41% who tried, 56% experienced difficulties such as long waiting lists or ineligibility.\n- A substantial proportion of people (39%) reported difficulties accessing support from friends and family; reduced in-person contact affected the perceived quality of support and disrupted collective mourning practices, whilst the wider social difficulties of the pandemic compounded feelings of isolation.\n\n\nImplications for policy and practice- Further investment in the provision of tailored bereavement support is needed to meet the diverse needs and backgrounds of bereaved people, including support that is culturally and crisis/context competent, and group-based support for those with shared experiences and characteristics.\n- To raise awareness of support options, information on grief and bereavement services should be provided proactively following a death and made available in online and community settings, with GPs and other primary care providers better resourced to signpost to appropriate support.\n- Following compassionate communities approaches, expanded provision of informal community-based support and activities could help with isolation, whilst longer-term educational and societal initiatives are needed to bolster community support for people experiencing death, dying and bereavement.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Emily J Harrop", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Silvia Goss", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Damian JJ Farnell", - "author_inst": "School of Dentistry, Cardiff University" - }, - { - "author_name": "Mirella Longo", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Anthony Byrne", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Kali Barawi", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Anna Torrens-Burton", - "author_inst": "PRIME Centre, Cardiff University" - }, - { - "author_name": "Annmarie Nelson", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Kathy Seddon", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Linda Machin", - "author_inst": "Keele University" - }, - { - "author_name": "Eileen Sutton", - "author_inst": "Palliative and End of Life Care Research Group, University of Bristol" - }, - { - "author_name": "Audrey Roulston", - "author_inst": "Queen's University Bristol" - }, - { - "author_name": "Anne Finucane", - "author_inst": "Clinical Psychology, School of Health in Social Science, University of Edinburgh" - }, - { - "author_name": "Alison Penny", - "author_inst": "National Bereavement Alliance" - }, - { - "author_name": "Kirsten V Smith", - "author_inst": "Centre for Anxiety Disorders and Trauma, Department of Experimental Psychology, University of Oxford" - }, - { - "author_name": "Stephanie Sivell", - "author_inst": "Marie Curie Palliative Care Research Centre, Cardiff University" - }, - { - "author_name": "Lucy E Selman", - "author_inst": "Palliative and End of Life Care Research Group, Population Health Sciences, Bristol Medical School, University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.14.448343", "rel_title": "COVID-eVax, an electroporated plasmid DNA vaccine candidate encoding the SARS-CoV-2 Receptor Binding Domain, elicits protective immune responses in animal models of COVID-19", @@ -723343,6 +724648,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.09.21258648", + "rel_title": "SARS-CoV-2-antibody response in health care workers after vaccination or natural infection in a longitudinal observational study", + "rel_date": "2021-06-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258648", + "rel_abs": "BackgroundFollowing a year of development, several vaccines have been approved to contain the global COVID-19 pandemic. Real world comparative data on immune response following vaccination or natural infection are rare.\n\nMethodsWe conducted a longitudinal observational study in employees at a secondary care hospital affected by the COVID-19 pandemic. Comparisons were made about the presence of anti-SARS-CoV-2 immunglobulin G (IgG) antibody ratio after natural infection, or vaccination with one or two doses of BioNTech/Pfizer (BNT162b2), or one dose of AstraZenca (Vaxzevria) vaccine.\n\nResultsWe found a 100% humoral response rate in participants after 2 doses of BNT162b2 vaccine. The antibody ratio in participants with one dose BNT162b2 and Vaxzevria did not differ significantly to those with previous PCR-confirmed infection, whereas this was significantly lower in comparison to two doses of BioNTech/Pfizer. We could not identify a correlation with previous comorbidities, obesity or age within this study. Smoking showed a negative effect on the antibody response (p=0.006)\n\nConclusionOur data provide an overview about humoral immune response after natural SARS-CoV-2 infection or following vaccination, and supports the usage of booster vaccinations, especially in patients after a natural SARS-CoV-2 infection.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jonas Herzberg", + "author_inst": "Department of Surgery - Krankenhaus Reinbek St. Adolf-Stift, Reinbek, Germany" + }, + { + "author_name": "Tanja Vollmer", + "author_inst": "Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW, Bad Oeynhausen, Ruhr University Bochum, Bochum, Germany" + }, + { + "author_name": "Bastian Fischer", + "author_inst": "Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW, Bad Oeynhausen, Ruhr University Bochum, Bochum, Germany" + }, + { + "author_name": "Heiko Becher", + "author_inst": "Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" + }, + { + "author_name": "Ann-Kristin Becker", + "author_inst": "Asklepios Klinik Harburg, Hamburg, Germany" + }, + { + "author_name": "Human Honarpisheh", + "author_inst": "Department of Surgery - Krankenhaus Reinbek St. Adolf-Stift, Reinbek, Germany" + }, + { + "author_name": "Salman Yousuf Guraya", + "author_inst": "Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates" + }, + { + "author_name": "Tim Strate", + "author_inst": "Department of Surgery - Krankenhaus Reinbek St. Adolf-Stift, Reinbek, Germany" + }, + { + "author_name": "Cornelius Knabbe", + "author_inst": "Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW, Bad Oeynhausen, Ruhr University Bochum, Bochum, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.10.21257898", "rel_title": "SARS-COV-2 VIRUS INFECTED PATIENT IDENTIFICATION THROUGH CANINE OLFACTIVE DETECTION ON AXILLARY SWEAT SAMPLES", @@ -724747,37 +726103,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.09.21258234", - "rel_title": "Personal space Increases during the COVID-19 Pandemic in Response to Real and Virtual Humans", - "rel_date": "2021-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258234", - "rel_abs": "Typically, people maintain a certain distance from others (\"personal space\") during daily life, in a largely automatic, unconscious manner. However during the COVID-19 pandemic, social distancing recommendations led to deliberate expansions of personal space outside of intimate social circles. In the laboratory, personal space preferences are quite stable over repeated measurements. Here, we collected such measurements both before and during the pandemic in the same individuals, using both conventional and virtual reality-based techniques. We found that the size of personal space, and discomfort ratings in response to personal space intrusions, increased significantly during the COVID-19 pandemic, in response to both real humans and virtual \"others\". Moreover, this increase in personal space requirements correlated with the perceived, not the actual, risk of being infected with COVID-19 - even in a virtual reality environment in which there was no possibility of infection. Thus, quantification of personal space may reveal some of the psychological effects of the pandemic, and subsequent progress towards recovery.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Daphne J Holt", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Sarah Zapetis", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Baktash Babadi", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Roger B.H. Tootell", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.08.21258525", "rel_title": "COVID19, Consumption and Inequality: A Systematic Analysis of Rural Population of India", @@ -724973,6 +726298,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2021.06.09.21258612", + "rel_title": "Second wave of COVID-19 in India could be predicted with genomic surveillance of SARS-CoV-2 variants coupled with epidemiological data: A tool for future", + "rel_date": "2021-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258612", + "rel_abs": "India recently witnessed a devastating second wave of COVID-19, which peaked by the end of the first week of May 2021. We aimed to understand formation and spread of the second wave in the country. We analyzed time series distribution of the genomic sequence data for SARS-CoV-2 and correlated that with the epidemiological data for new cases and deaths, for the corresponding period of the second wave. Further we analyzed the phylodynamics of the circulating SARS-CoV-2 variants in the Indian population in the period of study. Our analysis shows that the first indications of arrival of the second wave were observable by the end of January 2021, and by the end of March, 2021 it was clearly indicated. B.1.617 lineage variants drove the wave, particularly B.1.617.2 (a.k.a. delta variant). Based on the observations of this study, we propose that genomic surveillance of the SARS-CoV-2 variants augmented with epidemiological data can be a promising tool for forecasting imminent COVID-19 waves.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ashutosh Kumar", + "author_inst": "Department of Anatomy, All India Institute of Medical Sciences-Patna, Bihar, India" + }, + { + "author_name": "Adil Asghar", + "author_inst": "Department of Anatomy, All India Institute of Medical Sciences-Patna" + }, + { + "author_name": "Prakhar Dwivedi", + "author_inst": "All India Institute of Medical Sciences-Patna, Bihar, India" + }, + { + "author_name": "Gopichand Kumar", + "author_inst": "Department of Anatomy, All India Institute of Medical Sciences-Patna, Bihar, India" + }, + { + "author_name": "Ravi K. Narayan", + "author_inst": "Department of Anatomy, All India Institute of Medical Sciences-Patna, Bihar, India" + }, + { + "author_name": "Rakesh K. Jha", + "author_inst": "Department of Anatomy, All India Institute of Medical Sciences-Patna, Bihar, India" + }, + { + "author_name": "Rakesh Parashar", + "author_inst": "India Health Lead, Oxford Policy Management Limited, Oxford, UK" + }, + { + "author_name": "Chetan Sahni", + "author_inst": "Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University (BHU), Varanasi, India" + }, + { + "author_name": "Sada N. Pandey", + "author_inst": "Department of Zoology, Banaras Hindu University (BHU), Varanasi, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.09.21257915", "rel_title": "REGEN-COV Antibody Cocktail in Outpatients with Covid-19", @@ -726701,41 +728077,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.06.08.21258444", - "rel_title": "Does reactogenicity after a second injection of the BNT162b2 vaccine predict spike IgG antibody levels in healthy Japanese subjects?", - "rel_date": "2021-06-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258444", - "rel_abs": "Adverse reactions are more common after the second injection of messenger RNA vaccines such as Pfizer/BioNTechs BNT162b2. We hypothesized that the degree and severity of reactogenicity after the second injection reflects the magnitude of antibody production against the SARS CoV-2 virus spike protein (spike IgG). Blood samples were obtained from 67 healthy Japanese healthcare workers three weeks after the first injection and two weeks after the second injection of the BNT162b2 vaccine to measure spike IgG levels. Using questionnaires, we calculated an adverse event (AE) score (0-11) for each participant. The geometric mean of spike IgG titers increased from 1,047 antibody units (AU/mL) (95% CI: 855-1282 AU/mL) after the first injection to 17,378 AU/mL (14,622-20,663 AU/mL) after the second injection. The median AE score increased from 2 to 5. Spike IgG levels after the second injection were negatively correlated with age and positively correlated with spike IgG after the first injection. AE scores after the second injection were not significantly associated with log-transformed spike IgG after the second injection, when adjusted for age, sex, and log-transformed spike IgG after the first injection. Although the sample size was relatively small, reactogenicity after the second injection may not accurately reflect antibody production.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Masaaki Takeuchi", - "author_inst": "University of Occupational and Environmental Health" - }, - { - "author_name": "Yukie Higa", - "author_inst": "University of Occupational and Environmental Health" - }, - { - "author_name": "Akina Esaki", - "author_inst": "University of Occupational and Environmental Health" - }, - { - "author_name": "Yosuke Nabeshima", - "author_inst": "University of Occupational and Environmental Health" - }, - { - "author_name": "Akemi Nakazono", - "author_inst": "University of Occupational and Environmental Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.08.21258434", "rel_title": "The impact of COVID-19 pandemic on influenza transmission: molecular and epidemiological evidence", @@ -726971,6 +728312,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.06.07.21258484", + "rel_title": "A functionally distinct neutrophil landscape in severe COVID-19 reveals opportunities for adjunctive therapies", + "rel_date": "2021-06-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258484", + "rel_abs": "Acute respiratory distress syndrome (ARDS) is a life-threatening syndrome of respiratory failure and diffuse alveolar damage that results from dysregulated local and systemic immune activation, causing pulmonary vascular, parenchymal and alveolar damage. SARS-CoV-2 infection has become the dominant cause of ARDS worldwide, and emerging evidence implicates neutrophils and their cytotoxic arsenal of effector functions as central drivers of immune-mediated lung injury in COVID-19 ARDS. However, a key outstanding question is whether COVID-19 drives a unique program of neutrophil activation or effector functions that contributes to the severe pathogenesis of this pandemic illness, and whether this unique neutrophil response can be targeted to attenuate disease. Using a combination of high-dimensional single cell analysis and ex vivo functional assays of neutrophils from patients with COVID-19 ARDS compared to non-COVID ARDS (caused by bacterial pneumonia), we identified a functionally distinct landscape of neutrophil activation in COVID-19 ARDS that was intrinsically programmed during SARS-CoV-2 infection. Furthermore, neutrophils in COVID-19 ARDS were functionally primed to produce high amounts of neutrophil extracellular traps (NETs). Surprisingly, this unique pathological program of neutrophil priming escaped conventional therapy with dexamethasone, thereby revealing a promising target for adjunctive immunotherapy in severe COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Rachita Panda", + "author_inst": "University of Calgary" + }, + { + "author_name": "Fernanda Vargas E Silva Castanheira", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jared Schlechte", + "author_inst": "University of Calgary" + }, + { + "author_name": "Bas GJ Surewaard", + "author_inst": "University of Calgary" + }, + { + "author_name": "Hanjoo Brian Shim", + "author_inst": "University of Calgary" + }, + { + "author_name": "Amanda Z Zucoloto", + "author_inst": "University of Calgary" + }, + { + "author_name": "Zdenka Slavikova", + "author_inst": "University of Calgary" + }, + { + "author_name": "Bryan G Yipp", + "author_inst": "University of Calgary" + }, + { + "author_name": "Paul Kubes", + "author_inst": "University of Calgary" + }, + { + "author_name": "Braedon McDonald", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.06.07.21258492", "rel_title": "Evaluating the utility of high-resolution proximity metrics in predicting the spread of COVID-19", @@ -728635,61 +730031,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.07.21258520", - "rel_title": "Post-Acute COVID Syndrome, the Aftermath of Mild to Severe COVID-19 in Brazilian Patients", - "rel_date": "2021-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258520", - "rel_abs": "ObjectiveTo describe persistent symptoms after acute COVID-19 in different spectrum of disease severity in a population from an upper/middle income country, and identify the main clinical features impacting the quality of life.\n\nDesignCross-sectional study.\n\nSettingOutpatient clinic from a public post-COVID-19 health center (CPC) at Bahia-Brazil, a state where 80% are black or mixed race.\n\nParticipantsPatients admitted between August 2020 and February 2021 with symptoms at least one month after the onset of COVID-19.\n\nMain outcome measuresPACS and related disorders such as hospitalization one month or later after disease onset, biochemical dysregulation and reduced quality of life (EQ-5D-5L questionnaire).\n\nResultsAmong 683 individuals assisted at CPC in this period, 602 were recruited. Patients had average of 52 ({+/-}14.6) years, 355 (59%) were female, 528 (88%) black/brown. Individuals were classified as mild (39.9%), moderate (27.9%) or severe (32.2%) during acute illness if outpatient, hospitalized non-UCI or UCI, respectively. Most patients reported a polysymptomatic profile, in median eight (IQR=6-9) acute symptoms. The most frequent residual symptoms were dyspnea (66%), fatigue (62%) and chest pain (43%). Women were more affected regardless disease severity at acute stage: presented more residual symptoms [4 (2-6) vs 3 (2-4)] and a higher impact in quality of life. Altered HbA1c [(184/275 (66.9%)], high CRP levels [195/484 (40.3%)] and anemia [143/545 (26.2%)] were the most common abnormalities in laboratory exams. 76 patients presented HbA1c above 6.4% although only 42 referred previous diagnosis of diabetes mellitus. After one month of disease onset, 30 patients required hospitalization, including seven cases with mild acute illness. Hospital admission after acute disease was required on 30 patients, seven (23%) were mild. Quality of life had been affected for 357/404 (88.4%) patients according to EuroQoL (EQ-5D-5L), mainly the domains of anxiety/depression [severe or extreme anxiety for 79/401 (19.7%)] and pain/discomfort [severe or extreme pain for 71/403 (17.6%)]. The median EuroQoL Global Score was 70 [IQR 50-80]. PACS symptoms such as dyspnea, chest pain, and fatigue, was associated with decreased quality of life.\n\nConclusionsPACS, such as dyspnea, chest pain and fatigue, occurred after variable degree of disease severity. Among this majority black/mixed-race patients, woman seemed to be more affected. Other consequences included post-acute hospitalization, and abnormal glucose metabolism and reduced quality of life.\n\nSummary BoxSection 1: What is already known on this topic:\n\n{checkmark}Post-Acute COVID Syndrome (PACS) comprises a set of persistent or new-onset symptoms after illness onset.\n{checkmark}As far as we know, there are no studies describing PACS in a population principally black and mixed-race. Additionally, few studies have addressed PACS among outpatients.\n\n\nSection 2: What this study adds:\n\n{checkmark}Similar PACS were reported after mild, moderate and severe illness. Dyspnea, fatigue and chest pain were the most prevalent symptoms in this population presenting majority of black/mixed-race patients.\n{checkmark}Women presented more residual symptoms, a higher frequency of myalgia and worse score for mobility, usual activities, anxiety/depression, and pain.\n{checkmark}Hospitalization may occur one month or later after mild or moderate/severe acute infection due to respiratory and vascular disorders. Abnormal glucose metabolism was detected in the absence of previous diagnosis of diabetes mellitus.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ana Paula Andrade Barreto", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "Lucimeire Cardoso Duarte", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "Thiago Cerqueira-Silva", - "author_inst": "Instituto Gon\u00e7alo Moniz (Fiocruz-Bahia), Salvador, Brazil" - }, - { - "author_name": "Marcio Andrade Barreto Filho", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "Aquiles Camelier", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "Natalia Machado Tavares", - "author_inst": "Instituto Gon\u00e7alo Moniz (Fiocruz-Bahia), Salvador, Brazil" - }, - { - "author_name": "Manoel Barral-Netto", - "author_inst": "Instituto Gon\u00e7alo Moniz (Fiocruz-Bahia), Salvador, Brazil" - }, - { - "author_name": "Viviane Sampaio Boaventura", - "author_inst": "Instituto Gon\u00e7alo Moniz (Fiocruz-Bahia), Salvador, Brazil" - }, - { - "author_name": "Marcelo Chalhoub", - "author_inst": "Hospital Especializado Oct\u00e1vio Mangabeira (HEOM), Salvador, Brazil" - }, - { - "author_name": "- CPC Group Study", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.08.21258284", "rel_title": "Highly-specific memory B cells generation after the 2nd dose of BNT162b2 vaccine compensate for the decline of serum antibodies and absence of mucosal IgA", @@ -728981,6 +730322,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2021.06.06.21258442", + "rel_title": "Financial Meltdown in Swing Hospitals during the COVID-19 Outbreak", + "rel_date": "2021-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258442", + "rel_abs": "Hospitals in Japan have complete autonomy in deciding whether to admit COVID-19 patients, similar to that of the US. Taking this into account, we estimated the effect of admitting COVID-19 patients on hospital profits, using instrumental variable (IV) regression. Using IVs related to government intervention enabled us to not only estimate the effect of admitting COVID-19 patients among \"swing hospitals,\" where both options (to admit or to not admit COVID-19 patients) could potentially be realized but to also evaluate the effect of government intervention on such hospitals. Our empirical results revealed that monthly profits per bed decreased by approximately JPY 600,000 ({approx} USD 6,000) among swing hospitals, which is 15 times the average monthly profits in 2019. This overwhelming financial damage indicates that it would be costly for swing hospitals to treat COVID-19 patients because of their low suitability for admitting such patients. Given the implications of our main results, we propose an alternative strategy to handling surges in patients with new infectious diseases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Reo Takaku", + "author_inst": "Hitotsubashi University" + }, + { + "author_name": "Izumi Yokoyama", + "author_inst": "Hitotsubashi University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.06.06.21258429", "rel_title": "The importance of time post-vaccination in determining the decrease in vaccine efficacy against SARS-CoV-2 variants of concern", @@ -730677,93 +732041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.08.21258531", - "rel_title": "The UK Coronavirus Job Retention Scheme and changes in diet, physical activity and sleep during the COVID-19 pandemic: Evidence from eight longitudinal studies", - "rel_date": "2021-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258531", - "rel_abs": "BackgroundIn March 2020 the UK implemented the Coronavirus Job Retention Scheme (furlough) to minimize job losses. Our aim was to investigate associations between furlough and diet, physical activity, and sleep during the early stages of the COVID-19 pandemic.\n\nMethodsWe analysed data from 25,092 participants aged 16 to 66 years from eight UK longitudinal studies. Changes in employment (including being furloughed) were defined by comparing employment status pre- and during the first lockdown. Health behaviours included fruit and vegetable consumption, physical activity, and sleeping patterns. Study-specific estimates obtained using modified Poisson regression, adjusting for socio-demographic characteristics and pre-pandemic health and health behaviours, were statistically pooled using random effects meta-analysis. Associations were also stratified by sex, age, and education.\n\nResultsAcross studies, between 8 and 25% of participants were furloughed. Compared to those who remained working, furloughed workers were slightly less likely to be physically inactive (RR:0.85, [0.75-0.97], I2=59%) and did not differ in diet and sleep behaviours, although findings for sleep were heterogenous (I2=85%). In stratified analyses, furlough was associated with low fruit and vegetable consumption among males (RR=1.11; 95%CI: 1.01-1.22; I2: 0%) but not females (RR=0.84; 95%CI: 0.68-1.04; I2: 65%). Considering change in these health behaviours, furloughed workers were more likely than those who remained working to report increased fruit and vegetable consumption, exercise, and hours of sleep.\n\nConclusionsThose furloughed exhibited broadly similar levels of health behaviours to those who remained in employment during the initial stages of the pandemic. There was little evidence to suggest that such social protection policies if used in the post-pandemic recovery period and during future economic crises would have adverse impacts on population health behaviours.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Bozena Wielgoszewska", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Jane Maddock", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Michael J Green", - "author_inst": "MRC/CSO Social & Public Health Sciences Unit, University of Glasgow" - }, - { - "author_name": "Giorgio Di Gessa", - "author_inst": "Institute of Epidemiology and Health Care, University College London" - }, - { - "author_name": "Sam Parsons", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Gareth J Griffith", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Jazz Croft", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Anna J Stevenson", - "author_inst": "Centre for Genomic and Experimental Medicine, University of Edinburgh" - }, - { - "author_name": "Charlotte Booth", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Richard J Silverwood", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "David Bann", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Praveetha Patalay", - "author_inst": "UCL" - }, - { - "author_name": "Alun D Hughes", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Nishi Chaturvedi", - "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" - }, - { - "author_name": "Laura D Howe", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" - }, - { - "author_name": "Emla Fitzsimons", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - }, - { - "author_name": "Srinivasa Vittal Katikireddi", - "author_inst": "MRC/CSO Social & Public Health Sciences Unit, University of Glasgow" - }, - { - "author_name": "George B Ploubidis", - "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.07.446560", "rel_title": "Mapping Potential Antigenic Drift Sites (PADS) on SARS-CoV-2 Spike in Continuous Epitope-Paratope Space", @@ -731043,6 +732320,41 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2021.06.08.447224", + "rel_title": "Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome: A Resource for SARS-CoV-2 Research", + "rel_date": "2021-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.08.447224", + "rel_abs": "BackgroundThe coronavirus nonstructural protein 5 (Nsp5) is a cysteine protease required for processing the viral polyprotein and is therefore crucial for viral replication. Nsp5 from several coronaviruses have also been found to cleave host proteins, disrupting molecular pathways involved in innate immunity. Nsp5 from the recently emerged SARS-CoV-2 virus interacts with and can cleave human proteins, which may be relevant to the pathogenesis of COVID-19. Based on the continuing global pandemic, and emerging understanding of coronavirus Nsp5-human protein interactions, we set out to predict what human proteins are cleaved by the coronavirus Nsp5 protease using a bioinformatics approach.\n\nResultsUsing a previously developed neural network trained on coronavirus Nsp5 cleavage sites (NetCorona), we made predictions of Nsp5 cleavage sites in all human proteins. Structures of human proteins in the Protein Data Bank containing a predicted Nsp5 cleavage site were then examined, generating a list of 92 human proteins with a highly predicted and accessible cleavage site. Of those, 48 are expected to be found in the same cellular compartment as Nsp5. Analysis of this targeted list of proteins revealed molecular pathways susceptible to Nsp5 cleavage and therefore relevant to coronavirus infection, including pathways involved in mRNA processing, cytokine response, cytoskeleton organization, and apoptosis.\n\nConclusionsThis study combines predictions of Nsp5 cleavage sites in human proteins with protein structure information and protein network analysis. We predicted cleavage sites in proteins recently shown to be cleaved in vitro by SARS-CoV-2 Nsp5, and we discuss how other potentially cleaved proteins may be relevant to coronavirus mediated immune dysregulation. The data presented here will assist in the design of more targeted experiments, to determine the role of coronavirus Nsp5 cleavage of host proteins, which is relevant to understanding the molecular pathology of SARS-CoV-2 infection.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Benjamin M Scott", + "author_inst": "Concordia University" + }, + { + "author_name": "Vincent Lacasse", + "author_inst": "McGill University" + }, + { + "author_name": "Ditte G Blom", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Peter D Tonner", + "author_inst": "National Institute of Standards and Technology" + }, + { + "author_name": "Nikolaj S Blom", + "author_inst": "Technical University of Denmark" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.06.08.447588", "rel_title": "Targeting of Protein Kinase CK2 Elicits Antiviral Activity on Bovine Coronavirus Infection", @@ -732579,37 +733891,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.03.21258312", - "rel_title": "Outcomes of SARS-CoV-2 Infection in Patients with Chronic Liver Disease and Cirrhosis: a N3C Study", - "rel_date": "2021-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258312", - "rel_abs": "Background and AimsIn patients with chronic liver diseases (CLD) with or without cirrhosis, existing data on the risk of adverse outcomes with SARS-CoV-2 infection have been mixed or have limited generalizability. We used the National COVID Cohort Collaborative (N3C) Data Enclave, a harmonized electronic health record (EHR) dataset of 5.9 million nationally-representative, diverse, and gender-balanced patients, to describe outcomes in patients with CLD and cirrhosis with SARS-CoV-2.\n\nMethodsWe identified all chronic liver diseases patients with and without cirrhosis who had SARS-CoV-2 testing documented in the N3C Data Enclave as of data release date 5/15/2021. The primary outcome was 30-day all-cause mortality. Survival analysis methods were used to estimate cumulative incidences of death, hospitalization, and mechanical ventilation, and to calculate the associations of SARS-CoV-2 infection, presence of cirrhosis, and demographic and clinical factors to 30-day mortality.\n\nResultsWe isolated 217,143 patients with CLD: 129,097 (59%) without cirrhosis and SARS-CoV-2 negative, 25,844 (12%) without cirrhosis and SARS-CoV-2 positive, 54,065 (25%) with cirrhosis and SARS-CoV-2 negative, and 8,137 (4%) with cirrhosis and SARS-CoV-2 positive. Among CLD patients without cirrhosis, 30-day all-cause mortality rates were 0.4% in SARS-CoV-2 negative patients and 1.8% in positive patients. Among CLD patients with cirrhosis, 30-day all-cause mortality rates were 4.0% in SARS-CoV-2 negative patients and 9.7% in positive patients.\n\nCompared to those who tested SARS-CoV-2 negative, SARS-CoV-2 positivity was associated with more than two-fold (aHR 2.43, 95% CI 2.23-2.64) hazard of death at 30 days among patients with cirrhosis. Compared to patients without cirrhosis, the presence of cirrhosis was associated with a three-fold (aHR 3.39, 95% CI 2.96-3.89) hazard of death at 30 days among patients who tested SARS-CoV-2 positive. Age (aHR 1.03 per year, 95% CI 1.03-1.04) was associated with death at 30 days among patients with cirrhosis who were SARS-CoV-2 positive.\n\nConclusionsIn this study of nearly 220,000 CLD patients, we found SARS-CoV-2 infection in patients with cirrhosis was associated with 2.43-times mortality hazard, and the presence of cirrhosis among CLD patients infected with SARS-CoV-2 were associated with 3.39-times mortality hazard. Compared to previous studies, our use of a nationally-representative, diverse, and gender-balanced dataset enables wide generalizability of these findings.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jin Ge", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mark J. Pletcher", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jennifer C Lai", - "author_inst": "UCSF" - }, - { - "author_name": "- N3C Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2021.06.07.447287", "rel_title": "A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses", @@ -732945,6 +734226,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.06.07.447321", + "rel_title": "E156/G and Arg158, Phe-157/del mutation in NTD of spike protein in B.1.167.2 lineage of SARS-CoV-2 leads to immune evasion through antibody escape", + "rel_date": "2021-06-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.07.447321", + "rel_abs": "Emerging variants of SARS-CoV-2 with better immune escape mechanisms and higher transmissibility remains a persistent threat across the globe. B.1.617.2 (Delta) variant was first emerged from Maharashtra, India in December, 2020. This variant is classified to be a major cause and concern of the second wave of COVID-19 in India. In the present study, we explored the genomic and structural basis of this variant through computational analysis, protein modelling and molecular dynamics (MD) simulations approach. B.1.617.2 variant carried E156G and Arg158, Phe-157/del mutations in NTD of spike protein. These mutations in N-terminal domain (NTD) of spike protein of B.1.617.2 variant revealed more rigidity and reduced flexibility compared to spike protein of Wuhan isolate. Further, docking and MD simulation study with 4A8 monoclonal antibody which was reported to bind NTD of spike protein suggested reduced binding of B.1.617.2 spike protein compared to that of spike protein of Wuhan isolate. The results of the present study demonstrate the possible case of immune escape and thereby fitness advantage of the new variant and further warrants demonstration through experimental evidence. Our study identified the probable mechanism through which B.1.617.2 variant is more pathogenically evolved with higher transmissibility as compared to the wild-type.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC=\"FIGDIR/small/447321v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (23K):\norg.highwire.dtl.DTLVardef@b92cborg.highwire.dtl.DTLVardef@1d261f7org.highwire.dtl.DTLVardef@11da73eorg.highwire.dtl.DTLVardef@1cef6ca_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Armi Chaudhari", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Dinesh Kumar", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Madhvi Joshi", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Amrutlal Patel", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Chaitanya Joshi", + "author_inst": "Gujarat Biotechnology Research Centre" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2021.06.07.447389", "rel_title": "Evolutionary velocity with protein language models", @@ -734325,33 +735641,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.02.21258221", - "rel_title": "Classifying Texas counties using ARIMA Models on COVID-19 daily confirmed cases: the impact of political affiliation and face covering orders", - "rel_date": "2021-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21258221", - "rel_abs": "The aim of this paper is to investigate whether the 254 Texas counties in the United States can be grouped in a meaningful way according to the characteristics of the ARIMA or seasonal ARIMA models fitting the logarithm of daily confirmed cases of the Coronavirus Disease 2019 (COVID-19) for 254 counties in Texas of the United States. We analyze clusters of the models non-seasonal parameters (p, d, q), distinguishing between county-level political affiliations and face covering orders, and also consider county-level population and poverty rate. Using data from March 4, 2020 to March 15, 2021, we find that 223 of the total 254 counties are clustered into 23 model parameters (p, d, q), while the number of cases in the remaining 31 counties could not be successfully fitted to ARIMA models. We also find the impact of the county-level infection rate and the county-level poverty rate on clusters of counties with different political affiliations and face covering orders. Further, we find that the infection rate and the poverty rate had a significant high positive correlation, and Democrat-leaning counties, which tend to have large populations, had a higher correlation coefficient between infection rate and poverty rate. We also observe a significant high positive correlation between the infection rate and the number of cumulative cases in Republican counties that had not imposed a face covering order.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hao Jiang", - "author_inst": "Southern Methodist University" - }, - { - "author_name": "Brigitta Pulins", - "author_inst": "Southern Methodist University" - }, - { - "author_name": "Aurelie Thiele", - "author_inst": "Southern Methodist University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.02.21258257", "rel_title": "Efficacy of clarithromycin on COVID-19 pneumonia without oxygen administration; protocol for multicenter, open-label, randomized-controlled, 3-armed parallel group comparison, exploratory trial (CAME COVID study)", @@ -734543,6 +735832,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.02.21258229", + "rel_title": "Vaccine nationalism and the dynamics and control of SARS-CoV-2", + "rel_date": "2021-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21258229", + "rel_abs": "Vaccines provide powerful tools to mitigate the enormous public health and economic costs that the ongoing SARS-CoV-2 pandemic continues to exert globally, yet vaccine distribution remains unequal between countries. To examine the potential epidemiological and evolutionary impacts of vaccine nationalism, we extend previous models to include simple scenarios of stockpiling. In general, we find that stockpiling vaccines by countries with high availability leads to large increases in infections in countries with low vaccine availability, the magnitude of which depends on the strength and duration of natural and vaccinal immunity. Additionally, a number of subtleties arise when the populations and transmission rates in each country differ depending on evolutionary assumptions and vaccine availability. Furthermore, the movement of infected individuals between countries combined with the possibility of increases in viral transmissibility may greatly magnify local and combined infection numbers, suggesting that countries with high vaccine availability must invest in surveillance strategies to prevent case importation. Dose-sharing is likely a high-return strategy because equitable allocation brings non-linear benefits and also alleviates costs of surveillance (e.g. border testing, genomic surveillance) in settings where doses are sufficient to maintain cases at low numbers. Across a range of immunological scenarios, we find that vaccine sharing is also a powerful tool to decrease the potential for antigenic evolution, especially if infections after the waning of natural immunity contribute most to evolutionary potential. Overall, our results stress the importance of equitable global vaccine distribution.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Caroline E Wagner", + "author_inst": "McGill University" + }, + { + "author_name": "Chadi M. Saad-Roy", + "author_inst": "Princeton University" + }, + { + "author_name": "Sinead E. Morris", + "author_inst": "Columbia University" + }, + { + "author_name": "Rachel E. Baker", + "author_inst": "Princeton University" + }, + { + "author_name": "Michael J Mina", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Jeremy Farrar", + "author_inst": "The Wellcome Trust" + }, + { + "author_name": "Edward C Holmes", + "author_inst": "University of Sydney" + }, + { + "author_name": "Oliver G. Pybus", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrea L. Graham", + "author_inst": "Princeton University" + }, + { + "author_name": "Ezekiel J. Emanuel", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Simon A. Levin", + "author_inst": "Princeton University" + }, + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Princeton University" + }, + { + "author_name": "Bryan T. Grenfell", + "author_inst": "Princeton University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.03.21258241", "rel_title": "Multisystemic cellular tropism of SARS-CoV-2 in autopsies of COVID-19 patients", @@ -735787,89 +737143,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.04.21258316", - "rel_title": "A Prospective Observational Study to Investigate Performance of a Chest X-ray Artificial Intelligence Diagnostic Support Tool Across 12 U.S. Hospitals", - "rel_date": "2021-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.04.21258316", - "rel_abs": "ImportanceAn artificial intelligence (AI)-based model to predict COVID-19 likelihood from chest x-ray (CXR) findings can serve as an important adjunct to accelerate immediate clinical decision making and improve clinical decision making. Despite significant efforts, many limitations and biases exist in previously developed AI diagnostic models for COVID-19. Utilizing a large set of local and international CXR images, we developed an AI model with high performance on temporal and external validation.\n\nObjectiveInvestigate real-time performance of an AI-enabled COVID-19 diagnostic support system across a 12-hospital system.\n\nDesignProspective observational study.\n\nSettingLabeled frontal CXR images (samples of COVID-19 and non-COVID-19) from the M Health Fairview (Minnesota, USA), Valencian Region Medical ImageBank (Spain), MIMIC-CXR, Open-I 2013 Chest X-ray Collection, GitHub COVID-19 Image Data Collection (International), Indiana University (Indiana, USA), and Emory University (Georgia, USA)\n\nParticipantsInternal (training, temporal, and real-time validation): 51,592 CXRs; Public: 27,424 CXRs; External (Indiana University): 10,002 CXRs; External (Emory University): 2002 CXRs\n\nMain Outcome and MeasureModel performance assessed via receiver operating characteristic (ROC), Precision-Recall curves, and F1 score.\n\nResultsPatients that were COVID-19 positive had significantly higher COVID-19 Diagnostic Scores (median .1 [IQR: 0.0-0.8] vs median 0.0 [IQR: 0.0-0.1], p < 0.001) than patients that were COVID-19 negative. Pre-implementation the AI-model performed well on temporal validation (AUROC 0.8) and external validation (AUROC 0.76 at Indiana U, AUROC 0.72 at Emory U). The model was noted to have unrealistic performance (AUROC > 0.95) using publicly available databases. Real-time model performance was unchanged over 19 weeks of implementation (AUROC 0.70). On subgroup analysis, the model had improved discrimination for patients with \"severe\" as compared to \"mild or moderate\" disease, p < 0.001. Model performance was highest in Asians and lowest in whites and similar between males and females.\n\nConclusions and RelevanceAI-based diagnostic tools may serve as an adjunct, but not replacement, for clinical decision support of COVID-19 diagnosis, which largely hinges on exposure history, signs, and symptoms. While AI-based tools have not yet reached full diagnostic potential in COVID-19, they may still offer valuable information to clinicians taken into consideration along with clinical signs and symptoms.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ju Sun", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Le Peng", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Taihui Li", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Dyah Adila", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Zach Zaiman", - "author_inst": "Emory University" - }, - { - "author_name": "Genevieve Melton", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Nicholas E Ingraham", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Eric Murray", - "author_inst": "M Health Fairview" - }, - { - "author_name": "Daniel Boley", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Sean Switzer", - "author_inst": "University of Minnesota" - }, - { - "author_name": "John L Burns", - "author_inst": "Indiana University" - }, - { - "author_name": "Kun Huang", - "author_inst": "Indiana University" - }, - { - "author_name": "Tadashi Allen", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Scott D Steenburg", - "author_inst": "Indiana University" - }, - { - "author_name": "Judy Wawira Gichoya", - "author_inst": "Emory University" - }, - { - "author_name": "Erich Kummerfeld", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Christopher J Tignanelli", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.06.03.21258240", "rel_title": "Aggregating probabilistic predictions of the safety, efficacy, and timing of a COVID-19 vaccine", @@ -736145,6 +737418,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.02.21258184", + "rel_title": "Passively Sensing SARS-CoV-2 RNA in Public Transit Buses", + "rel_date": "2021-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21258184", + "rel_abs": "Affordably tracking the transmission of respiratory infectious diseases in urban transport infrastructures can inform individuals about potential exposure to diseases and guide public policymakers to prepare timely responses based on geographical transmission in different areas in the city. Towards that end, we designed and tested a method to detect SARS-CoV-2 RNA in the air filters of public buses, revealing that air filters could be used as passive fabric sensors for the detection of viral presence. We placed and retrieved filters in the existing HVAC systems of public buses to test for the presence of trapped SARS-CoV-2 RNA using phenol-chloroform extraction and RT-qPCR. SARS-CoV-2 RNA was detected in 14% (5/37) of public bus filters tested in Seattle, Washington, from August 2020 to March 2021. These results indicate that this sensing system is feasible and that, if scaled, this method could provide a unique lens into the geographically relevant transmission of SARS-CoV-2 through public transit rider vectors, pooling samples of riders over time in a passive manner without installing any additional systems on transit vehicles.\n\nSynopsisPassive sensing of viral presence on urban transit infrastructure is proven, with forward-looking benefits for tracking pandemic spread.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jason S Hoffman", + "author_inst": "University of Washington" + }, + { + "author_name": "Matthew Hirano", + "author_inst": "University of Washington" + }, + { + "author_name": "Nuttada Panpradist", + "author_inst": "University of Washington" + }, + { + "author_name": "Joseph Breda", + "author_inst": "University of Washington" + }, + { + "author_name": "Parker Ruth", + "author_inst": "University of Washington" + }, + { + "author_name": "Yuanyi Xu", + "author_inst": "University of Washington" + }, + { + "author_name": "Jonathan Lester", + "author_inst": "Microsoft Research" + }, + { + "author_name": "Bichlien Nguyen", + "author_inst": "Microsoft Research" + }, + { + "author_name": "Luis Ceze", + "author_inst": "University of Washington" + }, + { + "author_name": "Shwetak N Patel", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.06.02.21258242", "rel_title": "Antibody Response after Second-dose of ChAdOx1-nCOV (CovishieldTM) and BBV-152 (CovaxinTM) among Health Care Workers in India: Final Results of Cross-sectional Coronavirus Vaccine-induced Antibody Titre (COVAT) study", @@ -737829,69 +739157,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.05.31.21258129", - "rel_title": "Physical integrity of medical exam gloves with repeated applications of disinfecting agents: evidence for extended use", - "rel_date": "2021-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.31.21258129", - "rel_abs": "BackgroundThe COVID-19 pandemic has created global shortages of personal protective equipment (PPE) such as medical exam gloves, forcing healthcare workers to either forgo or reuse PPE to keep themselves and patients safe from infection. In severely resource-constrained situations, limited cycles of disinfection and extended use of gloves is recommended by the U.S. Centers for Disease Control and Prevention (CDC) to conserve supplies. However, these guidelines are based on limited evidence.\n\nMethodsSerial cycles of hand hygiene were performed on gloved hands using alcohol-based hand rub (ABHR) (six and ten cycles), 0.1% sodium hypochlorite (bleach) solution (ten cycles), or soap and water (ten cycles) on three types of latex and three types of nitrile medical exam gloves, purchased in the United States and India. A modified FDA-approved water-leak test was performed to evaluate glove integrity after repeated applications of these disinfecting agents. 80 gloves per disinfectant-glove type combination were tested. Within each glove type the proportion of gloves that failed the water-leak test for each disinfectant was compared to that of the control using a non-inferiority design with a non-inferiority margin of five percentage points. Results were also aggregated by glove material, and combined for overall results.\n\nFindingsWhen aggregated by glove material, the dilute bleach exposure demonstrated the lowest difference in proportion failed between treatment and control arms: -2.5 percentage points (95% CI: -5.3 to 0.3) for nitrile, 0.6 percentage points (95% CI: -2.6 to 3.8) for non-powdered latex. For US-purchased gloves tested with six and ten applications of ABHR, the mean difference in failure risk between treatment and control gloves was within the prespecified non-inferiority margin of five percentage points or less, though some findings were inconclusive because confidence intervals extended beyond the non-inferiority margin. The aggregated difference in failure risk between treatment and control gloves was 3.5 percentage points (0.6 to 6.4) for soap and water, and 2.3 percentage points (-0.5 to 5.0) and 5.0 percentage points (1.8 to 8.2) for 10 and 6 applications of ABHR, respectively. The majority of leaks occurred in the interdigital webs (35%) and on the fingers (34%).\n\nConclusionCurrent guidelines do not recommend extended use of a single-use PPE under normal supply conditions. However, our findings indicate that some combinations of glove types and disinfection methods may allow for extended use under crisis conditions. We found that ten applications of dilute bleach solution have the least impact on glove integrity, compared to repeated applications of ABHR and soap and water. However, the majority of glove and exposure combinations were inconclusive with respect to non-inferiority with a 5 percentage point non-inferiority margin. Testing specific glove and disinfectant combinations may be worthwhile for settings facing glove shortages during which extended use is necessary. The modified water-leak testing method used here is a low-resource method that could easily be reproduced in different contexts.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Jared S Shless", - "author_inst": "Department of Bioengineering, College of Engineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, CA 94720" - }, - { - "author_name": "Yoshika S Crider", - "author_inst": "Energy and Resources Group, University of California, Berkeley, 345 Giannini Hall, Berkeley, CA 94720" - }, - { - "author_name": "Helen O Pitchik", - "author_inst": "Division of Epidemiology, School of Public Health, University of California, Berkeley, 2121 Berkeley Way, Berkeley, CA 4720" - }, - { - "author_name": "Alliya S Qazi", - "author_inst": "Department of Surgery, University of California, Irvine School of Medicine, 333 City West Blvd., Suite 1600, Orange, CA 92868" - }, - { - "author_name": "Ashley Styczynski", - "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Lane 134, Palo Alto, CA 94305" - }, - { - "author_name": "Roger LeMesurier", - "author_inst": "Independent researcher, San Francisco, CA 94110" - }, - { - "author_name": "Daniel Haik", - "author_inst": "Department of Surgery, University of California, Irvine School of Medicine, 333 City West Blvd., Suite 1600, Orange, CA 92868" - }, - { - "author_name": "Laura H Kwong", - "author_inst": "Stanford University, Woods Institute for the Environment, 473 Via Ortega, Palo Alto, CA 94305" - }, - { - "author_name": "Christopher Leboa", - "author_inst": "Stanford University, Woods Institute for the Environment, 473 Via Ortega, Palo Alto, CA 94305" - }, - { - "author_name": "Arnab Bhattacharya", - "author_inst": "Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, India 400005" - }, - { - "author_name": "Youssef K Hamidi", - "author_inst": "Mechanical Engineering Program, College of Science and Engineering, University of Houston-Clear Lake, Houston, TX 77058" - }, - { - "author_name": "Robert N Phalen", - "author_inst": "Occupational Safety and Health Program, College of Science and Engineering, University of Houston-Clear Lake, Houston, TX 77058" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.01.21258147", "rel_title": "Minimum manufacturing costs, national prices and estimated global availability of new repurposed therapies for COVID-19.", @@ -738211,6 +739476,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.02.446468", + "rel_title": "Pathogenic neutrophilia drives acute respiratory distress syndrome in severe COVID-19 patients", + "rel_date": "2021-06-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.02.446468", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing COVID-19 pandemic have caused [~]40 million cases and over 648,000 deaths in the United States alone. Troubling disparities in COVID-19-associated mortality emerged early, with nearly 70% of deaths confined to Black/African-American (AA) patients in some areas, yet targeted studies within this demographic are scant. Multi-omics single-cell analyses of immune profiles from airways and matching blood samples of Black/AA patients revealed low viral load, yet pronounced and persistent pulmonary neutrophilia with advanced features of cytokine release syndrome and acute respiratory distress syndrome (ARDS), including exacerbated production of IL-8, IL-1{beta}, IL-6, and CCL3/4 along with elevated levels of neutrophil elastase and myeloperoxidase. Circulating S100A12+/IFITM2+ mature neutrophils are recruited via the IL-8/CXCR2 axis, which emerges as a potential therapeutic target to reduce pathogenic neutrophilia and constrain ARDS in severe COVID-19.\n\nGraphical AbstractThe lung pathology due to severe COVID-19 is marked by a perpetual pathogenic neutrophilia, leading to acute respiratory distress syndrome (ARDS) even in the absence of viral burden. Circulating mature neutrophils are recruited to the airways via IL-8 (CXCL8)/CXCR2 chemotaxis. Recently migrated neutrophils further differentiate into a transcriptionally active and hyperinflammatory state, with an exacerbated expression of IL-8 (CXCL8), IL-1{beta} (IL1B), CCL3, CCL4, neutrophil elastase (NE), and myeloperoxidase (MPO) activity. Airway neutrophils and recruited inflammatory monocytes further increase their production of IL-8 (CXCL8), perpetuating lung neutrophilia in a feedforward loop. MdCs and T cells produce IL-1{beta} and TNF, driving neutrophils reprogramming and survival.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC=\"FIGDIR/small/446468v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (43K):\norg.highwire.dtl.DTLVardef@81fd3aorg.highwire.dtl.DTLVardef@181e63org.highwire.dtl.DTLVardef@172fedcorg.highwire.dtl.DTLVardef@ba55a7_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Devon J. Eddins", + "author_inst": "Emory University" + }, + { + "author_name": "Junkai Yang", + "author_inst": "Emory University" + }, + { + "author_name": "Astrid Kosters", + "author_inst": "Emory University" + }, + { + "author_name": "Vincent Giacalone", + "author_inst": "Emory University" + }, + { + "author_name": "Ximo Pechuan", + "author_inst": "Genentech Inc." + }, + { + "author_name": "Joshua D. Chandler", + "author_inst": "Emory University" + }, + { + "author_name": "Jinyoung Eum", + "author_inst": "Emory University" + }, + { + "author_name": "Benjamin R. Babcock", + "author_inst": "Emory University" + }, + { + "author_name": "Brian S. Dobosh", + "author_inst": "Emory University" + }, + { + "author_name": "Mindy R. Hernandez", + "author_inst": "Emory University" + }, + { + "author_name": "Fathma Abdulkhader", + "author_inst": "Emory University" + }, + { + "author_name": "Genoah L. Collins", + "author_inst": "Emory University" + }, + { + "author_name": "Richard P. Ramonell", + "author_inst": "Emory University" + }, + { + "author_name": "Christine Moussion", + "author_inst": "Genentech Inc." + }, + { + "author_name": "Darya Orlova", + "author_inst": "Genentech Inc." + }, + { + "author_name": "Ignacio Sanz", + "author_inst": "Emory University" + }, + { + "author_name": "Frances Eun-Hyung Lee", + "author_inst": "Emory University" + }, + { + "author_name": "Rabindra Tirouvanziam", + "author_inst": "Emory University" + }, + { + "author_name": "Eliver Ghosn", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.06.03.446959", "rel_title": "The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner", @@ -739779,129 +741135,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.26.21257063", - "rel_title": "Evaluation of the INDICAID COVID-19 Rapid Antigen Test in symptomatic populations and asymptomatic community testing", - "rel_date": "2021-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257063", - "rel_abs": "BackgroundAs the COVID-19 pandemic continues to cause substantial morbidity and mortality, there is an increased need for rapid, accessible assays for SARS-CoV-2 detection.\n\nMethodsHere we present a clinical evaluation and real-world implementation of the INDICAID COVID-19 Rapid Antigen Test (INDICAID Rapid Test). A multi-site clinical evaluation of the INDICAID Rapid Test using prospectively collected samples from symptomatic subjects was performed. The INDICAID Rapid Test was then implemented at COVID-19 outbreak screening centers in Hong Kong to screen individuals for COVID-19 to prioritize confirmatory RT-PCR testing among asymptomatic populations.\n\nResultsThe clinical evaluation in symptomatic patient populations demonstrated a positive percent agreement and negative percent agreement of 85.3% (95% confidence interval [95% CI]: 75.6% - 91.6%) and 94.9% (95% CI: 91.6% - 96.9%), respectively, when compared to laboratory-based RT-PCR testing. When used during outbreak testing of 22,994 asymptomatic patients, the INDICAID Rapid Test demonstrated a positive percent agreement of 84.2% (95% CI: 69.6% - 92.6%) and a negative percent agreement of 99.9% (95% CI: 99.9% - 100%) compared to laboratory-based RT-PCR testing. When incorporated in a testing algorithm, the INDICAID Rapid Test reduced time to confirmatory positive result from an average 10.85 hours (standard RT-PCR only) to 0.84 hours, depending on the algorithm.\n\nConclusionThe INDICAID Rapid Test has excellent performance when compared to laboratory-based RT-PCR testing, and when used in tandem with RT-PCR, reduces the time to confirmatory positive result.\n\nSummaryIn clinical evaluations, the INDICAID COVID-19 Rapid Antigen Test demonstrated high sensitivity and specificity in symptomatic and asymptomatic patient populations. When used in tandem with RT-PCR testing, the INDICAID Rapid Test expedited confirmatory results and may help reduce SARS-CoV-2 outbreaks.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Ricky Chiu", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Noah Kojima", - "author_inst": "UCLA" - }, - { - "author_name": "Garrett Mosley", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Kwok Kin Cheng", - "author_inst": "Phase Scientific" - }, - { - "author_name": "David Pereira", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Matthew Brobeck", - "author_inst": "Contractor" - }, - { - "author_name": "Tsun Leung Chan", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Jonpaul Sze-Tsing Zee", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Harsha Kittur", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Tenny Chung", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Eric Tsang", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Kajal Maran", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Raymond Wai-Hung Yung", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Alex Chin-Pang Leung", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Ryan Siu", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Jessica Ng", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Tsz Hei Choi", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Mei Wai Fung", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Sean Parkin", - "author_inst": "CityHealth Urgent Care" - }, - { - "author_name": "Wai Sing Chan", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Ho Yin Lam", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Koon Kung Lee", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Felix C Chao", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Stephen Ka-Kung Ho", - "author_inst": "Contractor" - }, - { - "author_name": "Dan MArshak", - "author_inst": "Phase Scientific" - }, - { - "author_name": "Edmond Shiu-Kwan Ma", - "author_inst": "Hong Kong Sanatorium and Hospital" - }, - { - "author_name": "Jeffrey D Klausner", - "author_inst": "USC School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.01.21258124", "rel_title": "Regular testing of asymptomatic healthcare workers identifies cost-efficient SARS-CoV-2 preventive measures", @@ -740125,6 +741358,25 @@ "type": "new results", "category": "cancer biology" }, + { + "rel_doi": "10.1101/2021.05.27.21257908", + "rel_title": "Policy and Effectiveness of Covid-19 Response", + "rel_date": "2021-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257908", + "rel_abs": "A comparative analysis of selected national jurisdictions with respect to Covid-19 policy response indicated that factors such as effective communications and effective targeted intervention in the environments of higher epidemiological risk can be the key factors in the overall effectiveness of the epidemiological response minimizing both the impact of the epidemics and disruptions in the life of the society.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Serge Dolgikh", + "author_inst": "National Aviation University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.27.21257929", "rel_title": "Impact of vaccination and undetected cases on the COVID-19 pandemic dynamics in Qatar in 2021", @@ -741529,81 +742781,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.29.21257760", - "rel_title": "Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec", - "rel_date": "2021-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.29.21257760", - "rel_abs": "The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess the viral diversity of the outbreak. We report 264 viral genomes from 242 individuals (both staff and patients) with associated clinical features and outcomes, as well as longitudinal samples, technical replicates and the first publicly disseminated SARS-CoV-2 genomes in Quebec. Viral lineage assessment identified multiple subclades in both hospitals, with a predominant subclade in the Verdun outbreak, indicative of hospital-acquired transmission. Dimensionality reduction identified two subclades that evaded supervised lineage assignment methods, including Pangolin, and identified certain symptoms (headache, myalgia and sore throat) that are significantly associated with favorable patient outcomes. We also address certain limitations of standard SARS-CoV-2 bioinformatics procedures, notably when presented with multiple viral haplotypes.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Bastien Pare", - "author_inst": "Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal" - }, - { - "author_name": "Marieke Rozendaal", - "author_inst": "CHU Sainte-Justine Research Centre" - }, - { - "author_name": "Sacha Morin", - "author_inst": "Department of Computer Science and Operational Research, University of Montreal" - }, - { - "author_name": "Raphael Poujol", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Fatima Mostefai", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Jean-Christophe Grenier", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Lea Kaufmann", - "author_inst": "Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal" - }, - { - "author_name": "Henry Xing", - "author_inst": "CHU Sainte-Justine Research Centre" - }, - { - "author_name": "Miguelle Sanchez", - "author_inst": "Department of microbiology and infectious diseases, Hopital de Verdun" - }, - { - "author_name": "Ariane Yechouron", - "author_inst": "Department of microbiology and infectious diseases, Hopital de Verdun" - }, - { - "author_name": "Ronald Racette", - "author_inst": "Department of Emergency Medicine, Hopital de Verdun" - }, - { - "author_name": "Julie Hussin", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Guy Wolf", - "author_inst": "Mila - Quebec AI Institute, Montreal" - }, - { - "author_name": "Ivan Pavlov", - "author_inst": "Department of Emergency Medicine, Hopital de Verdun" - }, - { - "author_name": "Martin A Smith", - "author_inst": "University of Montreal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.31.21255594", "rel_title": "Signatures of mast cell activation are associated with severe COVID-19", @@ -741835,6 +743012,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.31.446420", + "rel_title": "Virucidal activity of a proprietary blend of plant-based oils (Viruxal) against SARS-CoV-2 and influenza viruses - an in vitro study", + "rel_date": "2021-06-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.31.446420", + "rel_abs": "BackgroundThe emergence of a novel coronavirus known as SARS-CoV-2 resulting in a global pandemic COVID-19 has led to a dramatic loss of life worldwide and presented an unprecedented challenge to public health. Viruxal is a medical device in a form of a nasal and oral spay containing a a proprietary blend of plant-based oils which acts against enveloped viruses. The aim of this study was to evaluate the virus deactivation activity of Viruxal against SARS-CoV-2 and Influenza A(H1N1) viruses.\n\nMethodsAn assay to detect virucidal activity was performed with four concentrations of Viruxal on two virus suspensions. Assessments were made based on log reduction values measured from the assay.\n\nResultsViruxal exhibited virucidal activity by reducing virus titer more than 90% for the enveloped viruses SARS-CoV-2 and influenza A(H1N1) after 30 minutes contact.\n\nConclusionsViruxal was validated for its potential usefulness as a medical device for treatment and prevention of enveloped respiratory viruses.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jon Magnus Kristjansson", + "author_inst": "Kerecis" + }, + { + "author_name": "Ottar Rolfsson", + "author_inst": "University of Iceland" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.01.446516", "rel_title": "SARS-CoV-2 cell-to-cell spread occurs rapidly and is insensitive to antibody neutralization", @@ -743019,45 +744219,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.31.446476", - "rel_title": "COVID-19 Mortality is Associated with Impaired Innate Immunity in Pre-existing Health Conditions", - "rel_date": "2021-05-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.31.446476", - "rel_abs": "BackgroundCOVID-19 poses a life-threatening endangerment to individuals with chronic diseases. However, not all comorbidities affect COVID-19 prognosis equally. Some increase the risk of COVID-19 related death by more than six folds while others show little to no impact. To prevent severe outcomes, it is critical that we comprehend pre-existing molecular abnormalities in common health conditions that predispose patients to poor prognoses. In this study, we aim to discover some of these molecular risk factors by associating gene expression dysregulations in common health conditions with COVID-19 mortality rates in different cohorts.\n\nMethodsWe focused on fourteen pre-existing health conditions, for which age-and-sex-adjusted hazard ratios of COVID-19 mortality have been documented. For each health condition, we analyzed existing transcriptomics data to identify differentially expressed genes (DEGs) between affected individuals and unaffected individuals. We then tested if fold changes of any DEG in these pre-existing conditions were correlated with hazard ratios of COVID-19 mortality to discover molecular risk factors. We performed gene set enrichment analysis to identify functional groups overrepresented in these risk factor genes and examined their relationships with the COVID-19 disease pathway.\n\nResultsWe found that upregulated expression of 70 genes and downregulated expression of 181 genes in pre-existing health conditions were correlated with increased risk of COVID-19 related death. These genes were significantly enriched with endoplasmic reticulum (ER) function, proinflammatory reaction, and interferon production that participate in viral transcription and immune responses to viral infections.\n\nConclusionsImpaired innate immunity in pre-existing health conditions are associated with increased hazard of COVID-19 mortality. The discovered molecular risk factors are potential prognostic biomarkers and targets for therapeutic interventions.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matthew E Lee", - "author_inst": "Arizona State University" - }, - { - "author_name": "Yung Chang", - "author_inst": "Arizona State University" - }, - { - "author_name": "Navid Ahmadinejad", - "author_inst": "Arizona State University" - }, - { - "author_name": "Crista E Johnson-Agbakwu", - "author_inst": "Valleywise Health Medical Center" - }, - { - "author_name": "Celeste Bailey", - "author_inst": "Valleywise Health Medical Center" - }, - { - "author_name": "Li Liu", - "author_inst": "Arizona State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.05.31.446421", "rel_title": "Accelerated Antibody Discovery Targeting the SARS-CoV-2 Spike Protein for COVID-19 Therapeutic Potential", @@ -743332,6 +744493,61 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.05.27.21257952", + "rel_title": "Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation", + "rel_date": "2021-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257952", + "rel_abs": "Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. B.1.1.7 (VOC-202012/01) has become the predominant variant in many countries and a new lineage (VOC-202102/02) harboring the E484K escape mutation in the B.1.1.7 background emerged in February 20211. This variant is of concern due to reduced neutralizing activity by vaccine-elicited antibodies2,3. However, it is not known whether this single amino acid change leads to an altered immune response. Here, we investigate differences in the immune transcriptome in hospitalized patients infected with either B.1.1.7 (n=28) or B.1.1.7+E484K (n=12). RNA-seq conducted on PBMCs isolated within five days after the onset of COVID symptoms demonstrated elevated activation of specific immune pathways, including JAK-STAT signaling, in B.1.1.7+E484K patients as compared to B.1.1.7. Longitudinal transcriptome studies demonstrated a delayed dampening of interferon-activated pathways in B.1.1.7+E484K patients. Prior vaccination with BNT162b vaccine (n=8 one dose; n=1 two doses) reduced the transcriptome inflammatory response to B.1.1.7+E484K infection relative to unvaccinated patients. Lastly, the immune transcriptome of patients infected with additional variants (B.1.258, B.1.1.163 and B.1.7.7) displayed a reduced activation compared to patients infected with B.1.1.7. Acquisition of the E484K substitution in the B.1.1.7 background elicits an altered immune response, which could impact disease progression.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Hye Kyung Lee", + "author_inst": "National Institute of Diabetes, Digestive and Kidney Diseases" + }, + { + "author_name": "Ludwig Knabl", + "author_inst": "TyrolPath, Zams, Austria" + }, + { + "author_name": "Ludwig Knabl Sr.", + "author_inst": "Krankenhaus St. Vinzenz, Zams, Austria" + }, + { + "author_name": "Manuel Wieser", + "author_inst": "TyrolPath, Zams, Austria" + }, + { + "author_name": "Anna Mur", + "author_inst": "Division of Internal Medicine, Krankenhaus Kufstein, Kufstein, Austria" + }, + { + "author_name": "August Zabernigg", + "author_inst": "Division of Internal Medicine, Krankenhaus Kufstein, Kufstein, Austria" + }, + { + "author_name": "Jana Schumacher", + "author_inst": "Division of Internal Medicine, Krankenhaus St. Johann, St. Johann, Austria" + }, + { + "author_name": "Norbert Kaiser", + "author_inst": "Division of Internal Medicine, Krankenhaus St. Johann, St. Johann, Austria" + }, + { + "author_name": "Priscilla A. Furth", + "author_inst": "Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA" + }, + { + "author_name": "Lothar Hennighausen", + "author_inst": "National Institute of Diabetes, Digestive and Kidney Diseases" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.27.21257868", "rel_title": "Time scale performance of rapid antigen testing for SARS-COV-2: evaluation of ten rapid antigen assays", @@ -744656,33 +745872,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.28.21254613", - "rel_title": "Antibody Response to CoronaVac Vaccine in Indonesian COVID-19 Survivor", - "rel_date": "2021-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21254613", - "rel_abs": "Several studies have shown that individuals with previous history of SARS-CoV-2 infection had boosted antibody response after single dose of mRNA or adenovirus-vectored vaccines. We wondered whether single dose CoronaVac, a whole-inactivated vaccine, could be considered for COVID-19 survivors in Indonesia. We measured IgG anti-RBD titre among 18 survivors and 37 non-survivors. Among survivors, there were 9 survivors with positive antibody titre (seropositive) before vaccination and 9 seronegative survivors. All respondents received two doses of CoronaVac vaccine at 14-days interval. We found no significant antibody titre difference between non-survivor at 14 or 28 days after second dose as well as seronegative survivor at at 14 days after second dose. Seropositive survivors were rapidly boosted after first dose with higher antibody titer than non-survivors and seronegative survivors after second dose. However, antibody titer did not differ between first and second dose among seropositive survivors. Seropositive COVID-19 survivors could receive single dose of CoronaVac vaccine which could potentially ease the vaccine supply constrain. A long-term follow-up must be conducted to observe difference in antibody response and persistence.\n\nArticle Summary LineSeropositive COVID-19 survivors had significantly higher antibody response after first dose of CoronaVac vaccine compared to non-survivors and seronegative survivors after second dose of vaccine.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rahmat Azhari Kemal", - "author_inst": "Faculty of Medicine, Universitas Riau" - }, - { - "author_name": "Dita Kartika Sari", - "author_inst": "Department of Anatomy, Faculty of Medicine, Universitas Riau" - }, - { - "author_name": "Ariza Julia Paulina", - "author_inst": "Department of Clinical Pathology, Faculty of Medicine, Universitas Riau" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.26.21257834", "rel_title": "Development and external validation of a diagnostic multivariable prediction model for a prompt identification of cases at high risk for SARS-COV-2 infection among patients admitted to the emergency department", @@ -744934,6 +746123,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.27.21257932", + "rel_title": "COVID-19 testing among children, parental preferences for testing venues and acceptability of school-based testing: a survey of US parents", + "rel_date": "2021-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257932", + "rel_abs": "In a national survey of 2,074 US parents conducted in March 2021, 35.9% reported their youngest child had been tested at least once for COVID-19. Parents preferred testing venue choice was the pediatricians office. Only half of parent surveyed (50.6%) reported that they would allow their child to be tested for COVID-19 at school/daycare if it was required.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Chloe A Teasdale", + "author_inst": "CUNY Graduate School of Public Health and Health Policy" + }, + { + "author_name": "Luisa N Borrell", + "author_inst": "CUNY Graduate School of Public Health" + }, + { + "author_name": "Yanhan Shen", + "author_inst": "CUNY Graduate School of Public Health and Health Policy" + }, + { + "author_name": "Spencer Kimball", + "author_inst": "Emerson College" + }, + { + "author_name": "Michael L Rinke", + "author_inst": "Childrens Hospital of Montefiore and Albert Einstein College of Medicine" + }, + { + "author_name": "Sasha A Fleary", + "author_inst": "CUNY Graduate School of Public Health and Health Policy" + }, + { + "author_name": "Denis Nash", + "author_inst": "CUNY Graduate School of Public Health and Health Policy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.05.26.21257861", "rel_title": "Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater", @@ -746341,33 +747573,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.27.21257938", - "rel_title": "Non-pharmaceutical interventions and the emergence of pathogen variants", - "rel_date": "2021-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257938", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWNon-pharmaceutical interventions (NPIs), such as social distancing and contact tracing, are important public health measures that can reduce pathogen transmission. In addition to playing a crucial role in suppressing transmission, NPIs influence pathogen evolution by mediating mutation supply, restricting the availability of susceptible hosts, and altering the strength of selection for novel variants. Yet it is unclear how NPIs might affect the emergence of novel variants that are able to escape pre-existing immunity (partially or fully), are more transmissible, or cause greater mortality. We analyse a stochastic two-strain epidemiological model to determine how the strength and timing of NPIs affects the emergence of variants with similar or contrasting life-history characteristics to the wildtype. We show that, while stronger and timelier NPIs generally reduce the likelihood of variant emergence, it is possible for more transmissible variants with high cross immunity to have a greater probability of emerging at intermediate levels of NPIs. This is because intermediate levels of NPIs allow an epidemic of the wildtype that is neither too small (facilitating high mutation supply), nor too large (leaving a large pool of susceptible hosts), to prevent a novel variant becoming established in the host population. However, since one cannot predict the characteristics of a variant, the best strategy to prevent emergence is likely to be implementation of strong, timely NPIs.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ben Ashby", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Cameron A Smith", - "author_inst": "University of Bath" - }, - { - "author_name": "Robin N Thompson", - "author_inst": "University of Warwick" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.28.21258006", "rel_title": "Fear, Anxiety, Stress, and Depression of novel coronavirus (COVID-19) pandemic among patients and their healthcare workers", @@ -746623,6 +747828,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.24.21257581", + "rel_title": "Covid-19 and Mental Health of Individuals with Different Personalities", + "rel_date": "2021-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257581", + "rel_abs": "Several studies have been devoted to establishing the effects of the Covid-19 pandemic on mental health across gender, age and ethnicity. However, much less attention has been paid to the differential effect of lockdown according to different personalities. We do this using the UKHLS longitudinal dataset, representative of the UK population. The UKHLS dataset allows us to assess the mental health of the same respondent during the Covid-19 period and the year before based on their personality \"Big Five\" traits and cognitive skills. We find that during the Covid-19 period individuals who have more Extrovert and Open personality report a higher mental health deterioration, while the ones scoring higher in Agreeableness are less affected. The effect of Openness is particularly strong: one more standard deviation predict one more symptom on the GHQ12 test for about 1 respondent over 4. In female respondents, Cognitive Skills and Openness are particularly strong predictors of deterioration. Neuroticism seems to predict more mental health deterioration, as it is normal to expect, but this effect is not significant in the main specifications of the estimated model. The studys results are robust to the inclusion of potential confounding variables such as changes in: physical health, household income and job status (like unemployed or furloughed).", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Eugenio Proto", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Anwen Zhang", + "author_inst": "University of Glasgow" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.05.26.21257847", "rel_title": "Recovery from the COVID-19 pandemic by mass vaccination: emergent lessons from the United States and India", @@ -748299,45 +749527,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.24.21257707", - "rel_title": "Does immune recognition of SARS-CoV2 epitopes vary between different ethnic groups?", - "rel_date": "2021-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257707", - "rel_abs": "The SARS-CoV2 mediated Covid-19 pandemic has impacted humankind at an unprecedented scale. While substantial research efforts have focused towards understand the mechanisms of viral infection and developing vaccines/ therapeutics, factors affecting the susceptibility to SARS-CoV2 infection and manifestation of Covid-19 remain less explored. Given that the Human Leukocyte Antigen (HLA) system is known to vary among ethnic populations, it is likely to affect the recognition of the virus, and in turn, the susceptibility to Covid-19. To understand this, we used bioinformatic tools to probe all SARS-CoV2 peptides which could elicit T-cell response in humans. We also tried to answer the intriguing question of whether these potential epitopes were equally immunogenic across ethnicities, by studying the distribution of HLA alleles among different populations and their share of cognate epitopes. We provide evidence that the newer mutations in SARS-CoV2 are unlikely to alter the T-cell mediated immunogenic responses among the studied ethnic populations. The work presented herein is expected to bolster our understanding of the pandemic, by providing insights into differential immunological response of ethnic populations to the virus as well as by gauging the possible effects of mutations in SARS-CoV2 on efficacy of potential epitope-based vaccines through evaluating [~]40000 viral genomes.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Tungadri Bose", - "author_inst": "Tata Consultancy Services Ltd." - }, - { - "author_name": "Namrata Pant", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - }, - { - "author_name": "Nishal Kumar Pinna", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - }, - { - "author_name": "Subhrajit Bhar", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - }, - { - "author_name": "Anirban Dutta", - "author_inst": "Tata Consultancy Services" - }, - { - "author_name": "Sharmila S Mande", - "author_inst": "Tata Consultancy Services Limited" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.24.21257703", "rel_title": "COVID-19 mass testing: harnessing the power of wastewater epidemiology", @@ -748753,6 +749942,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.24.21257705", + "rel_title": "Emergence of a new SARS-CoV-2 variant from GR clade with a novel S glycoprotein mutation V1230L in West Bengal, India", + "rel_date": "2021-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257705", + "rel_abs": "India is currently facing the devastating second wave of COVID-19 pandemic resulting in approximately 4000 deaths per day. To control this pandemic continuous mutational surveillance and genomic epidemiology of circulating strains is very important. In this study, we performed mutational analysis of the protein coding genes of SARS-CoV-2 strains (n=2000) collected during January 2021 to March 2021. Our data revealed the emergence of a new variant in West Bengal, India, which is characterized by the presence of 11 co-existing mutations including D614G, P681H and V1230L in S-glycoprotein. This new variant was identified in 70 out of 412 sequences submitted from West Bengal. Interestingly, among these 70 sequences, 16 sequences also harbored E484K in the S glycoprotein. Phylogenetic analysis revealed strains of this new variant emerged from GR clade (B.1.1) and formed a new cluster. We propose to name this variant as GRL or lineage B.1.1/S:V1230L due to the presence of V1230L in S glycoprotein along with GR clade specific mutations. Co-occurrence of P681H, previously observed in UK variant, and E484K, previously observed in South African variant and California variant, demonstrates the convergent evolution of SARS-CoV-2 mutation. V1230L, present within the transmembrane domain of S2 subunit of S glycoprotein, has not yet been reported from any country. Substitution of valine with more hydrophobic amino acid leucine at position 1230 of the transmembrane domain, having role in S protein binding to the viral envelope, could strengthen the interaction of S protein with the viral envelope and also increase the deposition of S protein to the viral envelope, and thus positively regulate virus infection. P618H and E484K mutation have already been demonstrated in favor of increased infectivity and immune invasion respectively. Therefore, the new variant having G614G, P618H, P1230L and E484K is expected to have better infectivity, transmissibility and immune invasion characteristics, which may pose additional threat along with B.1.617 in the ongoing COVID-19 pandemic in India.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rakesh Sarkar", + "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India" + }, + { + "author_name": "Ritubrita Saha", + "author_inst": "ICMR-NICED, Kolkata, West Bengal, India" + }, + { + "author_name": "Pratik Mallick", + "author_inst": "St. Xavier's College, Kolkata, West Bengal, India" + }, + { + "author_name": "Ranjana Sharma", + "author_inst": "ICMR-NICED, Kolkata, West Bengal, India" + }, + { + "author_name": "Amandeep Kaur", + "author_inst": "Guru Nanak Institute of Pharmaceutical Science and Technology, Kolkata, West Bengal, India" + }, + { + "author_name": "Shanta Dutta", + "author_inst": "ICMR-NICED, Kolkata, West Bengal, India" + }, + { + "author_name": "Dr. Mamta Chawla-Sarkar", + "author_inst": "ICMR-NICED, Kolkata, West Bengal, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.26.442666", "rel_title": "Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence", @@ -750069,85 +751301,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.21.21257624", - "rel_title": "Monoclonal Antibody Treatment, Prophylaxis and Vaccines Combined to Reduce SARS CoV-2 Spread", - "rel_date": "2021-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.21257624", - "rel_abs": "BackgroundAntiviral monoclonal antibodies (mAbs) developed for treatment of COVID-19 reduce the magnitude and duration of viral shedding and can thus potentially contribute to reducing transmission of the causative virus, severe acute respiratory coronavirus 2 (SARS-CoV-2). However, use of these mAbs in combination with a vaccine program has not been considered in public health strategic planning.\n\nMethodsWe developed an agent-based model to characterize SARS-CoV-2 transmission in the US population during an aggressive phase of the pandemic (October 2020 to April 2021), and simulated the effects on infections and mortality of combining mAbs as treatment and post-exposure prophylaxis (PEP) with a vaccine program plus non-pharmaceutical interventions. We also interrogated the impact of rapid diagnostic testing, increased mAb supply, and vaccine rollout.\n\nFindingsAllocation of mAbs as PEP or targeting those [≥]65 years provided the greatest incremental benefits relative to vaccine in averting infections and deaths, by up to 17% and 41%, respectively. Rapid testing, facilitating earlier diagnosis and mAb use, amplified these benefits. The model was sensitive to mAb supply; doubling supply further reduced infections and mortality, by up to two-fold, relative to vaccine. mAbs continued to provide incremental benefits even as proportion of the vaccinated population increased.\n\nInterpretationUse of anti-viral mAbs as treatment and PEP in combination with a vaccination program would substantially reduce SARS-CoV-2 transmission and pandemic burden. These results may help guide resource allocation and patient management decisions for COVID-19 and can also be used to inform public health policy for current and future pandemic preparedness.\n\nFundingRegeneron Pharmaceuticals.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Mohamed A. Kamal", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Andreas Kuznik", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Luyuan Qi", - "author_inst": "Certara; Paris, France" - }, - { - "author_name": "Witold Wi\u0119cek", - "author_inst": "Certara; London, United Kingdom" - }, - { - "author_name": "Mohamed Hussein", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Hazem E. Hassan", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Kashyap Patel", - "author_inst": "Certara; Princeton, New Jersey, USA" - }, - { - "author_name": "Thomas Obadia", - "author_inst": "Certara; Paris, France" - }, - { - "author_name": "Masood Khaksar Toroghi", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Daniela J. Conrado", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Nidal Al-Huniti", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Roman Casciano", - "author_inst": "Certara; Princeton, New Jersey, USA" - }, - { - "author_name": "Meagan P. O'Brien", - "author_inst": "Regeneron Pharmaceuticals; Tarrytown, NY, USA" - }, - { - "author_name": "Ruanne V. Barnabas", - "author_inst": "Department of Global Health, University of Washington; Seattle, Washington, USA" - }, - { - "author_name": "Myron S. Cohen", - "author_inst": "Institute for Global Health and Infectious Diseases, University of North Carolina; Chapel Hill, North Carolina, USA" - }, - { - "author_name": "Patrick F. Smith", - "author_inst": "Certara; Princeton, New Jersey, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.21.21257631", "rel_title": "Detecting COVID-19 Related Pneumonia on CT Scans using Hyperdimensional Computing", @@ -750295,6 +751448,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.23.21257672", + "rel_title": "Racial disparities in prevalence, determinants, and impacts of COVID-19 in pregnancy: Protocol for a study using data from New Jersey hospitals", + "rel_date": "2021-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.23.21257672", + "rel_abs": "IntroductionRacial and ethnic disparities in COVID-19 related infections, hospitalizations, and deaths have been well-documented. However, little research has examined racial and ethnic disparities in COVID-19 prevalence, determinants, and impacts among pregnant women. Within the United States, New Jersey was an early epicenter of the pandemic and experienced high rates of disease in the fall of 2020.\n\nMethodsThis study uses data from two New Jersey hospitals, which implemented universal testing of COVID-19 of pregnant women admitted for labor and delivery starting in March 2020. We will estimate prevalence of COVID-19 between March 2020 and November 2020 and compare prevalence rates across race and ethnicity. We will conduct multivariable logistic regression analysis to examine the associations of COVID-19 infection with patient demographic and health status predictors. We will also use multivariable linear and logistic regressions to examine the impact of COVID-19 symptomatic and asymptomatic infection on maternal and infant birth outcomes.\n\nDiscussionThis study will generate important policy implications on birth equity in the time of COVID-19 and guide future research studies related to COVID-19 in pregnant women. Results of this study will help to guide interventions and policies to center safe, accessible, and equitable maternity care within the strategic response to the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Slawa Rokicki", + "author_inst": "Rutgers School of Public Health" + }, + { + "author_name": "Pauline Nguyen", + "author_inst": "RWJBarnabas Health" + }, + { + "author_name": "Alaine Sharpe", + "author_inst": "RWJBarnabas Health" + }, + { + "author_name": "Dyese Taylor", + "author_inst": "RWJBarnabas Health" + }, + { + "author_name": "Suzanne Spernal", + "author_inst": "RWJBarnabas Health" + }, + { + "author_name": "Archana Raghunath", + "author_inst": "Rutgers School of Public Health" + }, + { + "author_name": "Leslie Kantor", + "author_inst": "Rutgers School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.23.21257679", "rel_title": "Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State", @@ -751923,93 +753119,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.22.21257658", - "rel_title": "Effectiveness of COVID-19 vaccines against the B.1.617.2 variant", - "rel_date": "2021-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.22.21257658", - "rel_abs": "BackgroundThe B.1.617.2 COVID-19 variant has contributed to the surge in cases in India and has now been detected across the globe, including a notable increase in cases in the UK. We estimate the effectiveness of the BNT162b2 and ChAdOx1 COVID-19 vaccines against this variant.\n\nMethodsA test negative case control design was used to estimate the effectiveness of vaccination against symptomatic disease with both variants over the period that B.1.617.2 began circulating with cases identified based on sequencing and S-gene target status. Data on all symptomatic sequenced cases of COVID-19 in England was used to estimate the proportion of cases with B.1.617.2 compared to the predominant strain (B.1.1.7) by vaccination status.\n\nResultsEffectiveness was notably lower after 1 dose of vaccine with B.1.617.2 cases 33.5% (95%CI: 20.6 to 44.3) compared to B.1.1.7 cases 51.1% (95%CI: 47.3 to 54.7) with similar results for both vaccines. With BNT162b2 2 dose effectiveness reduced from 93.4% (95%CI: 90.4 to 95.5) with B.1.1.7 to 87.9% (95%CI: 78.2 to 93.2) with B.1.617.2. With ChAdOx1 2 dose effectiveness reduced from 66.1% (95% CI: 54.0 to 75.0) with B.1.1.7 to 59.8% (95%CI: 28.9 to 77.3) with B.1.617.2. Sequenced cases detected after 1 or 2 doses of vaccination had a higher odds of infection with B.1.617.2 compared to unvaccinated cases (OR 1.40; 95%CI: 1.13-1.75).\n\nConclusionsAfter 2 doses of either vaccine there were only modest differences in vaccine effectiveness with the B.1.617.2 variant. Absolute differences in vaccine effectiveness were more marked with dose 1. This would support maximising vaccine uptake with two doses among vulnerable groups.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Jamie Lopez Bernal", - "author_inst": "Public Health England" - }, - { - "author_name": "Nick Andrews", - "author_inst": "Public Health England" - }, - { - "author_name": "Charlotte Gower", - "author_inst": "Public Health England" - }, - { - "author_name": "Eileen Gallagher", - "author_inst": "Public Health England" - }, - { - "author_name": "Ruth Simmons", - "author_inst": "Public Health England" - }, - { - "author_name": "Simon Thelwall", - "author_inst": "Public Health England" - }, - { - "author_name": "Elise Tessier", - "author_inst": "Public Health England" - }, - { - "author_name": "Natalie Groves", - "author_inst": "Public Health England" - }, - { - "author_name": "Gavin Dabrera", - "author_inst": "Public Health England" - }, - { - "author_name": "Richard Myers", - "author_inst": "Public Health England" - }, - { - "author_name": "Colin Campbell", - "author_inst": "Public Health England" - }, - { - "author_name": "Gayatri Amirthalingam", - "author_inst": "Public Health England" - }, - { - "author_name": "Matt Edmunds", - "author_inst": "Public Health England" - }, - { - "author_name": "Maria Zambon", - "author_inst": "Public Health England" - }, - { - "author_name": "Kevin Brown", - "author_inst": "Public Health England" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "Public Health England" - }, - { - "author_name": "Meera Chand", - "author_inst": "Public Health England" - }, - { - "author_name": "Mary Ramsay", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.22.21257649", "rel_title": "The COVID in the Context of Pregnancy, Infancy and Parenting (CoCoPIP) Study: protocol for a longitudinal study of parental mental health, social interactions, physical growth, and cognitive development of infants during the pandemic.", @@ -752393,6 +753502,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.24.445443", + "rel_title": "Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core", + "rel_date": "2021-05-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.24.445443", + "rel_abs": "The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes the preparation of the fusion machinery by dissociation of the S1 domains. We report the development of bottom-up coarse-grained (CG) models validated with cryo-electron tomography (cryo-ET) data, and the use of CG molecular dynamics simulations to investigate the dynamical mechanisms involved in viral binding and exposure of the S2 trimeric core. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces. The multivalent interaction cyclically and processively induces S1 dissociation, thereby exposing the S2 core containing the fusion machinery. Our simulations thus reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alexander J. Pak", + "author_inst": "Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Ch" + }, + { + "author_name": "Alvin Yu", + "author_inst": "Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Ch" + }, + { + "author_name": "Zunlong Ke", + "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK" + }, + { + "author_name": "John A. G. Briggs", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Gregory A. Voth", + "author_inst": "University of Chicago" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.05.24.445424", "rel_title": "Isolation of SARS-CoV-2 B.1.1.28.2 P2 variant and pathogenicity comparison with D614G variant in hamster model", @@ -753829,165 +754973,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.05.18.21257396", - "rel_title": "A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program", - "rel_date": "2021-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257396", - "rel_abs": "The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n=35) or hospitalization (n=42) due to severe COVID-19 using genome-wide association summary from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828= 53 and nrs505922=59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p=1.32 x 10-199), and thrombosis ORrs505922 1.33, p=2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p=4.12 x 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p=2.26x 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p=6.48 x10-23, lupus OR 0.84, p=3.97 x 10-06. PheWAS stratified by genetic ancestry demonstrated differences in genotype-phenotype associations across ancestry. LMNA (rs581342) associated with neutropenia OR 1.29 p=4.1 x 10-13 among Veterans of African ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Anurag Verma", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph" - }, - { - "author_name": "Noah L. Tsao", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi" - }, - { - "author_name": "Lauren O. Thomann", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Yuk-Lam Ho", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Sudha K. Iyengar", - "author_inst": "Departments of Population and Quantitative Health Sciences, Ophthalmology and Visual Sciences and Genetics and Genome Sciences, Case Western Reserve University," - }, - { - "author_name": "Shiuh-Wen Luoh", - "author_inst": "VA Portland Health Care System, Portland OR, USA" - }, - { - "author_name": "Rotonya Carr", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph" - }, - { - "author_name": "Dana C. Crawford", - "author_inst": "Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA" - }, - { - "author_name": "Jimmy T. Efird", - "author_inst": "Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, USA." - }, - { - "author_name": "Giulio Genovese", - "author_inst": "Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA." - }, - { - "author_name": "Adriana Hung", - "author_inst": "Tennessee Valley Healthcare System (Nashville VA) , Nashville, Tennessee, USA" - }, - { - "author_name": "Kerry L. Ivey", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Michael G. Levin", - "author_inst": "Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Julie Lynch", - "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, USA." - }, - { - "author_name": "Pradeep Natarajan", - "author_inst": "Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA." - }, - { - "author_name": "Saiju Pyarajan", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA;Harvard Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Alexander Bick", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA;Vanderbilt University, Nashville, Tennessee, USA" - }, - { - "author_name": "Lauren Costa", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Giulio Genovese", - "author_inst": "Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA." - }, - { - "author_name": "Richard Hauger", - "author_inst": "Department of Psychiatry, University of California, San Diego, La Jolla, CA; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, " - }, - { - "author_name": "Ravi Madduri", - "author_inst": "University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, USA;Data Science and Learning Division, Arg" - }, - { - "author_name": "Gita A. Pathak", - "author_inst": "Department of Psychiatry, Yale School of Medicine, Connecticut, USA" - }, - { - "author_name": "Renato Polimanti", - "author_inst": "Department of Psychiatry, Yale School of Medicine, Connecticut, USA" - }, - { - "author_name": "Benjamin F. Voight", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph" - }, - { - "author_name": "Marijana Vujkovic", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph" - }, - { - "author_name": "Maryam Zekavat", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Hongyu Zhao", - "author_inst": "VA Connecticut Healthcare System, West Haven, CT, USA" - }, - { - "author_name": "Marylyn Ritchie", - "author_inst": "Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Kyong-Mi Chang", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA" - }, - { - "author_name": "Kelly Cho", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Juan P Casas", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Philip S Tsao", - "author_inst": "VA Palo Alto Health Care System, Palo Alto, California, USA" - }, - { - "author_name": "J. Michael Gaziano", - "author_inst": "Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Christopher O?Donnell", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA" - }, - { - "author_name": "Scott M. Damrauer", - "author_inst": "Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi" - }, - { - "author_name": "Katherine P. Liao", - "author_inst": "VA Boston Healthcare System, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.05.17.21257134", "rel_title": "Heterologous vaccination strategy for containing COVID-19 pandemic", @@ -754459,6 +755444,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.21.21257575", + "rel_title": "Measurement of multiple SARS-CoV-2 antibody titer after vaccination represents individual vaccine response and contributes to individually appropriate vaccination schedules", + "rel_date": "2021-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.21257575", + "rel_abs": "The SARS-CoV-2 mRNA vaccine BNT162b2 (Pfizer-BioNTech) has become a game-changer in the COVID-19 crisis. Faster and wider coverage of vaccine supply is urgently needed, although vaccine supply is far from abundant in many countries and regions. There is no denying that Japan is vaccinating at a slower pace than in many other countries. At the end of April 2021, it had administered less than 2% of the population, according to the statistics website Our World in Data.1 Single-dose vaccination may be considered to induce an adequate antibody response in individuals with prior infection,2-5 which can lead to more effective vaccine distribution to people in serious need. However, multiple antibody responses in populations with various backgrounds, including prior COVID-19 infection, underlying diseases, and age, have not been investigated sufficiently. Due to the lack of antibody measurement data, antibody follow-up measurement recommendations have yet to be suggested. Accumulation of available data regarding quantitative antibody titer will lead to the establishment of personally customized schedules, including antibody follow-up, and will balance both faster delivery of vaccines and confirmation of effective vaccination.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Kenji Ota", + "author_inst": "Nagasaki University Hospital" + }, + { + "author_name": "Katsunori Yanagihara", + "author_inst": "Nagasaki University Hospital" + }, + { + "author_name": "Satoshi Murakami", + "author_inst": "Abbott Japan" + }, + { + "author_name": "Hiroshi Mukae", + "author_inst": "Nagasaki University Hospital" + }, + { + "author_name": "Shigeru Kohno", + "author_inst": "Nagasaki University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.21.21257442", "rel_title": "T-cell and antibody immunity after COVID-19 mRNA vaccines in healthy and immunocompromised subjects-An exploratory study.", @@ -756063,45 +757083,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.20.21257523", - "rel_title": "Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in Asymptomatic and Symptomatic populations at an Institution of Higher Education", - "rel_date": "2021-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257523", - "rel_abs": "Clinical evidence for asymptomatic cases of coronavirus disease (COVID-19) has reinforced the significance of effective surveillance testing programs. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays are considered the gold standard for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. However, the labor and resource requirements can be prohibitive with respect to large testing volumes associated with the pandemic. Pooled testing algorithms may serve to increase testing capacity with more efficient resource utilization. Due to the lack of carefully curated cohorts, there is limited evidence for the applicability of RT-PCR pooling in asymptomatic COVID-19 cases. In this study, we compared the analytical sensitivity of the TaqMan SARS-CoV-2 Pooling Assay to detect one positive sample in a pool of five anterior nare swabs in symptomatic and asymptomatic cohorts at an institute of higher education. Positive pools were deconvoluted and each individual sample was retested using the TaqPath COVID-19 Combo Kit. Both assays target the open reading frame (ORF) 1ab, nucleocapsid (N), and spike (S) gene of the strain that originated in Wuhan, Hubei, China. Qualitative results demonstrated absolute agreement between pooled and deconvoluted samples in both cohorts. Independent t-test performed on Ct shifts confirmed an insignificant difference between cohorts with p-values of 0.306 (Orf1ab), 0.147 (N), and 0.052 (S). All negative pools were correctly reported as negative. Thus, pooled PCR testing up to five samples is a valid method for surveillance testing of students and staff in a university setting, especially when the prevalence is expected to be low.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Troy Ganz", - "author_inst": "northeastern university" - }, - { - "author_name": "Sarah Sanderson", - "author_inst": "northeastern university" - }, - { - "author_name": "Connor Baush", - "author_inst": "northeastern university" - }, - { - "author_name": "Melanie Mejia", - "author_inst": "northeastern university" - }, - { - "author_name": "Manoj Gandhi", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Jared Auclair", - "author_inst": "Northeastern University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.19.21257470", "rel_title": "RT-qPCR half reaction optimization for the detection of SARS-CoV-2", @@ -756437,6 +757418,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.20.21257557", + "rel_title": "Early Detection of COVID-19 Outbreaks Using Human Mobility Data", + "rel_date": "2021-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257557", + "rel_abs": "BackgroundContact mixing plays a key role in the spread of COVID-19. Thus, mobility restrictions of varying degrees up to and including nationwide lockdowns have been implemented in over 200 countries. To appropriately target the timing, location, and severity of measures intended to encourage social distancing at a country level, it is essential to predict when and where outbreaks will occur, and how widespread they will be.\n\nMethodsWe analyze aggregated, anonymized health data and cell phone mobility data from Israel. We develop predictive models for daily new cases and the test positivity rate over the next 7 days for different geographic regions in Israel. We evaluate model goodness of fit using root mean squared error (RMSE). We use these predictions in a five-tier categorization scheme to predict the severity of COVID-19 in each region over the next week. We measure magnitude accuracy (MA), the extent to which the correct severity tier is predicted.\n\nResultsModels using mobility data outperformed models that did not use mobility data, reducing RMSE by 17.3% when predicting new cases and by 10.2% when predicting the test positivity rate. The best set of predictors for new cases consisted of 1-day lag of past 7-day average new cases, along with a measure of internal movement within a region. The best set of predictors for the test positivity rate consisted of 3-days lag of past 7-day average test positivity rate, along with the same measure of internal movement. Using these predictors, RMSE was 4.812 cases per 100,000 people when predicting new cases and 0.79% when predicting the test positivity rate. MA in predicting new cases was 0.775, and accuracy of prediction to within one tier was 1.0. MA in predicting the test positivity rate was 0.820, and accuracy to within one tier was 0.998.\n\nConclusionsUsing anonymized, macro-level data human mobility data along with health data aids predictions of when and where COVID-19 outbreaks are likely to occur. Our method provides a useful tool for government decision makers, particularly in the post-vaccination era, when focused interventions are needed to contain COVID-19 outbreaks while mitigating the collateral damage of more global restrictions.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Grace Guan", + "author_inst": "Stanford University" + }, + { + "author_name": "Yotam Dery", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Matan Yechezkel", + "author_inst": "Tel Aviv university" + }, + { + "author_name": "Irad Ben-Gal", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Dan Yamin", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Margaret Brandeau", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.20.21257461", "rel_title": "Efficacy Estimates for Various COVID-19 Vaccines: What we Know from the Literature and Reports", @@ -757713,29 +758733,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.05.18.21257416", - "rel_title": "Integrating health behavior theories to predict COVID-19 vaccine acceptance: differences between medical students and nursing students in Israel", - "rel_date": "2021-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257416", - "rel_abs": "BackgroundThis study aimed to explore behavioral-related factors predicting the intention of getting a COVID-19 vaccine among medical and nursing students using an integrative model combining the Health Belief Model (HBM) and the Theory of Planned Behavior (TPB).\n\nMethodsA cross-sectional online survey was conducted among medical and nursing students aged > 18 years in their clinical years in Israel between 27 August and 28 September 2020. Hierarchical logistic regression was used to predict acceptance of a COVID-19 vaccine.\n\nResultsA total number of 628 participants completed the survey. Medical students expressed higher intentions of getting vaccinated against COVID-19 than nursing students (88.1% vs. 76.2%, p < 0.01). The integrated model based on HBM and TPB was able to explain 66% of the variance (adjusted R2 = 0.66). Participants were more likely to be willing to get vaccinated if they reported higher levels of perceived susceptibility, benefits, barriers, cues to action, attitude, self-efficacy and anticipated regret. Two interaction effects revealed that male nurses had a higher intention of getting vaccinated than did female nurses and that susceptibility is a predictor of the intention of getting vaccinated only among nurses.\n\nConclusionsThis study demonstrates that both models considered (i.e., HBM and TPB) are important for predicting the intention of getting a COVID-19 vaccine among medical and nursing students, and can help better guide intervention programs, based on components from both models. Our findings also highlight the importance of paying attention to a targeted group of female nurses, who expressed low vaccine acceptance.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hila Rosental", - "author_inst": "Bar-Ilan University" - }, - { - "author_name": "Liora Shmueli", - "author_inst": "Bar-Ilan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.05.18.21257426", "rel_title": "Modeling waning and boosting of COVID-19 in Canada with vaccination", @@ -757927,6 +758924,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.05.19.21257430", + "rel_title": "CovidMulti-Net: A Parallel-Dilated Multi Scale Feature Fusion Architecture for the Identification of COVID-19 Cases from Chest X-ray Images", + "rel_date": "2021-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257430", + "rel_abs": "The COVID-19 pandemic is an emerging respiratory infectious disease, having a significant impact on the health and life of many people around the world. Therefore, early identification of COVID-19 patients is the fastest way to restrain the spread of the pandemic. However, as the number of cases grows at an alarming pace, most developing countries are now facing a shortage of medical resources and testing kits. Besides, using testing kits to detect COVID-19 cases is a time-consuming, expensive, and cumbersome procedure. Faced with these obstacles, most physicians, researchers, and engineers have advocated for the advancement of computer-aided deep learning models to assist healthcare professionals in quickly and inexpensively recognize COVID-19 cases from chest X-ray (CXR) images. With this motivation, this paper proposes a \"CovidMulti-Net\" architecture based on the transfer learning concept to classify COVID-19 cases from normal and other pneumonia cases using three publicly available datasets that include 1341, 1341, and 446 CXR images from healthy samples and 902, 1564, and 1193 CXR images infected with Viral Pneumonia, Bacterial Pneumonia, and COVID-19 diseases. In the proposed framework, features from CXR images are extracted using three well-known pre-trained models, including DenseNet-169, ResNet-50, and VGG-19. The extracted features are then fed into a concatenate layer, making a robust hybrid model. The proposed framework achieved a classification accuracy of 99.4%, 95.2%, and 94.8% for 2-Class, 3-Class, and 4-Class datasets, exceeding all the other state-of-the-art models. These results suggest that the \"CovidMulti-Net\" frameworks ability to discriminate individuals with COVID-19 infection from healthy ones and provides the opportunity to be used as a diagnostic model in clinics and hospitals. We also made all the materials publicly accessible for the research community at: https://github.com/saikat15010/CovidMulti-Net-Architecture.git.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Md. Saikat Islam Khan", + "author_inst": "Mawlana Bhashani Science and Technology University" + }, + { + "author_name": "Anichur Rahman", + "author_inst": "Mawlana Bhashani Science and Technology University" + }, + { + "author_name": "Md. Razaul Karim", + "author_inst": "Mawlana Bhashani Science and Technology University" + }, + { + "author_name": "Nasima Islam Bithi", + "author_inst": "Mawlana Bhashani Science and Technology University" + }, + { + "author_name": "Shahab Band", + "author_inst": "National Institute of Textile Engineering and Research (NITER), National University of Sciences" + }, + { + "author_name": "Abdollah Dehzangi", + "author_inst": "Rutgers University" + }, + { + "author_name": "Hamid Alinejad-Rokny", + "author_inst": "UNSW Sydney" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.05.18.21255620", "rel_title": "Emergence and spread of the potential variant of interest (VOI) B.1.1.519 predominantly present in Mexico.", @@ -759767,33 +760807,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.18.444723", - "rel_title": "The effect of SARS-COV-2 Infections on Amyloid Formation of Serum Amyloid A", - "rel_date": "2021-05-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.18.444723", - "rel_abs": "A marker for the severeness and disease progress of COVID-19 is overexpression of serum amyloid A (SAA) to levels that in other diseases are associated with a risk for SAA amyloidosis. In order to understand whether SAA amyloidosis could also be a long-term risk of SARS-COV-2 infections we have used long all-atom molecular dynamic simulations to study the effect of a SARS-COV-2 protein segment on SAA amyloid formation. Sampling over 40 {micro}s we find that presence of the nine-residue segment SK9, located at the C-terminus of the Envelope protein, increases the propensity for SAA fibril formation by three mechanisms: it reduces the stability of the lipid-transporting hexamer shifting the equilibrium toward monomers, it increases the frequency of aggregation-prone configurations in the resulting chains, and it raises the stability of SAA fibrils. Our results therefore suggest that SAA amyloidosis and related pathologies may be a long-term risk of SARS-COV-2 infections.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Asis K Jana", - "author_inst": "Dept. of Chemistry and Biochemistry, University of Oklahoma" - }, - { - "author_name": "Augustus B. Greenwood", - "author_inst": "Departement of Chemistry and Biochemistry, University of Oklahoma" - }, - { - "author_name": "Ulrich H.E. Hansmann", - "author_inst": "University of Oklahoma" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.05.19.444569", "rel_title": "Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection", @@ -760089,6 +761102,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.05.18.21256801", + "rel_title": "Evaluation of the Family Liaison Officer (FLO) role during the COVID-19 Pandemic", + "rel_date": "2021-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21256801", + "rel_abs": "ObjectivesDuring the first wave of COVID-19 heavy restrictions were placed on hospital visitations in the United Kingdom. To support communication between families and patients a central London hospital introduced the role of the Family Liaison Officer. Communication within healthcare settings is often the subject of contention, particularly for patients families. During periods of crisis communication can become strained for patients and their families. We aimed to evaluate the rapid implementation of this role to provide guidance if it was required in the future and to explore the potential for this to become a standard role.\n\nDesignService evaluation\n\nSettingSingle National Health Service hospital in London.\n\nMethodsSemi-structured video interviews with a convenience sample of 12 participants. Data were analysed using Framework Analysis.\n\nParticipantsFamily Liaison Officers (n=5) and colleagues who experienced working alongside them (n=7).\n\nResultsKey themes were identified from the interviews pertaining to the role, the team, the impact and the future. Two versions of the role emerged though the process based on the Family Liaison Officers previous background: Clinical Family Liaison Officers (primarily nurses) and Pastoral Family Liaison Officers (primarily play specialists). Both the Family Liaison Officers and their colleagues agreed that the role had a very positive impact on the wards during this time. Negative aspects of the role, such as a lack of induction, boundaries or clear structure were also discussed.\n\nConclusionThe Family Liaison Officer was a key role during the pandemic in facilitating communication between patient, clinical team and family. The challenges associated with the role reflect the speed in which it was implemented but it was evident to those in the role and clinicians who the role was supporting that it has potential to help improve hospital communication, and the work of healthcare staff outside of a pandemic.\n\nStrengths and limitations of this studyO_LIThis was an in-depth evaluation of the Family Liaison Officer role from the perspective of those in the role and the clinical team who they were providing support.\nC_LIO_LIThe sample included representation of the different disciplines who worked in the FLO role.\nC_LIO_LIThe evaluation only represents the professional perspective and not the experience of the family.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Luke Hughes", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Lisa Anderton", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Rachel M Taylor", + "author_inst": "University College London Hospitals NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.05.18.444742", "rel_title": "Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating Variants", @@ -763073,57 +764113,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.13.21257152", - "rel_title": "Distinct Mucoinflammatory Phenotype and the Immunomodulatory Long Noncoding Transcripts Associated with SARS-CoV-2 Airway Infection", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257152", - "rel_abs": "Respiratory epithelial cells are the primary target for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We investigated the 3D human airway tissue model to evaluate innate epithelial cell responses to SARS-CoV-2 infection. A SARS-CoV-2 clinical isolate productively infected the 3D-airway model with a time-dependent increase in viral load (VL) and concurrent upregulation of airway immunomodulatory factors (IL-6, ICAM-1, and SCGB1A1) and respiratory mucins (MUC5AC, MUC5B, MUC2, and MUC4), and differential modulation of select long noncoding RNAs (lncRNAs i.e., LASI, TOSL, NEAT1, and MALAT1). Next, we examined these immunomodulators in the COVID-19 patient nasopharyngeal swab samples collected from subjects with high- or low-VLs ([~]100-fold difference). As compared to low-VL, high-VL patients had prominent mucoinflammatory signature with elevated expression of IL-6, ICAM-1, SCGB1A1, SPDEF, MUC5AC, MUC5B, and MUC4. Interestingly, LASI, TOSL, and NEAT1 lncRNA expressions were also markedly elevated in high-VL patients with no change in MALAT1 expression. In addition, dual-staining of LASI and SARS-CoV-2 nucleocapsid N1 RNA showed predominantly nuclear/perinuclear localization at 24 hpi in 3D-airway model as well as in high-VL COVID-19 patient nasopharyngeal cells, which exhibited high MUC5AC immunopositivity. Collectively, these findings suggest SARS-CoV-2 induced lncRNAs may play a role in acute mucoinflammatory response observed in symptomatic COVID-19 patients.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Dinesh Devadoss", - "author_inst": "Florida International University" - }, - { - "author_name": "Arpan Acharya", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Marko Manevski", - "author_inst": "Florida International University" - }, - { - "author_name": "Kabita Pandey", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Glen M Borchert", - "author_inst": "University of South Alabama" - }, - { - "author_name": "Madhavan Nair", - "author_inst": "Florida International University" - }, - { - "author_name": "Mehdi S Mirsaeidi", - "author_inst": "University of Miami" - }, - { - "author_name": "Siddappa N Byrareddy", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Hitendra S Chand", - "author_inst": "Florida International University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.15.21257254", "rel_title": "Inhibitor screening of Spike variants reveals the heterogeneity of neutralizing antibodies to COVID-19 infection and vaccination", @@ -763431,6 +764420,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.14.21257247", + "rel_title": "Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257247", + "rel_abs": "The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID-19 cases in Europe and 59% of COVID-19 cases in the U.S. It is defined by the N501Y mutation in the receptor binding domain (RBD) of the Spike (S) protein, and a few other mutations. These include two mutations in the N terminal domain (NTD) of the S protein, HV69-70del and Y144del (also known as Y145del due to the presence of tyrosine at both positions). We recently identified several emerging SARS-CoV-2 variants of concerns, characterized by Membrane (M) protein mutations, including I82T and V70L. We now identify a sub-lineage of B.1.1.7 that emerged through sequential acquisitions of M:V70L in November 2020 followed by a novel S:D178H mutation first observed in early February 2021. The percentage of B.1.1.7 isolates in the U.S. that belong to this sub-lineage increased from 0.15% in February 2021 to 1.8% in April 2021. To date this sub-lineage appears to be U.S.-specific with reported cases in 31 states, including Hawaii. As of April 2021 it constituted 36.8% of all B.1.1.7 isolates in Washington. Phylogenetic analysis and transmission inference with Nextstrain suggests this sub-lineage likely originated in either California or Washington. Structural analysis revealed that the S:D178H mutation is in the NTD of the S protein and close to two other signature mutations of B.1.1.7, HV69-70del and Y144del. It is surface exposed and may alter NTD tertiary configuration or accessibility, and thus has the potential to affect neutralization by NTD directed antibodies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lishuang Shen", + "author_inst": "Children's Hospital of Los Angeles" + }, + { + "author_name": "Jennifer Dien Bard", + "author_inst": "Children's Hospital of Los Angeles" + }, + { + "author_name": "Timothy J Triche", + "author_inst": "Children's Hospital of Los Angeles" + }, + { + "author_name": "Alexander R Judkins", + "author_inst": "Children's Hospital of Los Angeles" + }, + { + "author_name": "Jaclyn A Biegel", + "author_inst": "Children's Hospital of Los Angeles" + }, + { + "author_name": "Xiaowu Gai", + "author_inst": "Children's Hospital of Los Angeles" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.17.21257309", "rel_title": "Mitigating the psychological impacts of COVID-19 restrictions: The Behavioural Activation in Social Isolation (BASIL) pilot randomised controlled trial to prevent depression and loneliness among older people with long term conditions", @@ -764915,85 +765943,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.05.18.21256128", - "rel_title": "Phylogenomics and population genomics of SARS-CoV-2 in Mexico reveals variants of interest (VOI) and a mutation in the Nucleocapsid protein associated with symptomatic versus asymptomatic carriers", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21256128", - "rel_abs": "Understanding the evolution of SARS-CoV-2 virus in various regions of the world during the Covid19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A RT-qPCR screening and phylogenomics reconstructions directed a sequence/structure analysis of the Spike glycoprotein, revealing mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show Spike protein mutations in the N-terminal domain (i.e., R190M), in the receptor-binding motif (i.e., T478K, E484K), within the S1-S2 subdomains (i.e., P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest (VOI) we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of Single Nucleotide Variants (SNVs) from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the Nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades, so we propose an additional VOI, 20A/N:194L.V2 (B.1.243). Our results highlight the dual and complementary role of Spike and Nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage.\n\nIMPACT STATEMENTFollowing self-sampling, screening of mutations of concern, and a combined phylogenomic and population genetics pipeline, we reveal the appearance of three VOI with mutations in the Spike protein, P.4 (B.1.1.28.4) and 20B/478K.V1 (B.1.1.222, leading to B.1.1.519), and in the Nucleocapsid protein, 20A/N:194L.V2 (B.1.243), in Mexico during the pre-vaccination stage. The mutation S194L in the Nucleocapsid was found to associate with symptomatic patients versus asymptomatic carriers in the population investigated. Our research can aid epidemiological genomics efforts during the vaccination stage in Mexico by contributing with a combined analytical platform and information about variants within different genetic lineages with the potential to evolve into variants of concern (VOC).", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Francisco Barona-Gomez", - "author_inst": "Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Luis Delaye", - "author_inst": "Departamento de Ingenieria Genetica, Unidad Irapuato, Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Erik Diaz-Valenzuela", - "author_inst": "Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Fabien Plisson", - "author_inst": "Conacyt - Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Arely Cruz-Perez", - "author_inst": "Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Mauricio Diaz-Sanchez", - "author_inst": "Molecular Biology Research & Development Department, GrupoT4, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Christian A Garcia-Sepulveda", - "author_inst": "Facultad de Medicina, Universidad Autonoma de San Luis Potosi, San Luis Potosi, Mexico." - }, - { - "author_name": "Alejandro Sanchez-Flores", - "author_inst": "Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico." - }, - { - "author_name": "Rafael Perez-Abreu", - "author_inst": "Centro de Investigacion en Matematicas AC (CIMAT), Sede Aguascalientes, Aguascalientes, Mexico." - }, - { - "author_name": "Francisco J Valencia-Valdespino", - "author_inst": "Prothesia, Monterrey, Nuevo Leon, Mexico." - }, - { - "author_name": "Alejandra Natali Vega-Magana", - "author_inst": "Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisc" - }, - { - "author_name": "J. Francisco Munoz-Valle", - "author_inst": "Institute for Research in Biomedical Sciences, University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco, Mexico." - }, - { - "author_name": "Octavio P Garcia-Gonzalez", - "author_inst": "Molecular Biology Research & Development Department, GrupoT4, Irapuato, Guanajuato, Mexico." - }, - { - "author_name": "Sofia Bernal-Silva", - "author_inst": "Centro de Investigacion en Ciencias de la Salud y Biomedicina, Universidad Autonoma de San Luis Potosi, San Luis Potosi, Mexico." - }, - { - "author_name": "Andreu Comas-Garcia", - "author_inst": "Centro de Investigacion en Ciencias de la Salud y Biomedicina, Universidad Autonoma de San Luis Potosi, San Luis Potosi, Mexico." - }, - { - "author_name": "Angelica Cibrian Jaramillo", - "author_inst": "Unidad de Genomica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.05.18.21257259", "rel_title": "SARS-CoV-2 Vaccine-Induced Antibody Response and Reinfection in Persons with Past Natural Infection", @@ -765201,6 +766150,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.17.21257337", + "rel_title": "Pregnancy and birth outcomes after SARS-CoV-2 vaccination in pregnancy", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257337", + "rel_abs": "BackgroundSARS-CoV-2 infection during pregnancy is associated with significant maternal morbidity and increased rates of preterm birth. For this reason, COVID-19 vaccine administration in pregnancy has been endorsed by multiple professional societies including ACOG and SMFM despite exclusion of pregnant women from initial clinical trials of vaccine safety and efficacy. However, to date little data exists regarding outcomes after COVID-19 vaccination of pregnant patients.\n\nStudy DesignA comprehensive vaccine registry was combined with a delivery database for an integrated healthcare system to create a delivery cohort including vaccinated patients. Maternal sociodemographic data were examined univariately for factors associated with COVID-19 vaccination. Pregnancy and birth outcomes were analyzed, including a composite measure of maternal and neonatal pregnancy complications, the Adverse Outcome Index.\n\nResultsOf 2002 patients in the delivery cohort, 140 (7.0%) received a COVID-19 vaccination during pregnancy and 212 (10.6%) experienced a COVID-19 infection during pregnancy. The median gestational age at first vaccination was 32 weeks (range 13 6/7-40 4/7), and patients vaccinated during pregnancy were less likely than unvaccinated patients to experience COVID-19 infection prior to delivery (1.4% (2/140) vs. 11.3% (210/1862)) P<0.001No maternal COVID-19 infections occurred after vaccination during pregnancy.\n\nFactors significantly associated with increased likelihood of vaccination included older age, higher level of maternal education, lower pre-pregnancy BMI, and use of infertility treatment for the current pregnancy. Tobacco or other substance use, Hispanic ethnicity, and higher gravidity were associated with a lower likelihood of vaccination. No significant difference in the composite adverse outcome (5.0% (7/140) vs. 4.9% (91/1862) P=0.95) or other maternal or neonatal complications, including thromboembolic events and preterm birth, was observed in vaccinated mothers compared to unvaccinated patients.\n\nConclusionsVaccinated pregnant women in this birth cohort were less likely to experience COVID-19 infection compared to unvaccinated pregnant patients, and COVID-19 vaccination during pregnancy was not associated with increased pregnancy or delivery complications. Significant sociodemographic disparities in vaccine uptake and/or access were observed among pregnant patients, and future efforts should focus on outreach to low-uptake populations.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Regan N Theiler", + "author_inst": "Mayo clinic" + }, + { + "author_name": "Myra Wick", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Amy Weaver", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Ramila Mehta", + "author_inst": "Mayo clinic" + }, + { + "author_name": "Abinash Virk", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Melanie Swift", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.05.17.21257197", "rel_title": "Long-lasting neutralizing antibody responses in SARS-CoV-2 seropositive individuals are robustly boosted by immunization with the CoronaVac and BNT162b2 vaccines", @@ -766641,81 +767629,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.17.21257223", - "rel_title": "Serial interval of COVID-19 and the effect of Variant B.1.1.7: analyses from a prospective community cohort study (Virus Watch).", - "rel_date": "2021-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257223", - "rel_abs": "IntroductionIncreased transmissibility of B.1.17 variant of concern (VOC) in the UK may explain its rapid emergence and global spread. We analysed data from putative household infector - infectee pairs in the Virus Watch Community cohort study to assess the serial interval of COVID-19 and whether this was affected by emergence of the B.1.17 variant.\n\nMethodsThe Virus Watch study is an online, prospective, community cohort study following up entire households in England and Wales during the COVID-19 pandemic. Putative household infector-infectee pairs were identified where more than one person in the household had a positive swab matched to an illness episode. Data on whether individual infections were caused by the B.1.1.7 variant were not available. We therefore developed a classification system based on the percentage of cases estimated to be due to B.1.17 in national surveillance data for different English regions and study weeks.\n\nResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)).\n\nConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Cyril Roman Geismar", - "author_inst": "University College London" - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "University College London" - }, - { - "author_name": "Vincent Grigori Nguyen", - "author_inst": "University College London" - }, - { - "author_name": "Wing Lam Erica Fong", - "author_inst": "University College London" - }, - { - "author_name": "Madhumita Shrotri", - "author_inst": "University College London" - }, - { - "author_name": "Sarah Beale", - "author_inst": "University College London" - }, - { - "author_name": "Alison Rodger", - "author_inst": "University College London" - }, - { - "author_name": "Vasileios Lampos", - "author_inst": "University College London" - }, - { - "author_name": "Thomas Edward Byrne", - "author_inst": "University College London" - }, - { - "author_name": "Jana Kovar", - "author_inst": "University College London" - }, - { - "author_name": "Annalan Navaratnam", - "author_inst": "University College London" - }, - { - "author_name": "Parth Patel", - "author_inst": "University College London" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "University College London" - }, - { - "author_name": "- Virus Watch Collaborative", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.13.21257146", "rel_title": "Sociodemographic inequality in COVID-19 vaccination coverage amongst elderly adults in England: a national linked data study", @@ -767059,6 +767972,153 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.13.21257065", + "rel_title": "HLA-B*15:01 is associated with asymptomatic SARS-CoV-2 infection", + "rel_date": "2021-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257065", + "rel_abs": "Despite some inconsistent reporting of symptoms, studies have demonstrated that at least 20% of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will remain asymptomatic. Although most global efforts have focused on understanding factors underlying severe illness in COVID-19 (coronavirus disease of 2019), the examination of asymptomatic infection provides a unique opportunity to consider early disease and immunologic features promoting rapid viral clearance. Owing to its critical role in the immune response, we postulated that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection. We enrolled 29,947 individuals registered in the National Marrow Donor Program for whom high-resolution HLA genotyping data were available in the UCSF Citizen Science smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n=1428) was comprised of unvaccinated, self-identified subjects who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci (HLA-A, -B, -C, -DRB1, -DQB1) with disease course and identified a strong association of HLA-B*15:01 with asymptomatic infection, and reproduced this association in two independent cohorts. Suggesting that this genetic association is due to pre-existing T-cell immunity, we show that T cells from pre-pandemic individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF, and 100% of the reactive cells displayed memory phenotype. Finally, we characterize the protein structure of HLA-B*15:01-peptide complexes, demonstrating that the NQKLIANQF peptide from SARS-CoV-2, and the highly homologous NQKLIANAF from seasonal coronaviruses OC43-CoV and HKU1-CoV, share similar ability to be stabilized and presented by HLA-B*15:01, providing the molecular basis for T-cell cross-reactivity and HLA-B*15:01-mediated pre-existing immunity.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Danillo G Augusto", + "author_inst": "Department of Neurology, University of California, San Francisco and Programa de Pos-Graduacao em Genetica, Universidade Federal do Parana, Curitiba, Brazil" + }, + { + "author_name": "Tasneem Yusufali", + "author_inst": "Department of Neurology, University of California, San Francisco" + }, + { + "author_name": "Joseph J Sabatino Jr.", + "author_inst": "Department of Neurology, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Noah D Peyser", + "author_inst": "Division of Cardiology, Department of Medicine, University of California, San Francisco" + }, + { + "author_name": "Lawton D. Murdolo", + "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia." + }, + { + "author_name": "Xochitl Butcher", + "author_inst": "Division of Cardiology, Department of Medicine, University of California, San Francisco" + }, + { + "author_name": "Victoria Murray", + "author_inst": "Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Vivian Pae", + "author_inst": "Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Sannidhi Sarvadhavabhatla", + "author_inst": "Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Fiona Beltran", + "author_inst": "Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Gurjot Gill", + "author_inst": "Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, US" + }, + { + "author_name": "Kara Lynch", + "author_inst": "Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Cassandra Yun", + "author_inst": "Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Colin Maguire", + "author_inst": "University of Utah, Clinical and Translational Science Institute, Salt Lake City, UT" + }, + { + "author_name": "Michael J. Peluso", + "author_inst": "Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Rebecca Hoh", + "author_inst": "Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Timothy J. Henrich", + "author_inst": "Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Steven G. Deeks", + "author_inst": "Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Michelle Davidson", + "author_inst": "Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Scott Lu", + "author_inst": "Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Sarah A. Goldberg", + "author_inst": "Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "J. Daniel Kelly", + "author_inst": "Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Jeffrey N. Martin", + "author_inst": "Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Cynthia A. Viera-Green", + "author_inst": "CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota" + }, + { + "author_name": "Stephen R. Spellman", + "author_inst": "CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota" + }, + { + "author_name": "David J. Langton", + "author_inst": "ExplantLab, The Biosphere, Newcastle Helix, Newcastle-upon-Tyne, UK" + }, + { + "author_name": "Sulggi Lee", + "author_inst": "Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA" + }, + { + "author_name": "Gregory M Marcus", + "author_inst": "Division of Cardiology, Department of Medicine, University of California, San Francisco" + }, + { + "author_name": "Jeffrey E Olgin", + "author_inst": "Division of Cardiology, Department of Medicine, University of California, San Francisco" + }, + { + "author_name": "Mark J Pletcher", + "author_inst": "Department of Epidemiology and Biostatistics and Division of General Internal Medicine, University of California, San Francisco" + }, + { + "author_name": "Stephanie Gras", + "author_inst": "Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia." + }, + { + "author_name": "Martin Maiers", + "author_inst": "National Marrow Donor Program, Minneapolis, MN" + }, + { + "author_name": "Jill A Hollenbach", + "author_inst": "Department of Neurology and Department of Epidemiology and Biostatistics, University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.16.21257288", "rel_title": "Monitoring of anti-SARS-CoV-2 IgG antibody immune response in infected and immunised healthcare workers in Hungary: a real-world longitudinal cohort study", @@ -768866,33 +769926,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.12.21257079", - "rel_title": "Computational modelling of COVID-19: A study of compliance and superspreaders", - "rel_date": "2021-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257079", - "rel_abs": "BackgroundThe success of social distancing implementations of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) depends heavily on population compliance. Mathematical modelling has been used extensively to assess the rate of viral transmission from behavioural responses. Previous epidemics of SARS-Cov-2 have been characterised by superspreaders, a small number of individuals who transmit a disease to a large group of individuals, who contribute to the stochasticity (or randomness) of transmission compared to other pathogens such as Influenza. This growing evidence proves an urgent matter to understand transmission routes in order to target and combat outbreaks.\n\nObjectiveTo investigate the role of superspreaders in the rate of viral transmission with various levels of compliance.\n\nMethodA SEIRS inspired social network model is adapted and calibrated to observe the infected links of a general population with and without superspreaders on four compliance levels. Local and global connection parameters are adjusted to simulate close contact networks and travel restrictions respectively and each performance assessed. The mean and standard deviation of infections with superspreaders and non-superspreaders were calculated for each compliance level.\n\nResultsIncreased levels of compliance of superspreaders proves a significant reduction in infections. Assuming long-lasting immunity, superspreaders could potentially slow down the spread due to their high connectivity.\n\nDiscussionThe main advantage of applying the network model is to capture the heterogeneity and locality of social networks, including the role of superspreaders in epidemic dynamics. The main challenge is the immediate attention on social settings with targeted interventions to tackle superspreaders in future empirical work.\n\nConclusionSuperspreaders play a central role in slowing down infection spread following compliance guidelines. It is crucial to adjust social distancing measures to prevent future outbreaks accompanied by population-wide testing and effective tracing.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Faith MY Lee", - "author_inst": "University College London" - }, - { - "author_name": "Maria Perez-Ortiz", - "author_inst": "University College London" - }, - { - "author_name": "John Shawe-Taylor", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.12.21257117", "rel_title": "Seven-day COVID-19 quarantine may be too short: assessing post-quarantine transmission risk in four university cohorts", @@ -769132,6 +770165,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.12.21257125", + "rel_title": "COVID-19 Serology in New York State Using a Multiplex Microsphere Immunoassay", + "rel_date": "2021-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257125", + "rel_abs": "The emergence of SARS-CoV-2, leading to COVID-19, necessitated the development of new molecular and serological tests. Here, we describe a multiplexed serological assay developed as the global pandemic moved into New York State in the spring of 2020. The original microsphere immunoassay used a target antigen from the SARS-CoV-1 virus responsible for the 2003 SARS outbreak, but evolved to incorporate multiple SARS-CoV-2 protein antigens (nucleocapsid, spike and spike domains, spike and nucleocapsid proteins from seasonal human coronaviruses). Besides being highly versatile due to multiplex capabilities, the assay was highly specific and sensitive and adaptable to measuring both total antibodies and antibody isotypes. While determining the assay performance characteristics, we were able to identify antibody production patterns (e.g., kinetics of isotypes, individual variations) for total antibodies and individual antibody classes. Overall, the results provide insights into the laboratory response to new serology needs, and how the evolution and fine-tuning of a serology assay helped contribute to a better understanding of the antibody response to SARS-CoV-2.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Danielle T. Hunt", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Jennifer L. Yates", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Karen E. Kulas", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Kyle Carson", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Theresa Lamson", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Valerie Demarest", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Andrea Furuya", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Kelly Howard", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Mary Marchewka", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Randy Stone", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Heidi Tucker", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Casey Warszycki", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "Jim Yee", + "author_inst": "Weill Cornell Medicine/New York Presbyterian Hospital/Weill Cornell Medical Campus" + }, + { + "author_name": "He S. Yang", + "author_inst": "Weill Cornell Medicine/New York Presbyterian Hospital/Weill Cornell Medical Campus" + }, + { + "author_name": "Sabrina Racine-Brzostek", + "author_inst": "Weill Cornell Medicine/New York Presbyterian Hospital/Weill Cornell Medical Campus" + }, + { + "author_name": "Zhen Zhao", + "author_inst": "Weill Cornell Medicine/New York Presbyterian Hospital/Weill Cornell Medical Campus" + }, + { + "author_name": "Monir Ejemel", + "author_inst": "MassBiologics of the University of Massachusetts Medical School" + }, + { + "author_name": "Qi Li", + "author_inst": "MassBiologics of the University of Massachusetts Medical School" + }, + { + "author_name": "Yang Wang", + "author_inst": "MassBiologics of the University of Massachusetts Medical School" + }, + { + "author_name": "Sebastian Fernando", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Francesca La Carpia", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Eldad A. Hod", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Kathleen A. McDonough", + "author_inst": "Wadsworth Center/New York State Department of Health" + }, + { + "author_name": "William T. Lee", + "author_inst": "Wadsworth Center/New York State Department of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.15.21256814", "rel_title": "Fatal breakthrough infection after anti-BCMA CAR-T therapy highlights suboptimal immune response to SARS-CoV-2 vaccination in myeloma patients", @@ -770704,109 +771848,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.13.21257129", - "rel_title": "Immune Responses to COVID-19 mRNA Vaccines in Patients with Solid Tumors on Active, Immunosuppressive Cancer Therapy", - "rel_date": "2021-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257129", - "rel_abs": "Vaccines against SARS-CoV-2 have shown high efficacy, but immunocompromised participants were excluded from controlled clinical trials. We compared immune responses to the Pfizer/BioNTech mRNA vaccine in solid tumor patients (n=53) on active cytotoxic anti-cancer therapy to a control cohort (n=50) as an observational study. Using live SARS-CoV-2 assays, neutralizing antibodies were detected in 67% and 80% of cancer patients after the first and second immunizations, respectively, with a 3-fold increase in median titers after the booster. Similar trends were observed in serum antibodies against the receptor-binding domain (RBD) and S2 regions of Spike protein, and in IFN{gamma}+ Spike-specific T cells. Yet the magnitude of each of these responses was diminished relative to the control cohort. We therefore quantified RBD- and Spike S1-specific memory B cell subsets as predictors of anamnestic responses to additional immunizations. After the second vaccination, Spike-specific plasma cell-biased memory B cells were observed in most cancer patients at levels similar to those of the control cohort after the first immunization. We initiated an interventional phase 1 trial of a third booster shot (NCT04936997); primary outcomes were immune responses with a secondary outcome of safety. After a third immunization, the 20 participants demonstrated an increase in antibody responses, with a median 3-fold increase in virus-neutralizing titers. Yet no improvement was observed in T cell responses at 1 week after the booster immunization. There were mild adverse events, primarily injection site myalgia, with no serious adverse events after a month of follow-up. These results suggest that a third vaccination improves humoral immunity against COVID-19 in cancer patients on active chemotherapy with no severe adverse events.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Rachna T Shroff", - "author_inst": "University of Arizona" - }, - { - "author_name": "Pavani Chalasani", - "author_inst": "University of Arizona" - }, - { - "author_name": "Ran Wei", - "author_inst": "University of Arizona" - }, - { - "author_name": "Daniel Pennington", - "author_inst": "University of Arizona" - }, - { - "author_name": "Grace Quirk", - "author_inst": "University of Arizona" - }, - { - "author_name": "Marta V Schoenle", - "author_inst": "University of Arizona" - }, - { - "author_name": "Kameron L Peyton", - "author_inst": "University of Arizona" - }, - { - "author_name": "Jennifer L Uhrlaub", - "author_inst": "University of Arizona" - }, - { - "author_name": "Tyler J Ripperger", - "author_inst": "University of Arizona" - }, - { - "author_name": "Mladen Jergovic", - "author_inst": "University of Arizona" - }, - { - "author_name": "Shelby Dalgai", - "author_inst": "University of Arizona" - }, - { - "author_name": "Alexander Wolf", - "author_inst": "University of Arizona" - }, - { - "author_name": "Rebecca D Whitmer", - "author_inst": "University of Arizona" - }, - { - "author_name": "Hytham Hammad", - "author_inst": "University of Arizona" - }, - { - "author_name": "Amy Carrier", - "author_inst": "University of Arizona" - }, - { - "author_name": "Aaron J Scott", - "author_inst": "University of Arizona" - }, - { - "author_name": "Janko Nikolich-Zugich", - "author_inst": "University of Arizona" - }, - { - "author_name": "Michael Worobey", - "author_inst": "University of Arizona" - }, - { - "author_name": "Ryan Sprissler", - "author_inst": "University of Arizona" - }, - { - "author_name": "Michael D Dake", - "author_inst": "University of Arizona" - }, - { - "author_name": "Bonnie J LaFleur", - "author_inst": "University of Arizona" - }, - { - "author_name": "Deepta Bhattacharya", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.07.21256823", "rel_title": "Evolution of human antibody responses up to one year after SARS-CoV-2 infection", @@ -771066,6 +772107,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.11.21257053", + "rel_title": "Analysis of 472,688 severe cases of COVID-19 in Brazil showed lower mortality in those vaccinated against influenza", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257053", + "rel_abs": "ObjectiveTo analyze the severe cases of COVID-19 in Brazil in 2020 and compare those vaccinated and unvaccinated against influenza in invasive ventilation, admission in Intensive Care Unit (ICU) and deaths.\n\nMethodCross-sectional study with public data from the OpenDataSUS platform, regarding confirmed severe cases for COVID-19 in Brazil in the year 2020. Data were analyzed by SPSS, from the chi-square test of independence and binary logistic regression.\n\nResultsThe population was 472,688 cases and 177,640 deaths, with a lethality of 37.58% in severe cases. The test of independence was highly significant in vaccinated survivors (<0.0001), and regression showed an almost twofold odds ratio for invasive ventilation, ICU admission, and death in unvaccinated cases.\n\nConclusionWe recommend mass influenza vaccination as an adjuvant in combating the COVID-19 pandemic in Brazil.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Daniele Melo Sardinha", + "author_inst": "Instituto Evandro Chagas" + }, + { + "author_name": "Diana da Costa Lobato", + "author_inst": "SESPA" + }, + { + "author_name": "Ana Lucia da Silva Ferreira", + "author_inst": "Universidade do Estado do Para" + }, + { + "author_name": "Karla Valeria Batista Lima", + "author_inst": "Instituto Evandro Chagas" + }, + { + "author_name": "Ricardo Jose de Paula Souza e Guimaraes", + "author_inst": "Instituto Evandro Chagas" + }, + { + "author_name": "Luana Nepomuceno Gondim Costa Lima", + "author_inst": "Instituto Evandro Chagas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.07.21256847", "rel_title": "Risk of COVID-19 epidemic resurgence with the introduction of vaccination passes", @@ -773470,57 +774550,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.12.443948", - "rel_title": "Plasmacytoid dendritic cells produce type I interferon and reduce viral replication in airway epithelial cells after SARS-CoV-2 infection", - "rel_date": "2021-05-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.12.443948", - "rel_abs": "Infection with SARS-CoV-2 has caused a pandemic of unprecedented dimensions. SARS-CoV-2 infects airway and lung cells causing viral pneumonia. The importance of type I interferon (IFN) production for the control of SARS-CoV-2 infection is highlighted by the increased severity of COVID-19 in patients with inborn errors of type I IFN response or auto-antibodies against IFN-. Plasmacytoid dendritic cells (pDCs) are a unique immune cell population specialized in recognizing and controlling viral infections through the production of high concentrations of type I IFN. In this study, we isolated pDCs from healthy donors and showed that pDCs are able to recognize SARS-CoV-2 and rapidly produce large amounts of type I IFN. Sensing of SARS-CoV-2 by pDCs was independent of viral replication since pDCs were also able to recognize UV-inactivated SARS-CoV-2 and produce type I IFN. Transcriptional profiling of SARS-CoV-2 and UV-SARS-CoV-2 stimulated pDCs also showed a rapid type I and III IFN response as well as induction of several chemokines, and the induction of apoptosis in pDCs. Moreover, we modeled SARS-CoV-2 infection in the lung using primary human airway epithelial cells (pHAEs) and showed that co-culture of pDCs with SARS-CoV-2 infected pHAEs induces an antiviral response and upregulation of antigen presentation in pHAE cells. Importantly, the presence of pDCs in the co-culture results in control of SARS-CoV-2 replication in pHAEs. Our study identifies pDCs as one of the key cells that can recognize SARS-CoV-2 infection, produce type I and III IFN and control viral replication in infected cells.\n\nImportanceType I interferons (IFNs) are a major part of the innate immune defense against viral infections. The importance of type I interferon (IFN) production for the control of SARS-CoV-2 infection is highlighted by the increased severity of COVID-19 in patients with defects in the type I IFN response. Interestingly, many cells are not able to produce type I IFN after being infected with SARS-CoV-2 and cannot control viral infection. In this study we show that plasmacytoid dendritic cells are able to recognize SARS-CoV-2 and produce type I IFN, and that pDCs are able to help control viral infection in SARS-CoV-2 infected airway epithelial cells.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Luisa Cervantes-Barragan", - "author_inst": "Emory University" - }, - { - "author_name": "Abigail Vanderheiden", - "author_inst": "Emory University" - }, - { - "author_name": "Charlotte J Royer", - "author_inst": "Emory University" - }, - { - "author_name": "Meredith E Davis-Gardner", - "author_inst": "Emory University" - }, - { - "author_name": "Philipp Ralfs", - "author_inst": "Emory University" - }, - { - "author_name": "Tatiana Chirkova", - "author_inst": "Emory University" - }, - { - "author_name": "Larry J Anderson", - "author_inst": "University of Emory School of Medicine" - }, - { - "author_name": "Arash Grakoui", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Mehul S Suthar", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.09.21250610", "rel_title": "Pooling of samples for SARS-CoV-2 detection using rapid antigen tests", @@ -773736,6 +774765,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.06.21256768", + "rel_title": "Antibody Response to COVID-19 vaccination in Patients Receiving Dialysis", + "rel_date": "2021-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256768", + "rel_abs": "BackgroundPatients receiving dialysis may mount impaired responses to COVID19 vaccination.\n\nMethodsWe report antibody response to vaccination from 1140 patients without, and 493 patients with pre-vaccination SARS-CoV-2 RBD antibody. We used commercially available assays (Siemens) to test remainder plasma monthly in association with vaccination date and type, and assess prevalence of absent total receptor binding antibody, and absent or attenuated (index value < 10) semiquantitative receptor binding domain IgG index values. We used Poisson regression to evaluate risk factors for absent or attenuated response to vaccination.\n\nResultsAmong patients who were seronegative versus seropositive before vaccination, 62% and 56% were [≥]65 years old, 20% and 24% were Hispanic, and 22% and 23% were Black. Median IgG index values rose steadily over time, and were higher among the seropositive than in the seronegative patients after completing vaccination (150 [25th, 75th percentile 23.2, 150.0] versus 41.6 [11.3, 150.0]). Among 610 patients who completed vaccination (assessed [≥]14 days later, median 29 days later), the prevalence of absent total RBD response, and absent and attenuated semiquantitative IgG response was 4.4% (95% CI 3.1, 6.4%), 3.4% (2.4, 5.2%), and 14.3% (11.7, 17.3%) respectively. Risk factors for absent or attenuated response included longer vintage of end-stage kidney disease, and lower pre-vaccination serum albumin.\n\nConclusionsMore than one in five patients receiving dialysis had evidence of an attenuated immune response to COVID19 vaccination.\n\nSignificance statementPatients receiving dialysis face high likelihood of severe COVID19; at the same time, vaccination may be less efficacious, as prior data indicate impaired immune responses to influenza and Hepatitis B vaccination. We found that 22% of patients receiving dialysis had suboptimal responses to vaccination, irrespective of whether or not they had evidence of prior SARS-CoV-2 infection. Poorer health status and longer duration of end-stage kidney disease increased likelihood of suboptimal response. Ongoing vigilance for COVID19 in dialysis facilities and studies of modified vaccination dosing schedules will be critical to protecting patients receiving dialysis.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Shuchi Anand", + "author_inst": "Stanford" + }, + { + "author_name": "Maria E Montez-Rath", + "author_inst": "Stanford University" + }, + { + "author_name": "Jialin Han", + "author_inst": "Stanford University" + }, + { + "author_name": "Pablo Garcia", + "author_inst": "Stanford University" + }, + { + "author_name": "LinaCel Cadden", + "author_inst": "Ascend Clinical Laboratory" + }, + { + "author_name": "Patti Hunsader", + "author_inst": "Ascend Clinical Laboratory" + }, + { + "author_name": "Russell Kerschmann", + "author_inst": "Ascend Clinical Laboratory" + }, + { + "author_name": "Paul Beyer", + "author_inst": "Ascend Clinical Laboratory" + }, + { + "author_name": "Mary Dittrich", + "author_inst": "US Renal Care" + }, + { + "author_name": "Geoffrey A Block", + "author_inst": "US Renal Care" + }, + { + "author_name": "Scott D Boyd", + "author_inst": "Stanford University" + }, + { + "author_name": "Julie Parsonnet", + "author_inst": "Stanford University" + }, + { + "author_name": "Glenn M Chertow", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.05.09.21256929", "rel_title": "INFLUENCE OF NOVEL CORONAVIRUS DISEASE (COVID-19) ON PARKINSONS DISEASE: SYSTEMATIC REVIEW", @@ -775288,61 +776384,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.05.11.443686", - "rel_title": "Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations", - "rel_date": "2021-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.11.443686", - "rel_abs": "The UK variant of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), known as B.1.1.7, harbors several point mutations and deletions on the spike (s) protein, which potentially alter its structural epitopes to evade host immunity while enhancing host receptor binding. Here we report the cryo-EM structures of the S protein of B.1.1.7 in its apo form and in the receptor ACE2-bound form. One or two of the three receptor binding domains (RBDs) were in the open conformation but no fully closed form was observed. In the ACE-bound form, all three RBDs were engaged in receptor binding. The B.1.1.7-specific A570D mutation introduced a salt bridge switch that could modulate the opening and closing of the RBD. Furthermore, the N501Y mutation in the RBD introduced a favorable {pi}-{pi} interaction manifested in enhanced ACE2 binding affinity. The N501Y mutation abolished the neutralization activity of one of the three potent neutralizing antibodies (nAbs). Cryo-EM showed that the cocktail of other two nAbs simultaneously bound to all three RBDs. Furthermore, the nAb cocktail synergistically neutralized different SARS-CoV-2 pseudovirus strains, including the B.1.1.7.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Tzu-Jing Yang", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Pei-Yu Yu", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Yuan-Chih Chang", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Kang-Hao Liang", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Hsian-Cheng Tso", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Meng-Ru Ho", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Wan-Yu Chen", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Hsiu-Ting Lin", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Han-Chung Wu", - "author_inst": "Academia Sinica" - }, - { - "author_name": "Shang-Te Danny Hsu", - "author_inst": "Academia Sinica" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.05.12.443228", "rel_title": "Interferon-armed RBD dimer enhances the immunogenicity of RBD for sterilizing immunity against SARS-CoV-2", @@ -775682,6 +776723,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.10.443532", + "rel_title": "Analysis of the Role of N-glycosylation in Cell-surface expression, Function and Binding Properties of SARS-CoV-2 receptor ACE2", + "rel_date": "2021-05-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.10.443532", + "rel_abs": "Human angiotensin I-converting enzyme 2 (hACE2) is a type-I transmembrane glycoprotein that serves as the major cell entry receptor for SARS-CoV and SARS-CoV-2. The viral spike (S) protein is required for attachment to ACE2 and subsequent virus-host cell membrane fusion. Previous work has demonstrated the presence of N-linked glycans in ACE2. N-glycosylation is implicated in many biological activities, including protein folding, protein activity, and cell surface expression of biomolecules. However, the contribution of N-glycosylation to ACE2 function is poorly understood. Here, we examined the role of N-glycosylation in the activity and localization of two species with different susceptibility to SARS-CoV-2 infection, porcine ACE2 (pACE2) and hACE2. The elimination of N-glycosylation by tunicamycin (TM) treatment or mutagenesis, showed that N-glycosylation is critical for the proper cell surface expression of ACE2 but not for its carboxiprotease activity. Furthermore, nonglycosylable ACE2 localized predominantly in the endoplasmic reticulum (ER) and not at the cell surface. Our data also revealed that binding of SARS-CoV and SARS-CoV-2 S protein to porcine or human ACE2 was not affected by deglycosylation of ACE2 or S proteins, suggesting that N-glycosylation plays no role in the interaction between SARS coronaviruses and the ACE2 receptor. Impairment of hACE2 N-glycosylation decreased cell to cell fusion mediated by SARS-CoV S protein but not SARS-CoV-2 S protein. Finally, we found that hACE2 N-glycosylation is required for an efficient viral entry of SARS-CoV/SARS-CoV-2 S pseudotyped viruses, which could be the result of low cell surface expression of the deglycosylated ACE2 receptor.\n\nImportanceElucidating the role of glycosylation in the virus-receptor interaction is important for the development of approaches that disrupt infection. In this study, we show that deglycosylation of both ACE2 and S had a minimal effect on the Spike-ACE2 interaction. In addition, we found that removal of N-glycans of ACE2 impaired its ability to support an efficient transduction of SARS-CoV and SARS-CoV-2 S pseudotyped viruses. Our data suggest that the role of deglycosylation of ACE2 on reducing infection is likely due to a reduced expression of the viral receptor on the cell surface. These findings offer insight into the glycan structure and function of ACE2, and potentially suggest that future antiviral therapies against coronaviruses and other coronavirus-related illnesses involving inhibition of ACE2 recruitment to the cell membrane could be developed.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alberto Brandariz-Nu\u00f1ez", + "author_inst": "University of Illinois at Urbana Champaign" + }, + { + "author_name": "Raymond R Rowland", + "author_inst": "Kansas State University" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.10.443524", "rel_title": "CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.", @@ -778082,37 +779146,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.05.11.21256876", - "rel_title": "The Impact of Control and Mitigation Strategies during the Second Wave of COVID-19 Infections in Spain and Italy", - "rel_date": "2021-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256876", - "rel_abs": "European countries struggled to fight against the second and the third waves of the COVID-19 pandemic, as the Test-Trace-Isolate (TTI) strategy widely adopted over the summer and early fall failed to effectively contain the spread of the disease. In this paper, we shed light on the effectiveness of such a strategy in two European countries (Spain and Italy) by analysing data from June to December 2020, collected via a large-scale online citizen survey with 95,251 answers in Spain and 43,393 answers in Italy. Through our analysis, we identify several weaknesses in each of the three pillars of the TTI strategy: testing, tracing and isolating. Moreover, we analyse the respondents self-reported behaviour before and after the mitigation strategies were deployed during the second wave of infections. We find that the changes in the participants behaviour were more pronounced in Italy than in Spain, whereas in both countries, respondents reported being very compliant with individual protection measures, such as wearing facial masks or frequently disinfecting their hands. Finally, we analyse the participants perceptions about their governments measures and the safety of everyday activities and places regarding the risk of getting an infection. We find that the perceived risk is often gender- and age-dependent and not aligned with the risk level identified by the literature. This finding emphasises the importance of deploying public-health communication campaigns to debunk misconceptions about SARS-CoV-2. Overall, our work shows the value of online citizen surveys to quickly and cheaply collect large-scale data to support and evaluate policy decisions to contrast the spread of the disease.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Marco De Nadai", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Kristof Roomp", - "author_inst": "The European Laboratory for Learning and Intelligent Systems (ELLIS), Alicante Unit" - }, - { - "author_name": "Bruno Lepri", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Nuria Oliver", - "author_inst": "The European Laboratory for Learning and Intelligent Systems (ELLIS), Alicante Unit" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.10.21256995", "rel_title": "Magnetofluidic platform for rapid multiplexed screening of SARS-CoV-2 variants and respiratory pathogens", @@ -778420,6 +779453,89 @@ "type": "confirmatory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.05.11.443384", + "rel_title": "Structure and mechanism of SARS-CoV-2 Spike N679-V687 deletion variant elucidate cell-type specific evolution of viral fitness", + "rel_date": "2021-05-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.11.443384", + "rel_abs": "As the global burden of SARS-CoV-2 infections escalates, so does the evolution of viral variants which is of particular concern due to their potential for increased transmissibility and pathology. In addition to this entrenched variant diversity in circulation, RNA viruses can also display genetic diversity within single infected hosts with co-existing viral variants evolving differently in distinct cell types. The BriS{Delta} variant, originally identified as a viral subpopulation by passaging SARS-CoV-2 isolate hCoV-19/England/02/2020, comprises in the spike glycoprotein an eight amino-acid deletion encompassing the furin recognition motif and S1/S2 cleavage site. Here, we elucidate the structure, function and molecular dynamics of this variant spike providing mechanistic insight into how the deletion correlates to viral cell tropism, ACE2 receptor binding and infectivity of this SARS-CoV-2 variant. Moreover, our study reveals long-range allosteric communication between functional regions within the spike that differ in wild-type and deletion variant. Our results support a view of SARS-CoV-2 probing multiple evolutionary trajectories in distinct cell types within the same infected host.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Kapil Gupta", + "author_inst": "University of Bristol" + }, + { + "author_name": "Christine Toelzer", + "author_inst": "University of Bristol" + }, + { + "author_name": "Maia Kavanagh Williamson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Deborah Shoemark", + "author_inst": "University of Bristol" + }, + { + "author_name": "A. Sofia F. Oliveira", + "author_inst": "University of Bristol" + }, + { + "author_name": "David A Matthews", + "author_inst": "University of Bristol" + }, + { + "author_name": "Abdulaziz Almuqrin", + "author_inst": "University of Bristol" + }, + { + "author_name": "Oskar Staufer", + "author_inst": "Max Planck Institute for Medical Research" + }, + { + "author_name": "Sathish K.N. Yadav", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ufuk Borucu", + "author_inst": "University of Bristol" + }, + { + "author_name": "Frederic Garzoni", + "author_inst": "Imophoron Ltd, Bristol" + }, + { + "author_name": "Daniel Fitzgerald", + "author_inst": "Halo Therapeutics Ltd, Bristol" + }, + { + "author_name": "Joachim Spatz", + "author_inst": "Max Planck Institute for Medical Research" + }, + { + "author_name": "Adrian J Mulholland", + "author_inst": "University of Bristol" + }, + { + "author_name": "Andrew D. Davidson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Christiane Schaffitzel", + "author_inst": "University of Bristol" + }, + { + "author_name": "Imre Berger", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.05.11.443477", "rel_title": "Viral shedding and transmission after natural infection and vaccination in an animal model of SARS-CoV-2 propagation", @@ -780100,45 +781216,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.10.21256951", - "rel_title": "The impact of COVID-19 pandemic on the provision of ambulatory care for patients with chronic neurological diseases in Japan: evaluation of an administrative claims database", - "rel_date": "2021-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256951", - "rel_abs": "BackgroundThe COVID-19 pandemic has affected not only the emergency medical system, but also patients regular ambulatory care. The number of patients visiting outpatient internal medicine clinics decreased during March-April 2020 compared to 2019. Moreover, the ban on telephone re-examination for outpatient clinics in lieu of ambulatory care for chronic diseases has been lifted since March 2020. In this context, we investigate the impact of the COVID-19 pandemic on ambulatory care at Japanese outpatient clinics for patients with chronic neurological diseases during the first half of 2020.\n\nMethodsWe collected data from the administrative claims database by DeSC Healthcare. Serial changes in the frequency of subsequent outpatient visits to clinics or hospitals (excluding large hospitals with beds >200) for chronic ambulatory care of epilepsy, migraine, Parkinsons disease (PD), and Alzheimers disease were measured. We also evaluated the utilization rate of telephone re-examination at outpatient clinics.\n\nResultsSince April 2020, the monthly count of outpatient clinic visits for epilepsy or PD decreased slightly but significantly. The use of telephone re-examination was facility-dependent, and it was used in less than 5% of all outpatient clinic visits for the examined neurological diseases in May 2020. The utilization rate of telephone re-examination was not associated with age or the neurological diseases of interest.\n\nConclusionThe impact of the COVID-19 pandemic on ambulatory care for several chronic neurological diseases may have been relatively limited, in terms of the frequency or type of outpatient visit, during the first half of 2020 in Japan.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kenichiro Sato", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Tatsuo Mano", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Yoshiki Niimi", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Atsushi Iwata", - "author_inst": "Tokyo Metropolitan Geriatric Institute" - }, - { - "author_name": "Tatsushi Toda", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Takeshi Iwatsubo", - "author_inst": "University of Tokyo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.05.08.21256775", "rel_title": "Intra-host evolution provides for continuous emergence of SARS-CoV-2 variants", @@ -780466,6 +781543,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.10.21255146", + "rel_title": "A population-level analysis of the protective effects of androgen deprivation therapy against COVID-19 disease incidence and severity", + "rel_date": "2021-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21255146", + "rel_abs": "ImportanceThe incidence and severity of coronavirus disease 19 (COVID-19) is higher in men. Sex hormones potentially offer one explanation for differences by sex.\n\nObjectiveTo determine whether men exposed to androgen deprivation therapy (ADT) have lower incidence and severity of COVID-19.\n\nDesignWe conducted an observational study of male Veterans treated in the Veterans Health Administration from February 15th to July 15th, 2020. We developed a propensity score model to predict the likelihood to undergo Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) testing. We performed multivariable logistic regression modeling adjusted with inverse probability weighting to examine the relationship between ADT and COVID-19 incidence. We conducted logistic regression analysis among COVID-19 patients to test the association between ADT and COVID-19 severity.\n\nSettingThe U.S. Department of Veterans Affairs\n\nParticipantsThe study sample consisted of 6,250,417 male Veterans who were alive as of February 15, 2020.\n\nExposureExposure to ADT was defined as having any prescription for a luteinizing hormone releasing hormone analogue or an antiandrogen in the six months prior to the index date.\n\nMain Outcomes and MeasuresTo assess incidence, we used a binary variable indicating any positive reverse transcriptase polymerase chain reaction SARS-CoV-2 test result through July 15, 2020. To measure severity, we constructed a binary variable indicating whether a patient was admitted to the intensive care unit, placed on mechanical ventilation, or dead in the 60 days following a positive test up to July 15, 2020.\n\nResultsWe identified 246,087 patients who had been tested for SARS-CoV-2, of whom 3,057 were exposed to ADT, and 36,096 patients with cancer and no ADT exposure. Of these, 295 ADT patients and 2,427 other cancer patients had COVID-19 illness. In the primary, propensity-weighted comparison of ADT patients to cancer patients not on ADT, ADT was associated with decreased likelihood of testing positive for SARS-CoV-2 (adjusted OR, 0.88 [95% CI, 0.81-0.95]; p=0.001). ADT was associated with fewer severe COVID-19 outcomes (OR 0.72 [95% CI 0.53-0.96]; p=0.03).\n\nConclusions and RelevanceADT is associated with reduced incidence and severity of COVID-19 amongst male Veterans. Repurposing of drugs that modulate androgen production and/or action may represent viable potential treatments for COVID-19.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSDoes androgen deprivation therapy (ADT) lower incidence and severity of COVID-19?\n\nFindingsIn this observational study of male Veterans treated in the Veterans Healthcare System, ADT was associated with decreased likelihood of testing positive for SARS-CoV-2 (adjusted OR, 0.88 [95% CI, 0.81-0.95]; p=0.001). ADT was also associated with fewer severe COVID-19 outcomes (OR 0.72 [95% CI 0.53-0.96]; p=0.03).\n\nMeaningThe use of androgen deprivation therapy may be protective against SARS-CoV-2 infection and modulate severity of COVID-19 outcomes.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kyung Lee", + "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT" + }, + { + "author_name": "Kent Heberer", + "author_inst": "VA Palo Alto Healthcare System, Palo Alto, CA" + }, + { + "author_name": "Anthony Gao", + "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT" + }, + { + "author_name": "Daniel J Becker", + "author_inst": "VA New York Harbor Healthcare System, New York, NY" + }, + { + "author_name": "Stacy Loeb", + "author_inst": "VA New York Harbor Healthcare System, New York, NY" + }, + { + "author_name": "Daniel Makarov", + "author_inst": "VA New York Harbor Healthcare System, New York, NY" + }, + { + "author_name": "Barbara Gulanski", + "author_inst": "Cooperative Studies Program Clinical Epidemiology Research Center (CSP CERC), VA Connecticut Healthcare System, West Haven, CT" + }, + { + "author_name": "Scott Duvall", + "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT" + }, + { + "author_name": "Mihaela Aslan", + "author_inst": "Cooperative Studies Program Clinical Epidemiology Research Center (CSP CERC), VA Connecticut Healthcare System, West Haven, CT" + }, + { + "author_name": "Jennifer Lee", + "author_inst": "VA Palo Alto Healthcare System, Palo Alto, CA" + }, + { + "author_name": "Richard Hauger", + "author_inst": "Center of Excellence for Stress and Mental Health (CESAMH), VA San Diego Healthcare System, San Diego, CA" + }, + { + "author_name": "Mei-Chung Shih", + "author_inst": "VA Palo Alto Healthcare System, Palo Alto, CA" + }, + { + "author_name": "Julie Lynch", + "author_inst": "VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT" + }, + { + "author_name": "Matthew Rettig", + "author_inst": "VA Greater Los Angeles Healthcare System, Los Angeles, CA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "urology" + }, { "rel_doi": "10.1101/2021.05.10.21256192", "rel_title": "High Dose Convalescent Plasma in COVID-19: Results from the randomized Trial CAPSID", @@ -782490,133 +783638,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.07.443175", - "rel_title": "Vaccination boosts naturally enhanced neutralizing breadth to SARS-CoV-2 one year after infection", - "rel_date": "2021-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.07.443175", - "rel_abs": "Over one year after its inception, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several excellent vaccines. Progress in controlling the pandemic is slowed by the emergence of variants that appear to be more transmissible and more resistant to antibodies1,2. Here we report on a cohort of 63 COVID-19-convalescent individuals assessed at 1.3, 6.2 and 12 months after infection, 41% of whom also received mRNA vaccines3,4. In the absence of vaccination antibody reactivity to the receptor binding domain (RBD) of SARS-CoV-2, neutralizing activity and the number of RBD-specific memory B cells remain relatively stable from 6 to 12 months. Vaccination increases all components of the humoral response, and as expected, results in serum neutralizing activities against variants of concern that are comparable to or greater than neutralizing activity against the original Wuhan Hu-1 achieved by vaccination of naive individuals2,5-8. The mechanism underlying these broad-based responses involves ongoing antibody somatic mutation, memory B cell clonal turnover, and development of monoclonal antibodies that are exceptionally resistant to SARS-CoV-2 RBD mutations, including those found in variants of concern4,9. In addition, B cell clones expressing broad and potent antibodies are selectively retained in the repertoire over time and expand dramatically after vaccination. The data suggest that immunity in convalescent individuals will be very long lasting and that convalescent individuals who receive available mRNA vaccines will produce antibodies and memory B cells that should be protective against circulating SARS-CoV-2 variants.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Zijun Wang", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Dennis Schaefer-Babajew", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Shlomo Finkin", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Charlotte Viant", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Christian Gaebler", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Hans- Heinrich Hoffmann", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Christopher O Barnes", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Melissa Cipolla", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Victor Ramos", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Thiago Y Oliveira", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Alice Cho", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Fabian Schmidt", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Justin Da Silva", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Eva Bednarski", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Lauren Aguado", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Jim Yee", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Mridushi Daga", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Martina Turroja", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Katrina G Millard", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Mila Jankovic", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Anna Gazumyan", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Zhen Zhao", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Charles M Rice", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Paul D Bieniasz", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Marina Caskey", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Michel C Nussenzweig", - "author_inst": "The Rockefeller University" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.08.443275", "rel_title": "In-vivo Protection from SARS-CoV-2 infection by ATN-161 in k18-hACE2 transgenic mice", @@ -782936,6 +783957,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.07.443177", + "rel_title": "Mathematical Analysis and Topology of SARS-CoV-2, Bonding with Cells and Unbonding", + "rel_date": "2021-05-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.07.443177", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWWe consider the structure of the novel coronavirus (SARS-Cov-2) in terms of the number of spikes that are critical in bonding with the cells in the host. Bonding formation is considered for selection criteria with and without any treatments. Functional mappings from the discrete space of spikes and cells and their analysis are performed. We found that careful mathematical constructions help in understanding the treatment impacts, and the role of vaccines within a host. Smales famous 2-D horseshoe examples inspired us to create 3-D visualizations and understand the topological diffusion of spikes from one human organ to another organ. The pharma industry will benefit from such an analysis for designing efficient treatment and vaccine strategies.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Arni S.R. Srinivasa Rao", + "author_inst": "Laboratory for Theory and Modeling, MCG, Augusta, U.S.A." + }, + { + "author_name": "Steven Krantz", + "author_inst": "Washington University in St. Louis, MO, U.S.A." + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.05.08.443212", "rel_title": "The role of host cell glycans on virus infectivity: The SARS-CoV-2 case", @@ -784244,33 +785288,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.05.21256257", - "rel_title": "A Rapid and Reliable Liquid Chromatography/Mass Spectrometry Method for SARS-CoV-2 Diagnostics from Gargle Solutions and Saliva", - "rel_date": "2021-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256257", - "rel_abs": "We describe a rapid liquid chromatography/mass spectrometry (LC/MS) method for the direct detection and quantitation of SARS-CoV-2 nucleoprotein in gargle solutions and saliva. The method is based on a multiple-reaction monitoring (MRM) mass spectrometry approach with a total cycle time of 5 minutes per analysis and allows the detection and accurate quantitation of SARS-CoV-2 nucleoprotein as low as 500 amol/{micro}l. We improved the sample preparation protocol of our recent piloting SARS-CoV-2 LC/MS study regarding sensitivity, reproducibility, and compatibility with a complementary reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) analysis of the same sample. The aim of this work is to promote diagnostic tools that allow identifying and monitoring SARS-CoV-2 infections by LC/MS methods in a routine clinical environment.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Marc Kipping", - "author_inst": "Martin Luther University Halle-Wittenberg" - }, - { - "author_name": "Dirk Taenzler", - "author_inst": "Martin Luther University Halle-Wittenberg" - }, - { - "author_name": "Andrea Sinz", - "author_inst": "Martin Luther University Halle-Wittenberg" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.05.21256475", "rel_title": "Extracorporeal membrane oxygenation in COVID-19 patients and in-hospital mortality: results from the Brazilian Registry using a propensity score matched analysis", @@ -784578,6 +785595,249 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.04.21256571", + "rel_title": "Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses", + "rel_date": "2021-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256571", + "rel_abs": "It is unclear whether prior endemic coronavirus infections affect COVID-19 severity. Here, we show that in cases of fatal COVID-19, antibody responses to the SARS-COV-2 spike are directed against epitopes shared with endemic beta-coronaviruses in the S2 subunit of the SARS-CoV-2 spike protein. This immune response is associated with the compromised production of a de novo SARS-CoV-2 spike response among individuals with fatal COVID-19 outcomes.", + "rel_num_authors": 57, + "rel_authors": [ + { + "author_name": "Anna L McNaughton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Robert S Paton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Matthew Edmans", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jonathan Youngs", + "author_inst": "Institute of Infection & Immunity, St. Georges University of London, London, UK" + }, + { + "author_name": "Judith Wellens", + "author_inst": "University of Oxford" + }, + { + "author_name": "Prabhjeet Phalora", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alex Fyfe", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sandra Belij-Rammerstorfer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jai Bolton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jonathan Ball", + "author_inst": "Intensive Care Medicine, St. Georges University Hospital NHS Trust, London UK" + }, + { + "author_name": "George Carnell", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Wanwisa Dejnirattisai", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christina Dold", + "author_inst": "University of Oxford" + }, + { + "author_name": "David W Eyre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philip Hopkins", + "author_inst": "Kings College, London, UK" + }, + { + "author_name": "Alison Howarth", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK" + }, + { + "author_name": "Kreepa Kooblall", + "author_inst": "University of Oxford" + }, + { + "author_name": "Hannah Klim", + "author_inst": "University of Oxford" + }, + { + "author_name": "Susannah Leaver", + "author_inst": "St. Georges University Hospital NHS Trust, London UK" + }, + { + "author_name": "Lian Lee", + "author_inst": "University of Oxford" + }, + { + "author_name": "Cesar Lopez-Camacho", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sheila F Lumley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Derek Macallan", + "author_inst": "St. Georges University Hospital NHS Trust, London UK" + }, + { + "author_name": "Alexander J Mentzer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicholas Provine", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jeremy Ratcliff", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jose Slon-Compos", + "author_inst": "University of Oxford" + }, + { + "author_name": "Donal Skelly", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lucas Stolle", + "author_inst": "University of Oxford" + }, + { + "author_name": "Piyada Supasa", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nigel Temperton", + "author_inst": "University of Kent" + }, + { + "author_name": "Chris Walker", + "author_inst": "Meso-Scale" + }, + { + "author_name": "Beibei Wang", + "author_inst": "University of Oxford" + }, + { + "author_name": "Duncan Wyncoll", + "author_inst": "Guys and St Thomas Hospital NHS Foundation Trust" + }, + { + "author_name": "- OPTIC consortium", + "author_inst": "" + }, + { + "author_name": "- SNBTS consortium", + "author_inst": "" + }, + { + "author_name": "Peter Simmonds", + "author_inst": "University of Oxford" + }, + { + "author_name": "Teresa Lambe", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kenneth Baillie", + "author_inst": "University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Malcolm G Semple", + "author_inst": "University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Peter IM Openshaw", + "author_inst": "Imperial College, London" + }, + { + "author_name": "- ISARIC4C consortium", + "author_inst": "" + }, + { + "author_name": "Uri Obolski", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Marc Turner", + "author_inst": "Scottish National Blood Transfusion Service" + }, + { + "author_name": "Miles Carroll", + "author_inst": "University of Oxford" + }, + { + "author_name": "Juthathip Mongkolsapaya", + "author_inst": "University of Oxford" + }, + { + "author_name": "Gavin Screaton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Stephen H Kennedy", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lisa Jarvis", + "author_inst": "Scottish National Blood Transfusion Service" + }, + { + "author_name": "Eleanor Barnes", + "author_inst": "University of Oxford" + }, + { + "author_name": "Susanna Dunachie", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jose Lourenco", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philippa C Matthews", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tihana Bicanic", + "author_inst": "St. Georges University of London, London, UK" + }, + { + "author_name": "Paul Klenerman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sunetra Gupta", + "author_inst": "University of Oxford" + }, + { + "author_name": "Craig Peter Thompson", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.06.21256403", "rel_title": "Detection of persistent SARS-CoV-2 IgG antibodies in oral mucosal fluid and upper respiratory tract specimens following COVID-19 mRNA vaccination", @@ -786398,53 +787658,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.04.21256599", - "rel_title": "Derivation and external validation of a simple risk score to predict in-hospital mortality in patients hospitalized for COVID-19", - "rel_date": "2021-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256599", - "rel_abs": "BackgroundAs SARS-CoV-2 continues to spread, and hospitals are treating a large number of patients with COVID-19, easy-to-use risk models that predict hospital mortality can assist in clinical decision making and triage.\n\nObjectiveAs SARS-CoV-2 continues to spread, easy-to-use risk models that predict hospital mortality can assist in clinical decision making and triage. We aimed to develop a risk score model for in-hospital mortality in patients hospitalized with COVID-19 that was robust across hospitals and used clinical factors that are readily available and measured standardly across hospitals.\n\nMethodsIn this observational study we developed a risk score model using data collected by trained abstractors for patients in 20 diverse hospitals across the state of Michigan (Mi-COVID19) who were discharged between March 5, 2020 and August 14, 2020. Patients who tested positive for SARS-CoV-2 during hospitalization or were discharged with an ICD-10 code for COVID-19 (U07.1) were included. We employed an iterative forward selection approach to consider the inclusion of 145 potential risk factors available at hospital presentation. Model performance was externally validated with patients from 19 hospitals in the Mi-COVID19 registry not used in model development. We shared the model in an easy-to-use online application that allows the user to predict in-hospital mortality risk for a patient if they have any subset of the variables in the final model.\n\nResultsOur final model includes the patients age, first recorded respiratory rate, first recorded pulse oximetry, highest creatinine level on day of presentation, and hospitals COVID-19 mortality rate. No other factors showed sufficient incremental model improvement to warrant inclusion. The AUC for the derivation and validation sets were .796 and .829 respectively.\n\nConclusionsRisk of in-hospital mortality in COVID-19 patients can be reliably estimated using a few factors, which are standardly measured and available to physicians very early in a hospital encounter.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Charlotte Z Mann", - "author_inst": "University of Michigan" - }, - { - "author_name": "Chelsea Abshire", - "author_inst": "Michigan Value Collaborative" - }, - { - "author_name": "Monica Yost", - "author_inst": "Michigan Value Collaborative" - }, - { - "author_name": "Scott Kaatz", - "author_inst": "Henry Ford Hospital" - }, - { - "author_name": "Lakshmi Swaminathan", - "author_inst": "St. Joseph Mercy Hospital" - }, - { - "author_name": "Scott A Flanders", - "author_inst": "University of Michigan" - }, - { - "author_name": "Hallie C Prescott", - "author_inst": "University of Michigan" - }, - { - "author_name": "Johann A Gagnon-Bartsch", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.05.04.21256609", "rel_title": "SARS-CoV-2 infection and reinfection in a seroepidemiological workplace cohort in the United States", @@ -786916,6 +788129,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.05.442873", + "rel_title": "Diversity and selection of SARS-CoV-2 minority variants in the early New York City outbreak", + "rel_date": "2021-05-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.05.442873", + "rel_abs": "High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller, and use of replicate sequencing have the most significant impact on single nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false negative rates. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intrahost viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intrahost variation, viral diversity, and viral evolution.\n\nIMPORTANCEWhen viruses replicate inside a host, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus, nor strongly beneficial, can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in inclusion of false positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant calling tools. We used simulated and synthetic data to test their performance against a true set of variants, and then used these studies to inform variant identification in data from clinical SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Allison Roder", + "author_inst": "Systems Genomics Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases" + }, + { + "author_name": "Katherine E Johnson", + "author_inst": "Center for Genomics and Systems Biology, Department of Biology, New York University" + }, + { + "author_name": "Marissa Knoll", + "author_inst": "Center for Genomics and Systems Biology, Department of Biology, New York University" + }, + { + "author_name": "Mohammed Khalfan", + "author_inst": "Center for Genomics and Systems Biology, Department of Biology, New York University" + }, + { + "author_name": "Bessie Wang", + "author_inst": "New York University" + }, + { + "author_name": "Stephanie Banakis", + "author_inst": "Systems Genomics Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases" + }, + { + "author_name": "Allie Kreitman", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Christopher Mederos", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Jung-Ho Youn", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Rachel Mercado", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Wei Wang", + "author_inst": "J Craig Venter Institute" + }, + { + "author_name": "Denis Ruchnewitz", + "author_inst": "Institute for Biological Physics, University of Cologne" + }, + { + "author_name": "Marie I Samanovic", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Mark J Mulligan", + "author_inst": "New York University Langone Medical Center" + }, + { + "author_name": "Michael Laessig", + "author_inst": "Institute for Biological Physics, University of Cologne" + }, + { + "author_name": "Marta Luksza", + "author_inst": "Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sanchita Das", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "David Gresham", + "author_inst": "New York University" + }, + { + "author_name": "Elodie Ghedin", + "author_inst": "Systems Genomics Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.06.442935", "rel_title": "A novel class of TMPRSS2 inhibitors potently block SARS-CoV-2 and MERS-CoV viral entry and protect human epithelial lung cells", @@ -788147,61 +789451,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.01.21256090", - "rel_title": "Effect of commuting on the risk of COVID-19 and COVID-19-induced anxiety", - "rel_date": "2021-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256090", - "rel_abs": "BackgroundTo prevent the spread of coronavirus disease (COVID-19), it is important to avoid 3Cs (closed spaces, crowded places, and close-contact settings). However, the risk of contact with an unspecified number of people is inevitable while commuting to and from work. In this study, we investigated the relationship between commuting, and the risk of COVID-19 and COVID-19-induced anxiety.\n\nMethodsAn internet-based questionnaire survey was conducted to obtain a dataset from 27036 respondents. One-way commuting time was evaluated using a five-case method. The commuting distance was estimated using zip codes of the home and workplace. Logistic regression analysis was performed with the following outcomes: COVID-19 risk, close contact, infection anxiety, and infection anxiety due to commuting. Commuting distance and commuting time were analyzed separately in the model. We excluded participants with incalculable commuting distance, commuting distance exceeding 300 km, commuting distance of 0 km, or who telecommuted at least once a week.\n\nResultsThe total number of participants included in the analysis was 14038. The adjusted odds ratios (aORs) of using public transportation for severe acute respiratory syndrome coronavirus 2 infection were 4.17 (95% confidence interval [CI]: 2.51-6.93) (commuting time) and 5.18 (95% CI: 3.06-8.78) (commuting distance). The aOR of COVID-19 diagnosis decreased significantly with increasing commuting distance. The aORs of using public transportation to infection anxiety were 1.44 (95% CI: 1.31-1.59) (commuting time) and 1.45 (95% CI: 1.32-1.60) (commuting distance). The longer the commuting time, the more the aOR increased..\n\nConclusionsCOVID-19 risk, close contact, and infection anxiety were all associated with the use of public transportation during commuting. Both commuting distance and time were associated with infection anxiety due to commuting, and the strength of the association increased with increase in commuting time distance. Since transportation by commuting is associated with COVID-19 risk and anxiety, we recommend the use of telecommuting and other means of work.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Hajime Ando", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Kazunori Ikegami", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hisashi Eguchi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "- the CORoNaWork project", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.05.01.21256442", "rel_title": "Prevalence of anxiety, depression, and stress among teachers during the COVID-19 pandemic: Systematic review", @@ -788489,6 +789738,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.03.21256468", + "rel_title": "Lipid-Modulating Agents for Prevention or Treatment of COVID-19 in Randomized Trials", + "rel_date": "2021-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21256468", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is associated with systemic inflammation, endothelial activation, and multi-organ manifestations. Lipid modulating agents may be useful in treating patients with COVID-19. They may inhibit viral entry by lipid raft disruption or ameliorate the inflammatory response and endothelial activation. In addition, dyslipidemia with lower high-density lipoprotein cholesterol and higher triglycerides portends worse outcome in patients with COVID-19. Upon a systematic search, 40 RCTs with lipid modulating agents were identified, including 17 statin trials, 14 omega-3 fatty acids RCTs, 3 fibrates RCTs, 5 niacin RCTs, and 1 dalcetrapib RCT for management or prevention of COVID-19. This manuscript summarizes the ongoing or completed randomized controlled trials (RCTs) of lipid modulating agents in COVID-19 and the implications of these trials for patient management.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Azita H. H. Talasaz", + "author_inst": "Tehran Heart Center" + }, + { + "author_name": "Parham Sadeghipour", + "author_inst": "Cardiovascular Intervention Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Maryam Aghakouchakzadeh", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Isaac Dreyfus", + "author_inst": "NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, New York" + }, + { + "author_name": "Hessam Kakavand", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Hamid Ariannejad", + "author_inst": "Tehran Heart Center" + }, + { + "author_name": "Aakriti Gupta", + "author_inst": "CUMC" + }, + { + "author_name": "Mahesh Madhavan", + "author_inst": "NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, New York" + }, + { + "author_name": "Benjamin Van tassell", + "author_inst": "VCU" + }, + { + "author_name": "David Jimenez", + "author_inst": "Respiratory Department, Hospital Ramon y Cajal and Medicine Department, Universidad de Alcal" + }, + { + "author_name": "Manuel Monreal", + "author_inst": "Department of Internal Medicine, Hospital Universitari Germans Trials i Pujol" + }, + { + "author_name": "Muthiah Vaduganathan", + "author_inst": "Division of cardiovascular Medicine Division, Brigham and Women Hospital, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "John Fanikos", + "author_inst": "Department of Pharmacy, Brigham and Women Hospital, Harvard Medical School, Boston, MA, USA." + }, + { + "author_name": "Dave Dixon", + "author_inst": "VCU" + }, + { + "author_name": "Gregory Piazza", + "author_inst": "Division of cardiovascular Medicine Division, Brigham and Women Hospital, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Sahil Parikh", + "author_inst": "wYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, New York" + }, + { + "author_name": "Deepak Bhatt", + "author_inst": "Division of cardiovascular Medicine Division, Brigham and Women Hospital, Harvard Medical School, Boston, MA, USA." + }, + { + "author_name": "Gregory Lip", + "author_inst": "Liverpool Centre for Cardiovascular Science, Liverpool Heart and Chest Hospital, University of Liverpool, Liverpool, United Kingdom." + }, + { + "author_name": "Gregg Stone", + "author_inst": "Clinical Trials Center, Cardiovascular Research Foundation, New York, NY, USA." + }, + { + "author_name": "Harlan Krumholz", + "author_inst": "Yale University" + }, + { + "author_name": "Peter Libby", + "author_inst": "Division of cardiovascular Medicine Division, Brigham and Women Hospital, Harvard Medical School, Boston, MA, USA." + }, + { + "author_name": "Samuel Goldhaber", + "author_inst": "Division of cardiovascular Medicine Division, Brigham and Women Hospital, Harvard Medical School, Boston, MA, USA." + }, + { + "author_name": "Behnood Bikdeli", + "author_inst": "Division of cardiovascular Medicine Division, Brigham and Women Hospital, Harvard Medical School, Boston, MA, USA." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.05.02.21256473", "rel_title": "Does the Data Tell the True Story? A Modelling Study of Early COVID-19 Pandemic Suppression and Mitigation Strategies in Ghana", @@ -790109,25 +791465,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.01.21256389", - "rel_title": "Latin American Registry of renal involvement in COVID-19 disease. The relevance of assessing proteinuria throughout the clinical course.", - "rel_date": "2021-05-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256389", - "rel_abs": "The Latin American Society of Nephrology and Hypertension carried out a cohort prospective, multinational registry of patients with kidney impairment associated to COVID-19 in Latin America through open invitation in order to describe the characteristics of the disease in the region. A population of 870 patients from 12 countries were included. Median age was 63 years (54-74), most of patients were male (68.4%) and had comorbidities (87.2%). Acute kidney injury (AKI) was hospital-acquired in 64.7% and non-oliguric in 59.9%. Multiorgan dysfunction syndrome (MODS) due to COVID-19 and volume depletion were the main causes of AKI (59.2% and 35.7% respectively). Kidney replacement therapy was started in 46.2%. Non-recovery of renal function was observed in 65.3%. 71.5% of patients were admitted to ICU and 72.2% underwent mechanical ventilation. Proteinuria at admission was present in 62.4% of patients and proteinuria during hospital-stay occurred in 37.5%. Those patients with proteinuria at admission had higher burden of comorbidities, higher baseline sCr, higher mortality and MODS was severe. On the other hand, patients with de novo proteinuria had lower burden of comorbidities and near normal sCr at admission, but showed adverse course of disease and higher in-mortality. COVID-19 MODS was the main cause of AKI in both groups. All-cause mortality was 57.4%, and it was associated to age, chronic cardiac disease, fluid depletion, COVID-19 MODS, non-recovery of renal function, ICU admission, vasopressors, in-hospital complications and hospital stay. In conclusion, our study contributes to a better knowledge of this condition and highlights the relevance of the detection of proteinuria throughout the clinical course.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Raul Lombardi", - "author_inst": "Hospital de Clinicas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.05.01.21256452", "rel_title": "A hemagglutination-based, semi-quantitative test for point-of-care determination of SARS-CoV-2 antibody levels", @@ -790399,6 +791736,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.30.21256406", + "rel_title": "Development of in-house, indirect ELISAs for the detection of SARS-CoV-2 spike protein-associated serology in COVID-19 patients in Panama.", + "rel_date": "2021-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256406", + "rel_abs": "COVID-19 is the name of the acute respiratory disease caused by the new coronavirus SARS-CoV-2, a close relative of those that caused the severe outbreaks of SARS and MERS several years ago. Since first appearance on December of 2019, the COVID-19 pandemic has cause extremely high levels of mortality, morbidity, global economic breakdown and the consequent human suffering. While vaccination efforts are not extensive and rapid enough, the main tools to keep the virus under control are still keeping physical distancing, reinforce personal hygiene measures, using masks and early diagnosis of virus infected persons, either symptomatic or not. The main diagnostic test for the confirmation of symptomatic individuals is the detection of viral RNA by reverse transcriptase - quantitative real time PCR (RT-PCR). Additionally, serology techniques, such as ELISA are extremely useful to measure the antibodies generated in humans after virus contact, as well as the direct presence of viral antigens. In this study we aim to assemble and evaluate four ELISAs assays to measure the presence of IgG or IgM specific for the viral Spike protein in COVID-19 patients, using either the full recombinant SARS-CoV-2 Spike protein or the fragment corresponding to the receptor binding domain. As a control, we also analyzed a group of prepandemic serum samples obtained before 2017.\n\nStrong reactivity was observed against both antigens. A few prepandemic samples displayed high OD values, suggesting the possibility of some crossreactivity. All four assays show very good repeatability, both intra- and inter-assay; however, no clear relationship could be detected between positivity and time of sample collection for serology. Receiver operating characteristic analysis allowed the definition of cutoffs and evaluation of performance for each ELISA by estimation of the area under the curve. This performance parameter was high for all tests (AUC range: 0.98-0.995). Multiple comparisons between tests revealed no significant difference between each other (P values: 0.24-0.95). Our results show that both antigens are very effective to reveal both specific IgG and IgM antibodies, with high sensitivity (range 0.929-0.99) and specificity (range 0.933-0.977). The estimated congruence with the RT-PCR test, as estimated by Cohens Kappa, indicates a high agreement in all cases (range 0.874-0.937). This test will allow health authorities to have a new tool to estimate seroprevalence, and to manage and improve the serious sanitary situation created by this virus.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Carolina de la Guardia", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Giselle Rangel", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Alcibiades Villarreal", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Amador Goodridge", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Patricia L Fernandez", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Ricardo Lleonart", + "author_inst": "INDICASAT AIP" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.01.21256441", "rel_title": "Point of care testing for detection of coronaviruses including SARS-CoV-2 from saliva without treating RNA in advance", @@ -791493,33 +792869,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.30.21256366", - "rel_title": "Age-dependent association between SARS-CoV-2 cases reported by passive surveillance and viral load in wastewater", - "rel_date": "2021-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256366", - "rel_abs": "The true number of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is difficult to estimate using a case-reporting system (i.e., passive surveillance) alone because of asymptomatic infection. While wastewater-based epidemiology has been implemented as an alternative/additional monitoring tool to reduce reporting bias, the relationship between passive and wastewater surveillance data has yet to be explicitly examined. Since there is strong age dependency in the symptomatic ratio of SARS-CoV-2 infections, this study aimed to estimate i) an age-dependent association between the number of reported cases and the viral load in wastewater and ii) the time lag between those time series. The viral load in wastewater was modeled as a combination of contributions from different age groups virus shedding, incorporating the delay, and fitted with daily case count data collected from the Massachusetts Department of Public Health and SARS-CoV-2 RNA concentrations in wastewater collected by the Massachusetts Water Resources Authority. The estimated lag between the time series of viral loads in wastewater and of reported cases was 10.8 days (95% confidence interval =[10.2, 11.6]) for wastewater treatment plants northern area and 8.8 days [8.4, 9.1] for southern area. The estimated contribution rate of a reported case to the viral load in wastewater in the 0-19 yr age group was 0.38 [0.35, 0.41] for northern area and 0.40 [0.37, 0.43] for southern area, that in the 80+ yr age group was 0.67 [0.65, 0.69] for northern area and 0.51 [0.49, 0.52] for southern area. The estimated lag between those time series suggested the predictability of reported cases ten days later using viral loads in wastewater. The contribution of a reported case in passive surveillance to the viral load in wastewater differed by age, suggesting a large variation in viral shedding kinetics among age groups.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ryosuke Omori", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Fuminari Miura", - "author_inst": "Ehime University" - }, - { - "author_name": "Masaaki Kitajima", - "author_inst": "Hokkaido University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.30.21256385", "rel_title": "The immediate and longer-term impact of the COVID-19 pandemic on the mental health and wellbeing of older adults in England", @@ -791675,6 +793024,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2021.05.01.21255871", + "rel_title": "Passive and active immunity in infants born to mothers with SARS-CoV-2 infection during pregnancy: Prospective cohort study", + "rel_date": "2021-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21255871", + "rel_abs": "OBJECTIVETo investigate maternal immunoglobulins (IgM, IgG) response to SARS-CoV-2 infection during pregnancy and IgG transplacental transfer, to characterize neonatal antibody response to SARS-CoV-2 infection, and to longitudinally follow actively- and passively-acquired SARS-CoV-2 antibodies in infants.\n\nDESIGNA prospective observational study.\n\nSETTINGA public healthcare system in Santa Clara County (CA, USA).\n\nPARTICIPANTSWomen with SARS-CoV-2 infection during pregnancy and their infants were enrolled between April 15, 2020 and March 31, 2021.\n\nOUTCOMESSARS-CoV-2 serology analyses in the cord and maternal blood at delivery and longitudinally in infant blood between birth and 28 weeks of life.\n\nRESULTSOf 145 mothers who tested positive for SARS-CoV-2 during pregnancy, 86 had symptomatic infections: 78 with mild-moderate symptoms, and eight with severe-critical symptoms. Of the 147 newborns, two infants showed seroconversion at two weeks of age with high levels of IgM and IgG, including one premature infant with confirmed intrapartum infection. The seropositivity rates of the mothers at delivery was 65% (95% CI 0.56-0.73) and the cord blood was 58% (95% CI 0.49-0.66). IgG levels significantly correlated between the maternal and cord blood (Rs= 0.93, p< 0.0001). IgG transplacental transfer ratio was significantly higher when the first maternal positive PCR was 60-180 days before delivery compared to <60 days (1.2 vs. 0.6, p=<0.0001). Infant IgG negative conversion rate over follow-up periods of 1-4, 5-12, and 13-28 weeks were 8% (4/48), 12% (3/25), and 38% (5/13), respectively. The IgG seropositivity in the infants was positively related to IgG levels in the cord blood and persisted up to six months of age.\n\nCONCLUSIONSMaternal SARS-CoV-2 IgG is efficiently transferred across the placenta when infections occur more than two months before delivery. Maternally-derived passive immunity may protect infants up to six months of life. Neonates mount a strong antibody response to perinatal SARS-CoV-2 infection.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Dongli Song MD, PhD", + "author_inst": "Santa Clara Valley Medical Center, Stanford University School of Medicine" + }, + { + "author_name": "Mary Prahl MD, PhD", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Stephanie Gaw MD", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sudha Rani Narasimhan MD, IBCLC", + "author_inst": "Santa Clara Valley Medical Center, Stanford University School of Medicine" + }, + { + "author_name": "Daljeet S Rai MD", + "author_inst": "Stanford University, School of Medicine" + }, + { + "author_name": "Angela Huang RNC, MPH", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Claudia Flores BA", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Christine Y Lin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Unurzul Jigmeddagva MD", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alan H.B. Wu PhD", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Lakshmi Warrier", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Justine Levan PhD", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Catherine B.T. Nguyen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Perri Callaway PhD", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Lila Farrington PhD", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Gonzalo R Acevedo Phd", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Anna Vaaben MS", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Veronica J Gonzalez MD", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Phuong Nguyen MBA", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Elda Atmosfera CLS, MT", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Constance Marleau MT", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Christina Anderson MD", + "author_inst": "Santa Clara Valley Medical Center, Stanford University School of Medicine" + }, + { + "author_name": "Sonya Misra MD, MPH", + "author_inst": "Santa Clara Valley Medical Center, Stanford University School of Medicine" + }, + { + "author_name": "Monica Setemmle MD", + "author_inst": "Santa Clara Valley Medical Center, Stanford University School of Medicine" + }, + { + "author_name": "Maria Cortes DNP", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Jennifer McAuley NNP", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Nicole Metz RNC, BSN", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Rupalee Patel DNP", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Matthew Nudelman MD", + "author_inst": "Santa Clara Valley Medical Center" + }, + { + "author_name": "Susan Abraham MD", + "author_inst": "Santa Clara Valley Medical Center, Stanford University School of Medicine" + }, + { + "author_name": "James Byrne MD", + "author_inst": "Santa Clara Valley Medical Center, Stanford University School of Medicine" + }, + { + "author_name": "Priya Jegatheesan MD", + "author_inst": "Santa Clara Valley Medical Center, Stanford University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.30.21256060", "rel_title": "GP73 is a glucogenic hormone regulating SARS-CoV-2-induced hyperglycemia", @@ -793239,61 +794731,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.04.29.21256291", - "rel_title": "Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19", - "rel_date": "2021-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256291", - "rel_abs": "COVID-19 is a pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various disease conditions. The aim of this retrospective and observational pilot study was to examine the potential value of cfDNA plasma concentrations as a correlative biomarker in hospitalized COVID-19 patients. Lithium-Heparin plasma samples were obtained from twenty-one COVID-19 patients during hospitalization in the University Medical Center of Mainz, Germany, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). cfDNA plasma concentrations of COVID-19 patients ranged between 247.5 and 6346.25 ng/ml and the mean concentrations were 1831 {+/-} 1388 ng/ml ({+/-} standard deviation). Correlations were found between cfDNA levels and the occurrence of acute respiratory distress symptom (ARDS), acute kidney injury (AKI), myositis, neurological complications, bacterial superinfection and disease severity as defined by sepsis-related organ failure assessment score (SOFA) score. D-Dimer and C-reactive-protein (CRP), determined by clinical laboratory analysis, showed the highest correlations with cfDNA levels. The results of this observational study suggest that cfDNA plasma concentrations may serve as a predictive biomarker of disease severity in COVID-19. Prospective studies enrolling larger patient cohorts are ongoing to test this hypothesis.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Katharina Hoeter", - "author_inst": "Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany" - }, - { - "author_name": "Elmo Neuberger", - "author_inst": "Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Germany" - }, - { - "author_name": "Susanne Fischer", - "author_inst": "Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany" - }, - { - "author_name": "Manuel Herbst", - "author_inst": "Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center Mainz, Germany" - }, - { - "author_name": "Ema Juskeviciute", - "author_inst": "Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Germany." - }, - { - "author_name": "Heidi Rossmann", - "author_inst": "Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Germany" - }, - { - "author_name": "Martin F Sprinzl", - "author_inst": "Department of Internal Medicine I, University Medical Center of the Johannes Gutenberg-University Mainz, Germany." - }, - { - "author_name": "Perikles Simon", - "author_inst": "Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Germany" - }, - { - "author_name": "Marc Bodenstein", - "author_inst": "Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany" - }, - { - "author_name": "Michael K.E. Sch\u00e4fer", - "author_inst": "Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University of Mainz, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.27.21256207", "rel_title": "SARS-CoV-2 antibodies remain detectable 12 months after infection and antibody magnitude is associated with age and COVID-19 severity", @@ -793717,6 +795154,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.29.21256358", + "rel_title": "Transition in Learning Approach for Undergraduate Medical Students of Bangladesh in Covid 19 Pandemic: A Situation Analysis", + "rel_date": "2021-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256358", + "rel_abs": "BackgroundThe outbreak of Covid-19 pandemic has fundamentally transformed the landscape of medical education system upside down worldwide. This unanticipated transition without any pre build infrastructure has made this altered prospect more challenging in Bangladesh. Though many countries across the world utilize Web Based Learning (WBL), but medical students of Bangladesh are mostly unfamiliar and unaccustomed with this newly imposed online learning avenue. Therefore, this study has evaluated the familiarity, usage, attitude of students towards online class and figured out the barriers witnessed by students in Bangladesh prospect.\n\nMethodsThis cross sectional, questionnaire based study was conducted in medical colleges across Bangladesh. A questionnaire linked to google form were distributed to undergraduate medical students all over Bangladesh through different social platforms. The answered questionnaires were automatically stored in Google drive in a specific email ID.\n\nResultsA total of 1708 students participated. Among the respondents 45.1% were satisfied with online class. Though most students (45.8%) think online class is not effective like traditional lectures but 47.4% agrees to the point that online class should have complementary role in medical education. One of the strong attitude of medical students revealed that, most of them undoubtedly in unison (49.5% disagree, 30.3% strongly disagree) with that online class can never replace traditional class. 77.2% students responded that web based learning is interactive. 54.9% students pointed out interrupted internet connections with low speed during class which is a barrier to WBL. 83.2% of the respondents complained about facing audio visual problem in class which is attributed to poor network connectivity. Most students (74.8%) found online classes costly and 53.8% needed technical supports for online class.\n\nConclusionThis study finding can suggest a potential reform for online class in Bangladesh. Addressing the obstacles and expectations can execute a fruitful web based learning in Bangladesh.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Fatiha Tasmin Jeenia", + "author_inst": "Chattagram international Medical College" + }, + { + "author_name": "Md Jamal Uddin Tanin", + "author_inst": "National Hospital" + }, + { + "author_name": "Jannatul Ferdoush", + "author_inst": "BGC Trust Medical College" + }, + { + "author_name": "Fatema Johora", + "author_inst": "Army Medical College, Bogura" + }, + { + "author_name": "Afroza Hoque", + "author_inst": "Chattagram International Medical College" + }, + { + "author_name": "Asma Akter Abbasy", + "author_inst": "Brahmanbaria Medical College" + }, + { + "author_name": "Halima Sadia", + "author_inst": "Army Medical College, Chattogram" + }, + { + "author_name": "Rehnuma Urmi", + "author_inst": "Chittagong Medical College" + }, + { + "author_name": "Priyanka Moitra", + "author_inst": "Colonel Malek Medical College" + }, + { + "author_name": "Quazi Sahely Sarah", + "author_inst": "Jashore Medical College" + }, + { + "author_name": "Maliha Ata", + "author_inst": "Chattagram maa O Shishu Medical College" + }, + { + "author_name": "Kohinoor Parveen", + "author_inst": "Rangamati Medical College" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2021.04.29.21256327", "rel_title": "COVID-19 and pregnancy: An umbrella review of clinical presentation, vertical transmission, and maternal and perinatal outcomes", @@ -794941,85 +796441,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.27.21256193", - "rel_title": "Real-world effectiveness of Ad26.COV2.S adenoviral vector vaccine for COVID-19", - "rel_date": "2021-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256193", - "rel_abs": "In light of the massive and rapid vaccination campaign against COVID-19, continuous real-world effectiveness and safety assessment of the FDA-authorized vaccines is critical to amplify transparency, build public trust, and ultimately improve overall health outcomes. In this study, we leveraged large-scale longitudinal curation of electronic health records (EHRs) from the multi-state Mayo Clinic health system (MN, AZ, FL, WN, IA). We compared the infection rate of 2,195 individuals who received a single dose of the Ad26.COV2.S vaccine from Johnson & Johnson (J&J) to the infection rate of 21,950 unvaccinated, propensity-matched individuals between February 27th and April 14th 2021. Of the 1,779 vaccinated individuals with at least two weeks of follow-up, only 3 (0.17%) tested positive for SARS-CoV-2 15 days or more after vaccination compared to 128 of 17,744 (0.72%) unvaccinated individuals (4.34 fold reduction rate). This corresponds to a vaccine effectiveness of 76.7% (95% CI: 30.3-95.3%) in preventing SARS-CoV-2 infection with onset at least two weeks after vaccination. This data is consistent with the clinical trial-reported efficacy of Ad26.COV2.S in preventing moderate to severe COVID-19 with onset at least 14 days after vaccine administration (66.9%; 95% CI: 59.0-73.4%). Due to the recent authorization of the Ad26.COV2.S vaccine, there are not yet enough hospitalizations, ICU admissions, or deaths within this cohort to robustly assess the effect of vaccination on COVID-19 severity, but these outcomes will be continually assessed in near-real-time with our platform. Collectively, this study provides further evidence that a single dose of Ad26.COV2.S is highly effective in preventing SARS-CoV-2 infection and reaffirms the urgent need to continue mass vaccination efforts globally.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Juan Corchado-Garcia", - "author_inst": "nference" - }, - { - "author_name": "David Puyraimond-Zemmour", - "author_inst": "nference" - }, - { - "author_name": "Travis Hughes", - "author_inst": "nference" - }, - { - "author_name": "Tudor Cristea-Platon", - "author_inst": "nference" - }, - { - "author_name": "Patrick Lenehan", - "author_inst": "nference" - }, - { - "author_name": "Colin Pawlowski", - "author_inst": "nference" - }, - { - "author_name": "Sairam Bade", - "author_inst": "nference Labs" - }, - { - "author_name": "John C OHoro", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Gregory J Gores", - "author_inst": "nference" - }, - { - "author_name": "Amy W Williams", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Andrew D Badley", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "John Halamka", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Abinash Virk", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Melanie D Swift", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Tyler Wagner", - "author_inst": "nference" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.29.21256255", "rel_title": "Objective and Subjective COVID-19 Vaccine Reactogenicity by Age and Vaccine Manufacturer", @@ -795195,6 +796616,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.29.21256002", + "rel_title": "SARS-CoV-2 sculpts the immune system to induce sustained virus-specific nai\u0308ve-like and memory B cell responses", + "rel_date": "2021-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256002", + "rel_abs": "SARS-CoV-2 infection induces virus-reactive memory B cells expressing unmutated antibodies, which hints at their emergence from naive B cells. Yet, the dynamics of virus-specific naive B cells and their impact on immunity and immunopathology remain unclear. Here, we longitudinally studied moderate to severe COVID-19 patients to dissect SARS-CoV-2-specific B cell responses overtime. We found a broad virus-specific antibody response during acute infection, which evolved into an IgG1-dominated response during convalescence. Acute infection was associated with increased mature B cell progenitors in the circulation and the unexpected expansion of virus-targeting naive-like B cells that further augmented during convalescence together with virus-specific memory B cells. In addition to a transitory increase in tissue-homing CXCR3+ plasmablasts and extrafollicular memory B cells, most COVID-19 patients showed persistent activation of CD4+ and CD8+ T cells along with transient or long-lasting changes of key innate immune cells. Remarkably, virus-specific antibodies and the frequency of naive B cells were among the major variables defining distinct immune signatures associated with disease severity and inflammation. Aside from providing new insights into the complexity of the immune response to SARS-CoV-2, our findings indicate that the de novo recruitment of mature B cell precursors into the periphery may be central to the induction of antiviral immunity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Leire de Campos-Mata", + "author_inst": "Translational Clinical Research Program, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain" + }, + { + "author_name": "Sonia Tejedor Vaquero", + "author_inst": "Translational Clinical Research Program, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain" + }, + { + "author_name": "Roser Tach\u00f3-Pi\u00f1ot", + "author_inst": "Translational Clinical Research Program, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain" + }, + { + "author_name": "Janet Pi\u00f1ero", + "author_inst": "Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra Uni" + }, + { + "author_name": "Emilie K. Grasset", + "author_inst": "Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" + }, + { + "author_name": "Itziar Arrieta Aldea", + "author_inst": "Department of Infectious Diseases, Hospital Del Mar, Hospital del Mar Medical Research Institute (IMIM), 08003, Barcelona, Spain" + }, + { + "author_name": "Natalia Rodrigo Melero", + "author_inst": "Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08004 Barcelona" + }, + { + "author_name": "Carlo Carolis", + "author_inst": "Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08004 Barcelona" + }, + { + "author_name": "Juan P. Horcajada", + "author_inst": "4Department of Infectious Diseases, Hospital Del Mar, Hospital del Mar Medical Research Institute (IMIM), 08003, Barcelona, Spain" + }, + { + "author_name": "Andrea Cerutti", + "author_inst": "Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain; Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, Ne" + }, + { + "author_name": "Judit Villar-Garc\u00eda", + "author_inst": "Department of Infectious Diseases, Hospital Del Mar, Hospital del Mar Medical Research Institute (IMIM), 08003, Barcelona, Spain" + }, + { + "author_name": "Giuliana Magri", + "author_inst": "Translational Clinical Research Program, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.30.440988", "rel_title": "Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals", @@ -796621,73 +798105,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.28.441832", - "rel_title": "An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose.", - "rel_date": "2021-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.28.441832", - "rel_abs": "Development of efficacious single dose vaccines would substantially aid efforts to stop the uncontrolled spread of the COVID-19 pandemic. We evaluated enveloped virus-like particles (eVLPs) expressing various forms of the SARS-CoV-2 spike protein and several adjuvants in an effort to identify a COVID-19 vaccine candidate efficacious after a single dose. The eVLPs expressing a modified prefusion form of SARS-CoV-2 spike protein were selected as they induced the highest antibody binding titers and neutralizing activity after a single injection in mice. Formulation of SARS-CoV-2 S eVLPs with aluminum phosphate resulted in balanced induction of IgG2 and IgG1 isotypes and antibody binding and neutralization titers were undiminished for more than 3 months after a single immunization. A single dose of this candidate, VBI-2902a (prefusion S eVLPs formulated with aluminum phosphate), protected Syrian golden hamsters from challenge with SARS-CoV-2 and supports the on-going clinical evaluation of VBI-2902a as a potential single dose vaccine against COVID-19.\n\nHighlightsO_LIVBI-2902a is a VLP-based vaccine candidate against SARS-COV-2\nC_LIO_LIVBI-2902a contains VLPs pseudotyped with a modified prefusion SARS-COV-2 S in Alum.\nC_LIO_LIVBI-2902a induces robust neutralization antibody response against SARS-COV-2 S\nC_LIO_LIVBI-2902a protects hamsters from SARS-CoV-2 induced lung inflammation\nC_LIO_LIA single dose of VBI-2902a provides protective benefit in hamsters\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Anne-Catherine Fluckiger", - "author_inst": "VBIvaccines" - }, - { - "author_name": "Barthelemy Ontsouka", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Jasminka Bozic", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Abebaw Diress", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Tanvir Ahmed", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Tamara Berthoud", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Mingmin Liao", - "author_inst": "VIDO, University of Saskatchewan" - }, - { - "author_name": "Anh Tran", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Diana Duque", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Michael McCluskie", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Francisco Diaz-Mitoma", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "David E Anderson", - "author_inst": "VBI Vaccines" - }, - { - "author_name": "Catalina Soare", - "author_inst": "VBI Vaccines" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.29.441258", "rel_title": "Allelic variation in Class I HLA determines pre-existing memory responses to SARS-CoV-2 that shape the CD8+ T cell repertoire upon viral exposure", @@ -797043,6 +798460,37 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.04.29.441933", + "rel_title": "Possible link between higher transmissibility of B.1.617 and B.1.1.7 variants of SARS-CoV-2 and increased structural stability of its spike protein and hACE2 affinity", + "rel_date": "2021-04-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.29.441933", + "rel_abs": "The Severe Acute syndrome corona Virus 2 (SARS-CoV-2) outbreak in December 2019 has caused a global pandemic. The rapid mutation rate in the virus has caused alarming situations worldwide and is being attributed to the false negativity in RT-PCR tests, which also might lead to inefficacy of the available drugs. It has also increased the chances of reinfection and immune escape. We have performed Molecular Dynamic simulations of three different Spike-ACE2 complexes, namely Wildtype (WT), B.1.1.7 variant (N501Y Spike mutant) and B.1.617 variant (L452R, E484Q Spike mutant) and compared their dynamics, binding energy and molecular interactions. Our result shows that mutation has caused the increase in the binding energy between the Spike and hACE2. In the case of B.1.617 variant, the mutations at L452R and E484Q increased the stability and intra-chain interactions in the Spike protein, which may change the interaction ability of human antibodies to this Spike variant. Further, we found that the B.1.1.7 variant had increased hydrogen interaction with LYS353 of hACE2 and more binding affinity in comparison to WT. The current study provides the biophysical basis for understanding the molecular mechanism and rationale behind the increase in the transmissivity and infectivity of the mutants compared to wild-type SARS-CoV-2.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vipul Kumar", + "author_inst": "Department of Biochemical Engineering & Biotechnology, DAILAB, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi-110016" + }, + { + "author_name": "Jasdeep Singh", + "author_inst": "Jamia Hamdard" + }, + { + "author_name": "Seyad E. Hasnain", + "author_inst": "Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, 110016" + }, + { + "author_name": "Durai Sundar", + "author_inst": "Department of Biochemical Engineering & Biotechnology, DAILAB, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi-110016" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.04.27.21256151", "rel_title": "BNT162b2 vaccination induces SARS-CoV-2 specific antibody secretion into human milk with minimal transfer of vaccine mRNA", @@ -798519,73 +799967,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.26.21256152", - "rel_title": "Effectiveness of portable air filtration on reducing indoor aerosol counts: preclinical observational trials", - "rel_date": "2021-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256152", - "rel_abs": "ObjectiveTo assess the effectiveness of aerosol filtration by portable air cleaning devices with high efficiency particulate air (HEPA) filters used in addition to standard building heating ventilation and air-conditioning (HVAC).\n\nMethodsTest rooms, including a hospital single-patient room, were filled with test aerosol to simulate aerosol movement. Aerosol counts were measured over time with various portable air cleaning devices and room ventilation systems to quantify the aerosol concentration reduction rate and overall clearance rate.\n\nResultsPortable air cleaners were very effective in removing aerosols, especially for the devices with high flow rate. In a small control room, the aerosols were cleared 4 to 5 times faster with portable air cleaners than the room with HVAC alone. A single bed hospital room equipped with an excellent ventilation rate ([~] 14 air changes per hour) can clear the aerosols in 20 minutes. However, with the addition of two air cleaners, the clearance time became 3 times faster (in 6 minutes and 30 seconds).\n\nConclusionsPortable air cleaning devices with HEPA filtration were highly effective at removing aerosols. To clear aerosols (above 90% clearance) in under 10 minutes requires around 25 air changes per hour; readily feasible with air cleaners. Inexpensive portable air cleaning devices should be considered for small and enclosed spaces in health care settings such as inpatient rooms, personal protective equipment donning/doffing stations, and staff tea rooms. Portable air cleaners are particularly important where there is limited ability to reduce aerosol transmission with building HVAC ventilation.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Junghoon Lee", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Max Rounds", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Forbes McGain", - "author_inst": "Intensive Care, Western Health, Melbourne, Australia" - }, - { - "author_name": "Robyn Schofield", - "author_inst": "School of Earth Sciences, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Grant Skidmore", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Imogen Wadlow", - "author_inst": "School of Earth Sciences, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Kevin Kevin", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Ashley Stevens", - "author_inst": "5 Hospital Engineering, Royal Melbourne Hospital, Melbourne, Australia" - }, - { - "author_name": "Caroline Marshall", - "author_inst": "Infection Prevention and Surveillance Service, Royal Melbourne Hospital, Melbourne, Australia" - }, - { - "author_name": "Lou Irving", - "author_inst": "Respiratory Medicine, Royal Melbourne Hospital, Melbourne, Australia" - }, - { - "author_name": "Marion Kainer", - "author_inst": "Department of Infectious Diseases, Western Health, Melbourne, Australia" - }, - { - "author_name": "Kirsty Buising", - "author_inst": "Victorian Infectious Diseases service, Royal Melbourne Hospital, Melbourne, Australia" - }, - { - "author_name": "Jason Monty", - "author_inst": "Department of Mechanical Engineering, University of Melbourne, Melbourne, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.26.21256154", "rel_title": "Optimal use of COVID19 Ag-RDT screening at border crossings to prevent community transmission: a modeling analysis", @@ -798973,6 +800354,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.27.441707", + "rel_title": "Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant", + "rel_date": "2021-04-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.27.441707", + "rel_abs": "The global circulation of newly emerging variants of SARS-CoV-2 is a new threat to public health due to their increased transmissibility and immune evasion. Moreover, currently available vaccines and therapeutic antibodies were shown to be less effective against new variants, in particular, the South African (SA) variant, termed 501Y.V2 or B.1.351. To assess the efficacy of the CT-P59 monoclonal antibody against the SA variant, we sought to perform as in vitro binding and neutralization assays, and in vivo animal studies. CT-P59 neutralized B.1.1.7 variant to a similar extent as to wild type virus. CT-P59 showed reduced binding affinity against a RBD (receptor binding domain) triple mutant containing mutations defining B.1.351 (K417N/E484K/N501Y) also showed reduced potency against the SA variant in live virus and pseudovirus neutralization assay systems. However, in vivo ferret challenge studies demonstrated that a therapeutic dosage of CT-P59 was able to decrease B.1.351 viral load in the upper and lower respiratory tracts, comparable to that observed for the wild type virus. Overall, although CT-P59 showed reduced in vitro neutralizing activity against the SA variant, sufficient antiviral effect in B.1.351-infected animals was confirmed with a clinical dosage of CT-P59, suggesting that CT-P59 has therapeutic potential for COVID-19 patients infected with SA variant.\n\nHighlightsO_LICT-P59 significantly inhibit B.1.1.7 variant to a similar extent as to wild type virus\nC_LIO_LICT-P59 showed reduced potency against the B.1.351 variant in in vitro studies\nC_LIO_LITherapeutic dosage of CT-P59 showed in vivo neutralizing potency against B.1.351 in ferret challenge study.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Soo-Young Lee", + "author_inst": "Celltrion" + }, + { + "author_name": "Dong-Kyun Ryu", + "author_inst": "Celltrion" + }, + { + "author_name": "Young Ki Choi", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Penny Moore", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Carel A van Baalen", + "author_inst": "Viroclinics" + }, + { + "author_name": "rina song", + "author_inst": "Celltrion" + }, + { + "author_name": "Aloys SL Tijsma", + "author_inst": "Viroclinics" + }, + { + "author_name": "Thandeka Gwete-Moyo", + "author_inst": "National Institute for Communicable Disease" + }, + { + "author_name": "Minsoo Kim", + "author_inst": "Celltrion" + }, + { + "author_name": "Young-Il Kim", + "author_inst": "Chungbuk National University" + }, + { + "author_name": "Cheolmin Kim", + "author_inst": "Celltrion" + }, + { + "author_name": "Jong-In Kim", + "author_inst": "celltrion" + }, + { + "author_name": "Ki-Sung Kwon", + "author_inst": "Celltrion" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.27.440939", "rel_title": "Massively Multiplexed Affinity Characterization of Therapeutic Antibodies Against SARS-CoV-2 Variants", @@ -800377,89 +801825,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.04.23.21255973", - "rel_title": "EVIDENCE FOR BIOLOGICAL AGE ACCELERATION AND TELOMERE2 SHORTENING IN COVID-19 SURVIVORS", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255973", - "rel_abs": "Introduction & Backgroundthe SARS-CoV-2 infection determines the COVID-19 syndrome characterized, in the worst cases, by severe respiratory distress, pulmonary and cardiac fibrosis, inflammatory cytokines release, and immunodepression. This condition has led to the death of about 2.15% of the total infected world population so far. Among survivors, the presence of the so-called post-COVID19 syndrome (PPCS) is a common finding. In patients who survived the SARS-CoV-2 infection, overt PPCS presents one or more symptoms such as fatigue, dyspnea, memory loss, sleep disorders, and difficulty concentrating. The pathophysiology of PPCS is currently poorly understood, and whether epigenetic mechanisms are involved in this process is unexplored.\n\nMethods & ResultsIn this study, a cohort of 117 COVID19 survivors (post-COVID19) and 144 non-infected volunteers (COVID19-free) were analyzed using pyrosequencing of defined CpG islands previously identified as suitable for biological age determination. Besides, telomere length (TL) and ACE2 and DPP4 receptor expression were determined. The results show a consistent biological age increase in the post-covid population (58,44 {+/-} 14,66 ChronoAge Vs. 67,18 {+/-} 10,86 BioAge, P<0,0001), determining a DeltaAge acceleration of 10,45 {+/-} 7,29 years (+5.25 years above range of normality) compared to 3,68 {+/-} 8,17 years for the COVID19-free population (P<0,0001). A significant telomere shortening parallels this finding in the post-COVID19 cohort compared to COVID19-free subjects (post-COVID19 TL: 3,03 {+/-} 2,39 Kb vs. COVID19-free: 10,67 {+/-} 11,69 Kb; P<0,0001). Additionally, ACE2 expression was decreased in post-COVID19 patients compare to COVID19-free, while DPP-4 did not change.\n\nConclusionIn light of these observations, we hypothesize that some epigenetic alterations are associated with the post-COVID19 condition, particularly in the younger (<60 years). Although the consequences of such modifications on the long-term clinical outcome remain unclear, they might indicate a direction to investigate the pathophysiological basis of the post-COVID19 syndrome.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Alessia Mongelli", - "author_inst": "ICS MAUGERI S.P.A." - }, - { - "author_name": "veronica barbi", - "author_inst": "ICS Maugeri Pavia" - }, - { - "author_name": "michela gottardi zamperla", - "author_inst": "ICS Maugeri Pavia" - }, - { - "author_name": "sandra atlante", - "author_inst": "ICS Maugeri PAVIA" - }, - { - "author_name": "Luana Forleo", - "author_inst": "ICS Maugeri" - }, - { - "author_name": "Marialisa Nesta", - "author_inst": "policlinico Gemelli" - }, - { - "author_name": "massimo massetti", - "author_inst": "policlinico Gemelli" - }, - { - "author_name": "alfredo pontecorvi", - "author_inst": "policlinico Gemelli" - }, - { - "author_name": "simona nanni", - "author_inst": "Policlinico Gemelli" - }, - { - "author_name": "antonella farsetti", - "author_inst": "Institute for Systems Analysis and Computer Science \"A. Ruberti\"" - }, - { - "author_name": "oronzo catalano", - "author_inst": "ICS Maugeri Pavia" - }, - { - "author_name": "maurizio bussotti", - "author_inst": "ICS Maugeri Milano" - }, - { - "author_name": "laura dalla vecchia", - "author_inst": "ICS MAUGERI MILANO" - }, - { - "author_name": "tiziana bachetti", - "author_inst": "ICS Maugeri Pavia" - }, - { - "author_name": "fabio martelli", - "author_inst": "Policlinico San Donato" - }, - { - "author_name": "maria teresa la rovere", - "author_inst": "ICS Maugeri MONTESCANO" - }, - { - "author_name": "carlo gaetano", - "author_inst": "ICS Maugeri Pavia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.21.21255782", "rel_title": "Mathematical modeling suggests pre-existing immunity to SARS-CoV-2", @@ -800778,6 +802143,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.27.21256140", + "rel_title": "Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256140", + "rel_abs": "We assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1,000 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samples were analyzed for SARS-CoV-2 RNA concentrations during a six-month time period that overlapped with fall 2020 and winter 2021 COVID-19 outbreaks in each municipality. We fit a single regression model to estimate reported case rates in the six municipalities from SARS-CoV-2 RNA concentrations collected daily from corresponding wastewater treatment facilities. Results demonstrate the ability of SARS-CoV-2 RNA concentrations in primary sludge to estimate COVID-19 reported case rates across treatment facilities and wastewater catchments, with coverage probabilities ranging from 0.94 to 0.96. Leave-one-out cross validation suggests that the model can be broadly applied to wastewater catchments that range in more than one order of magnitude in population served. Estimation of case rates from wastewater data can be useful in locations with limited testing availability or testing disparities, or delays in individual COVID-19 testing programs.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Alessandro Zulli", + "author_inst": "Yale University" + }, + { + "author_name": "Annabelle Pan", + "author_inst": "Yale University" + }, + { + "author_name": "Stephen M. Bart", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Forrest W. Crawford", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Edward H Kaplan", + "author_inst": "Yale University" + }, + { + "author_name": "Matthew Cartter", + "author_inst": "Connecticut Department of Health" + }, + { + "author_name": "Albert Ko", + "author_inst": "Yale University School of Public Health" + }, + { + "author_name": "Duncan Cozens", + "author_inst": "Connecticut Agricultural Experimental Station" + }, + { + "author_name": "Marcela Sanchez", + "author_inst": "Yale University" + }, + { + "author_name": "Doug E Brackney", + "author_inst": "The Connecticut Agricultural Experiment Station" + }, + { + "author_name": "Jordan Peccia", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.22.21255955", "rel_title": "Approximate Reciprocal Relationship Between Two Cause-Specific Hazard Ratios in COVID-19 Data With Mutually Exclusive Events", @@ -802078,33 +803502,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.27.441661", - "rel_title": "Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets", - "rel_date": "2021-04-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.27.441661", - "rel_abs": "The functions of RNA are often tied to its structure, hence analyzing structure is of significant interest when studying cellular processes. Recently, large-scale structure probing (SP) studies have enabled assessment of global structure-function relationships via standard data summarizations or local folding. Here, we approach structure quantification from a hairpin-centric perspective where putative hairpins are identified in SP datasets and used as a means to capture local structural effects. This has the advantage of rapid processing of big (e.g., transcriptome-wide) data as RNA folding is circumvented, yet it captures more information than simple data summarizations. We reformulate a statistical learning algorithm we previously developed to significantly improve precision of hairpin detection, then introduce a novel nucleotide-wise measure, termed the hairpin-derived structure level (HDSL), which captures local structuredness by accounting for the presence of likely hairpin elements. Applying HDSL to data from recent studies recapitulates, strengthens, and expands on their findings which were obtained by more comprehensive folding algorithms, yet our analyses are orders of magnitude faster. These results demonstrate that hairpin detection is a promising avenue for global and rapid structure-function analysis, furthering our understanding of RNA biology and the principal features which drive biological insights from SP data.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pierce Radecki", - "author_inst": "UC Davis" - }, - { - "author_name": "Rahul Uppuluri", - "author_inst": "UC Davis" - }, - { - "author_name": "Sharon Aviran", - "author_inst": "UC Davis" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.04.26.21256081", "rel_title": "Clinical validation of RCSMS: a rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva", @@ -802328,6 +803725,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.26.441280", + "rel_title": "SARS-CoV-2 Entry Protein TMPRSS2 and Its Homologue, TMPRSS4 Adopts Structural Fold Similar to Blood Coagulation and Complement Pathway Related Proteins", + "rel_date": "2021-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.26.441280", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes TMPRSS2 receptor to enter target human cells and subsequently causes coronavirus disease 19 (COVID-19). TMPRSS2 belongs to the type II serine proteases of subfamily TMPRSS, which is characterized by the presence of the serine-protease domain. TMPRSS4 is another TMPRSS member, which has a domain architecture similar to TMPRSS2. TMPRSS2 and TMPRSS4 have been shown to be involved in SARS-CoV-2 infection. However, their normal physiological roles have not been explored in detail. In this study, we analyzed the amino acid sequences and predicted 3D structures of TMPRSS2 and TMPRSS4 to understand their functional aspects at the protein domain level. Our results suggest that these proteins are likely to have common functions based on their conserved domain organization. Furthermore, we show that the predicted 3D structure of their serine protease domain has significant similarity to that of plasminogen which dissolves blood clot, and of other blood coagulation related proteins. Additionally, molecular docking analyses of inhibitors of four blood coagulation and anticoagulation factors show the same high specificity to TMPRSS2 and TMPRSS4 3D structures. Hence, our observations are consistent with the blood coagulopathy observed in COVID-19 patients and their predicted functions based on the sequence and structural analyses offer avenues to understand better and explore therapeutic approaches for this disease.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "VIJAYKUMAR Yogesh MULEY", + "author_inst": "Instituto de Neurobiologia, Universidad Nacional Autonoma de Mexico, Queretaro, 76230, Mexico" + }, + { + "author_name": "Amit Singh", + "author_inst": "Institute of Molecular Biosciences, University of Graz, Graz, Austria" + }, + { + "author_name": "Karl Gruber", + "author_inst": "Institute of Molecular Biosciences, University of Graz, Graz, Austria" + }, + { + "author_name": "Alfredo Varela-Echavarria", + "author_inst": "Instituto de Neurobiologia, Universidad Nacional Autonoma de Mexico, Queretaro, Mexico" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.04.24.21256045", "rel_title": "Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests", @@ -803848,129 +805276,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.04.25.441271", - "rel_title": "Production of a Highly Immunogenic Antigen from SARS-CoV-2 by Covalent Coupling of the Receptor Binding Domain of Spike Protein to a Multimeric Carrier", - "rel_date": "2021-04-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.25.441271", - "rel_abs": "Since the discovery of SARS-CoV-2, several antigens have been proposed to be part of COVID-19 vaccines. The receptor binding domain (RBD) of Spike protein is one of the promising candidates to develop effective vaccines since it can induce potent neutralizing antibodies. We previously reported the production of RBD in Pichia pastoris and showed it is structurally identical to the protein produced in mammalian HEK-293T cells. In this work we designed an RBD multimer construct with the purpose of increasing RBD immunogenicity. We produced multimeric particles by a transpeptidation reaction between the RBD expressed in P. pastoris and Lumazine Synthase from Brucella abortus (BLS), which is a highly immunogenic and very stable decameric protein of 170 kDa. We vaccinated mice with two doses 30 days apart, and then we measured humoral immune response. When the number of RBD copies coupled to BLS was high (6-7 RBD molecules per BLS decamer, in average), the immune response was significantly better than that elicited by RBD alone or even by RBD-BLS comprising low number of RBD copies (1-2 RBD molecules per BLS decamer). Remarkably, the construct with high number of RBD copies induced high IgG titers with high neutralizing capacity. Furthermore, a superior immune response was observed when Al(OH)3 adjuvant was added to this formulation, exhibiting a higher titer of neutralizing antibodies. Altogether our results suggest that RBD covalent coupled to BLS forming a multimer-particle shows an advantageous architecture to the antigen-presentation to the immune system which enhances immune responses. This new antigen should be considered a potent candidate for a protein-based vaccine.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "- Argentinian AntiCovid Consortium", - "author_inst": "-" - }, - { - "author_name": "Paula M. Berguer", - "author_inst": "Fundaci\u00f3n Instituto Leloir, IIBBA, Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas (CONICET), Buenos Aires, Argentina." - }, - { - "author_name": "Matias Blaustein", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Luis Bredeston", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioqu\u00edmica. Departamento de Qu\u00edmica Biol\u00f3gica. Junin 965 C1113AAD. Buenos Aires, Argentina. CONICET-Universi" - }, - { - "author_name": "Patricio O. Craig", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Qu\u00edmica Biol\u00f3gica. Buenos Aires, Argentina. CONICET-Universidad de Buenos" - }, - { - "author_name": "Fernanda Elias", - "author_inst": "Instituto de Ciencia y Tecnolog\u00eda Dr. C\u00e9sar Milstein (Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas-Fundaci\u00f3n Pablo Cassar\u00e1). Saladillo 2468 (C1440" - }, - { - "author_name": "Paola C. Farr\u00e9", - "author_inst": "Laboratorio Pablo Cassara S.R.L." - }, - { - "author_name": "Natalia B. Fern\u00e1ndez", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Hern\u00e1n G. Gentili", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Yamila G\u00e1ndola", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Javier Gasulla", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Gustavo E. Gudesblat", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Mar\u00eda G. Herrera", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Lorena I. Iba\u00f1ez", - "author_inst": "Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas (CONICET). Departamento de Qu\u00edmica Inorg\u00e1nica, Anal\u00edtica y Qu\u00edmica F\u00edsica, Facultad de Ciencias Exact" - }, - { - "author_name": "Tommy Idrovo-Hidalgo", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Alejnadro D Nadra", - "author_inst": "Universidad de Buenos Aires" - }, - { - "author_name": "Diego G. Noseda", - "author_inst": "Universidad Nacional de San Mart\u00edn - CONICET. Instituto de Investigaciones Biotecnol\u00f3gicas (IIBio). San Mart\u00edn, Buenos Aires, Argentina." - }, - { - "author_name": "Carlos H. Pav\u00e1n", - "author_inst": "Universidad de Buenos Aires, Facultad de Farmacia y Bioqu\u00edmica. Buenos Aires, Argentina. CONICET-Universidad de Buenos Aires. Facultad de Medicina. LANAIS-PROEM" - }, - { - "author_name": "Mar\u00eda F. Pavan", - "author_inst": "Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas (CONICET). Departamento de Qu\u00edmica Inorg\u00e1nica, Anal\u00edtica y Qu\u00edmica F\u00edsica, Facultad de Ciencias Exact" - }, - { - "author_name": "Mar\u00eda F. Pignataro", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Ernesto Roman", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Qu\u00edmica Biol\u00f3gica. Buenos Aires, Argentina. CONICET-Universidad de Buenos" - }, - { - "author_name": "Lucas A.M Ruberto", - "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioqu\u00edmica. Departamento de Microbiolog\u00eda, Inmunolog\u00eda, Biotecnolog\u00eda y Gen\u00e9tica. Buenos Aires, Argentina. C" - }, - { - "author_name": "Natalia Rubinstein", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Mar\u00eda V. Sanchez", - "author_inst": "Instituto de Medicina y Biolog\u00eda Experimental de Cuyo (IMBECU).Centro Cient\u00edfico Tecnol\u00f3gico de Mendoza ( CCT-Mendoza), CONICET, Universidad Nacional de Cuyo, (" - }, - { - "author_name": "Javier Santos", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Instituto de Biociencias, Biot" - }, - { - "author_name": "Diana E. Wetzler", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Qu\u00edmica Biol\u00f3gica. Buenos Aires, Argentina. CONICET-Universidad de Buenos" - }, - { - "author_name": "Alicia M. Zelada", - "author_inst": "Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiolog\u00eda y Biolog\u00eda Molecular y Celular. Laboratorio de Agrobiotecnolog" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.04.25.441372", "rel_title": "Control-theoretic immune tradeoffs explain SARS-CoV-2 virulence and transmission variation", @@ -804230,6 +805535,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.24.21256042", + "rel_title": "A Novel Evidence-Based Predictor Tool for Hospitalization and Length of Stay: Insights from COVID19 Patients in New York City", + "rel_date": "2021-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.24.21256042", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) has evolved into a true global pandemic infecting more than 30 million people worldwide. Predictive models for key outcomes have the potential to optimize resource utilization and patient outcome as outbreaks continue to occur worldwide. We aimed to design and internally validate a web-based calculator predictive of hospitalization and length of stay (LOS) in a large cohort of COVID-19 positive patients presenting to the Emergency Department (ED) in a New York City health system.\n\nMethodsThe study cohort consisted of consecutive adult (>18 years) patients presenting to the ED of one of the Mount Sinai Health System hospitals between March, 2020 and April, 2020 who were diagnosed with COVID-19. Logistic regression was utilized to construct predictive models for hospitalization and prolonged (>3 days) LOS. Discrimination was evaluated using area under the receiver operating curve (AUC). Internal validation with bootstrapping was performed, and a web-based calculator was implemented.\n\nResultsThe cohort consisted of 5859 patients with a hospitalization rate of 65% and a prolonged LOS rate of 75% among hospitalized patients. Independent predictors of hospitalization included older age (OR=6.29; 95% CI [1.83-2.63], >65 vs. 18-44), male sex (OR=1.35 [1.17-1.55]), chronic obstructive pulmonary disease (OR=1.74; [1.00-3.03]), hypertension (OR=1.39; [1.13-1.70]), diabetes (OR=1.45; [1.16-1.81]), chronic kidney disease (OR=1.69; [1.23-2.32]), elevated maximum temperature (OR=4.98; [4.28-5.79]), and low minimum oxygen saturation (OR=13.40; [10.59-16.96]). Predictors of extended LOS included older age (OR=1.03 [1.02-1.04], per year), chronic kidney disease (OR=1.91 [1.35-2.71]), elevated maximum temperature (OR=2.91 [2.40- 3.53]), and low minimum percent oxygen saturation (OR=3.89 [3.16-4.79]). AUCs of 0.881 and 0.770 were achieved for hospitalization and LOS, respectively. A calculator was made available under the following URL: https://covid19-outcome-prediction.shinyapps.io/COVID19_Hospitalization_Calculator/\n\nConclusionThe prediction tool derived from this study can be used to optimize resource allocation, guide quality of care, and assist in designing future studies on the triage and management of patients with COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Maan El Halabi", + "author_inst": "Mount Sinai West Medical Center" + }, + { + "author_name": "James Feghali", + "author_inst": "Johns Hopkins University School of Medicine, Department of Neurosurgery" + }, + { + "author_name": "Paulino Tallon de Lara", + "author_inst": "Mount Sinai West Medical Center" + }, + { + "author_name": "Bharat Narasimhan", + "author_inst": "Mount Sinai West Medical Center" + }, + { + "author_name": "Kam Ho", + "author_inst": "Mount Sinai West Medical Center" + }, + { + "author_name": "Joseph Saabeyi", + "author_inst": "Mount Sinai West Medical Center" + }, + { + "author_name": "Judy Huang", + "author_inst": "Johns Hopkins University School of Medicine, Department of Neurosurgery" + }, + { + "author_name": "Georgina Osorio", + "author_inst": "Mount Sinai West Medical Center" + }, + { + "author_name": "Joseph Mathew", + "author_inst": "Mount Sinai West Medical Center" + }, + { + "author_name": "Juan Wisnivesky", + "author_inst": "Mount Sinai Hospital" + }, + { + "author_name": "David Steiger", + "author_inst": "Mount Sinai West Medical Center, Division of Pulmonary and Critical Care Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.04.25.441361", "rel_title": "Conserved in 186 countries the RBD fraction of SARS CoV-2 S-protein with in-silicoT500S mutation strongly blocks ACE2 rejecting the viral spike; A Molecular-docking analysis.", @@ -805462,41 +806826,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.23.21256007", - "rel_title": "Effects of the COVID-19 Pandemic on Park Use in U.S. Cities", - "rel_date": "2021-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21256007", - "rel_abs": "IntroductionThe COVID-19 pandemic focused attention on city parks as important public resources. However, it is unknown how city park use in 2020 compared to prior years and whether COVID-19 may have exacerbated racial/ethnic inequities in access. Moreover, traditional methods of measuring park use present major drawbacks.\n\nMethodsWe analyzed monthly mobility data derived from a large panel of smartphone devices, cross-referenced with a database of parks locations sourced from local agencies. We assessed park use trends in 44 of the 50 most populous U.S. cities from January 2018 to November 2020 using interrupted time series regressions. We also compared parks to other city amenities (e.g., gyms and libraries).\n\nResultsBased on a sample of 5,559 city parks, park visits declined by 14.6% (95% CI [9.2, 19.7], p < 0.001) from March through November 2020, compared to prior levels and trends. When we segmented the COVID-19 period by time of widespread closures (March-April) and partial-to-full reopenings (May-November), we estimated a larger reduction during closures (35.7% reduction, 95% CI [33.5, 37.8], p < 0.001) compared to the reduction during reopenings (8.0% reduction, 95% CI [1.9, 13.7], p = 0.001). Reductions for other amenities were more prolonged. In park service areas where a greater proportion of residents were White, reopening was associated with more visits, suggesting that racial privilege influenced access.\n\nConclusionsSmartphone mobility data can address a data availability gap for monitoring park use. Park use only declined modestly in 2020. Opportunities exist to make access more racially equitable.\n\nSignificance statementParks are public resources that promote health. Little is known about how parks have been used during the COVID-19 pandemic, when parks have become particularly important public spaces. This study introduces an approach to monitor park use over time, using location data from smartphones. This approach enabled the authors to evaluate trends in park use during the pandemic, including major gaps in visits to parks according to whether they mostly served White residents or residents of color. This big data approach offers advantages over traditional methods for monitoring park use and can help city officials to identify and address inequities in park access.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jonathan Jay", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Felicia Heykoop", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Linda Hwang", - "author_inst": "Trust for Public Land" - }, - { - "author_name": "Jorrit de Jong", - "author_inst": "Harvard Kennedy School of Government" - }, - { - "author_name": "Michelle Kondo", - "author_inst": "United States Forest Service" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.21.21255880", "rel_title": "Efficacy of universal masking for source control and personal protection from simulated cough and exhaled aerosols in a room", @@ -805780,6 +807109,57 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.04.20.21255670", + "rel_title": "Protection of previous SARS-CoV-2 infection is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel", + "rel_date": "2021-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255670", + "rel_abs": "Worldwide shortage of vaccination against SARS-CoV-2 infection while the pandemic is still uncontrolled leads many states to the dilemma whether or not to vaccinate previously infected persons. Understanding the level of protection of previous infection compared to that of vaccination is critical for policy making. We analyze an updated individual-level database of the entire population of Israel to assess the protection efficacy of both prior infection and vaccination in preventing subsequent SARS-CoV-2 infection, hospitalization with COVID-19, severe disease, and death due to COVID-19. Vaccination was highly effective with overall estimated efficacy for documented infection of 92{middle dot}8% (CI:[92{middle dot}6, 93{middle dot}0]); hospitalization 94{middle dot}2% (CI:[93{middle dot}6, 94{middle dot}7]); severe illness 94{middle dot}4% (CI:[93{middle dot}6, 95{middle dot}0]); and death 93{middle dot}7% (CI:[92{middle dot}5, 94{middle dot}7]). Similarly, the overall estimated level of protection from prior SARS-CoV-2 infection for documented infection is 94{middle dot}8% (CI:[94{middle dot}4, 95{middle dot}1]); hospitalization 94{middle dot}1% (CI:[91{middle dot}9, 95{middle dot}7]); and severe illness 96{middle dot}4% (CI:[92{middle dot}5, 98{middle dot}3]). Our results question the need to vaccinate previously-infected individuals.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yair Goldberg", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Micha Mandel", + "author_inst": "The Hebrew University of Jerusalem" + }, + { + "author_name": "Yonatan Woodbridge", + "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center" + }, + { + "author_name": "Ronen Fluss", + "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center" + }, + { + "author_name": "Ilya Novikov", + "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center" + }, + { + "author_name": "Rami Yaari", + "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center" + }, + { + "author_name": "Arnona Ziv", + "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center" + }, + { + "author_name": "Laurence Freedman", + "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center" + }, + { + "author_name": "Amit Huppert", + "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.20.21255818", "rel_title": "Estimating the total morbidity burden of COVID-19", @@ -807148,57 +808528,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.04.22.441041", - "rel_title": "Prefusion conformation of SARS-CoV-2 receptor-binding domain favors interactions with human receptor ACE2", - "rel_date": "2021-04-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.22.441041", - "rel_abs": "A new coronavirus pandemic COVID-19, caused by Severe Acute Respiratory Syndrome coronavirus (SARS-CoV-2), poses a serious threat across continents, leading the World Health Organization to declare a Public Health Emergency of International Concern. In order to block the entry of the virus into human host cells, major therapeutic and vaccine design efforts are now targeting the interactions between the SARS-CoV-2 spike (S) glycoprotein and the human cellular membrane receptor angiotensin-converting enzyme, hACE2. By analyzing cryo-EM structures of SARS-CoV-2 and SARS-CoV-1, we report here that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) that binds with hACE2 has expanded in size, undergoing a large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits higher intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction has caused a significant structural rigidification, favoring proteolytic processing of S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification in the RBD dynamics and their likely impact on infectivity.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nitesh Kumawat", - "author_inst": "School of Mathematics, Statistics and Computational Sciences, Central University of Rajasthan, Bandarsindri, Ajmer, India." - }, - { - "author_name": "Andrejs Tucs", - "author_inst": "Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan" - }, - { - "author_name": "Soumen Bera", - "author_inst": "Department of Microbiology, University of Tennessee, Knoxville, USA" - }, - { - "author_name": "Gennady N. Chuev", - "author_inst": "Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia." - }, - { - "author_name": "Marina V. Fedotova", - "author_inst": "G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia." - }, - { - "author_name": "Koji Tsuda", - "author_inst": "Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan" - }, - { - "author_name": "Sergey E. Kruchinin", - "author_inst": "G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russia." - }, - { - "author_name": "Adnan Sljoka", - "author_inst": "RIKEN Center for Advanced Intelligence Project, Tokyo, Japan." - }, - { - "author_name": "AMIT CHAKRABORTY", - "author_inst": "Sikkim University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.04.20.440658", "rel_title": "Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients", @@ -807718,6 +809047,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.04.20.21255792", + "rel_title": "Retrospective Assessment of Treatments of Hospitalized Covid-19 Patients", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255792", + "rel_abs": "Infection with SARS-Cov-2 virus, is associated with significant morbidity and mortality, in addition to the economic burden it has put on the country. While waiting for a vaccine that gives adequate protection, it is necessary to understand the course of the infection and identify drugs that could reduce its impact. The results of this multicenter study involving 1035 hospitalized patients in Pune, identified diabetes, hypertension and low lymphocyte counts as predictors of mortality. There is also an indication that multiple comorbidities add to risk of severe disease and mortality. Data from metformin treated diabetics raises the possibility of considering repurposing of this drug in a larger study. It is also noted that Hydroxychloroquine, dexamethasone, azithromycin and remdesivir were associated with lower overall mortality. Diabetes and hypertension put Covid infected patients at greater risk of death, coexistence of both diseases further augment the risk, and must be aggressively treated.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Ravindra Ghooi", + "author_inst": "Task Force on Repurposing Drugs for Covid 19 (TFORD), Venture Centre, Pune." + }, + { + "author_name": "Chitra Lele", + "author_inst": "Task Force on Repurposing Drugs for Covid 19 (TFORD), Venture Centre, Pune." + }, + { + "author_name": "Madhur Motwani", + "author_inst": "Task Force on Repurposing Drugs for Covid 19 (TFORD), Venture Centre, Pune." + }, + { + "author_name": "Santosh Dixit", + "author_inst": "Task Force on Repurposing Drugs for Covid 19 (TFORD), Venture Centre, Pune." + }, + { + "author_name": "Premnath Venugopalan", + "author_inst": "Task Force on Repurposing Drugs for Covid 19 (TFORD), Venture Centre, Pune." + }, + { + "author_name": "Sundeep Salvi", + "author_inst": "Pulmocare Research and Education (PURE) Foundation, Pune" + }, + { + "author_name": "Shreepad Bhat", + "author_inst": "Smt. Kashibai, Navale Medical College and General Hospital, Narhe, Pune" + }, + { + "author_name": "Piyush Chaudhari", + "author_inst": "Jehangir Hospital, Pune" + }, + { + "author_name": "Pradeep D'Costa", + "author_inst": "Sahyadri Superspeciality Hospitals, Pune" + }, + { + "author_name": "Ashwini Jahagirdar", + "author_inst": "Sahyadri Superspeciality Hospitals, Pune" + }, + { + "author_name": "Abhay Mane", + "author_inst": "Smt. Kashibai, Navale Medical College and General Hospital, Narhe, Pune" + }, + { + "author_name": "Vikram Padbidri", + "author_inst": "Jehangir Hospital, Pune" + }, + { + "author_name": "Chetan Pande", + "author_inst": "Sahyadri Superspeciality Hospitals, Pune" + }, + { + "author_name": "Urvi Shukla", + "author_inst": "Symbiosis University Hospital and Research Centre, Lavale, Pune." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.20.21255816", "rel_title": "Systematic review of the association between ABO blood type and COVID-19 incidence and mortality", @@ -809042,41 +810442,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.15.21252192", - "rel_title": "Previous COVID-19 infection but not Long-COVID is associated with increased adverse events following BNT162b2/Pfizer vaccination", - "rel_date": "2021-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21252192", - "rel_abs": "ImportanceUnderstanding Adverse Events (AEs) associated with SARS-CoV-2 vaccination has public health implications, especially with regards to vaccine hesitancy.\n\nObjectiveTo establish whether individuals with prior history of COVID-19 were more likely to experience AEs after BNT162b2/Pfizer vaccination, than those without previous COVID-19, and whether COVID-19-vaccination interval influenced AE severity.\n\nDesignAn observational study explored AEs after vaccination. Participants were invited to complete an electronic survey, capturing self-reported COVID-19 symptoms, PCR/antibody results, and AEs following first dose of BNT162b2/Pfizer vaccine. In a subset where PCR/antibody results could be verified, a sensitivity analysis was conducted.\n\nSettingThree North-East England hospital Trusts in the United Kingdom.\n\nParticipantsHealthcare workers formed an opportunistic sample - 265 of 974 reported prior positive SARS-CoV-2 PCR and/or antibody.\n\nExposureAll participants had received their first dose of BNT162b2/Pfizer vaccine.\n\nMain Outcomes and MeasuresNature, severity, duration, and onset of self-reported AEs (reported via a modified version of the FDA Toxicity Grading Scale for vaccine-associated AEs), was compared between those with and without a prior history of COVID-19, using 2-way ANCOVA and logistic regression. Effects of age, gender, illness-vaccine interval, and ongoing symptoms ( Long-COVID) on AEs, were also explored.\n\nResultsOf 974 respondents (81% female, mean age 48), 265 (27%) reported previous COVID-19 infection. Within this group (symptoms median 8.9 months pre-vaccination), 30 (11%) complained of Long-COVID. The proportion reporting one moderate/severe symptom was higher in the previous COVID-19 group (56% v 47%, OR=1.5 [95%CI, 1.1-2.0], p=.009), with fever, fatigue, myalgia-arthralgia and lymphadenopathy significantly more common. There was no significant relationship between illness-vaccine interval and symptom composite score (rs=0.09, p=.44). Long-COVID was not associated with worse AEs in comparison to the group without previous COVID-19. In the smaller sensitivity analysis cohort (412 people) similar findings were obtained although only myalgia and arthralgia remained significant.\n\nConclusions and RelevancePrior COVID-19 infection but not ongoing Long-COVID symptoms were associated with an increase in the risk of self-reported adverse events following BNT162b2/Pfizer vaccination. COVID-19 illness-vaccination interval did not significantly influence AEs. This data can support education around vaccine-associated AEs and, through improved understanding, help to combat vaccine hesitancy.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes previous COVID-19 infection or Long-COVID increase the frequency of Adverse Events (AEs) following first dose of BNT162b2/Pfizer vaccination?\n\nFindingsIn a survey-based observational study, healthcare workers in the United Kingdom reported AEs experienced after their first dose of BNT162b2/Pfizer vaccine. Prior COVID-19 infection, but not Long-COVID, were associated with increased risk of self-reported AEs including lymphadenopathy post-vaccination. Duration since COVID-19 infection did not affect severity of AEs.\n\nMeaningOur study can inform education and understanding of AEs associated with COVID-19 vaccination and help to combat vaccine hesitancy.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rachael Kathleen Raw", - "author_inst": "Newcastle University" - }, - { - "author_name": "Clive Kelly", - "author_inst": "South Tees Hospitals NHS Foundation Trust" - }, - { - "author_name": "Jon Rees", - "author_inst": "Sunderland University" - }, - { - "author_name": "Caroline Wroe", - "author_inst": "South Tees Hospitals NHS Foundation Trust" - }, - { - "author_name": "David Robert Chadwick", - "author_inst": "South Tees Hospitals NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.14.21255443", "rel_title": "Association of in-hospital use of ACE-I/ARB and COVID-19 outcomes in African American population", @@ -809336,6 +810701,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.15.21255348", + "rel_title": "Patient symptoms and experience following COVID-19: results from a UK wide survey", + "rel_date": "2021-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255348", + "rel_abs": "ObjectivesTo investigate the experience of people who continue to be unwell after acute COVID-19, often referred to as long COVID, both in terms of their symptoms and their interactions with healthcare.\n\nDesignWe conducted a mixed-methods analysis (quantitative and qualitative) of responses to a survey accessed through a UK online post-COVID support and information hub between April 2020 and December 2020 about peoples experiences after having acute COVID-19.\n\nParticipantsOf 3290 respondents, 78% were female, median age range 45-54 years, 92.1% reported white ethnicity; 12.7% had been hospitalised. 494 respondents (16.5%) completed the survey between 4 and 8 weeks of the onset of their symptoms, 641 (21.4%) between 8 and 12 weeks and 1865 (62.1%) more than 12 weeks after.\n\nResultsThe ongoing symptoms most frequently reported were; breathing problems (92.1%), fatigue (83.3%), muscle weakness or joint stiffness (50.6%), sleep disturbances (46.2%), problems with mental abilities (45.9%) changes in mood, including anxiety and depression (43.1%) and cough (42.3%). Symptoms did not appear to be related to the severity of the acute illness or to the presence of pre-existing medical conditions. Analysis of free text responses revealed three main themes (1) Experience of living with COVID-19 - physical and psychological symptoms that fluctuate unpredictably; (2) Interactions with healthcare; (3) Implications for the future - their own condition, society and the healthcare system and the need for research\n\nConclusionPeople living with persistent problems after the acute phase of COVID-19 report multiple and varying symptoms that are not necessarily associated with initial disease severity or the presence of pre-existing health conditions. Many have substantial unmet needs and experience barriers to accessing healthcare. Consideration of patient perspective and experiences will assist in the planning of services to address this.\n\nEthical approvalEthical approval was granted by Imperial College Research and Integrity Team (IREC; 20IC6625).\n\nWhat we already know on this subjectO_LIMany people who develop COVID-19 will go on to endure persistent symptoms past the acute phase of the disease, commonly termed long-COVID.\nC_LIO_LIKnowledge gaps exist regarding the lived experience and symptom frequency, in people with long-COVID, particularly in those who were not admitted to hospital during the acute phase of their illness.\nC_LI\n\nWhat this study addsO_LIThe findings from this large population, many of whom were not hospitalised during the acute phase of their illness, demonstrate the varying patterns and persistence of symptoms of long-COVID, which do not appear to be associated with severity of the acute phase of the disease or pre-existing medical conditions.\nC_LIO_LIQualitative findings revealing the patient experience of long-COVID symptoms, healthcare, and suggestions for future research and service adaptation.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Sara C Buttery", + "author_inst": "NHLI Imperial College" + }, + { + "author_name": "Keir E J Philip", + "author_inst": "Imperial College London" + }, + { + "author_name": "Parris J Williams", + "author_inst": "Imperial College London" + }, + { + "author_name": "Andrea Fallas", + "author_inst": "Asthma UK and British Lung Foundation Partnership, London UK" + }, + { + "author_name": "Brigitte West", + "author_inst": "Asthma UK and British Lung Foundation Partnership, London UK" + }, + { + "author_name": "Andrew Cumella", + "author_inst": "Asthma UK and British Lung Foundation Partnership, London UK" + }, + { + "author_name": "Cheryl Cheung", + "author_inst": "Asthma UK and British Lung Foundation Partnership, London UK" + }, + { + "author_name": "Samantha Walker", + "author_inst": "Asthma UK and British Lung Foundation Partnership, London UK" + }, + { + "author_name": "Jennifer K Quint", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michael I Polkey", + "author_inst": "Imperial College Hospital" + }, + { + "author_name": "Nicholas S Hopkinson", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.19.21255461", "rel_title": "Effects of BNT162b2 mRNA vaccine on Covid-19 infection and hospitalisation among older people: matched case control study for England", @@ -810947,53 +812371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.20.440654", - "rel_title": "Rapid and Efficient Inactivation of SARS-CoV-2 from Surfaces using UVC Light Emitting Diode Device", - "rel_date": "2021-04-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.440654", - "rel_abs": "Efforts are underway to develop countermeasures to prevent the environmental spread of COVID-19 pandemic caused by SARS-CoV-2. Physical decontamination methods like Ultraviolet radiation has shown to be promising. Here, we describe a novel device emitting ultraviolet C radiation (UVC), called NuvaWave, to rapidly and efficiently inactivate SARS-CoV-2. SARS-CoV-2 was dried on a chambered glass slides and introduced in a NuvaWave robotic testing unit. The robot simulated waving NuvaWave over the virus at a pre-determined UVC radiation dose of 1, 2, 4 and 8 seconds. Post-UVC exposure, virus was recovered and titered by plaque assay in Vero E6 cells. We observed that relative control (no UVC exposure), exposure of the virus to UVC for one or two seconds resulted in a >2.9 and 3.8 log10 reduction in viral titers, respectively. Exposure of the virus to UVC for four or eight seconds resulted in a reduction of greater than 4.7-log10 reduction in viral titers. The NuvaWave device inactivates SARS-CoV-2 on surfaces to below the limit of detection within one to four seconds of UVC irradiation. This device can be deployed to rapidly disinfect surfaces from SARS-CoV-2, and to assist in mitigating its spread in a variety of settings.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Varun Dwivedi", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Jun-Gyu Park", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Stephen Grenon", - "author_inst": "UV Innovators, Inc" - }, - { - "author_name": "Nicholas Medendorp Jr.", - "author_inst": "UV Innovators, Inc" - }, - { - "author_name": "Cory Hallam", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Jordi B Torrelles", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Luis Martinez-Sobrido", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Viraj Kulkarni", - "author_inst": "Texas Biomedical Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.20.440676", "rel_title": "Eicosanoid signaling as a therapeutic target in middle-aged mice with severe COVID-19", @@ -811265,6 +812642,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.04.14.21255507", + "rel_title": "A seq2seq model to forecast the COVID-19 cases, deaths and reproductive R numbers in US counties", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255507", + "rel_abs": "The global pandemic of coronavirus disease 2019 (COVID-19) has killed almost two million people worldwide and over 400 thousand in the United States (US). As the pandemic evolves, informed policy-making and strategic resource allocation relies on accurate forecasts. To predict the spread of the virus within US counties, we curated an array of county-level demographic and COVID-19-relevant health risk factors. In combination with the county-level case and death numbers curated by John Hopkins university, we developed a forecasting model using deep learning (DL). We implemented an autoencoder-based Seq2Seq model with gated recurrent units (GRUs) in the deep recurrent layers. We trained the model to predict future incident cases, deaths and the reproductive number, R. For most counties, it makes accurate predictions of new incident cases, deaths and R values, up to 30 days in the future. Our framework can also be used to predict other targets that are useful indices for policymaking, for example hospitalization or the occupancy of intensive care units. Our DL framework is publicly available on GitHub and can be adapted for other indices of the COVID-19 spread. We hope that our forecasts and model can help local governments in the continued fight against COVID-19.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yanli Zhang-James", + "author_inst": "SUNY Upstate Medical University" + }, + { + "author_name": "Jonathan L Hess", + "author_inst": "SUNY Upstate Medical University" + }, + { + "author_name": "Asif Salekin", + "author_inst": "Syracuse University, Syracuse, New York" + }, + { + "author_name": "Dongliang Wang", + "author_inst": "SUNY Upstate Medical University" + }, + { + "author_name": "Samuel Chen", + "author_inst": "SUNY Upstate Medical University" + }, + { + "author_name": "Peter Winkelstein", + "author_inst": "SUNY University at Buffalo" + }, + { + "author_name": "Christopher P Morley", + "author_inst": "Upstate Medical University" + }, + { + "author_name": "Stephen V Faraone", + "author_inst": "Upstate Medical University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.04.14.21255465", "rel_title": "Policies for Easing COVID-19 Pandemic Travel Restrictions", @@ -812677,89 +814101,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.13.21255345", - "rel_title": "Self-collected oral, nasal and saliva samples yield sensitivity comparable to professional-collected oro-nasopharyngeal swabs in SARS-CoV-2 diagnosis", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255345", - "rel_abs": "Summary/AbstractO_ST_ABSIntroductionC_ST_ABSContainment of the COVID-19 pandemic requires broad-scale testing. Laboratory capacities for real-time-PCR were increased, and are complemented by Ag-tests. However, sample-collection still requires qualified personnel and protective equipement, may produce transmission to others during conduct and travel, and is perceived uncomfortable. We tested sensitivity of three simplified self-sampling techniques compared to professional-collected combined oro-nasopharyngeal samples (cOP/NP).\n\nMethodsFrom 62 symptomatic COVID-19 outpatients, we obtained simultaneously three self- and one professional-collected sample after initial confirmation in a testing centre: (i) combination swab (tongue, cheek, both nasal vestibula, MS, (ii) saliva sponge combined with both nasal vestibula, SN, and (iii) gargled tap water, GW, (iv) professionally-collected cOP/NP (standard). We compared the results of SARS-CoV-2 PCR-assays detecting E-gene and ORF1ab for the different sample types and performed bivariate statistical analysis to determine the variables reducing sensitivity of the self-collecting procedures.\n\nResultsSARS-CoV-2 RNA was detected in all 62 professionally-collected cOP/NP. MS and SN samples showed a sensitivity of 95.2% (95%CI 86.5-99.0) and GW samples of 88.7% (78.1-95.3). Compared to the median ct-values of cOP/NP samples for E-gene (20.7) and ORF1ab (20.2) these were higher for MS (22.6 and 21.8), SN (23.3 and 22.3), and for GW (30.3 and 29.8).\n\nFor MS and SN samples but not for GW specimens, false negativity in bivariate analysis was associated with non-German mother-tongue, number of sampling errors, and with symptom duration. For symptom duration of [≤]8 days, test sensitivity for SN samples was 98.2% (95%CI 90.4-100.0) and for MS 96.4% (95%CI 87.7-99.6) and drops after day 8 below 90%.\n\nDiscussionThe study is limited to sensitivity of self-collection in symptomatic patients. Still, in this group, self-collected oral/nasal/saliva samples are reliable alternatives to professional-collected cOP/NP samples, if symptom duration does not exceed eight days and operational errors are minimized. Self-sampling could contribute to up-scaling of safe and efficient testing.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Maximilian Gertler", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Eva Krause", - "author_inst": "Robert Koch Institute - Centre for Biological Threats and Special Pathogens, Division Highly Pathogenic Viruses ZBS1, Berlin, Germany" - }, - { - "author_name": "Welmoed van Loon", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Niklas Krug", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Franka Kausch", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Chiara Rohardt", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Heike Roessig", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Medical D" - }, - { - "author_name": "Janine Michel", - "author_inst": "Robert Koch Institute - Centre for Biological Threats and Special Pathogens, Division Highly Pathogenic Viruses ZBS1, Berlin, Germany" - }, - { - "author_name": "Andreas Nitsche", - "author_inst": "Robert Koch Institute - Centre for Biological Threats and Special Pathogens, Division Highly Pathogenic Viruses ZBS1, Berlin, Germany" - }, - { - "author_name": "Marcus A. Mall", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Departmen" - }, - { - "author_name": "Olga Nikolai", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Franziska Hommes", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Susen Burock", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Charite C" - }, - { - "author_name": "Andreas K. Lindner", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Frank P. Mockenhaupt", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Institute of Tropical Medicine and Intern" - }, - { - "author_name": "Ulrich Pison", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin; Department of Anaesthesiology and Inte" - }, - { - "author_name": "Joachim Seybold", - "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health; Medical D" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.15.21255533", "rel_title": "Evaluation of seven different rapid methods for nucleic acid detection of SARS-COV-2 virus", @@ -813111,6 +814452,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.19.21255657", + "rel_title": "On whether therapeutic plasma exchange is an effective cure for severe/critical COVID-19 pneumonia", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255657", + "rel_abs": "BackgroundThere is a risk of novel mutations of SARS-CoV-2 that may render COVID-19 resistant to most of the therapies, including antiviral drugs. The evidence around the application of therapeutic plasma exchange (TPE) for the management of critically ill COVID-19 patients is still provisional and further investigations are needed to confirm its eventual beneficial effects.\n\nMethodsWe therefore carried out a single-centered retrospective observational non-placebo-controlled trial enrolling 73 inpatients from Baqiyatallah Hospital in Tehran (Iran) with diagnosis of COVID-19 pneumonia confirmed by real-time polymerase chain reaction (RT-PCR) on nasopharyngeal swabs and high-resolution computerized tomography chest scan. These patients were broken down into two groups: Group 1 (30 patients) receiving standard of care (corticosteroids, ceftriaxone, azithromycin, pantoprazole, hydroxychloroquine, lopinavir/ritonavir); and Group 2 (43 patients) receiving the above regimen plus TPE (replacing 2 liter of patients plasma by a solution, 50% of normal plasma and 50% of albumin at 5%) administered according to various time schedules. The follow-up time was 30 days and all-cause mortality was the endpoint.\n\nResultsDeaths were 6 (14%) in Group 2 and 14 (47%) in Group 1. However, different harmful risk factors prevailed among patients not receiving TPE rather than being equally split between the intervention and control group. We used an algorithm of Structural Equation Modeling (of STATA) to summarize a large pool of potential confounders into a single score (called with the descriptive name \"severity\"). Disease severity was significantly (Wilkinson rank sum test p-value=0.0000) lower among COVID-19 patients undergoing TPE (median: -2.82; range: -5.18; 7.96) as compared to those non receiving TPE (median: -1.35; range: -3.89; 8.84), confirming that treatment assignment involved a selection bias of patients according to the severity of COVID-19 at hospital admission. The adjustment for confounding was carried out using severity as covariate in Cox regression models. The univariate Hazard Ratio (HR) of 0.68 (95%CI: 0.26; 1.80; p=0.441) for TPE turned to 1.19 (95%CI: 0.43; 3.29; p=0.741) after adjusting for severity.\n\nConclusionsThe lower mortality observed among patients receiving TPE was due to a lower severity of COVID-19 rather than TPE effects.\n\nTRIAL REGISTRATIONIRCT registration number: IRCT20080901001165N58 (Iranian Registry of Clinical Trials)\n\nRegistration date: 2020-05-27, 1399/03/07 (retrospectively registered)", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Luca Cegolon", + "author_inst": "Local Health Unit N.2 \"Marca Trevigiana\"" + }, + { + "author_name": "Behzad Einollahi", + "author_inst": "Nephrology and Urology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Sina Imanizadeh", + "author_inst": "Student Research Committee (SRC), Baqiyatallah University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohammad Rezapour", + "author_inst": "Student Research Committee (SRC), Baqiyatallah University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohammad Javanbakht", + "author_inst": "Nephrology and Urology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohammad Nikpouraghdam", + "author_inst": "Nephrology and Urology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Hassan Abolghasemi", + "author_inst": "Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Giuseppe Mastrangelo", + "author_inst": "Padua University, Department of Cardiac, Thoracic, Vascular Sciences & Public Health, Padua, Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.04.14.21255511", "rel_title": "Survival analysis methods for analysis of hospitalization data: Application to COVID-19 patient hospitalization experience", @@ -814567,69 +815955,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.20.439992", - "rel_title": "Drug repurposing to face Covid-19: Celastrol, a potential leading drug capable of inhibiting SARS-CoV-2 replication and induced inflammation", - "rel_date": "2021-04-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.439992", - "rel_abs": "The global emergence of Covid-19 has caused huge human casualties. Clinical manifestations of the disease vary from asymptomatic to lethal, and the symptomatic form can be associated with cytokine storm and non-homeostatic inflammatory response. In face of the urgent demand for effective drugs to treat Covid-19, we have searched for candidate compounds using a drug repurposing approach based on in silico analysis followed by biological validation. Here we identified celastrol, a pentacyclic triterpene isolated from Tripterygium wilfordii Hook F - a plant used in traditional Chinese medicine - as one of the best compounds out of 39 repurposed drug candidates. Celastrol reverted gene expression signature from SARS-CoV-2-infected cells; bound with high-affinity energy to viral molecular targets such as main protease (Mpro) and receptor-biding domain (RBD); inhibited SARS-CoV-2 replication in monkey (Vero and Vero-ACE2) and human (Caco-2 and Calu-3) cell lines; and decreased interleukin-6 (IL-6) secretion in SARS-CoV-2-infected human cell lines. Interestingly, celastrol acted in a concentration-dependent manner, with undetectable signs of cytotoxicity. Therefore, celastrol is a promising lead drug candidate to treat Covid-19 due to its ability to suppress SARS-CoV-2 replication and IL-6 production in infected cells, two critical events in the pathophysiology of this disease.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Carlos A. Fuzo", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - }, - { - "author_name": "Ronaldo B. Martins", - "author_inst": "Departamento de Biologia Celular e Molecular e Bioagentes Patog\u00eanicos, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, B" - }, - { - "author_name": "Thais F.C. Fraga-Silva", - "author_inst": "Departamento de Bioqu\u00edmica e Imunologia. Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil." - }, - { - "author_name": "Martin K. Amstalden", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - }, - { - "author_name": "Thais Canassa-DeLeo", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - }, - { - "author_name": "Juliano P. Souza", - "author_inst": "Departamento de Biologia Celular e Molecular e Bioagentes Patog\u00eanicos, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, B" - }, - { - "author_name": "Thais M. Lima", - "author_inst": "Departamento de Biologia Celular e Molecular e Bioagentes Patog\u00eanicos, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, B" - }, - { - "author_name": "L\u00facia H. Faccioli", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - }, - { - "author_name": "Suzelei C. Fran\u00e7a", - "author_inst": "Unidade de Biotecnologia, Universidade de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto, SP, Brazil." - }, - { - "author_name": "V\u00e2nia L.D. Bonato", - "author_inst": "Departamento de Bioqu\u00edmica e Imunologia. Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, Brazil." - }, - { - "author_name": "Eurico A. Neto", - "author_inst": "Departamento de Biologia Celular e Molecular e Bioagentes Patog\u00eanicos, Faculdade de Medicina de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Preto, SP, B" - }, - { - "author_name": "Marcelo Dias-Baruffi", - "author_inst": "Departamento de An\u00e1lises Cl\u00ednicas, Toxicol\u00f3gicas e Bromatol\u00f3gicas. Faculdade de Ci\u00eancias Farmac\u00eauticas de Ribeir\u00e3o Preto, Universidade de S\u00e3o Paulo, Ribeir\u00e3o Pr" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.20.440651", "rel_title": "Comparison of Mucosal and Intramuscular Immunization against SARS-CoV-2 with Replication-Defective and Replicating Single-cycle Adenovirus Vaccines", @@ -814901,6 +816226,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.04.19.21255715", + "rel_title": "Identification of clinical features associated with mortality in COVID-19 patients", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255715", + "rel_abs": "BackgroundTo prevent infectious diseases, it is necessary to understand how they are spread and their clinical features. Early identification of risk factors and clinical features is needed to identify critically ill patients, provide suitable treatments, and prevent mortality.\n\nMethodsWe conducted a prospective study on COVID-19 patients referred to a tertiary hospital in Iran between March and November 2020. Of the 3008 patients (mean age 59.3{+/-}18.7 years, range 1 to 100 years), 1324 were women. We investigated COVID-19 related mortality and its association with clinical features including headache, chest pain, symptoms on CT, hospitalization, time to infection, history of neurological disorders, having a single or multiple risk factors, fever, myalgia, dizziness, seizure, abdominal pain, nausea, vomiting, diarrhoea and anorexia.\n\nFindingsThere was a significant association between COVID-19 mortality and old age, headache, chest pain, respiratory distress, low respiratory rate, oxygen saturation less than 93%, need for a mechanical ventilator, having symptoms on CT, hospitalization, time to infection, history of hypertension, neurological disorders, cardiovascular diseases and having a risk factor or multiple risk factors. In contrast, there was no significant association between mortality and gender, fever, myalgia, dizziness, seizure, abdominal pain, nausea, vomiting, diarrhoea and anorexia.\n\nInterpretationOur results might help identify early symptoms related to COVID-19 and better manage patients clinically.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Rahimeh Eskandarian", + "author_inst": "Semnan University of Medical Sciences" + }, + { + "author_name": "Zahra Alizadeh Sani", + "author_inst": "Omid hospital, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohaddeseh Behjati", + "author_inst": "Rajaei Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mehrdad Zahmatkesh", + "author_inst": "Semnan University of Medical Sciences" + }, + { + "author_name": "Azadeh Haddadi", + "author_inst": "Department of Biology, Faculy of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran." + }, + { + "author_name": "Kourosh Kakhi", + "author_inst": "Computer department, Monash University. Melbourne, Australia" + }, + { + "author_name": "Mohamad Roshanzamir", + "author_inst": "Department of Engineering, Fasa Branch, Islamic Azad University, Post Box No 364, Fasa, Fars 7461789818, Iran" + }, + { + "author_name": "Afshin Shoeibi", + "author_inst": "Computer Engineering Department, Ferdowsi University of Mashhad, Mashhad, Iran." + }, + { + "author_name": "Roohallah Alizadehsani", + "author_inst": "Deakin University" + }, + { + "author_name": "Sadiq Hussain", + "author_inst": "System Administrator, Dibrugarh University, Assam 786004, India" + }, + { + "author_name": "Fahime Khozeimeh", + "author_inst": "Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia" + }, + { + "author_name": "Vahideh Keyvani", + "author_inst": "Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran." + }, + { + "author_name": "Abbas Khosravi", + "author_inst": "Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia" + }, + { + "author_name": "Saeid Nahavandi", + "author_inst": "Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia" + }, + { + "author_name": "Sheikh Mohammed Shariful Islam", + "author_inst": "Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, VIC, 3220, Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.20.440678", "rel_title": "Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein", @@ -816725,97 +818125,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.15.440089", - "rel_title": "Substantial Differences in SARS-CoV-2 Antibody Responses Elicited by Natural Infection and mRNA Vaccination", - "rel_date": "2021-04-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.15.440089", - "rel_abs": "We analyzed data from two ongoing COVID-19 longitudinal serological surveys in Orange County, CA., between April 2020 and March 2021. A total of 8,476 finger stick blood specimens were collected before and after an aggressive mRNA vaccination campaign. IgG levels were determined using a multiplex antigen microarray containing 10 SARS-CoV-2 antigens, 4 SARS, 3 MERS, 12 Common CoV, and 8 Influenza antigens. Twenty-six percent of 3,347 specimens from unvaccinated Orange County residents in December 2020 were SARS-CoV-2 seropositive. The Ab response was predominantly against nucleocapsid (NP), full length spike and the spike S2 domain. Anti-receptor binding domain (RBD) reactivity was low and there was no cross-reactivity against SARS S1 or SARS RBD. An aggressive mRNA vaccination campaign at the UCI Medical Center started on December 16, 2020 and 6,724 healthcare workers were vaccinated within 3 weeks. Seroprevalence increased from 13% in December to 79% in January, 93% in February and 99% in March. mRNA vaccination induced much higher Ab levels especially against the RBD domain and significant cross-reactivity against SARS RBD and S1 was also observed. Nucleocapsid protein Abs can be used to distinguish individuals in a population of vaccinees to classify those who have been previously infected and those who have not, because nucleocapsid is not in the vaccine. Previously infected individuals developed higher Ab titers to the vaccine than those who have not been previously exposed. These results indicate that mRNA vaccination rapidly induces a much stronger and broader Ab response than SARS-CoV-2 infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Rafael Ramiro de Assis", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Aarti Jain", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Rie Nakajima", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Algis Jasinskas", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Saahir Khan", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Anton Palma", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Daniel M. Parker", - "author_inst": "University of California Irvine School of Medicine" - }, - { - "author_name": "Anthony Chau", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Amanda Leung", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Christina Grabar", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Fjolla Muqolli", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Ghali Khalil", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Jessica Colin Escobar", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Jenny Ventura", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Huw Davies", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Bruce Albala", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Bernadette Boden-Albala", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Sebastian Schubl", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Philip L Felgner", - "author_inst": "University of California Irvine School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.18.440366", "rel_title": "An Immune Cell Atlas Reveals Dynamic COVID-19 Specific Neutrophil Programming Amendable to Dexamethasone Therapy", @@ -817187,6 +818496,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.17.440288", + "rel_title": "Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein", + "rel_date": "2021-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.17.440288", + "rel_abs": "Tracking the evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through genomic surveillance programs is undoubtedly one of the key priorities in the current pandemic situation. Although the genome of SARS-CoV-2 acquires mutations at a slower rate compared with other RNA viruses, evolutionary pressures derived from the widespread circulation of SARS-CoV-2 in the human population have progressively favored the global emergence, though natural selection, of several variants of concern that carry multiple non-synonymous mutations in the spike glycoprotein. These are often placed in key sites within major antibody epitopes and may therefore confer resistance to neutralizing antibodies, leading to partial immune escape, or otherwise compensate infectivity deficits associated with other non-synonymous substitutions. As previously shown by other authors, several emerging variants carry recurrent deletion regions (RDRs) that display a partial overlap with antibody epitopes located in the spike N-terminal domain (NTD). Comparatively, very little attention has been directed towards spike insertion mutations prior to the emergence of the B.1.1.529 (omicron) lineage. This manuscript describes a single recurrent insertion region (RIR1) in the N-terminal domain of SARS-CoV-2 spike protein, characterized by at least 41 independent acquisitions of 1-8 additional codons between Val213 and Leu216 in different viral lineages. Even though RIR1 is unlikely to confer antibody escape, its association with two distinct formerly widespread lineages (A.2.5 and B.1.214.2), with the quickly spreading omicron and with other VOCs and VOIs warrants further investigation concerning its effects on spike structure and viral infectivity.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Marco Gerdol", + "author_inst": "University of Trieste" + }, + { + "author_name": "Klevia Dishnica", + "author_inst": "University of Verona" + }, + { + "author_name": "Alejandro Giorgetti", + "author_inst": "University of Verona" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.04.18.440296", "rel_title": "Molecular relationships between SARS-CoV-2 Spike protein and LIFR, a pneumonia protective IL-6 family cytokine", @@ -818563,65 +819899,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.04.16.21255618", - "rel_title": "Adverse effects of COVID-19 vaccination: machine learning and statistical approach to identify and classify incidences of morbidity and post-vaccination reactogenicity", - "rel_date": "2021-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255618", - "rel_abs": "Good vaccine safety and reliability are essential to prevent infectious disease spread. A small but significant number of apparent adverse reactions to the new COVID-19 vaccines have been reported. Here, we aim to identify possible common causes for such adverse reactions with a view to enabling strategies that reduce patient risk by using patient data to classify and characterise patients those at risk of such reactions. We examined patient medical histories and data documenting post-vaccination effects and outcomes. The data analyses were conducted by different statistical approaches followed by a set of machine learning classification algorithms. In most cases, similar features were significantly associated with poor patient reactions. These included patient prior illnesses, admission to hospitals and SARS-CoV-2 reinfection. The analyses indicated that patient age, gender, allergic history, taking other medications, type-2 diabetes, hypertension and heart disease are the most significant pre-existing factors associated with risk of poor outcome and long duration of hospital treatments, pyrexia, headache, dyspnoea, chills, fatigue, various kind of pain and dizziness are the most significant clinical predictors. The machine learning classifiers using medical history were also able to predict patients most likely to have complication-free vaccination with an accuracy score above 85%. Our study identifies profiles of individuals that may need extra monitoring and care (e.g., vaccination at a location with access to comprehensive clinical support) to reduce negative outcomes through classification approaches. Important classifiers achieving these reactions notably included allergic susceptibility and incidence of heart disease or type-2 diabetes.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Md. Martuza Ahamad", - "author_inst": "Bangabandhu Sheikh Mujibur Rahman Science and Technology University" - }, - { - "author_name": "Sakifa Aktar", - "author_inst": "Bangabandhu Sheikh Mujibur Rahman Science and Technology University" - }, - { - "author_name": "Md. Jamal Uddin", - "author_inst": "Bangabandhu Sheikh Mujibur Rahman Science and Technology University" - }, - { - "author_name": "Md. Rashed-Al-Mahfuz", - "author_inst": "University of Rajshahi" - }, - { - "author_name": "AKM Azad", - "author_inst": "University of Technology Sydney" - }, - { - "author_name": "Shahadat Uddin", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Salem A. Alyami", - "author_inst": "Imam Mohammad Ibn Saud Islamic University (IMSIU)" - }, - { - "author_name": "Iqbal H. Sarker", - "author_inst": "Chittagong University of Engineering & Technology" - }, - { - "author_name": "Pietro Lio", - "author_inst": "The University of Cambridge" - }, - { - "author_name": "Julian M.W. Quinn", - "author_inst": "The Garvan Institute of Medical Research" - }, - { - "author_name": "Mohammad Ali Moni", - "author_inst": "University of New south Wales" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.04.16.21255616", "rel_title": "Prevalence and Transmission of SARS-CoV-2 in Childcare Facilities: A Longitudinal Study", @@ -819001,6 +820278,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.15.21255569", + "rel_title": "Using rapid (point-of-care) tests for COVID-19: A decision analysis comparing the expected benefit of two screening strategies", + "rel_date": "2021-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255569", + "rel_abs": "BackgroundRapid tests for COVID-19 could be used to augment the otherwise limited laboratory-based testing capacity, but there are concerns that their utility may be compromised by their limited accuracy. The objective of this article is to compare the expected benefit (EB) of two screening strategies, one with rapid tests (SwRT) and another one without rapid tests [Formula].\n\nMethodsWe performed a decision analysis, with the overall EB defined as the proportion of correctly identified individuals minus the proportion of incorrectly identified individuals. Accordingly, the SwRT strategy will be deemed a better screening strategy if its lesser EB for COVID-19 free individuals is more than compensated by its greater EB for COVID-19 individuals. Otherwise, it will not.\n\nResultsAs expected, the EB for COVID-19 individuals was greater for the SwRT strategy, with a far superior ability to rule out the presence of COVID-19. In fact, under the scenario of interest (i.e., 8000 ID Now rapid tests in addition to 28185 lab-based RT-PCR tests), it identified almost 16% more COVID-19 individuals than the [Formula] strategy. In addition, the EB for COVID-19 free individuals was the same for both strategies, with a perfect ability at ruling in the presence of COVID-19.\n\nConclusionThe SwRT strategy identified more COVID-19 individuals and this gain was not obtained at the detriment of COVID-19 free individuals who were equally well identified by both strategies. Hence, the SwRT strategy is a better screening strategy for COVID-19. It represents an opportunity to curtail the spread of SARS-CoV-2 that we may not afford to miss with new more contagious variants becoming more and more common in Canada.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Raymond H Baillargeon", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Xavier Seyer", + "author_inst": "Not available" + }, + { + "author_name": "Ericka Bernard-Bedard", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.15.21255545", "rel_title": "Declines in life expectancy following the COVID-19 pandemic in provinces of Spain", @@ -820301,85 +821605,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.15.21253747", - "rel_title": "Multiplex Fragment Analysis Identifies SARS-CoV-2 Variants", - "rel_date": "2021-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21253747", - "rel_abs": "The rapid spread of SARS-CoV-2 Variants of Concern (VOC) necessitates systematic efforts for epidemiological surveillance. The current method for identifying variants is viral whole genome sequencing (WGS). Broad clinical adoption of sequencing is limited by costly equipment, bioinformatics support, technical expertise, and time for implementation. Here we describe a scalable, multiplex, non-sequencing-based capillary electrophoresis assay to affordably screen for SARS-CoV-2 VOC.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Andrew E Clark", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Zhaohui Wang", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Brandi L Cantarel", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Mohammed Kanchwala", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Chao Xing", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Li Chen", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Pei Irwin", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Yan Xu", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Dwight Oliver", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Francesca Lee", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Jeffrey R Gagan", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Jason Y Park", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Laura Filkins", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Alagarraju Muthukumar", - "author_inst": "UT Southwestern Medical Center, Dallas" - }, - { - "author_name": "Ravi Sarode", - "author_inst": "University of Texas Southwestern Medical" - }, - { - "author_name": "Jeffrey A SoRelle", - "author_inst": "University of Texas Southwestern Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.16.440173", "rel_title": "Viral neuroinvasion and neurotropism without neuronal damage in the hACE2 mouse model of COVID-19", @@ -820783,6 +822008,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.15.21255510", + "rel_title": "More than a year after the onset of the CoVid-19 pandemic in the UK: lessons learned from a minimalistic model capturing essential features including social awareness and policy making", + "rel_date": "2021-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255510", + "rel_abs": "The number of new daily SARS-CoV-2 infections experienced an abrupt increase during the last quarter of 2020 in almost every European country. The phenomenological explanation offered was a new mutation of the virus, first identified in the UK. We use publicly available data in combination with a time-delayed controlled SIR model, which captures the effects of preventive measures and concomitant social response on the spreading of the virus. The model, which has a unique transmission rate, enables us to reproduce the waves of infection occurred in the UK. This suggests that the new SARS-CoV-2 UK variant is as transmissible as previous strains. Our findings reveal that the sudden surge in cases was in fact related to the relaxation of preventive measures and social awareness. We also simulate the combined effects of restrictions and vaccination campaigns in 2021, demonstrating that lockdown policies are not fully effective to flatten the curve; fully effective mitigation can only be achieved via a vigorous vaccination campaign. As a matter of fact, incorporating recent data about vaccine efficacy, our simulations advocate that the UK might have overcome the worse of the CoVid-19 pandemic, provided that the vaccination campaign maintains a rate of approximately 140k jabs per day.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Miguel A Duran-Olivencia", + "author_inst": "Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK" + }, + { + "author_name": "Serafim Kalliadasis", + "author_inst": "Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.16.21255582", "rel_title": "Changes in eating habits and sedentary behavior during the COVID-19 pandemic in adolescents with chronic conditions", @@ -822039,37 +823287,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.13.21255328", - "rel_title": "Do people reduce compliance with COVID-19 guidelines following vaccination? A longitudinal analysis of matched UK adults", - "rel_date": "2021-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255328", - "rel_abs": "IntroductionCOVID-19 vaccines do not confer immediate immunity and vaccinated individuals may still be at risk of transmitting the virus. Governments have not exempted vaccinated individuals from behavioural measures to reduce the spread of COVID-19, such as practicing social distancing. However, vaccinated individuals may have reduced compliance with these measures, given lower perceived risks.\n\nMethodsWe used monthly panel data from October 2020 - March 2021 in the UK COVID-19 Social Study to assess changes in compliance following vaccination. Compliance was measured with two items on compliance with guidelines in general and compliance with social distancing. We used matching to create comparable groups of individuals by month of vaccination (January, February, or not vaccinated by February) and fixed effects regression to estimate changes in compliance over the study period.\n\nResultsCompliance increased between October 2020 - March 2021, regardless of vaccination status or month of vaccination. There was no clear evidence that vaccinated individuals decreased compliance relative to those who were not yet vaccinated.\n\nConclusionThere was little evidence that sample members vaccinated in January or February reduced compliance after receiving vaccination for COVID-19. Continued monitoring is required as younger individuals receive the vaccine, lockdown restrictions are lifted and individuals receive second doses of the vaccine.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Liam Wright", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Hei Wan Mak", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.13.21255336", "rel_title": "Trajectories of compliance with COVID-19 related guidelines: longitudinal analyses of 50,000 UK adults", @@ -822389,6 +823606,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.13.21255117", + "rel_title": "A distinct metabolic profile associated with a fatal outcome in COVID-19 patients during early epidemic in Italy", + "rel_date": "2021-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255117", + "rel_abs": "Leveraging the unique biological resource based upon the initial COVID-19 patients in Policlinico di Milano (Italy), our study provides the first metabolic profile associated with a fatal outcome. The identification of potential predictive biomarkers offers a vital opportunity to employ metabolomics in a clinical setting as diagnostic tool of disease prognosis upon hospital admission.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Elisa Saccon", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Alessandra Bandera", + "author_inst": "University of Milan" + }, + { + "author_name": "Mariarita Sciume", + "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" + }, + { + "author_name": "Flora Mikaeloff", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Abid Ali Lashari", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Stefano Aliberti", + "author_inst": "University of Milan, Milan, Italy" + }, + { + "author_name": "Michael Sachs", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Filippo Billi", + "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" + }, + { + "author_name": "Francesco Blasi", + "author_inst": "University of Milan, Milan, Italy" + }, + { + "author_name": "Erin Gabriel", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Giorgio Costantino", + "author_inst": "University of Milan, Milan, Italy" + }, + { + "author_name": "Pasquale Deroberto", + "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" + }, + { + "author_name": "Shuba Krishnan", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Andrea Gori", + "author_inst": "University of Milan, Milan, Italy" + }, + { + "author_name": "Flora Peyvandi", + "author_inst": "University of Milan, Milan, Italy" + }, + { + "author_name": "Luigia Scudeller", + "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" + }, + { + "author_name": "Christian L Lorson", + "author_inst": "University of Missouri, Columbia, USA" + }, + { + "author_name": "Luca Valenti", + "author_inst": "University of Milan, Milan, Italy" + }, + { + "author_name": "Kamlendra Singh", + "author_inst": "University of Missouri, Columbia, USA" + }, + { + "author_name": "Luca Baldini", + "author_inst": "University of Milan, Milan, Italy" + }, + { + "author_name": "Nicola Stefano Fracchiolla", + "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" + }, + { + "author_name": "Ujjwal Neogi", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.13.21255402", "rel_title": "Central obesity, smoking habit and hypertension are associated with a blunted serological response to COVID-19 mRNA vaccine", @@ -823933,57 +825253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.04.12.21254876", - "rel_title": "Behavioral nudges increase COVID-19 vaccinations: Two randomized controlled trials", - "rel_date": "2021-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21254876", - "rel_abs": "Fighting the COVID-19 pandemic requires quick and effective strategies to maximize vaccine uptake. We present two sequential randomized controlled trials (RCTs) that tackle this challenge with behavioral science insights. We deliver text-based nudges to UCLA Health patients one day (first RCT; N=113,229) and eight days (second RCT; N=90,662) after they receive notifications of vaccine eligibility. In the first RCT, text messages designed to make vaccination salient and easy to schedule boost appointment and vaccination rates by 86% and 26%, respectively. Nudges that make patients feel endowed with the vaccine heighten these effects, but addressing vaccine hesitancy via a video-based information intervention does not yield benefits beyond simple text. These results hold across ethnicity and age groups. By contrast, online experiments (N=2,003) soliciting hypothetical responses to the same messages reveal the opposite patterns, underscoring the importance of pilot-testing behavioral nudges in the real world before scaling them up. In the second RCT, we further find that receiving a second reminder boosts appointment and vaccination rates by 52% and 16%, respectively. Our findings suggest that text-based nudges can substantially increase and accelerate COVID-19 vaccinations at almost zero marginal cost, highlighting the promising role of behavioral science in addressing a critical component of the COVID-19 pandemic response.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hengchen Dai", - "author_inst": "Anderson School of Management, University of California Los Angeles, Los Angeles, California, 90095. USA" - }, - { - "author_name": "Silvia Saccardo", - "author_inst": "Department of Social and Decision Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213. USA" - }, - { - "author_name": "Maria A Han", - "author_inst": "Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, 90095. USA" - }, - { - "author_name": "Lily Roh", - "author_inst": "Office of Population Health and Accountable Care, University of California Los Angeles, 10960 Wilshire Blvd, Los Angeles, 90095. USA" - }, - { - "author_name": "Naveen Raja", - "author_inst": "Office of Population Health and Accountable Care, University of California Los Angeles, 10960 Wilshire Blvd, Los Angeles, 90095. USA" - }, - { - "author_name": "Sitaram Vangala", - "author_inst": "Department of Medicine Statistics Core, David Geffen School of Medicine, 1100 Glendon Avenue, Los Angeles, CA 90024, USA" - }, - { - "author_name": "Hardikkumar Modi", - "author_inst": "Office of Health Informatics and Analytics, University of California Los Angeles Health Sciences, Los Angeles, 90095. USA" - }, - { - "author_name": "Shital Pandya", - "author_inst": "Office of Health Informatics and Analytics, University of California Los Angeles Health Sciences, Los Angeles, 90095. USA" - }, - { - "author_name": "Daniel M Croymans", - "author_inst": "Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, 90095. USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.04.10.21255111", "rel_title": "Rapid spread and high impact of the Variant of Concern P.1 in the largest city of Brazil", @@ -824223,6 +825492,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.08.21254953", + "rel_title": "Analysis on Action Tracking Reports of COVID-19 Informs Control Strategies and Vaccine Delivery in Post-Pandemic Era", + "rel_date": "2021-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21254953", + "rel_abs": "Understanding the spread of SARS-CoV-2 provides important insights for control policies such as social-distancing interventions and vaccine delivery in the post-pandemic era. In this work, we take the advantage of action tracking reports of confirmed COVID-19 patients, which contain the mobility trajectory of patients. We analyzed reports of patients from April 2020 to January 2021 in China, a country where the residents are well-prepared for the \"new normal\" world following COVID-19 spread. We developed natural language processing (NLP) tools to transform the unstructured text of action-tracking reports to a structured network of social contacts. An epidemiology model was built on top of the network. Our analysis provides important insights for the development of control policies. Under the \"new normal\" conditions, we find that restaurants, locations less protected by mask-wearing, have a greater risk than any other location categories, including locations where people are present at higher densities (e.g., flight). We find that discouraging railway transports is crucial to avoid another wave of breakout during the Chunyun season (a period of travel in China with extremely high traffic load around the Chinese New Year). By formalizing the challenge of finding the optimal vaccine delivery among various different population groups as an optimization problem, our analysis helps to maximize the efficiency of vaccine delivery under the general situation of vaccine supply shortage. We are able to reduce the numbers of infections and deaths by 7.4% and 10.5% respectively with vaccine supply for only 1% of the population. Furthermore, with 10% vaccination rate, the numbers of infections and deaths further decrease by 52.6% and 78.1% respectively. Our work will be helpful in the design of effective policies regarding interventions, reopening, contact tracing and vaccine delivery in the \"new normal\" world following COVID-19 spread.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Xiaofei Sun", + "author_inst": "Shannon.AI" + }, + { + "author_name": "Tianjia Guan", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Tao Xue", + "author_inst": "School of Public Health, Peking University Health Science Centre" + }, + { + "author_name": "Chun Fan", + "author_inst": "Computer Center of Peking University" + }, + { + "author_name": "Meng Yang", + "author_inst": "MGI, BGI-Shenzhen" + }, + { + "author_name": "Yuxian Meng", + "author_inst": "Shannon.AI" + }, + { + "author_name": "Tianwei Zhang", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Bahabaike Jiangtulu", + "author_inst": "School of Public Health, Peking University Health Science Centre" + }, + { + "author_name": "Fei Wu", + "author_inst": "Department of Computer Science, Zhejiang University" + }, + { + "author_name": "Jiwei Li", + "author_inst": "Department of Computer Science, Zhejiang University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.12.21254610", "rel_title": "An Ecological Study to Investigate Links Between Atmospheric Pollutants From Farming and SARS-CoV-2 Mortality", @@ -825503,105 +826827,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.04.09.21255229", - "rel_title": "COVID-19 vaccine perceptions: An observational study on Reddit", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255229", - "rel_abs": "ObjectivesAs COVID-19 vaccinations accelerate in many countries, narratives skeptical of vaccination have also spread through social media. Open online forums like Reddit provide an opportunity to quantitatively examine COVID-19 vaccine perceptions over time. We examine COVID-19 misinformation on Reddit following vaccine scientific announcements.\n\nMethodsWe collected all posts on Reddit from January 1 2020 - December 14 2020 (n=266,840) that contained both COVID-19 and vaccine-related keywords. We used topic modeling to understand changes in word prevalence within topics after the release of vaccine trial data. Social network analysis was also conducted to determine the relationship between Reddit communities (subreddits) that shared COVID-19 vaccine posts, and the movement of posts between subreddits.\n\nResultsThere was an association between a Pfizer press release reporting 90% efficacy and increased discussion on vaccine misinformation. We observed an association between Johnson and Johnson temporarily halting its vaccine trials and reduced misinformation. We found that information skeptical of vaccination was first posted in a subreddit (r/Coronavirus) which favored accurate information and then reposted in subreddits associated with antivaccine beliefs and conspiracy theories (e.g. conspiracy, LockdownSkepticism).\n\nConclusionsOur findings can inform the development of interventions where individuals determine the accuracy of vaccine information, and communications campaigns to improve COVID-19 vaccine perceptions. Such efforts can increase individual- and population-level awareness of accurate and scientifically sound information regarding vaccines and thereby improve attitudes about vaccines. Further research is needed to understand how social media can contribute to COVID-19 vaccination services.\n\nFundingStudy was funded by the Yale Institute for Global Health and the Whitney and Betty MacMillan Center for International and Area Studies at Yale University. The funding bodies had no role in the design, analysis or interpretation of the data in the study.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Navin Kumar", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Isabel Corpus", - "author_inst": "Yale University" - }, - { - "author_name": "Meher Hans", - "author_inst": "Yale University" - }, - { - "author_name": "Nikhil Harle", - "author_inst": "Yale University" - }, - { - "author_name": "Nan Yang", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Curtis McDonald", - "author_inst": "Yale University" - }, - { - "author_name": "Shinpei Nakamura Sakai", - "author_inst": "Yale University" - }, - { - "author_name": "Kamila A Janmohamed", - "author_inst": "Yale University" - }, - { - "author_name": "Weiming Tang", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Jason L Schwartz", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "S Mo Jones-Jang", - "author_inst": "Boston College" - }, - { - "author_name": "Koustuv Saha", - "author_inst": "Georgia Tech" - }, - { - "author_name": "Shahan Ali Memon", - "author_inst": "New York University" - }, - { - "author_name": "Chris Bauch", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Munmun De Chaudhury", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Orestis Papakyriakopoulos", - "author_inst": "Princeton University" - }, - { - "author_name": "Joseph D Tucker", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Abhay Goyal", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Aman Tyagi", - "author_inst": "carnegie mellon university" - }, - { - "author_name": "Kaveh Khoshnood", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Saad Omer", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.09.21255195", "rel_title": "Ovarian follicular function is not altered by SARS-Cov-2 infection or BNT162b2 mRNA Covid-19 vaccination.", @@ -825997,6 +827222,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.12.21255343", + "rel_title": "Long COVID In Adults at 12 Months After Mild-to-Moderate SARS-CoV-2 Infection", + "rel_date": "2021-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255343", + "rel_abs": "BackgroundIn a proportion of patients recovered from the acute COVID-19 phase, a variable range of symptoms has been observed to persist for at least 6-months.\n\nObjectivesThe main aim of this study was to evaluate the prevalence of COVID-related symptoms 12-months after the onset of mild-to-moderate disease.\n\nMethodsProspective study based on structured questionnaires and additional outcomes.\n\nResults304/354 patients completing the survey at baseline also completed the follow-up interview (85.9%; median [range] age, 47 [18-76] years; 185 [60.9%] women). Persistence of at least one symptom at 12-months follow-up was reported by 161 patients (53.0%). The most commonly reported symptom of long COVID was felt tired (n=83, 27.3%), followed by smell or taste impairment (n=67, 22.0%), shortness of breath (n=39, 12.8%) and muscle pain (n=28, 9.2%). Being females (OR=1.64; 95% CI: 1.00-2.70), aged between 40-54 (OR=1.92; 95% CI: 1.07-3.44), having a BMI [≥]25 (OR=1.67; 95% CI: 1.00-2.78), and experiencing more symptoms during the acute phase of the disease (OR=8.71 for [≥]8 symptoms; 95% CI: 2.73-27.76) were associated with long COVID. Persistence of symptoms showed a significant impact on quality of life (p<0.0001) and depression scale scores (p=0.0102).\n\nConclusionMore than half of patients with previous mild-to-moderate symptomatic COVID-19 complained the persistence of at least one symptom 12-months after the onset of the illness.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Paolo Boscolo Rizzo", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Francesco Guida", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Jerry Polesel", + "author_inst": "Unit of Cancer Epidemiology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy" + }, + { + "author_name": "Alberto Vito Marcuzzo", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Vincenzo Capriotti", + "author_inst": "Department of Neurosciences, Section of Otolaryngology, Papa Giovanni XXIII General Hospital, Bergamo, Italy" + }, + { + "author_name": "Andrea D'Alessandro", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Enrico Zanelli", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Riccardo Marzolino", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Chiara Lazzarin", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Paolo Antonucci", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Erica Sacchet", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Margherita Tofanelli", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Daniele Borsetto", + "author_inst": "Department of ENT, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom" + }, + { + "author_name": "Nicoletta Gardenal", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Martino Pengo", + "author_inst": "Department of Cardiovascular, Neural and Metabolic Sciences, Istituto Auxologico Italiano IRCCS, Ospedale San Luca, Milano, Italy" + }, + { + "author_name": "Giancarlo Tirelli", + "author_inst": "Department of Medical, Surgical and Health Sciences, Section of Otolaryngology, University of Trieste, Trieste, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.09.21255193", "rel_title": "Case fatality rates for COVID-19 are higher than case fatality rates for motor vehicle accidents for individuals over 40 years of age", @@ -827545,49 +828849,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.10.439300", - "rel_title": "Combinatorial approach with mass spectrometry and lectin microarray dissected glycoproteomic features of virion-derived spike protein of SARS-CoV-2", - "rel_date": "2021-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.10.439300", - "rel_abs": "The COVID-19 pandemic caused by the novel coronavirus, SARS-CoV-2, has a global impact on public health. Since glycosylation of the viral envelope glycoproteins is known to be deeply associated with their immunogenicity, intensive studies on the glycans of its major glycoprotein, S protein, have been conducted. Nevertheless, the detailed site-specific glycan compositions of virion-associated S protein have not yet been clarified. Here, we conducted intensive glycoproteomic analyses of SARS-CoV-2 S protein using a combinatorial approach with two different technologies: mass spectrometry (MS) and lectin microarray. Using our unique MS1-based glycoproteomic technique, Glyco-RIDGE, in addition to MS2-based Byonic search, we identified 1,759 site-specific glycan compositions. The most frequent was HexNAc:Hex:Fuc:NeuAc:NeuGc = 6:6:1:0:0, suggesting a tri-antennary N-glycan terminating with LacNAc and having bisecting GlcNAc and a core fucose, which was found in 20 of 22 glycosylated sites. The subsequent lectin microarray analysis emphasized intensive outer arm fucosylation of glycans, which efficiently complemented the glycoproteomic features. The present results illustrate the high-resolution glycoproteomic features of SARS-CoV-2 S protein and significantly contribute to vaccine design, as well as the understanding of viral protein synthesis.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Takahiro Hiono", - "author_inst": "Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Scienc" - }, - { - "author_name": "Azusa Tomioka", - "author_inst": "Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Scienc" - }, - { - "author_name": "Hiroyuki Kaji", - "author_inst": "Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Scienc" - }, - { - "author_name": "Michihito Sasaki", - "author_inst": "Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan" - }, - { - "author_name": "Yasuko Orba", - "author_inst": "Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan" - }, - { - "author_name": "Hirofumi Sawa", - "author_inst": "Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan" - }, - { - "author_name": "Atsushi Kuno", - "author_inst": "Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Scienc" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.04.12.439473", "rel_title": "Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies", @@ -827771,6 +829032,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.12.439549", + "rel_title": "Interactions between SARS-CoV-2 N-protein and \u03b1-synuclein accelerate amyloid formation", + "rel_date": "2021-04-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.12.439549", + "rel_abs": "First cases that point at a correlation between SARS-CoV-2 infections and the development of Parkinsons disease have been reported. Currently it is unclear if there also is a direct causal link between these diseases. To obtain first insights into a possible molecular relation between viral infections and the aggregation of -synuclein protein into amyloid fibrils characteristic for Parkinsons disease, we investigated the effect of the presence of SARS-CoV-2 proteins on -synuclein aggregation. We show, in test tube experiments, that SARS-CoV-2 S-protein has no effect on -synuclein aggregation while SARS-CoV-2 N-protein considerably speeds up the aggregation process. We observe the formation of multi-protein complexes, and eventually amyloid fibrils. Microinjection of N-protein in SHSY-5Y cells disturbed the -synuclein proteostasis and increased cell death. Our results point toward direct interactions between the N-protein of SARS-CoV-2 and -synuclein as molecular basis for the observed coincidence between SARS-CoV-2 infections and Parkinsonism.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Slav Semerdzhiev", + "author_inst": "University of Twente" + }, + { + "author_name": "Mohammad Amin Abolghassemi Fakhree", + "author_inst": "University of Twente" + }, + { + "author_name": "Ine Segers-Nolten", + "author_inst": "University of Twente" + }, + { + "author_name": "Christian Blum", + "author_inst": "University of Twente" + }, + { + "author_name": "Mireille M.A.E. Claessens", + "author_inst": "University of Twente" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.04.12.439478", "rel_title": "Epitope profiling of coronavirus-binding antibodies using computational structural modelling", @@ -829283,49 +830579,6 @@ "type": "confirmatory results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.04.08.439088", - "rel_title": "The homology analysis of ACE2 gene and its distinct expression in laboratory and wild animals", - "rel_date": "2021-04-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.08.439088", - "rel_abs": "Angiotensin-converting enzyme-2 (ACE2) has been recognized as an entry receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into the host cells while bats has been suspected as natural host of SARS-CoV-2. However, the detail of intermediate host or the route of transmission of SARS-CoV-2 is still unclear. In this study, we analyze the conservation of ACE2 gene in 11 laboratory and wild animals that live in close proximity either with Bats or human and further investigated its RNA and protein expression pattern in wild bats, mice and tree shrew. We verified that the wild-bats and mice were belonged to Hipposideros pomona and Rattus norvegicus, respectively. ACE2 gene is highly conserved among all 11 animals species at the DNA level. Phylogenetic analysis based on the ACE2 nucleotide sequences revealed that wild bat and Tree shrew were forming a cluster close to human. We further report that ACE2 RNA expression pattern is highly species-specific in different tissues of different animals. Most notably, we found that the expression pattern of ACE2 RNA and protein are very different in each animal species. In summary, our results suggested that ACE2 gene is highly conserved among all 11 animals species. However, different relative expression pattern of ACE2 RNA and protein in each animal species is interesting. Further research is needed to clarify the possible connection between different relative expression pattern of ACE2 RNA and protein in different laboratory and wild animal species and the susceptibility to SARS-CoV-2 infection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gang Wang", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Zhang A-Mei", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Wang Binghui", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Jianhua Yin", - "author_inst": "Kunming University of Science and technology" - }, - { - "author_name": "Feng Yue", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Zulqarnain Baloch", - "author_inst": "Kunming University of Science and technology" - }, - { - "author_name": "Xue-shan Xia", - "author_inst": "Kunming University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.09.439203", "rel_title": "A trimeric hydrophobic zipper mediates the intramembrane assembly of SARS-CoV-2 spike", @@ -829757,6 +831010,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.09.439154", + "rel_title": "Atypical N-glycosylation of SARS-CoV-2 impairs the efficient binding of Spike-RBM to the human-host receptor hACE2", + "rel_date": "2021-04-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.09.439154", + "rel_abs": "SARS-CoV-2 internalization by human host cells relies on the molecular binding of its spike glycoprotein (SGP) to the angiotensin-converting-enzyme-2 (hACE2) receptor. It remains unknown whether atypical N-glycosylation of SGP modulates SARS-CoV-2 tropism for infections. Here, we address this question through an extensive bioinformatics analysis of publicly available structural and genetic data. We identified two atypical sequons (sequences of N-glycosylation: NGV 481-483 and NGV 501-503), strategically located on the receptor-binding motif (RBM) of SGP and facing the hACE2 receptor. Interestingly, the cryo-electron microscopy structure of trimeric SGP in complex with potent-neutralizing antibodies from convalescent patients revealed covalently-linked N-glycans in NGV 481-483 atypical sequons. Furthermore, NGV 501-503 atypical sequon involves the asparagine-501 residue, whose highly-transmissible mutation N501Y is present in circulating variants of major concerns and affects the SGP-hACE2 binding-interface through the well-known hotspot-353. These findings suggest that atypical SGP post-translational modifications modulate the SGP-hACE2 binding-affinity affecting consequently SARS-CoV-2 transmission and pathogenesis.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gustavo Gamez", + "author_inst": "University of Antioquia" + }, + { + "author_name": "Juan A Hermoso", + "author_inst": "Spanish National Research Council- CSIC" + }, + { + "author_name": "Cesar Carrasco-Lopez", + "author_inst": "Princeton University" + }, + { + "author_name": "Alejandro Gomez Mejia", + "author_inst": "University Hospital Zurich" + }, + { + "author_name": "Carlos Muskus", + "author_inst": "University of Antioquia" + }, + { + "author_name": "Sven Hammerschmidt", + "author_inst": "University of Greifswald" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.04.08.21254580", "rel_title": "North West London Covid-19 Vaccination Programme: Real-world evidence for Vaccine uptake and effectiveness.", @@ -831085,45 +832377,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.06.21255013", - "rel_title": "Reduction in the 2020 Life Expectancy in Brazil after COVID-19", - "rel_date": "2021-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21255013", - "rel_abs": "Brazil has the second-largest number of COVID-19 deaths worldwide. We use data on reported deaths to measure and compare the death toll across states from a demographic perspective. We estimate a decline in 2020 life expectancy at birth of 1.94 years, resulting in a mortality level not seen since 2013. The reduction in life expectancy at age 65 was 1.58 years, setting Brazil back to 2009 levels. The decline was larger for males, widening by 2.3% and 5.4% the female-male gap in life expectancy at birth and at age 65, respectively. Among states, Amazonas lost 59.6% of the improvements in life expectancy at birth since 2000. With 2021 COVID-19 deaths at about 43% of the total 2020 figures (as of mid-March) the demographic effect is likely to be even higher this year.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Marcia C. Castro", - "author_inst": "Department of Global Health and Population, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Susie Gurzenda", - "author_inst": "Department of Global Health and Population, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Cassio M. Turra", - "author_inst": "Demography Department, Cedeplar, Universidade Federal de Minas Gerais" - }, - { - "author_name": "Sun Kim", - "author_inst": "Department of Global Health and Population, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Theresa Andrasfay", - "author_inst": "Leonard Davis School of Gerontology, University of Southern California" - }, - { - "author_name": "Noreen Goldman", - "author_inst": "Office of Population Research, Princeton University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.07.21255071", "rel_title": "Results Availability and Timeliness of Registered COVID-19 Clinical Trials: A Cross-Sectional Study", @@ -831403,6 +832656,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.06.21255017", + "rel_title": "Short-range exposure to airborne virus transmission and current guidelines", + "rel_date": "2021-04-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21255017", + "rel_abs": "After the Spanish flu pandemic, it was apparent that airborne transmission was crucial to spreading virus contagion, and research responded by producing several fundamental works like the experiments of Duguid [J. Hyg. 44:6, 1946] and the model of Wells [Am. J. Hyg., 20:611-18,1934]. These seminal works have been pillars to past and current guidelines published by health organizations. However, in about one century, understanding of turbulent aerosol transport by jets and plumes has enormously progressed and it is now time to use this body of developed knowledge. In this work, we use detailed experiments and accurate computationally-intensive numerical simulations of droplet-laden turbulent puffs emitted during sneezes in a wide range of environmental conditions. We consider the same emission - number of drops, drop size distribution and initial velocity - and we change environmental parameters as temperature and humidity, and we observe strong variation in droplets evaporation or condensation in accordance with their local temperature and humidity microenvironment. We assume that 3% of the initial droplet volume is made of non-volatile matter. Our systematic analysis confirms that droplets lifetime is always about one order of magnitude larger compared to previous predictions, in some cases up to 200 times. Finally, we have been able to produce original virus exposure maps, which can be a useful instrument for health scientists and practitioners to calibrate new guidelines to prevent short-range airborne disease transmission.\n\nSignificance StatementViolent expiratory events represent an important route for the spread of respiratory viruses, as the SARS-CoV-2 virus. We use finely-resolved experiments and simulations to quantify how the turbulent cloud of moist air exhaled during a sneeze largely increases the airborne time and the lifespan of virus-loaded droplets. By providing visualizations of the spatial distribution of the virus copies, we highlight the high infection risk associated with droplets that remain airborne in the near proximity of an infected individual. The present study aims at raising awareness among public health authorities about this infection risk, which is grossly underestimated by current guidelines.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jietuo Wang", + "author_inst": "University of Padova" + }, + { + "author_name": "Mobin Alipour", + "author_inst": "TU Wien" + }, + { + "author_name": "Giovanni Soligo", + "author_inst": "Okinawa Institute of Science and Technology" + }, + { + "author_name": "Alessio Roccon", + "author_inst": "TU Wien" + }, + { + "author_name": "Marco De Paoli", + "author_inst": "TU Wien" + }, + { + "author_name": "Francesco Picano", + "author_inst": "University of Padova" + }, + { + "author_name": "Alfredo Soldati", + "author_inst": "TU Wien" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.06.21254995", "rel_title": "Performance Comparison of a Flow Cytometry-based and Two Commercial Chemiluminescent Immunoassays for Detection and Quantification of Antibodies Binding to SARS-CoV-2 Spike Protein", @@ -833171,45 +834467,6 @@ "type": "new results", "category": "synthetic biology" }, - { - "rel_doi": "10.1101/2021.04.06.438540", - "rel_title": "TMPRSS2 and RNA-dependent RNA polymerase are effective targets of therapeutic intervention for treatment of COVID-19 caused by SARS-CoV-2 variants (B.1.1.7 and B.1.351)", - "rel_date": "2021-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438540", - "rel_abs": "SARS-CoV-2 is a causative agent of COVID-19 pandemic and the development of therapeutic interventions is urgently needed. So far, monoclonal antibodies and drug repositioning are the main methods for drug development and this effort was partially successful. Since the beginning of COVID-19 pandemic, the emergence of SARS-CoV-2 variants has been reported in many parts of the world and the main concern is whether the current vaccines and therapeutics are still effective against these variant viruses. The viral entry and viral RNA-dependent RNA polymerase (RdRp) are the main targets of current drug development, thus the inhibitory effects of TMPRSS2 and RdRp inhibitors were compared among the early SARS-CoV-2 isolate (lineage A) and the two recent variants (lineage B.1.1.7 and lineage B.1.351) identified in the UK and South Africa, respectively. Our in vitro analysis of viral replication showed that the drugs targeting TMPRSS2 and RdRp are equally effective against the two variants of concern.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jihye Lee", - "author_inst": "Institut Pasteur Korea" - }, - { - "author_name": "JinAh Lee", - "author_inst": "Institut Pasteur Korea" - }, - { - "author_name": "Hyeon Ju Kim", - "author_inst": "Institut Pasteur Korea" - }, - { - "author_name": "Meehyun Ko", - "author_inst": "Institute Pasteur Korea" - }, - { - "author_name": "Youngmee Jee", - "author_inst": "Institut Pasteur Korea" - }, - { - "author_name": "Seungtaek Kim", - "author_inst": "Institut Pasteur Korea" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.07.438818", "rel_title": "Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody", @@ -833649,6 +834906,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.08.20205781", + "rel_title": "Safe and effective pool testing for SARS-CoV-2 detection", + "rel_date": "2021-04-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.20205781", + "rel_abs": "Background / ObjectivesThe global spread of SARS-CoV-2 is a serious public health issue. Large-scale surveillance screenings are crucial but can exceed diagnostic test capacities. We set out to optimize test conditions and implemented high throughput pool testing of respiratory swabs into SARS-CoV-2 diagnostics.\n\nStudy designIn preparation for pool testing, we determined the optimal pooling strategy and pool size. In addition, we measured the impact of vortexing prior to sample processing, compared pipette- and swab-pooling method as well as the sensitivity of three different PCR assays.\n\nResultsUsing optimized strategies for pooling, we systematically pooled 55,690 samples in a period of 44 weeks resulting in a reduction of 47,369 PCR reactions. In a low prevalence setting, we defined a preferable pool size of ten in a two-stage hierarchical pool testing strategy. Vortexing of the swabs increased cellular yield by a factor of 2.34, and sampling at or shortly after symptom onset was associated with higher viral loads. By comparing different pooling strategies, pipette-pooling was more efficient compared to swab-pooling.\n\nConclusionsFor implementing pooling strategies into high throughput diagnostics, we recommend to apply a pipette-pooling method, using pool sizes of ten samples, performing sensitivity validation of the PCR assays used, and vortexing swabs prior to analyses. Our data shows, that pool testing for SARS-CoV-2 detection is feasible and highly effective in a low prevalence setting.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Marie Wunsch", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Dominik Aschemeier", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Eva Heger", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Denise Ehrentraut", + "author_inst": "Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne" + }, + { + "author_name": "Jan Krueger", + "author_inst": "Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne" + }, + { + "author_name": "Martin Hufbauer", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Adnan S Syed", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Gibran Horemheb-Rubio", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Felix Dewald", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Irina Fish", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Maike Schlotz", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Henning Gruell", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Max Augustin", + "author_inst": "University of Cologne, Department I of Internal Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Clara Lehmann", + "author_inst": "University of Cologne, Department I of Internal Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Rolf Kaiser", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Elena Knops", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Steffi Silling", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + }, + { + "author_name": "Florian Klein", + "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.08.439071", "rel_title": "A repurposed drug screen identifies compounds that inhibit the binding of the COVID-19 spike protein to ACE2", @@ -835129,29 +836473,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.04.05.21254024", - "rel_title": "Strategies for antigen testing: An alternative approach to widespread PCR testing", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254024", - "rel_abs": "Multiple applications of low cost and rapid antigen tests for individuals, in parallel (at the same time) or at times sufficiently close to each other, when appropriately interpreted can considerably increase sensitivity of these tests, improving on their performance greatly. Under reasonable assumptions, this occurs when considering a positive to arise in a composite test if at least one of two underlying repeated tests are positive. Parallel Rapid Testing can potentially provide a form of testing that is accessible (combining wide availability and lack of expense) and quick. Moreover, it can provide a level of sensitivity that is comparable to seemingly more sophisticated but more expensive alternatives. In combination with sequential testing, this strategy offers an alternative method of testing that can be applied immediately and on a widespread basis.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sanjay G Reddy", - "author_inst": "The New School" - }, - { - "author_name": "Saumya Das", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.05.21254722", "rel_title": "Outcomes of COVID-19 Vaccination Efforts in Florida from December 14, 2020 to March 15, 2021 on Older Individuals", @@ -835367,6 +836688,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.05.21251104", + "rel_title": "Detection of two CAL.20C SARS-CoV-2 variants in Monterrey metropolitan area in Northeast Mexico", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21251104", + "rel_abs": "SARS-CoV-2 variants of concern (VOC) are a worldwide problem. CAL.20C is considered a VOC and its distribution should be monitored. We detected two CAL.20C variants in Monterrey, Mexico in patients who had no recent travel history. This indicates that this variant is now transmitted locally in Northeast Mexico.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kame A Galan-Huerta", + "author_inst": "Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Ana M Rivas-Estilla", + "author_inst": "Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Sonia A Lozano-Sepulveda", + "author_inst": "Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Natalia Martinez-Acuna", + "author_inst": "Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Daniel Arellanos-Soto", + "author_inst": "Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Roberto Montes-de-Oca-Luna", + "author_inst": "Secretaria de Salud de Nuevo Leon" + }, + { + "author_name": "Consuelo Trevi\u0148o-Garza", + "author_inst": "Secretaria de Salud de Nuevo Leon" + }, + { + "author_name": "Manuel E De-la-O-Cavazos", + "author_inst": "Secretaria de Salud de Nuevo Leon" + }, + { + "author_name": "Javier Ramos-Jimenez", + "author_inst": "Universidad Autonoma de Nuevo Leon" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.03.21254823", "rel_title": "A prospective observational safety study on ChAdOx1 nCoV- 19 corona virus vaccine (recombinant) use in healthcare workers- first results from India", @@ -836987,57 +838359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.04.06.21254840", - "rel_title": "Patient perspectives on healthcare at the time of COVID-19 and suggestions for care redesign after the pandemic: a qualitative study in all six WHO regions", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254840", - "rel_abs": "ObjectiveThe COVID-19 pandemic has triggered significant changes in healthcare. As they were mainly driven by professionals and are likely to influence healthcare in the future, it is of utmost importance to consider patients perspectives equally. We, therefore, explored the lived experiences of patients and patient representatives in all six World Health Organisation (WHO) regions regarding healthcare at the time of COVID-19 and extracted suggestions for care redesign after the pandemic.\n\nMethodsWe conducted semi-structured interviews until saturation. Thematic analysis followed a modified form of meaning condensation. We established rigour by transcript checking, inter-coder agreement, quote variation and standardised reporting.\n\nResultsDisadvantaged people experienced an unprecedented inequity in healthcare due to the pandemic. The main reasons were the reduction in public care services and limited access to information, transportation, technology and income. Stigmatisation from COVID-19 differed between cultural contexts and ranged from none to feeling \"ashamed\" and \"totally bashed\". Participants experienced telehealth as indispensable but with limitations. These included giving \"bad news\", such as having an eye removed because of melanoma, and the difficulty of providing end-of-life care over the phone. Patient representatives redefined their role and became indispensable influencers throughout the pandemic and beyond.\n\nConclusionWe reached out to individuals with a diversity of perspectives, including minorities and marginalised populations. A systematic exclusion of people with limited technology access increases inequity in healthcare and biases research findings. Since preferences and personal meanings drive behaviour and could be foundations for targeted interventions, they must be considered in all groups of people to increase societys resilience as a whole.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Tanja Stamm", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Yuki Seidler", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Margaret R Andrews", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Mohammad Eghbali", - "author_inst": "University of Social Welfare and Rehabilitation Sciences, Tehran, Iran" - }, - { - "author_name": "Juliet Kiguli", - "author_inst": "Makerere University, Kampala, Uganda" - }, - { - "author_name": "Valentin Ritschl", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Maisa Omara", - "author_inst": "Medical University of Vienna, Austria" - }, - { - "author_name": "Gertraud Schaffer", - "author_inst": "Oesterreichische Rheumaliga, Maria Alm, Austria" - }, - { - "author_name": "Erika Mosor", - "author_inst": "Medical University of Vienna, Austria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.04.05.21254952", "rel_title": "mRNA vaccination compared to infection elicits an IgG-predominant response with greater SARS-CoV-2 specificity and similar decrease in variant spike recognition", @@ -837437,6 +838758,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.04.06.21254961", + "rel_title": "It's possibly made us feel a little more alienated: How people from ethnic minority communities conceptualise COVID-19 and its influence on engagement with testing.", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21254961", + "rel_abs": "ObjectivesThe cultural beliefs, practices and experiences of ethnic minority groups, alongside structural inequalities and the political economy play a critical, but overlooked role in health promotion. The current study aims to address this deficit; understanding how these groups conceptualise COVID-19, and how this influences engagement in testing, with the future aim of developing targeted communications to address the challenges of testing uptake.\n\nMethodBlack (African and Caribbean) and South Asian (Indian, Pakistani and Bangladeshi) community members were purposefully recruited across the UK. Fifty-seven semi-structured interviews were conducted and analysed using principles of Grounded Theory.\n\nResultsThe findings illustrate that Black and South Asians conceptualise COVID-19 as a disease that makes them visible to others outside their community; in having more severe risk and suffering worst consequences; resulting in fear, stigmatisation and alienation. Views about COVID-19 were embedded in cultural beliefs, relating to culturally specific ideas around disease, such as ill-health being Gods will. Challenges brought about by the pandemic were conceptualised as one of many struggles, with the saliency of the virus contextualised against life experiences. These themes and others influenced engagement with COVID-19 testing. Testing was less about accessing timely and effective treatment for themselves, and more about acting to protect the family and community. Testing symbolised a loss of income, anxiety and isolation, accentuated by issues of mistrust of the system, and not being valued, or being treated unfairly.\n\nConclusionIn tackling these challenges, we conclude that health communications should focus on counterbalancing the mistrust, alienation and stigmatisation that act as barriers to testing, with trust built using local credible sources.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tushna F Vandrevala", + "author_inst": "Kingston University" + }, + { + "author_name": "Lailah Alidu", + "author_inst": "University of Kingston" + }, + { + "author_name": "Jane Hendy", + "author_inst": "Brunel University" + }, + { + "author_name": "Shuja Shafi", + "author_inst": "Mass Gathering" + }, + { + "author_name": "Aftab Ala", + "author_inst": "Royal Surrey County Hospital NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.06.21254963", "rel_title": "Impaired Humoral and Cellular Immunity after SARS-CoV2 BNT162b2 (Tozinameran) Prime-Boost Vaccination in Kidney Transplant Recipients", @@ -838817,53 +840173,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.02.21254493", - "rel_title": "Humoral response to Pfizer mRNA vaccine against SARS CoV2, in patients with autoimmune inflammatory rheumatic diseases and the impact on the rheumatic disease activity", - "rel_date": "2021-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21254493", - "rel_abs": "BackgroundThe registration trials of mRNA vaccines against SARS CoV2 did not address patients with autoimmune inflammatory rheumatoid diseases (AIRD).\n\nAimsTo assess the humoral response to mRNA vaccine against SARS CoV2, in AIRD patients treated with immunomodulating drugs and the impact on AIRD activity.\n\nMethodsConsecutive patients treated at the rheumatology institute who received their first SARS-CoV-2 (Pfizer) vaccine were recruited to the study, at their routine visit. The patients were invited for serology test 4-6 weeks after receiving the second dose of vaccine. IgG Antibodies (Ab) against SARS COV2 virus were detected using the SARS-Cov-2 IgG II Quant (Abbott) assay\n\nResultsOne hundred fifty-six consecutive patients (76% females) treated at a single rheumatology center (mean age (range) 59.1 (21-83) years), mean (range) disease duration 10.8 (1-55) years), were recruited to the study. Thirty-five percents of patients received conventional synthetic (cs)DMARDs only, 64% biological/targeted synthetic (b/ts) DMARDs, 34% received combined treatment with csDMARDs and b/tsDMARDs and 32% corticosteroids (mean dose(range) 5.8mg(2.5-20mg) prednisone). One hundred thirty-seven patients (88%) were seropositive for IgG Ab against SARS CoV2 virus (median 2832.5 AU/ml, range 58-29499). Nineteen (12%) patients had negative tests, 11/19 were treated with B cell depleting agents. The reported side effects of the vaccine were minor (muscle sore, headache, low grade fever). The rheumatic disease remained stable in all patients.\n\nConclusionsThe vast majority of AIRD patients developed a significant humoral response following the administration of the second dose of the Pfeizer mRNA vaccine against SARS CoV2 virus. Only minor side effects were reported and no apparent impact on AIRD activity was noted.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yolanda Braun-Moscovici", - "author_inst": "Rambam Health Care Campus" - }, - { - "author_name": "Marielle Kaplan", - "author_inst": "Biochemistry Laboratory, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Doron Markovits", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Samy Giryes", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Kochava Toledano", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Yonit Tavor", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Katya Dolnikov", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - }, - { - "author_name": "Alexandra Balbir-Gurman", - "author_inst": "B Shine Rheumatology Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion, Haifa" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2021.03.31.21254674", "rel_title": "Efficient Maternal to Neonatal transfer of SARS-CoV-2 and BNT162b2 antibodies", @@ -839355,6 +840664,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.31.21254739", + "rel_title": "Global-scale analysis and longitudinal assessment of COVID-19 incidence in the first six months", + "rel_date": "2021-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254739", + "rel_abs": "Studies examining factors responsible for COVID-19 incidence have mostly focused at the national or sub-national level. Here we undertake an analysis of COVID-19 cases at the global scale to identify key factors associated with disease incidence. A regression modeling framework was used to identify key variables associated with COVID-19 incidence, and to assess longitudinal trends in reported incidence at the country-level. New COVID-19 case dynamics in response to lockdowns was characterized via cluster analysis. Eleven variables were found to be independently associated with COVID-19 infections (p<1e-05) and a 4-variable model adequately explained global variations in COVID-19 cases (p<0.01). COVID-19 case trajectories for most countries followed the log-logistic curve. Six predominant country clusters summarized the differences in individual countrys response to lockdowns. Globally, economic and meteorological factors are important determinants of COVID-19 incidence. Analysis of longitudinal trends and lockdown effects on COVID-19 caseloads further highlights important nuances in country-specific responses to the pandemic. These findings on the first six months of the pandemic has important implications for additional phases of the disease currently underway in many countries.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "SUJOY GHOSH", + "author_inst": "DUKE NUS MEDICAL SCHOOL" + }, + { + "author_name": "SAIKAT SINHA ROY", + "author_inst": "Department of Economics, Jadavpur University, Kolkata, West Bengal, India" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.31.21254668", "rel_title": "First-in-Human Trial of a Recombinant Stabilized Prefusion SARS-CoV-2 Spike Protein Vaccine with Adjuvant of Aluminum Hydroxide and CpG 1018", @@ -840723,37 +842055,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.31.21254434", - "rel_title": "Impact of COVID-19 in Individuals with Autism Spectrum Disorders: Analysis of a National Private Claims Insurance Database", - "rel_date": "2021-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254434", - "rel_abs": "The COVID-19 pandemic continues to have a detrimental impact on individuals with disabilities. Data from FAIR Healths FH(R) NPIC (National Private Insurance Claims) database,1 one of the nations largest databases of private insurance claim records, were analyzed to understand the experiences of individuals with ASD in COVID-19 pandemic. Multivariate logistic regression models revealed that individuals with ASD + ID were nine times more likely to be hospitalized (OR = 9.3; 95% CI: 6.9 - 12.5) and were nearly six times more likely have an elevated length of hospital stay(OR = 5.9; 95% CI: 3.5 - 10.1) compared those without ASD + ID. These findings point to their need for prioritization in access to vaccines for preventing COVID-19 infection and morbidities.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Arun Karpur", - "author_inst": "Autism Speaks" - }, - { - "author_name": "Vijay Vasudevan", - "author_inst": "Autism Speaks" - }, - { - "author_name": "Andy J Shih", - "author_inst": "Autism Speaks" - }, - { - "author_name": "Thomas W Frazier", - "author_inst": "Autism Speaks, John Carroll University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.01.21254679", "rel_title": "Is convalescent plasma futile in COVID-19? A Bayesian re-analysis of the RECOVERY randomised controlled trial", @@ -841153,6 +842454,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.02.21253262", + "rel_title": "Antibodies against type-I Interferon: detection and association with severe clinical outcome in COVID-19 patients", + "rel_date": "2021-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21253262", + "rel_abs": "ObjectivesImpairment of type I interferon (IFN-I) immunity has been reported in critically-ill COVID-19 patients. This defect can be explained in a subset of patients by the presence of circulating autoantibodies (auto-Abs) against IFN-I. We set out to improve the detection and the quantification of IFN-I auto-Abs in a cohort of critically-ill COVID-19 patients, in order to better evaluate the prevalence of these Abs as the pandemic progresses, and how they correlate with the clinical course of the disease.\n\nMethodsThe concentration of anti-IFN-2 Abs was determined in the serum of 84 critically-ill COVID-19 patients who were admitted to ICU in Hospices Civils de Lyon, France using a commercially available kit (Thermo-Fisher, Catalog #BMS217).\n\nResultsA total of 21/84 (25%) critically-ill COVID-19 patients had circulating anti-IFN-2 Abs above cut-off (>34 ng.mL-1). Among them, 15/21 had Abs with neutralizing activity against IFN-2, i.e. 15/84 (18%) of critically-ill patients. In addition, we noticed an impairment of the IFN-I response in the majority of patients with neutralizing anti-IFN-2 Abs. There was no significant difference in the clinical characteristics or outcome of with or without neutralizing anti-IFN-2 auto-Abs. We detected anti-IFN-2 auto-Abs in COVID-19 patients sera throughout their ICU stay. Finally, we also found auto-Abs against multiple subtypes of IFN-I including IFN-{omega}.\n\nConclusionsWe reported that 18% of critically-ill COVID-19 patients were positive for IFN-I auto-Abs, confirming that the presence of these antibodies is associated with higher risk of developing a criticall COVID-19 form.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "David Goncalves", + "author_inst": "Immunology Department, Lyon-Sud Hospital, Hospices Civils de Lyon, Pierre-Benite, France" + }, + { + "author_name": "Mehdi Mezidi", + "author_inst": "Lyon University, CREATIS, CNRS UMR5220, Inserm U1044, INSA, Lyon, France, Intensive Care Unit, Hospices Civils de Lyon, Lyon, France" + }, + { + "author_name": "Paul Bastard", + "author_inst": "Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine" + }, + { + "author_name": "Magali Perret", + "author_inst": "Immunology Department, Lyon-Sud Hospital, Hospices Civils de Lyon, Pierre-Benite, France; International Center of Research in Infectiology, Lyon University, IN" + }, + { + "author_name": "Kahina Saker", + "author_inst": "Infective Agents Institute, Hospices Civils de Lyon, Lyon, France" + }, + { + "author_name": "Nicole Fabien", + "author_inst": "Immunology Department, Lyon-Sud Hospital, Hospices Civils de Lyon, Pierre-Benite, France" + }, + { + "author_name": "Remi Pescarmona", + "author_inst": "Immunology Department, Lyon-Sud Hospital, Hospices Civils de Lyon, Pierre-Benite, France; International Center of Research in Infectiology, Lyon University, IN" + }, + { + "author_name": "Christine Lombard", + "author_inst": "Immunology Department, Lyon-Sud Hospital, Hospices Civils de Lyon, Pierre-Benite, France" + }, + { + "author_name": "Thierry Walzer", + "author_inst": "International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France" + }, + { + "author_name": "Jean-Laurent Casanova", + "author_inst": "Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine" + }, + { + "author_name": "Alexandre Belot", + "author_inst": "International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France; National Referee Centre for Rheumatic a" + }, + { + "author_name": "Jean-Christophe Richard", + "author_inst": "Lyon University, CREATIS, CNRS UMR5220, Inserm U1044, INSA, Lyon, France, Intensive Care Unit, Hospices Civils de Lyon, Lyon, France" + }, + { + "author_name": "Sophie Trouillet-Assant", + "author_inst": "International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France; Infective Agents Institute, Hospices Ci" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.04.01.21252379", "rel_title": "Cross-reactive CD4+ T cells enhance SARS-CoV-2 immune responses upon infection and vaccination", @@ -842637,61 +844005,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.02.21254856", - "rel_title": "Background rates of hospitalizations and emergency department visits for selected thromboembolic and coagulation disorders in Ontario, Canada, 2015 to 2020, to inform COVID-19 vaccine safety surveillance", - "rel_date": "2021-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21254856", - "rel_abs": "ObjectiveThe objective of this study was to estimate background rates of selected thromboembolic and coagulation disorders in Ontario, Canada.\n\nDesignPopulation-based retrospective observational study using linked health administrative databases. Records of hospitalizations and emergency department visits were searched to identify cases using diagnostic codes from the International Statistical Classification of Diseases and Related Health Problems, Tenth Revision, Canada (ICD-10-CA).\n\nParticipantsAll Ontario residents.\n\nPrimary outcome measuresIncidence rates of stroke, deep vein thrombosis, pulmonary embolism, idiopathic thrombocytopenia, disseminated intravascular coagulation, and cerebral venous thrombosis during five pre-pandemic years (2015-2019, annually, averaged, and monthly average) and 2020.\n\nResultsThe average annual population was 14 million with 51% female. The mean annual rates during 2015-2019 were 127.1/100,000 population (95% confidence interval [CI], 126.2, 127.9) for ischemic stroke, 22.0/100,000 (95%CI, 21.6, 22.3) for intracerebral haemorrhage, 9.4 (95%CI, 9.2, 9.7) for subarachnoid haemorrhage, 86.8/100,000 (95%CI, 86.1, 87.5) for deep vein thrombosis, 63.7/100,000 (95%CI, 63.1, 64.3) for pulmonary embolism, 6.1/100,000 (95%CI, 5.9, 6.3) for idiopathic thrombocytopenia, 1.6/100,000 (95%CI, 1.5, 1.7) for disseminated intravascular coagulation, and 1.5/100,000 (95%CI, 1.4, 1.6) for cerebral venous thrombosis. Rates were lower in 2020 than during the pre-pandemic years for ischemic stroke, deep vein thrombosis, and idiopathic thrombocytopenia. Rates were generally consistent over time, except for pulmonary embolism, which increased from 57.1 to 68.5 per 100,000 between 2015 and 2019. Rates were higher for females than males for subarachnoid haemorrhage, pulmonary embolism, and cerebral venous thrombosis, and vice versa for ischemic stroke and intracerebral haemorrhage. Rates increased with age for most of these conditions, but idiopathic thrombocytopenia demonstrated a bimodal distribution with incidence peaks at 0-19 years and [≥]60 years.\n\nConclusionsOur estimated background rates help to contextualize observed events of these potential adverse events of special interest and to detect potential safety signals related to COVID-19 vaccines.\n\nStrengths and limitations of this study[tpltrtarr] Recent background rates of selected thromboembolic and coagulation disorders that are potential adverse events special interest related to COVID-19 vaccine are estimated.\n[tpltrtarr]Background rates during five pre-pandemic (2015-2019) years and 2020 will provide context for these events to identify vaccine safety signals.\n[tpltrtarr]We used recorded diagnostic codes in administrative data without information on clinical and/or diagnostic confirmation, and the validity of these data are imperfect, which may result in under or overestimation.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sharifa Nasreen", - "author_inst": "University of Toronto" - }, - { - "author_name": "Andrew Calzavara", - "author_inst": "ICES" - }, - { - "author_name": "Maria Sundaram", - "author_inst": "University of Toronto" - }, - { - "author_name": "Shannon E MacDonald", - "author_inst": "University of Alberta" - }, - { - "author_name": "Christiaan Righolt", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Menaka Pai", - "author_inst": "McMaster University" - }, - { - "author_name": "Thalia Field", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Lily W Zhou", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Sarah Wilson", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Jeff Kwong", - "author_inst": "ICES" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.02.438274", "rel_title": "Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN", @@ -843123,6 +844436,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.30.21254031", + "rel_title": "Clinical efficacy of Early Administration of Convalescent Plasma among COVID-19 Cases in Egypt", + "rel_date": "2021-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254031", + "rel_abs": "ImportanceEarly and effective treatment of COVID-19 is vital for control of SARS-CoV-2 infection\n\nObjectivesThe primary objective of the study was to assess the degree of clinical improvement in severe and critically ill COVID-19 patients, treated early with early CPT.\n\nDesignsAn interventional, single-arm, non-randomized clinical trial conducted in Egypt from April 15 to July 21, 2020.\n\nSettingsThis was a multi-centre study conducted in 3 hospitals in Egypt.\n\nParticipantsa total of 94 COVID-19 laboratory-confirmed patients using qRT-PCR were enrolled in the study.\n\nInterventionAll patients were administered with two plasma units (each unit is 200cc). The volume of donated plasma was 800cc.\n\nMain Outcome and MeasuresPrimary measure was the degree of clinical improvement among the COVID-19 patients who received CPT within seven days\n\nResultsA total of 94 patients were enrolled who received CPT either within seven days or after seven days of hospitalization. 82 were severely ill, 12 were critically ill. The average age remained 58 years ({+/-}SD 15.1 years). Male were 69% and 49% patients got cured while 51% died with CFR 51%. 75% deaths were above 45years of age. The symptoms were dyspnoea (55%), fever (52%), cough (46%), and loss of taste and smell (21%), and cyanosis (15%). The most common co-morbidities among the <40 years remained Diabetes Mellitus (21%) and Asthma (14%). Among 40-60 years Hypertension (56%), Diabetes Mellitus (39%) and among >60 years age group Hypertension (57%) and Chronic Heart Disease (24%) were reported. CPT within seven days remained significant as compared with the CPT after seven days with the number of days to cure (p=0.007) and ICU stay (P=0.008) among severely ill cured cases.\n\nConclusion and RelevanceAmong patients with COVID-19 and severe or critical illness, the use of CPT along with routine standard therapy resulted in a statistically significant improvement when administered within seven days of hospital admission. However, plasma transfusion, irrespective of days to transfusion may not help treat critically ill patients. The overall mean time to cure in severely ill patients was 15 days if CPT provided within seven days with 65% cure rate.\n\nTrial RegistrationClinical Intervention identifier: MOHP_COVID-19_Ver1.1", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Noha Asem", + "author_inst": "Cairo Univesity,Ministry of Health and Population" + }, + { + "author_name": "Hossam Hosny Massoud", + "author_inst": "Cairo University" + }, + { + "author_name": "Ehab Serag", + "author_inst": "Ministry of Health and Population" + }, + { + "author_name": "Mohamed Hassany", + "author_inst": "Ministry of Health and Population" + }, + { + "author_name": "Gehan ElAssal", + "author_inst": "Ain Shams university" + }, + { + "author_name": "Akram Abdelbary", + "author_inst": "Cairo University" + }, + { + "author_name": "Marwa Mohsen", + "author_inst": "Ministry of Health and Population" + }, + { + "author_name": "Amin Abdelbary", + "author_inst": "National Hepatology and Tropical medicine Research Institue" + }, + { + "author_name": "Samy Zaky", + "author_inst": "Al-Azhar University" + }, + { + "author_name": "Wagdy Amin", + "author_inst": "Ministry of Health and Population" + }, + { + "author_name": "Ehab Kamal", + "author_inst": "National Research Center,Ministry of Health and Population" + }, + { + "author_name": "Hamdy Ibrahem", + "author_inst": "Ministry of Health and Population" + }, + { + "author_name": "Ahmed Said Mohsen", + "author_inst": "Cairo University" + }, + { + "author_name": "Mohamed Ahmed Aly", + "author_inst": "National Research Center" + }, + { + "author_name": "Nancy Elgendy", + "author_inst": "Cairo University,Ministry of Health and Population" + }, + { + "author_name": "Mohamed Elbadry", + "author_inst": "Helwan University" + }, + { + "author_name": "Salwa Hassan Ahmed", + "author_inst": "Ministry of Health and Population" + }, + { + "author_name": "Naguib Nassif Shenouda", + "author_inst": "Ministry of Health and Population" + }, + { + "author_name": "Mohamed Abdelhamed Fathy", + "author_inst": "Ministry of Health and Population" + }, + { + "author_name": "Hala Zaid", + "author_inst": "Ministry of Health and Population" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.29.21254559", "rel_title": "RELATIONSHIP OF LIVER ENZYME LEVELS WITH THE CLINICAL COURSE OF COVID-19", @@ -844539,145 +845947,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.03.31.437925", - "rel_title": "SARS-CoV-2 immune evasion by variant B.1.427/B.1.429", - "rel_date": "2021-04-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.31.437925", - "rel_abs": "SARS-CoV-2 entry is mediated by the spike (S) glycoprotein which contains the receptor-binding domain (RBD) and the N-terminal domain (NTD) as the two main targets of neutralizing antibodies (Abs). A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429) was originally detected in California and is currently spreading throughout the US and 29 additional countries. It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R. Here, we assessed neutralizing Ab responses following natural infection or mRNA vaccination using pseudoviruses expressing the wildtype or the B.1.427/B.1.429 S protein. Plasma from vaccinated or convalescent individuals exhibited neutralizing titers, which were reduced 3-6 fold against the B.1.427/B.1.429 variant relative to wildtype pseudoviruses. The RBD L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific monoclonal antibodies (mAbs), including three clinical-stage mAbs. Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site. These data warrant closer monitoring of signal peptide variants and their involvement in immune evasion and show that Abs directed to the NTD impose a selection pressure driving SARS-CoV-2 viral evolution through conventional and unconventional escape mechanisms.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Matthew McCallum", - "author_inst": "University of Washington" - }, - { - "author_name": "Jessica Bassi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Anna De Marco", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Alex Chen", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Alexandra C Walls", - "author_inst": "University of Washington" - }, - { - "author_name": "Julia Di Iulio", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "M. Alejandra Tortorici", - "author_inst": "University of Washington" - }, - { - "author_name": "Mary-Jane Navarro", - "author_inst": "University of Washington" - }, - { - "author_name": "Chiara Silacci-Fregni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Christian Saliba", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Maria Agostini", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Dora Pinto", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Katja Culap", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Siro Bianchi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Stefano Jaconi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Elisabetta Cameroni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "John E Bowen", - "author_inst": "University of Washington" - }, - { - "author_name": "Sasha W Tiles", - "author_inst": "University of Washington" - }, - { - "author_name": "Matteo Samuele Pizzuto", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Sonja Bernasconi Guastalla", - "author_inst": "Independent physician" - }, - { - "author_name": "Giovanni Bona", - "author_inst": "Independent physician" - }, - { - "author_name": "Alessandra Franzetti Pellanda", - "author_inst": "Clinica Luganese Moncucco" - }, - { - "author_name": "Christian Garzoni", - "author_inst": "Clinica Luganese Moncucco" - }, - { - "author_name": "Wesley C Van Voorhis", - "author_inst": "University of Washington" - }, - { - "author_name": "Laura E Rosen", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Gyorgy C Snell", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Amalio Telenti", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Herbert W Virgin", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Luca Piccoli", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Davide Corti", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "David Veesler", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.01.438035", "rel_title": "The neutralization potency of anti-SARS-CoV-2 therapeutic human monoclonal antibodies is retained against novel viral variants", @@ -845061,6 +846330,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.31.437792", + "rel_title": "Hydrogel-based slow release of a receptor-binding domain subunit vaccine elicits neutralizing antibody responses against SARS-CoV-2", + "rel_date": "2021-04-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.31.437792", + "rel_abs": "The development of effective vaccines that can be rapidly manufactured and distributed worldwide is necessary to mitigate the devastating health and economic impacts of pandemics like COVID-19. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, which mediates host cell entry of the virus, is an appealing antigen for subunit vaccines because it is efficient to manufacture, highly stable, and a target for neutralizing antibodies. Unfortunately, RBD is poorly immunogenic. While most subunit vaccines are commonly formulated with adjuvants to enhance their immunogenicity, we found that clinically-relevant adjuvants Alum, AddaVax, and CpG/Alum were unable to elicit neutralizing responses following a prime-boost immunization. Here we show that sustained delivery of an RBD subunit vaccine comprising CpG/Alum adjuvant in an injectable polymer-nanoparticle (PNP) hydrogel elicited potent anti-RBD and anti-spike antibody titers, providing broader protection against SARS-CoV-2 variants of concern compared to bolus administration of the same vaccine and vaccines comprising other clinically-relevant adjuvant systems. Notably, a SARS-CoV-2 spike-pseudotyped lentivirus neutralization assay revealed that hydrogel-based vaccines elicited potent neutralizing responses when bolus vaccines did not. Together, these results suggest that slow delivery of RBD subunit vaccines with PNP hydrogels can significantly enhance the immunogenicity of RBD and induce neutralizing humoral immunity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Emily C. Gale", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Abigail E. Powell", + "author_inst": "Stanford University" + }, + { + "author_name": "Gillie A. Roth", + "author_inst": "Stanford University" + }, + { + "author_name": "Emily L. Meany", + "author_inst": "Stanford University" + }, + { + "author_name": "Jerry Yan", + "author_inst": "Stanford University" + }, + { + "author_name": "Ben S. Ou", + "author_inst": "Stanford University" + }, + { + "author_name": "Abigail K. Grosskopf", + "author_inst": "Stanford University" + }, + { + "author_name": "Julia Adamska", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Vittoria C. T. M. Picece", + "author_inst": "Stanford University" + }, + { + "author_name": "Bali Pulendran", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Peter S. Kim", + "author_inst": "Stanford University" + }, + { + "author_name": "Eric Appel", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.03.31.437918", "rel_title": "Structural dynamics of the \u03b2-coronavirus Mpro protease ligand binding sites", @@ -846673,33 +848005,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.30.21254635", - "rel_title": "Validity of markers and indexes of systemic inflammation in predicting mortality in COVID 19 infection : A hospital based cross sectional study", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254635", - "rel_abs": "BackgroundCOVID-19 is an ongoing global pandemic. It is a systemic infection with a significant impact on the hematopoietic and the immune system. In this study we aimed to evaluate the different inflammatory markers and indexes of systemic inflammatory response in predicting the mortality in patients with COVID 19.\n\nMethodsIn this cross sectional study, various inflammatory markers like D-dimer, CRP, serum ferritin, LDH and CBC derived indexes of inflammation were analyzed in predicting mortality in COVID 19 infection.\n\nResultsWe enrolled 302 COVID 19 patients who had a mean age of 54.51{+/-}15.39 yrs with 210 (69.5%) males. Among them 21% were asymptomatic and fever was the commonest among symptomatic patients. Majority of patients (66.7%) had no comorbidities and 20% had multiple comorbidities. On analyzing different hematological variables, survivors had statistically significant higher hemoglobin count, lymphocytes, monocytes, eosinophil and platelet count and lower leukocyte, neutrophil count. Inflammatory markers D-dimer, serum ferritin and LDH were significantly elevated among non survivors. Among the indexes of inflammation, only NLR showed significant higher values among non survivors.\n\nAll the inflammatory markers were able to predict mortality among the COVID 19 infected cases with a sensitivity and specificity of 85% and 65% for d dimer levels, 85% and 72% for serum ferritin, 85% and 72% for LDH, 85% and 51% for CRP levels respectively. Among the indexes of inflammation, validity of NLR was best in predicting mortality with 85% sensitivity and 51% specificity.\n\nConclusionAbnormalities in peripheral blood parameters and increase in inflammatory markers are common findings in COVID 19 infection. NLR was best at predicting mortality followed by D-dimer and serum ferritin levels\n\nContribution details\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@c4c8eaorg.highwire.dtl.DTLVardef@1627f25org.highwire.dtl.DTLVardef@1896e70org.highwire.dtl.DTLVardef@1b1b238org.highwire.dtl.DTLVardef@12b8087_HPS_FORMAT_FIGEXP M_TBL C_TBL", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Archana Baburao", - "author_inst": "Rajarajeswari Medical college and hospital" - }, - { - "author_name": "shylaja Shamsunder", - "author_inst": "Bhagawan mahaveer jain hospital" - }, - { - "author_name": "Rinki Das", - "author_inst": "Bhagawan Mahaveer Jain hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.29.21254334", "rel_title": "Estimating the asymptomatic proportion of SARS-CoV-2 infection in the general population: Analysis of a nationwide serosurvey in the Netherlands", @@ -846907,6 +848212,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.03.30.21254614", + "rel_title": "Prevalence and risk factors of internet gaming disorder and problematic internet use before and during the COVID-19 pandemic: A large online survey of Japanese adults", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254614", + "rel_abs": "Internet gaming disorder (IGD) and problematic internet use (PIU) are becoming increasingly detrimental in modern society, with serious consequences for daily functioning. IGD and PIU may be exacerbated by lifestyle changes imposed by the coronavirus 2019 (COVID-19) pandemic. This study investigated changes in IGD and PIU during the pandemic and risk factors for them. This study is a part of a larger online study on problematic smartphone use in Japan, originally planned in 2019, and expanded in August 2020 to include the impact of COVID-19. 51,246 adults completed an online survey during the pandemic (August 2020), in Japan. Of these, 3,938 had also completed the survey before the onset of the pandemic (December, 2019) and were used as the study population to determine how the pandemic has influenced IGD and PIU. IGD was assessed using the Internet Gaming Disorder Scale (IGDS). PIU was measured using the Compulsive Internet Use Scale (CIUS). The prevalence of probable IGD during COVID-19 was 4.1% [95%CI, 3.9% to 4.2%] overall (N=51,246), and 8.6% among younger people (age < 30), higher than reported before the pandemic (1 - 2.5%). Probable PIU was 7.8% [95%CI, 7.6% to 8.1%] overall, and 17.0% [95%CI, 15.9% to 18.2%] among younger people, also higher than reported before the pandemic (3.2 - 3.7%). Comparisons before and during the pandemic, revealed that probable IGD prevalence has increased 1.6 times, and probable PIU prevalence by 1.5 times (IGD: t3937 = 5.93, p < .001, PIU: t3937 = 6.95, p < .001). Youth (age < 30) and COVID-19 infection were strongly associated with IGD exacerbation (odds ratio, 2.10 [95%CI, 1.18 to 3.75] and 5.67 [95%CI, 1.33 to 24.16]). Internet gaming disorder and problematic internet use appear to be aggravated by the pandemic. In particular, younger persons and people infected with COVID-19 are at higher risk for Internet Gaming Disorder. Prevention of these problems is needed.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Taiki Oka", + "author_inst": "Advanced Telecommunications Research Institute International" + }, + { + "author_name": "Toshitaka Hamamura", + "author_inst": "Innovation center KDDI Research, Inc" + }, + { + "author_name": "Yuka Miyake", + "author_inst": "KDDI CORPORATION" + }, + { + "author_name": "Nao Kobayashi", + "author_inst": "KDDI CORPORATION" + }, + { + "author_name": "Masaru Honjo", + "author_inst": "Innovation center KDDI Research, Inc" + }, + { + "author_name": "Mitsuo Kawato", + "author_inst": "Advanced Telecommunications Research Institute International" + }, + { + "author_name": "Takatomi Kubo", + "author_inst": "Advanced Telecommunications Research Institute International" + }, + { + "author_name": "Toshinori Chiba", + "author_inst": "Advanced Telecommunications Research Institute International" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.03.29.21254527", "rel_title": "Health risk behaviours among people with severe mental ill health during the COVID-19 pandemic: analysis of linked cohort data", @@ -848151,29 +849503,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.29.21254583", - "rel_title": "Migration of households from New York City and the Second Peak in Covid-19 cases in New Jersey, Connecticut and New York Counties.", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254583", - "rel_abs": "The five boroughs of New York City (NYC) were early epicenters of the Covid-19 pandemic in the United States, with over 380,000 cases by May 31. High caseloads were also seen in nearby counties in New Jersey (NJ), Connecticut (CT) and New York (NY). The pandemic started in the area in March with an exponential rise in the number of daily cases, peaked in early April, briefly declined, and then, showed clear signs of a second peak in several counties. We will show that despite control measures such as lockdown and restriction of movement during the exponential rise in daily cases, there was a significant net migration of households from NYC boroughs to the neighboring counties in NJ, CT and NY State. We propose that the second peak in daily cases in these counties around NYC was due, in part, to the movement of people from NYC boroughs to these counties. We estimate the movement of people using \"Change of Address\" (CoA) data from the US Postal Service, provided under the \"Freedom of Information Act\" of 1967. To identify the timing of the second peak and the number of cases in it, we use a previously proposed SIR model, which accurately describes the early stages of the coronavirus pandemic in European countries. Subtracting the model fits from the data identified, we establish the timing and the number of cases, NCS, in the second peak. We then related the number of cases in the second peak to the county population density, P, and the excess Change of Address, ECoA, into each county using the simple model [Formula] which fits the data very well with = 0.68, {beta} = 0.31 (R2 = 0.74, p = 1.3e-8). We also find that the time between the first and second peaks was proportional to the distance of the county seat from NY Penn Station, suggesting that this migration of households and disease was a directed flow and not a diffusion process. Our analysis provides a simple method to use change of address data to track the spread of an infectious agent, such as SARS-Cov-2, due to migrations away from epicenters during the initial stages of a pandemic.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Adam T Schulman", - "author_inst": "Rutgers Robert Wood Johnson" - }, - { - "author_name": "Gyan Bhanot", - "author_inst": "Rutgers University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.29.21254581", "rel_title": "A new Reproduction Index Ri and its Usefulness for Germany's Covid19-Data", @@ -848545,6 +849874,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.03.29.21254122", + "rel_title": "Increased transmissibility of the B.1.1.7 SARS-CoV-2 variant: Evidence from contact tracing data in Oslo, January to February 2021", + "rel_date": "2021-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254122", + "rel_abs": "We use data from contact tracing in Oslo, Norway, to estimate the new SARS-CoV-2 B.1.1.7 lineages relative transmissibility. Within households, we find an increase in the secondary attack rate by 60% (20% 114%) compared to other variants. In general, we find a significant increase in the estimated reproduction number of 24% (95% CI 0% - 52%), or an absolute increase of 0.19 compared to other variants.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Jonas Christoffer Lindstr\u00f8m", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Solveig Engebretsen", + "author_inst": "Norwegian Computing Center" + }, + { + "author_name": "Anja Br\u00e5then Kristoffersen", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Gunnar \u00d8ivind Isaksson R\u00f8", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Alfonso Diz-Lois Palomares", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Kenth Eng\u00f8-Monsen", + "author_inst": "Telenor" + }, + { + "author_name": "Elisabeth Henie Madslien", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Frode Forland", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Karin Maria Nyg\u00e5rd", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Frode Hagen", + "author_inst": "Oslo Municipality Health Service" + }, + { + "author_name": "Ottar Wiklund", + "author_inst": "Oslo Municipality Health Service" + }, + { + "author_name": "Gunnar Gantzel", + "author_inst": "Olso Municipality Health Service" + }, + { + "author_name": "Arnoldo Frigessi", + "author_inst": "University of Oslo" + }, + { + "author_name": "Birgitte Freiesleben de Blasio", + "author_inst": "Norwegian Institute of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.23.21253630", "rel_title": "A patient satisfaction survey and educational package to improve the care of people hospitalised with COVID-19: an observational study, Liverpool, UK", @@ -850041,101 +851441,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.27.21253966", - "rel_title": "Clinical performance evaluation of SARS-CoV-2 rapid antigen testing in point of care usage in comparison to RT-qPCR", - "rel_date": "2021-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.27.21253966", - "rel_abs": "BackgroundAntigen rapid diagnostic tests (RDT) for SARS-CoV-2 are fast, broadly available, and inexpensive. Despite this, reliable clinical performance data is sparse.\n\nMethodsIn a prospective performance evaluation study, RDT from three manufacturers (NADAL(R), Panbio, MEDsan(R)) were compared to quantitative reverse transcription polymerase chain reaction (RT-qPCR) in 5 068 oropharyngeal swabs for detection of SARS-CoV-2 in a hospital setting. Viral load was derived from standardized RT-qPCR Cycle threshold (Ct) values. The data collection period ranged from November 12, 2020 to February 28, 2021.\n\nFindingsOverall, sensitivity of RDT compared to RT-qPCR was 42{middle dot}57% (95% CI 33{middle dot}38%-52{middle dot}31%), and specificity 99{middle dot}68% (95% CI 99{middle dot}48%-99{middle dot}80%). Sensitivity declined with decreasing viral load from 100% in samples with a deduced viral load of [≥]108 SARS-CoV-2 RNA copies per ml to 8{middle dot}82% in samples with a viral load lower than 104 SARS-CoV-2 RNA copies per ml. No significant differences in sensitivity or specificity could be observed between the three manufacturers, or between samples with and without spike protein variant B.1.1.7. The NPV in the study cohort was 98{middle dot}84%; the PPV in persons with typical COVID-19 symptoms was 97{middle dot}37%, and 28{middle dot}57% in persons without or with atypical symptoms.\n\nInterpretationRDT are a reliable method to diagnose SARS-CoV-2 infection in persons with high viral load. RDT are a valuable addition to RT-qPCR testing, as they reliably detect infectious persons with high viral loads before RT-qPCR results are available.\n\nFundingGerman Federal Ministry for Education and Science (BMBF), Free State of Bavaria\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMED an MedRxiv for articles including \"COVID-19\", \"COVID\", \"SARS-CoV-2\", \"coronavirus\" as well as \"antigen detection\", \"rapid antigen test\", \"Point-of-Care test\" in title or abstract, published between January 1, 2020 and February 28, 2021. The more than 150 RDT on the market at the end of February 2021 represent a huge expansion of diagnostic possibilities.1 Performance of currently available RDT is evaluated in several international studies, with heterogeneous results. Sensitivity values of RDT range from 0{middle dot}0%2 to 98{middle dot}3%3, specificity from 19{middle dot}4%4 to 100{middle dot}0%.2,5-14. Some of this data differs greatly from manufacturers data. However, these previously published performance evaluation studies were conducted under laboratory conditions using frozen swabs, or in small cohorts with middle-aged participants. Comparable RDT performance data from large-scale clinical usage is missing.5-19\n\nAdded value of this studyBased on previous examinations the real life opportunities and limitations of SARS-CoV-2 RDT as an instrument of hospital infection detection and control are still unclear as well as further study results are limited in transferability to general public. Our findings show that RDT performance in daily clinical routine is reliable in persons with high viral for punctual detection and isolation of infectious persons before RT-qPCR become available. In persons with lower viral load, or in case of asymptomatic patients SARS-CoV2 detection by RDT was unsuccessful. The general sensitivity of 42{middle dot}57% is too low to accept the RDT in clinical use as an alternative to RT-qPCR in diagnosis of COVID-19. Calculated specificity was 99.68%. The results are based on a huge study cohort with more than 5 000 participants including a representative ages structure with pediatric patients up to geriatric individuals, which portrays approximately the demographic structure of the local society.\n\nImplications of all the available evidenceDue to the low general sensitivity RDT in clinical use cannot be accepted as an alternative but as an addition to RT-qPCR in SARS-CoV-2 diagnosis. The benefit of early detection of highly infectious persons has to be seen in context of the effort of testing and isolation of false positive tested persons.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Isabell Wagenhaeuser", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Kerstin Knies", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Vera Rauschenberger", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Michael Eisenmann", - "author_inst": "Infection Control Unit, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Miriam McDonogh", - "author_inst": "Department of Orthopaedic Trauma, Hand, Plastic and Reconstructive Surgery, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Nils Petri", - "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Oliver Andres", - "author_inst": "Department of Pediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Sven Flemming", - "author_inst": "Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Micha Gawlik", - "author_inst": "Department of Psychiatry and Psychotherapy, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Michael Papsdorf", - "author_inst": "Department of Obstetrics and Gynecology, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Regina Taurines", - "author_inst": "Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Hartmut Boehm", - "author_inst": "Department of Oral and Maxillofacial Surgery, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Johannes Forster", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Dirk Weismann", - "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Benedikt Weissbrich", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Lars Doelken", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Johannes Liese", - "author_inst": "Department of Pediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Oliver Kurzai", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Ulrich Vogel", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Manuel Krone", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.26.21254422", "rel_title": "Targeting the Microbiome With KB109 in Outpatients with Mild to Moderate COVID-19 Reduced Medically Attended Acute Care Visits and Improved Symptom Duration in Patients With Comorbidities", @@ -850483,6 +851788,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.28.437363", + "rel_title": "SARS-CoV-2 variant B.1.1.7 caused HLA-A2+ CD8+ T cell epitope mutations for impaired cellular immune response", + "rel_date": "2021-03-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.28.437363", + "rel_abs": "The rapid spreading of the newly emerged SARS-CoV-2 variant, B.1.1.7, highlighted the requirements to better understand adaptive immune responses to this virus. Since CD8+ T cell responses play an important role in disease resolution and modulation in COVID-19 patients, it is essential to address whether these newly emerged mutations would result in altered immune responses. Here we evaluated the immune properties of the HLA-A2 restricted CD8+ T cell epitopes containing mutations from B.1.1.7, and furthermore performed a comprehensive analysis of the SARS-CoV-2 specific CD8+ T cell responses from COVID-19 convalescent patients and SARS-CoV-2 vaccinees recognizing the ancestral Wuhan strain compared to B.1.1.7. First, most of the predicted CD8+ T cell epitopes showed proper binding with HLA-A2, while epitopes from B.1.1.7 had lower binding capability than those from the ancestral strain. In addition, these peptides could effectively induced the activation and cytotoxicity of CD8+ T cells. Our results further showed that at least two site mutations in B.1.1.7 resulted in a decrease in CD8+ T cell activation and a possible immune evasion, namely A1708D mutation in ORF1ab1707-1716 and I2230T mutation in ORF1ab2230-2238. Our current analysis provides information that contributes to the understanding of SARS-CoV-2-specific CD8+ T cell responses elicited by infection of mutated strains or vaccination.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC=\"FIGDIR/small/437363v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@b9f2cdorg.highwire.dtl.DTLVardef@1f39e3dorg.highwire.dtl.DTLVardef@119c313org.highwire.dtl.DTLVardef@565388_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Chanchan Xiao", + "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, China" + }, + { + "author_name": "Lipeng Mao", + "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, China" + }, + { + "author_name": "Zhigang Wang", + "author_inst": "Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China" + }, + { + "author_name": "Guodong Zhu", + "author_inst": "Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou, China" + }, + { + "author_name": "Lijuan Gao", + "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, China" + }, + { + "author_name": "Jun Su", + "author_inst": "Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China" + }, + { + "author_name": "Xiongfei Chen", + "author_inst": "Guangzhou Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Jun Yuan", + "author_inst": "Guangzhou Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Yutian Hu", + "author_inst": "Meng Yi Center Limited, Macau, China" + }, + { + "author_name": "Zhinan Yin", + "author_inst": "Jinan University" + }, + { + "author_name": "Jun Xie", + "author_inst": "ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine" + }, + { + "author_name": "Weiqing Ji", + "author_inst": "ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine" + }, + { + "author_name": "Haitao Niu", + "author_inst": "Jinan University" + }, + { + "author_name": "Feng Gao", + "author_inst": "Jinan University" + }, + { + "author_name": "Oscar Junhong Luo", + "author_inst": "Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China" + }, + { + "author_name": "Lianbo Xiao", + "author_inst": "ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine" + }, + { + "author_name": "Pengcheng Wang", + "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, China" + }, + { + "author_name": "Guobing Chen", + "author_inst": "Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.28.437369", "rel_title": "Preliminary report on SARS-CoV-2 Spike mutation T478K", @@ -851635,69 +853027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, - { - "rel_doi": "10.1101/2021.03.25.21253908", - "rel_title": "A unique SARS-CoV-2 spike protein P681H strain detected in Israel", - "rel_date": "2021-03-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21253908", - "rel_abs": "Routine detection, surveillance and reporting of SARS-CoV-2 novel variants is important, as these threaten to hinder vaccination efforts. Herein we report a local novel strain that includes a non-synonymous mutation in the spike (S) protein - P681H and additional synonymous mutations. The P681H Israeli strain has not been associated with higher infection rates and was neutralized by sera from vaccinated individuals in comparable levels to the B.1.1.7 strain and a non-P681H strain from Israel.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Neta S Zuckerman", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Shay Fleishon", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Efrat Bucris", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Dana Bar-Ilan", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Michal Linial", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Itay Bar-Or", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Victoria Indenbaum", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Merav Weil", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "- Israel National Consortium for SARS-CoV-2 sequencing", - "author_inst": "" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Michal Mandelboim", - "author_inst": "Israel Ministry of Health" - }, - { - "author_name": "Orna Mor", - "author_inst": "Israel Ministry of Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.25.21254335", "rel_title": "Infliximab is associated with attenuated immunogenicity to BNT162b2 and ChAdOx1 nCoV-19 SARS-CoV-2 vaccines", @@ -852041,6 +853370,141 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.03.27.437323", + "rel_title": "High Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Non-Covalent Inhibitor", + "rel_date": "2021-03-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.27.437323", + "rel_abs": "Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel non-covalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (Mpro) by employing a scalable high throughput virtual screening (HTVS) framework and a targeted compound library of over 6.5 million molecules that could be readily ordered and purchased. Our HTVS framework leverages the U.S. supercomputing infrastructure achieving nearly 91% resource utilization and nearly 126 million docking calculations per hour. Downstream biochemical assays validate this Mpro inhibitor with an inhibition constant (Ki) of 2.9 {micro}M [95% CI 2.2, 4.0]. Further, using room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a cleft in the primary binding site of Mpro forming stable hydrogen bond and hydrophobic interactions. We then used multiple {micro}s-timescale molecular dynamics (MD) simulations, and machine learning (ML) techniques to elucidate how the bound ligand alters the conformational states accessed by Mpro, involving motions both proximal and distal to the binding site. Together, our results demonstrate how MCULE-5948770040 inhibits Mpro and offers a springboard for further therapeutic design.\n\nO_TEXTBOXSignificance StatementThe ongoing novel coronavirus pandemic (COVID-19) has prompted a global race towards finding effective therapeutics that can target the various viral proteins. Despite many virtual screening campaigns in development, the discovery of validated inhibitors for SARS-CoV-2 protein targets has been limited. We discover a novel inhibitor against the SARS-CoV-2 main protease. Our integrated platform applies downstream biochemical assays, X-ray crystallography, and atomistic simulations to obtain a comprehensive characterization of its inhibitory mechanism. Inhibiting Mpro can lead to significant biomedical advances in targeting SARS-CoV-2 treatment, as it plays a crucial role in viral replication.\n\nC_TEXTBOX", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Austin Clyde", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Stephanie Galanie", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Daniel W. Kneller", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Heng Ma", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Yadu Babuji", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Ben Blaiszik", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Alexander Brace", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Thomas Brettin", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Kyle Chard", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Ryan Chard", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Leighton Coates", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Ian Foster", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Darin Hauner", + "author_inst": "Pacific Northwest National Laboratory" + }, + { + "author_name": "Vilmos Kertesz", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Neeraj Kumar", + "author_inst": "Pacific Northwest National Laboratory" + }, + { + "author_name": "Hyungro Lee", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Zhuozhao Li", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Andre Merzky", + "author_inst": "Rutgers University" + }, + { + "author_name": "Jurgen G. Schmidt", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Li Tan", + "author_inst": "Brookhaven National Laboratory" + }, + { + "author_name": "Mikhail Titov", + "author_inst": "Rutgers University" + }, + { + "author_name": "Anda Trifan", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Matteo Turilli", + "author_inst": "Rutgers University" + }, + { + "author_name": "Hubertus Van Dam", + "author_inst": "Brookhaven National Laboratory" + }, + { + "author_name": "Srinivas C. Chennubhotla", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Shantenu Jha", + "author_inst": "Rutgers University" + }, + { + "author_name": "Andrey Kovalevsky", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Arvind Ramanathan", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Marti Head", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Rick Stevens", + "author_inst": "Argonne National Laboratory" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.03.08.21252449", "rel_title": "International attitudes on COVID-19 vaccination: repeat national cross-sectional surveys across 15 countries", @@ -853769,77 +855233,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.22.21254082", - "rel_title": "Epidemiology and transmission of COVID-19 in cases and close contacts in Georgia in the first four months of the epidemic", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254082", - "rel_abs": "BackgroundBetween February and June 2020, 917 COVID-19 cases and 14 COVID-19-related deaths were reported in Georgia. Early on, Georgia implemented non-pharmaceutical interventions (NPI) including extensive contact tracing and restrictions on movement.\n\nAimTo characterize the demographics of those tested and infected with COVID-19 in Georgia; to evaluate factors associated with transmission between cases and their contacts; and to determine how transmission varied due to NPI up to 24 June 2020.\n\nMethodsWe use data gathered by the Georgian National Center for Disease Control on all polymerase chain reaction tests conducted (among symptomatic patients, through routine testing and contact tracing); hospitalization data for confirmed cases, and contact tracing data. We calculated the number of contacts per index case, the secondary attack rate (% contacts infected), and effective R number (new cases per index case), and used logistic regression to estimate how age, gender, and contact type affected transmission.\n\nResultsMost contacts and transmission events were between family members. Contacts <40 years were less likely to be infected, while infected individuals >50 were more likely to die than younger patients. Contact tracing identified 917 index cases with mean 3.1 contacts tested per case, primarily family members. The overall secondary attack rate was 28% (95% confidence interval [CI]: 26-29%) and effective R number was 0.87 (95%CI 0.81-0.93), peaking at 1.1 (95%CI 0.98-1.2) during the period with strongest restrictions.\n\nConclusionGeorgia effectively controlled the COVID-19 epidemic in its early stages, although evidence does not suggest transmission was reduced during the strict lockdown period.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and MedRxiv for papers reporting research using contact tracing data to evaluate the characteristics of the COVID-19 epidemic in any country. A number of analyses were identified from Asia, including China, Taiwan, Maldives, Thailand, South Korea, and India, but none from other regions other than one previous analysis conducted in Europe, focusing on the first two months of the COVID-19 epidemic in Cyprus. Studies evaluated number of contacts and different contact types, secondary attack rate, and effective R number. However, none of these studies compared characteristics between different time periods or under varied levels of non-pharmaceutical interventions or restrictions on social mixing.\n\nAdded value of this studyIn this study, we use contact tracing data from Georgia from all cases identified in the first four months of the epidemic, as well as testing and hospitalization data, to evaluate the number and type of contacts, effective R number (new cases per index case), and secondary attack rate (proportion of contacts infected) in this population, and whether these measures changed before, during, and after the lockdown period. We also evaluated how the chance of transmission varied by type of index case and contact. Our results indicate that number of contacts remained relatively low throughout the study period, so although the secondary attack rate was relatively high (28%) compared to that seen in studies in Asia (10-15%), the effective R number was less than one overall, peaking at 1.1 (0.98-1.2) during the strictest lockdown period, with easing of restrictions corresponding to a lower effective R of 0.87 (0.77-0.97). Most transmission occurred between family members with transmission very low between co-workers, friends, neighbours, and medical personnel, indicating that the restrictions on social mixing were effective at keeping the epidemic under control during this period.\n\nImplications of all the available evidenceOur study presents the first analysis of the successful control of a COVID-19 epidemic in a European country, indicating that despite a high secondary attack rate, reduction in contacts outside the home, and a well-timed lockdown, were able to keep transmission under control.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Josephine G Walker", - "author_inst": "University of Bristol" - }, - { - "author_name": "Irine Tskhomelidze", - "author_inst": "The Task Force for Global Health" - }, - { - "author_name": "Adam Trickey", - "author_inst": "University of Bristol" - }, - { - "author_name": "Vladimer Getia", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Lia Gvinjilia", - "author_inst": "The Task Force for Global Health" - }, - { - "author_name": "Paata Imnadze", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Tinatin Kuchuloria", - "author_inst": "The Task Force for Global Health" - }, - { - "author_name": "Aaron G Lim", - "author_inst": "University of Bristol" - }, - { - "author_name": "Jack Stone", - "author_inst": "University of Bristol" - }, - { - "author_name": "Sophia Surguladze", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Maia Tsereteli", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Khatuna Zakhashvili", - "author_inst": "National Center for Disease Control and Public Health" - }, - { - "author_name": "Peter Vickerman", - "author_inst": "University of Bristol" - }, - { - "author_name": "Amiran Gamkrelidze", - "author_inst": "National Center for Disease Control and Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.22.21254139", "rel_title": "Acute Brain Ischemia, Infarction and Hemorrhage in Subjects Dying with or Without Autopsy-Proven Acute Pneumonia", @@ -854087,6 +855480,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.22.21254120", + "rel_title": "Multiplex Antibody Analysis of IgM, IgA and IgG to SARS-CoV-2 in Saliva and Serum from Infected Children and their Close Contacts", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254120", + "rel_abs": "COVID-19 affects children to a lesser extent than adults but they can still get infected and transmit SARS-CoV-2 to their contacts. Field deployable non-invasive sensitive diagnostic techniques are needed to evaluate the infectivity dynamics of the coronavirus in pediatric populations and guide public health interventions.\n\nWe evaluated the utility of high-throughput Luminex-based assays applied to saliva samples to quantify IgM, IgA and IgG antibodies against five SARS-CoV-2 spike (S) and nucleocapsid (N) antigens in the context of a contacts and infectivity longitudinal study. We compared the antibody levels obtained in saliva versus serum/plasma samples from a group of children and adults tested weekly by RT-PCR over 35 days and diagnosed as positive (n=58), and a group of children and adults who consistently tested negative over the follow up period (n=61), in the Summer of 2020 in Barcelona, Spain.\n\nAntibody levels in saliva samples from individuals with confirmed RT-PCR diagnosis of SARS-CoV-2 infection were significantly higher than in negative individuals and correlated with those measured in sera/plasmas. Higher levels of anti-S IgG were found in asymptomatic individuals that could indicate protection against disease in infected individuals. Higher anti-S IgG and IgM levels in serum/plasma and saliva, respectively, in infected children compared to infected adults could also be related to stronger clinical immunity in them. Among infected children, males had higher levels of saliva IgG to N and RBD than females. Despite overall correlation, individual clustering analysis suggested that responses that may not be detected in blood could be patent in saliva, and vice versa, and therefore that both measurements are complementary.\n\nIn addition to serum/plasma, measurement of SARS-CoV-2-specific saliva antibodies should be considered as a complementary non-invasive assay to better estimate the percentage of individuals who have experienced coronavirus infection. Saliva antibody detection could allow determining COVID-19 prevalence in pediatric populations, alternative to bleeding or nasal swab, and serological diagnosis following vaccination.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Carlota Dobano", + "author_inst": "ISGlobal" + }, + { + "author_name": "Selena Alonso", + "author_inst": "ISGlobal" + }, + { + "author_name": "Marta Vidal", + "author_inst": "ISGlobal" + }, + { + "author_name": "Alfons Jimenez", + "author_inst": "ISGlobal" + }, + { + "author_name": "Rocio Rubio", + "author_inst": "ISGlobal" + }, + { + "author_name": "Rebeca Santano", + "author_inst": "ISGlobal" + }, + { + "author_name": "Diana Barrios", + "author_inst": "ISGlobal" + }, + { + "author_name": "Gemma Pons Tomas", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Maria Mele Casas", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Maria Hernandez Garcia", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Monica Girona-Alarcon", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Laura Puyol", + "author_inst": "ISGlobal" + }, + { + "author_name": "Natalia Rodrigo Melero", + "author_inst": "CRG" + }, + { + "author_name": "Carlo Carolis", + "author_inst": "CRG" + }, + { + "author_name": "Aleix Garcia-Miquel", + "author_inst": "Fetal Medicine Research Center" + }, + { + "author_name": "Elisenda Bonet-Carne", + "author_inst": "Fetal Medicine Research Center" + }, + { + "author_name": "Joana Claverol", + "author_inst": "Fundacio Sant Joan de Deu" + }, + { + "author_name": "Marta Cubells", + "author_inst": "Fundacio Sant Joan de Deu" + }, + { + "author_name": "Claudia Fortuny", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Victoria Fumado", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Anna Codina", + "author_inst": "Institut de Recerca Sant Joan de Deu" + }, + { + "author_name": "Quique Bassat", + "author_inst": "ISGlobal" + }, + { + "author_name": "Carmen Munoz-Almagro", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Mariona Fernandez de Sevilla", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Eduard Gratacos", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Luis Izquierdo", + "author_inst": "Barcelona Institute for Global Health (ISGlobal)" + }, + { + "author_name": "Juan Jose Garcia-Garcia", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Ruth Aguilar", + "author_inst": "ISGlobal" + }, + { + "author_name": "Iolanda Jordan", + "author_inst": "Hospital Sant Joan de Deu" + }, + { + "author_name": "Gemma Moncunill", + "author_inst": "ISGlobal" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.22.21254078", "rel_title": "Chagas disease and SARS-CoV-2 coinfection does not lead to worse in-hospital outcomes: results from the Brazilian COVID-19 Registry", @@ -855535,41 +857063,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.03.23.21254209", - "rel_title": "Vascular Comorbidities Worsen Prognosis of Patients with Heart Failure Hospitalized with COVID-19", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254209", - "rel_abs": "BackgroundPrior diagnosis of heart failure (HF) is associated with increased length of hospital stay (LOS) and mortality from Coronavirus disease-2019 (COVID-19). Associations between substance use, venous thromboembolism (VTE), or peripheral arterial disease (PAD) and its effects on LOS or mortality in patients with HF hospitalized with COVID-19 remains unknown.\n\nObjectiveThis study identified risk factors associated with poor in-hospital outcomes among patients with HF hospitalized with COVID-19.\n\nMethodsCase control study was conducted of patients with prior diagnosis of HF hospitalized with COVID-19 at an academic tertiary care center from January 1, 2020 to February 28, 2021. Patients with HF hospitalized with COVID-19 with risk factors were compared with those without risk factors for clinical characteristics, length of stay (LOS), and mortality. Multivariate regression was conducted to identify multiple predictors of increased LOS and in-hospital mortality in patients with HF hospitalized with COVID-19.\n\nResultsTotal of 211 HF patients were hospitalized with COVID-19. Females had longer LOS than males (9 days vs. 7 days; p < 0.001). Compared with patients without peripheral arterial disease (PAD) or ischemic stroke, patients with PAD or ischemic stroke had longer LOS (7 days vs. 9 days; p = 0.012 and 7 days vs. 11 days, p < 0.001; respectively). Older patients (aged 65 and above) had increased in-hospital mortality compared to younger patients (Adjusted OR: 1.04; 95% CI: 1.00 - 1.07; p = 0.036). VTE increased mortality more than three-fold in patients with HF hospitalized with COVID-19 (Adjusted OR: 3.33; 95% CI: 1.29 - 8.43; p = 0.011).\n\nConclusionVascular diseases increase LOS and mortality in patients with HF hospitalized with COVID-19.\n\nKEY QUESTIONSO_ST_ABSWhat is already known about this subject?C_ST_ABS- Prior diagnosis of heart failure (HF) increases LOS and mortality in patients admitted to the hospital for COVID-19\n- Antiplatelet, anticoagulation, and statin therapy decreased venous thromboembolism (VTE) in patients admitted for COVID-19\n\n\nWhat does this study add?- This study showed that patients with COVID-19, HF, and VTE had a higher mortality rate than patients with COVID-19 and either HF or VTE, or patients with HF and/or VTE who did not have COVID-19.\n- This study showed that patients with HF hospitalized with COVID-19 had greater length of stay with prior diagnosis of peripheral arterial disease (PAD) or ischemic stroke\n\n\nHow might this impact on clinical practice?- Our findings demonstrate clinical relevance by showing supportive evidence for antiplatelet, anticoagulation, and statin therapy in HF patients hospitalized with COVID-19", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jacob Mok", - "author_inst": "The University of Tennessee Health Science Center College of Medicine Chattanooga" - }, - { - "author_name": "Juan Carlos Malpartida", - "author_inst": "The University of Tennessee Health Science Center College of Medicine Chattanooga" - }, - { - "author_name": "Joshua Davis", - "author_inst": "The University of Tennessee Health Science Center College of Medicine Chattanooga" - }, - { - "author_name": "Cuilan Gao", - "author_inst": "The University of Tennessee at Chattanooga" - }, - { - "author_name": "Harish Manyam", - "author_inst": "Erlanger Health System, Heart and Lung Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.03.23.21254214", "rel_title": "Mouth-rinses and SARS-CoV-2 viral load in saliva: A living systematic review", @@ -855849,6 +857342,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.25.21254360", + "rel_title": "Disparities in Excess Deaths from the COVID-19 Pandemic Among Migrant Workers in Kuwait", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254360", + "rel_abs": "BackgroundThe actual human cost of the pandemic cannot be viewed through the COVID-19 mortality rates alone. Especially when the pandemic is widening the existing health disparities among different subpopulations within the same society. In Kuwait, migrant workers were already disproportionately impacted by COVID-19 and its unintended consequences.\n\nObjectiveTo estimate the excess deaths in the pandemic year of 2020 among the Kuwaitis and non-Kuwaiti migrants.\n\nMethodsWe analyzed publicly available retrospective data on total annual mortality historically (2005 to 2019) and in 2020. We fitted a quasi-poisson generalized linear model adjusted for yearly trend and nationality to estimate the expected deaths in 2020 in the absence of the pandemic. We calculated excess deaths as the difference between observed and expected mortality for the year of the pandemic in both Kuwaitis and non-Kuwaitis.\n\nResultsIn the absence of the pandemic, we expect the total mortality in Kuwait to be 6629 (95% CI: 6472 to 6789) deaths. However, the observed total mortality in 2020 was 9975 deaths; about 3346 (3186 to 3503) more deaths above the historical trend. Deaths among migrant workers would have been approximately 71.9% (67.8 to 76.0) lower in the absence of the pandemic. On the other hand, deaths among Kuwaitis would have been 32.4% (29.3 to 35.6) lower if the country had not had the pandemic.\n\nConclusionThe mortality burden of the COVID-19 pandemic is substantially higher than what the official tally might suggest. Systematically disadvantaged migrant workers shouldered a larger burden of deaths in the pandemic year. Public health interventions must consider structural and societal determinants that give rise to the health disparities seen among migrant workers.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Barrak Alahmad", + "author_inst": "Harvard T.H. Chan School of Public Health; Faculty of Public Health, Kuwait University" + }, + { + "author_name": "Dawoud AlMekhled", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, Nursing, and Health Sciences, Monash University, Melbourne, Australia." + }, + { + "author_name": "Ayah Odeh", + "author_inst": "Department of Health Policy and Management, Faculty of Public Health, Kuwait University, Hawalli, Kuwait." + }, + { + "author_name": "Janvier Gasana", + "author_inst": "Department of Environmental and Occupational Health, Faculty of Public Health, Kuwait University, Hawalli, Kuwait." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.25.21254292", "rel_title": "Why ODE models for COVID-19 fail: Heterogeneity shapes epidemic dynamics", @@ -857033,61 +858557,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.24.21252635", - "rel_title": "Tenofovir-DF versus Hydroxychloroquine in the Treatment of Hospitalized Patients with COVID-19: An Observational Study (THEDICOV)", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21252635", - "rel_abs": "BackgroundAlthough several therapeutic agents have been suggested for the treatment of the disease caused by the Coronavirus of the year 2019 (COVID-19), no antiviral has yet demonstrated consistent efficacy.\n\nMethodsThe results of an observational study comparing Tenofovir-DF (TDF) with Hydroxychloroquine (HCQ) in the treatment of hospitalized patients with COVID-19 with evidence of pulmonary compromise and the vast majority with supplemental oxygen requirement are presented. Patients received HCQ consecutively at the dose of 400 mg. 12 hourly for 01 day and then 200 mg. every 8 to 12 hours PO for 5 to10 days; or TDF 300 mg. per day PO for 7 to 10 days. The primary outcomes of the study were the differences between the two groups regarding: hospital stay, the need for intensive care or mechanical ventilation (ICU / MV) and mortality.\n\nResults104 patients were included: 36 in the HCQ group and 68 in the TDF group. The unadjusted primary outcomes were: LOS (length of stay) 16.6 {+/-} 12.1 for HCQ versus 12.2 {+/-} 7.0 days for TDF (p = o.o102); need for admission to ICU / mechanical ventilation (MV): 61.1% for HCQ versus 11.8% for TDF (p = o.ooo); and mortality: 50.0% for HCQ and 8.8% for TDF (p = o.ooo). The patients in the HCQ group had significant differences at admission compared to those in the TDF group regarding: male sex, cardiovascular risk factor, greater respiratory involvement and higher glucose and creatinine levels, lower albumin levels and higher. Inflammatory markers. When the outcomes were adjusted for these baseline differences, in the multiple regression model for LOS, it was found that TDF decreased the hospital stay by 6.10 days (C.I.: -11.97 to -2.40, p = o.o42); In the logistic regression model for the need for ICU / MV, it was found that the use of TDF had an O.R. of 0.15 (C.I.: 0.03-0.76, p = o.o22); and for the Cox proportional hazards model for mortality, the H.R. was 0.16 for TDF (C.I.: 0.03-0.96, p = o.o41). In the estimation model of the treatment effects by regression adjustment, it was found that TDF decreased the stay by -6.38 days (C.I.: -12.34 to -0.42, p = o.o36); the need for ICU / MV at -41.74% (C.I.: -63.72 to -19.7, p = o.ooo); and mortality by -35.22% (C.I.: -56.47 to -13.96, p = o.oo1).\n\nConclusionTDF may be an effective antiviral in the treatment of COVID-19. Some of its advantages include: its wide availability, cost and oral presentation. Randomized clinical trials are imperatively required to confirm this possibility.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mario Cornejo-Giraldo", - "author_inst": "Hospital Nacional CASE - EsSalud. Universidad Catolica Santa Maria" - }, - { - "author_name": "Nelson Rosado", - "author_inst": "Hospital Nacional CASE - EsSalud. Universidad Catolica Santa Maria." - }, - { - "author_name": "Jesus Salinas", - "author_inst": "Hospital Nacional CASE - EsSalud. Universidad Catolica Santa Maria" - }, - { - "author_name": "Nelson Aspilcueta", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Eduardo Bernales", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Jimmy Lipa", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Johanna Coacalla", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Yoisi Flores", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Pamela Leon", - "author_inst": "Hospital Nacional CASE - EsSalud" - }, - { - "author_name": "Claudia Chamby", - "author_inst": "Hospital Nacional CASE - EsSalud" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.24.21253923", "rel_title": "Pattern of COVID-19 epidemics in Japan influenced by the control measures", @@ -857359,6 +858828,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.24.21252687", + "rel_title": "Hospital mortality in COVID-19 patients in Belgium treated with statins, ACE inhibitors and/or ARBs", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21252687", + "rel_abs": "The COVID-19 pandemic has disrupted life throughout the world. Newly developed vaccines promise relief to people who live in high-income countries, although vaccines and expensive new treatments are unlikely to arrive in time to help people who live in low-and middle-income countries. The pathogenesis of COVID-19 is characterized by endothelial dysfunction. Several widely available drugs like statins, ACE inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) have immunometabolic activities that (among other things) maintain or restore endothelial cell function. For this reason, we undertook an observational study in four Belgian hospitals to determine whether in-hospital treatment with these drugs could improve survival in 959 COVID-19 patients. We found that treatment with statins and ACEIs/ARBs reduced 28-day mortality in hospitalized COVID-19 patients. Moreover, combination treatment with these drugs resulted in a 3-fold reduction in the odds of hospital mortality (OR=0.33; 95% CI 0.17-0.69). These findings were in general agreement with other published studies. Additional observational studies and clinical trials are needed to convincingly show that in-hospital treatment with statins, ACEIs/ARBs, and especially their combination saves lives.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Geert Byttebier", + "author_inst": "Medaman BV, Belgium" + }, + { + "author_name": "Luc Belmans", + "author_inst": "Medaman BV, Belgium" + }, + { + "author_name": "Myriam Alexander", + "author_inst": "Open Health" + }, + { + "author_name": "Bo E.H. Saxberg", + "author_inst": "DDO Strategic Services, LLC" + }, + { + "author_name": "Bart De Spiegeleer", + "author_inst": "Ghent University" + }, + { + "author_name": "Anton De Spiegeleer", + "author_inst": "Ghent University" + }, + { + "author_name": "Nick Devreker", + "author_inst": "AZ Delta, Roeselare, Belgium" + }, + { + "author_name": "Jens Van Praet", + "author_inst": "Department of Nephrology and Infectious diseases, AZ Sint-Jan Brugge-Oostende AV, Belgium" + }, + { + "author_name": "Karolien Vanhove", + "author_inst": "AZ Vesalius, Tongeren, Belgium" + }, + { + "author_name": "Reinhilde Reybrouck", + "author_inst": "RZ Heilig Hart, Tienen, Belgium" + }, + { + "author_name": "Evelien Wynendaele", + "author_inst": "Ghent University" + }, + { + "author_name": "David Fedson", + "author_inst": "retired" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.24.21254260", "rel_title": "SARS-CoV-2 Antibody persistence in COVID-19 convalescent plasma donors", @@ -858767,41 +860299,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.24.21254270", - "rel_title": "Counties with lower insurance coverage are associated with both slower vaccine rollout and higher COVID-19 incidence across the United States", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254270", - "rel_abs": "Efficient and equitable vaccination distribution is a priority for effectively outcompeting the transmission of COVID-19 globally. A recent study from the Centers for Disease Control and Prevention (CDC) identified that US counties with high social vulnerability according to metrics such as poverty, unemployment, low income, and no high school diploma, have significantly lower rates of vaccination compared to the national average1. Here, we build upon this analysis to consider associations between county-level vaccination rates and 68 different demographic, socioeconomic, and environmental factors for 1,510 American counties with over 228 million individuals for which vaccination data was also available. Our analysis reveals that counties with high levels of uninsured individuals have significantly lower COVID-19 vaccination rates (Spearman correlation: -0.264), despite the fact that the CDC has mandated that all COVID-19 vaccines are free and cannot be denied to anyone based upon health insurance coverage or immigration status. Furthermore, we find that the counties with high levels of uninsured individuals tend to have the highest COVID-19 incidence rates in March 2021 relative to December 2020 (Spearman correlation: 0.388). Among the 68 factors analyzed, insurance coverage is the only factor which is highly correlated with both vaccination rate and change in COVID-19 incidence during the vaccination period (|Spearman correlation|> 0.25). We also find that counties with higher percentages of Black and Hispanic individuals have significantly lower vaccination rates (Spearman correlations: -0.128, -0.136) and lesser declines of COVID-incidence rates (Spearman correlations: 0.334, 0.330) during the vaccination period. Surprisingly however, after controlling for race, we find that the association between lack of insurance coverage and vaccination rate as well as COVID-19 incidence rates is largely driven by counties with a majority white population. Among the counties with high proportions of white residents (top 10% decile), the association between insurance coverage and vaccination rate is significant (Spearman correlation: -0.210, p-value: 0.002), but among counties with low proportions of white residents (bottom 10% decile) this association is not significant (Spearman correlation: 0.072, p-value: 0.088). Taken together, this study highlights the fact that intricate socioeconomic factors are correlated not just to COVID-19 vaccination rates, but also to COVID-19 incidence fluctuations, underscoring the need to improve COVID-19 vaccination campaigns in marginalized communities. The strong positive correlation between low levels of health insurance coverage and low vaccination rates is particularly concerning, and calls for improved public health messaging to emphasize the fact that health insurance is not required to be eligible for any of the FDA-authorized COVID-19 vaccines in the United States", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Emily Lindemer", - "author_inst": "nference" - }, - { - "author_name": "Mayank Choudhary", - "author_inst": "nference" - }, - { - "author_name": "Gregory Donadio", - "author_inst": "nference" - }, - { - "author_name": "Colin Pawlowski", - "author_inst": "nference" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.26.437014", "rel_title": "Aberrant glycosylation of anti-SARS-CoV-2 IgG is a pro-thrombotic stimulus for platelets", @@ -859069,6 +860566,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.24.21254199", + "rel_title": "Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave in Europe and the United States", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254199", + "rel_abs": "Given the narrowness of the initial testing criteria, the SARS-CoV-2 virus spread through cryptic transmission in January and February, setting the stage for the epidemic wave experienced in March and April, 2020. We use a global metapopulation epidemic model to provide a mechanistic understanding of the global dynamic underlying the establishment of the COVID-19 pandemic in Europe and the United States (US). The model is calibrated on international case introductions at the early stage of the pandemic. We find that widespread community transmission of SARS-CoV-2 was likely in several areas of Europe and the US by January 2020, and estimate that by early March, only 1 - 3 in 100 SARS-CoV-2 infections were detected by surveillance systems. Modeling results indicate international travel as the key driver of the introduction of SARS-CoV-2 with possible importation and transmission events as early as December, 2019. We characterize the resulting heterogeneous spatio-temporal spread of SARS-CoV-2 and the burden of the first COVID-19 wave (February-July 2020). We estimate infection attack rates ranging from 0.78%-15.2% in the US and 0.19%-13.2% in Europe. The spatial modeling of SARS-CoV-2 introductions and spreading provides insights into the design of innovative, model-driven surveillance systems and preparedness plans that have a broader initial capacity and indication for testing.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jessica T Davis", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Nicola Perra", + "author_inst": "Networks and Urban Systems Centre, University of Greenwich, London, UK" + }, + { + "author_name": "Kunpeng Mu", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Ana Pastore y Piontti", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA" + }, + { + "author_name": "Natalie E Dean", + "author_inst": "Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, USA" + }, + { + "author_name": "Corrado Gioannini", + "author_inst": "ISI Foundation, Turin, Italy" + }, + { + "author_name": "Maria Litvinova", + "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA" + }, + { + "author_name": "Stefano Merler", + "author_inst": "Bruno Kessler Foundation, Trento Italy" + }, + { + "author_name": "Luca Rossi", + "author_inst": "ISI Foundation, Turin, Italy" + }, + { + "author_name": "Kaiyuan Sun", + "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA" + }, + { + "author_name": "Xinyue Xiong", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "M. Elizabeth Halloran", + "author_inst": "Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA. USA" + }, + { + "author_name": "Ira M Longini", + "author_inst": "Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, USA" + }, + { + "author_name": "C\u00e9cile Viboud", + "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.26.21254416", "rel_title": "Exploring Integrated Environmental Viral Surveillance of Indoor Environments: A comparison of surface and bioaerosol environmental sampling in hospital rooms with COVID-19 patients", @@ -860732,57 +862312,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21253429", - "rel_title": "SARS-CoV-2 Seroprevalence in 12 Cities of India from July-December 2020", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253429", - "rel_abs": "ObjectivesWe sought to understand the spread of SARS-CoV-2 infection in urban India, which has surprisingly low COVID-19 deaths.\n\nDesignCross-sectional and trend analyses of seroprevalence in self-referred test populations, and of reported cases and COVID mortality data.\n\nParticipants448,518 self-referred individuals using a nationwide chain of private laboratories with central testing of SARS-CoV-2 antibodies and publicly available case and mortality data.\n\nSetting12 populous cities with nearly 92 million total population.\n\nMain outcome measuresSeropositivity trends and predictors (using a Bayesian geospatial model) and prevalence derived from mortality data and infection fatality rates (IFR).\n\nResultsFor the whole of India, 31% of the self-referred individuals undergoing antibody testing were seropositive for SARS-CoV-2 antibodies. Seropositivity was higher in females (35%) than in males (30%) overall and in nearly every age group. In these 12 cities, seroprevalence rose from about 18% in July to 41% by December, with steeper increases at ages <20 and 20-44 years than at older ages. The \"M-shaped\" age pattern is consistent with intergenerational transmission. Areas of higher childhood measles vaccination in earlier years had lower seropositivity. The patterns of increase in seropositivity and in peak cases and deaths varied substantially across cities. In Delhi, death rates and cases first peaked in June and again in November; Chennai had a single peak in July. Based local IFRs and COVID deaths (adjusted for undercounts), we estimate that 43%-65% of adults above age 20 had been infected (range of mid-estimates of 12%-77%) corresponding 26 to 36 million infected adults in these cities, or an average of 9-12 infected adults per confirmed case.\n\nConclusionEven with relatively low death rates, the large cities of India had remarkably high levels of SARS-CoV-2 infection. Vaccination strategies need to consider widespread intergenerational transmission.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Arokiaswamy Velumani", - "author_inst": "Thyrocare Laboratories" - }, - { - "author_name": "Chaitili Nikam", - "author_inst": "Thyrocare Laboratories" - }, - { - "author_name": "Wilson Suraweera", - "author_inst": "Centre for Global Health Research, University of Toronto" - }, - { - "author_name": "Sze Hang Fu", - "author_inst": "Centre for Global Health Research, University of Toronto" - }, - { - "author_name": "Hellen Gelband", - "author_inst": "Centre for Global Health Research, University of Toronto" - }, - { - "author_name": "Patrick E Brown", - "author_inst": "University of Toronto" - }, - { - "author_name": "Isaac Bogoch", - "author_inst": "University of Toronto" - }, - { - "author_name": "Nico Nagelkerke", - "author_inst": "Centre for Global Health Research, University of Toronto" - }, - { - "author_name": "Prabhat Jha", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.15.21253567", "rel_title": "Evaluation of pooling of samples for testing SARS-COV- 2 for mass screening of COVID-19", @@ -861010,6 +862539,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.17.21253751", + "rel_title": "Longitudinal determination of mRNA-vaccination induced strongly binding SARS-CoV-2 IgG antibodies in a cohort of healthcare workers with and without prior exposure to the novel coronavirus", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253751", + "rel_abs": "Mass vaccination against the disease caused by the novel coronavirus (COVID-19) was a crucial step in slowing the spread of SARS-CoV-2 in 2021. Even in the face of new variants, it still remains extremely important for reducing hospitalizations and COVID-19 deaths. Only limited data exists about the short- and long-term dynamics of humoral immune response. We present a longitudinal analysis of post-vaccination IgG levels in a cohort of 166 healthcare workers vaccinated with BNT162b2 with weekly follow-up until 35 days past the first dose and monthly follow-up up to 6 months post-vaccination. A subset of the patients continued with follow-up after 6 months and either received a booster dose or got infected during the Delta wave in Romania. Tests were carried out on 1697 samples using a CE-marked IgG ELISA assay developed in-house, containing S1 and N antigens of the wild type virus.\n\nParticipants infected with SARS-CoV-2 before vaccination mount a quick immune response, reaching peak IgG levels two weeks after the first dose, while IgG levels of previously uninfected participants mount gradually, increasing abruptly after the second dose. Overall higher IgG levels are maintained for the previously infected group 35-70 days after vaccination. The decrease of IgG levels is gradual, with lower overall values in the infection naive cohort even 7-8 months after vaccination, compared to the previously infected cohort. Administration of a booster dose yielded higher average IgG antibody levels than post second dose in the infection naive group and comparable levels in the previously infected group.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Monika Korodi", + "author_inst": "University of Pecs" + }, + { + "author_name": "Istvan Horvath", + "author_inst": "University of Pecs" + }, + { + "author_name": "Kinga Rakosi", + "author_inst": "Pro-Vitam Ltd" + }, + { + "author_name": "Zsuzsanna Jenei", + "author_inst": "Pro-Vitam Ltd" + }, + { + "author_name": "Gabriella Hudak", + "author_inst": "Pro-Vitam Ltd" + }, + { + "author_name": "Melinda Kakes", + "author_inst": "Promedical Center Ltd" + }, + { + "author_name": "Katalin Dallos-Fejer", + "author_inst": "Pro-Vitam Ltd" + }, + { + "author_name": "Eniko Simai", + "author_inst": "Benedek Geza Hospital for Rehabilitation of Cardiovascular Disease" + }, + { + "author_name": "Orsolya Pall", + "author_inst": "University of Pecs" + }, + { + "author_name": "Natalia Staver", + "author_inst": "Promedical Center Ltd" + }, + { + "author_name": "Violeta Briciu", + "author_inst": "Hospital for Infectious Diseases Cluj-Napoca" + }, + { + "author_name": "Mihaela Lupse", + "author_inst": "University of Medicine and Pharmacy Iuliu Hatieganu" + }, + { + "author_name": "Mirela Flonta", + "author_inst": "Hospital for Infectious Diseases Cluj-Napoca" + }, + { + "author_name": "Ariana Almas", + "author_inst": "Hospital for Infectious Diseases Cluj-Napoca" + }, + { + "author_name": "Victoria Birlutiu", + "author_inst": "Lucian Blaga University of Sibiu" + }, + { + "author_name": "Claudia Daniela Lupu", + "author_inst": "Lucian Blaga University of Sibiu" + }, + { + "author_name": "Andreea Magdalena Ghibu", + "author_inst": "Lucian Blaga University of Sibiu" + }, + { + "author_name": "Pianoschi Dana", + "author_inst": "Hospital for Infectious Diseases Cluj-Napoca" + }, + { + "author_name": "Livia-Maria Terza", + "author_inst": "Pro-Vitam Ltd" + }, + { + "author_name": "Szilard Fejer", + "author_inst": "Pro-Vitam Ltd" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.19.21253518", "rel_title": "Comparative assessment of SARS-CoV-2 serology in healthcare workers with Abbott Architect, Roche Elecsys and The Binding site ELISA immunoassays.", @@ -862318,57 +863942,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.24.436850", - "rel_title": "Factors Associated with Emerging and Re-emerging of SARS-CoV-2 Variants", - "rel_date": "2021-03-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.24.436850", - "rel_abs": "Global spread of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has triggered unprecedented scientific efforts, as well as containment and treatment measures. Despite these efforts, SARS-CoV-2 infections remain unmanageable in some parts of the world. Due to inherent mutability of RNA viruses, it is not surprising that the SARS-CoV-2 genome has been continuously evolving since its emergence. Recently, four functionally distinct variants, B.1.1.7, B.1.351, P.1 and CAL.20C, have been identified, and they appear to more infectious and transmissible than the original (Wuhan-Hu-1) virus. Here we provide evidence based upon a combination of bioinformatics and structural approaches that can explain the higher infectivity of the new variants. Our results show that the greater infectivity of SARS-CoV-2 than SARS-CoV can be attributed to a combination of several factors, including alternate receptors. Additionally, we show that new SARS-CoV-2 variants emerged in the background of D614G in Spike protein and P323L in RNA polymerase. The correlation analyses showed that all mutations in specific variants did not evolve simultaneously. Instead, some mutations evolved most likely to compensate for the viral fitness.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Austin N Spratt", - "author_inst": "Christopher S. Bond Life Sciences Center, University of Missouri," - }, - { - "author_name": "Saathvik K Kannan", - "author_inst": "Christopher S. Bond Life Sciences Center, University of Missouri" - }, - { - "author_name": "Lucas T Woods", - "author_inst": "Department of Biochemistry, University of Missouri, Columbia" - }, - { - "author_name": "Gary A Weisman", - "author_inst": "Department of Biochemistry, University of Missouri, Columbia" - }, - { - "author_name": "Thomas D Quinn", - "author_inst": "Department of Biochemistry, University of Missouri, Columbia" - }, - { - "author_name": "Christian L Lorson", - "author_inst": "Department of Veterinary Pathobiology, University of Missouri, Columbia" - }, - { - "author_name": "Anders Sonnerborg", - "author_inst": "Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge 14186, Stockholm, Sweden" - }, - { - "author_name": "Siddappa N Byrareddy", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Kamal Singh", - "author_inst": "University of Missouri" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.03.24.436822", "rel_title": "Arginine Methylation Regulates SARS-CoV-2 Nucleocapsid Protein Function and Viral Replication", @@ -862644,6 +864217,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.03.23.21253503", + "rel_title": "The role of classroom volume, natural ventilation and voice reduction in transmission risk of SARS-CoV2 in schools", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21253503", + "rel_abs": "Issues linked to aerosol physics within school buildings and related infection risk still lack a proper recognition in school safety regulations. In this theoretical work we try to shed more light on the critical role of air ventilation, classroom volume, occupancy, and face mask types (surgical vs ffp2) in controlling airborne transmission risk in educational settings. Limited spaces available in many schools require to precisely assess the occupancy/volume ratio in each classroom and to investigate the specific risk levels from aerosolization of viral loads from infective sources. Moreover, most schools are not provided with mechanical HVAC systems. Fundamental questions are therefore: how the specific classroom volume affects the long-range contagion risk in a given classroom? is linear social distancing the right way to assess a volumetric risk problem? How effective are other countermeasures like reduced speaking volume or equipping teachers with microphones? We present here the results of a numerical analysis based on the Gammaitoni-Nucci infection risk model and the consolidated Wells-Riley like approach, with SARS-CoV2 input data and geometric data from a typical high-school classroom in Italy. We investigated separately the case of infective asymptomatic student and infective asymptomatic teacher as source of viral quanta, taking into account thermal gradient effects on the air ventilation rates. First recommendations based on the volumetric nature of aerosol risk are suggested to extend the linear social distancing approach applied so far. Finally we discuss the concept of \"cumulative infection risk\" over multiple lesson+break cycles in Wells-Riley-like infection models. We believe that any attempt to proper model infection risk in closed environments with cycled changes of the source and the susceptible individuals, should carefully consider this point, particularly when modelling air ventilation breaks in classrooms.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alessandro Zivelonghi", + "author_inst": "ITCS \"Lorgna-Pindemonte\"" + }, + { + "author_name": "Massimo Lai", + "author_inst": "Certara" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.03.22.21254057", "rel_title": "Physical, cognitive and mental health impacts of COVID-19 following hospitalisation: a multi-centre prospective cohort study", @@ -863882,81 +865478,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.17.21253283", - "rel_title": "COVID-19 in Children with Brain-Based Developmental Disabilities: A Rapid Review Update", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253283", - "rel_abs": "ObjectiveInformation regarding the impact of COVID-19 in children with brain-based disabilities, or those at risk of developing such conditions, remains scarce. The objective was to evaluate if children with brain-based disabilities are more likely to (1) develop COVID-19, (2) develop complications from the disease, and (3) to have a poorer prognosis.\n\nStudy designWe conducted a rapid review using search strategies iteratively developed and tested by an experienced medical information specialist in consultation with the review team and a panel of knowledge users. Searches were initially performed on April 18th, 2021, and updated on October 31st, 2020. Four reviewers individually performed study selection using pilot-tested standardized forms. Single reviewers extracted the data using a standardized extraction form that included study characteristics, patients characteristics, and outcomes reported.\n\nResultsWe identified 1448 publications, of which 29 were included. Studies reported data on 2288 COVID-19 positive children, including 462 with a brain-based disability, and 72 at risk of developing such disability. Overall, the included studies showed a greater risk to develop severe COVID-19 disease in children with brain-based disabilities. Although mortality is very low, the case-fatality rate appeared to be higher in children with disabilities compared to children without disabilities.\n\nConclusionsOur review shows that children with brain-based disabilities are overrepresented in hospitalization numbers compared to children without disabilities. However, most studies included children that were hospitalized from COVID-19 in secondary and tertiary care centers. Results of this review should therefore be interpreted with caution.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Mich\u00e8le Dugas", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Th\u00e9o St\u00e9fan", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Johanie L\u00e9pine", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Patrick Blouin", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Andr\u00e9e-Anne Poirier", - "author_inst": "VITAM Research Center and INESSS" - }, - { - "author_name": "Val\u00e9rie Carnovale", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale" - }, - { - "author_name": "Benoit Mailhot", - "author_inst": "VITAM Research Center, CIUSSS de la Capitale-Nationale - Universit\u00e9 Laval" - }, - { - "author_name": "Becky Skidmore", - "author_inst": "Independent Information Specialist" - }, - { - "author_name": "Lena Faust", - "author_inst": "Patient partner, McGill University" - }, - { - "author_name": "Carrie Costello", - "author_inst": "Patient partner with the CHILD-BRIGHT Network" - }, - { - "author_name": "Donna Thomson", - "author_inst": "Patient partner with the CHILD-BRIGHT Network, and Kids Brain Health Network" - }, - { - "author_name": "Annette Majnemer", - "author_inst": "McGill University" - }, - { - "author_name": "Dan Goldowitz", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Steven P. Miller", - "author_inst": "University of Toronto" - }, - { - "author_name": "Annie LeBlanc", - "author_inst": "Universite Laval - VITAM Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.03.19.21253756", "rel_title": "Characterizing Post-Acute Sequelae of SARS-CoV-2 Infection across Claims and Electronic Health Record Databases", @@ -864180,6 +865701,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, + { + "rel_doi": "10.1101/2021.03.19.21253558", + "rel_title": "Argentine Registry of neurological manifestations due to coronavirus-19 (COVID-19)", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253558", + "rel_abs": "COVID-19 disease has spread around the world since December 2019. Neurological symptoms are part of its clinical spectrum.\n\nObjectiveTo know the neurological manifestations in patients infected by COVID-19 in Argentina.\n\nMethodsMulticenter study conducted in adults, from May 2020 to January 2021, with confirmed COVID-19 and neurological symptoms. Demographic variables, existence of systemic or neurological comorbidities, the form of onset of the infection, alteration in complementary studies and the degree of severity of neurological symptoms were recorded.\n\nResults817 patients from all over the country were included, 52% male, mean age 38 years, most of them without comorbidities or previous neurological pathology. The first symptom of the infection was neurological in 56.2% of the cases, predominantly headache (69%), then anosmia / ageusia (66%). Myalgias (52%), allodynia / hyperalgesia (18%), and asthenia (6%) were also reported. 3.2% showed diffuse CNS involvement such as encephalopathy or seizures. 1.7% had cerebrovascular complications. Sleep disorders were observed in 3.2%. 6 patients were reported with Guillain Barre (GBS), peripheral neuropathy (3.4%), tongue paresthesia (0.6%), hearing loss (0.4%), plexopathy (0.3%). The severity of neurological symptoms was correlated with age and the existence of comorbidities.\n\nConclusionsOur results, similar to those of other countries, show two types of neurological symptoms associated with COVID-19: some potentially disabling or fatal such as GBS or encephalitis, and others less devastating, but more frequent such as headache or anosmia that demand increasingly long-term care.", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Mariana Bendersky", + "author_inst": "University of Buenos Aires school of medicine, ENyS, CONICET" + }, + { + "author_name": "Lucas Alessandro", + "author_inst": "FLENI" + }, + { + "author_name": "Franco Appiani", + "author_inst": "FUNDACION FAVALORO" + }, + { + "author_name": "Brenda Borrego Guerrero", + "author_inst": "SANATORIO TANDIL" + }, + { + "author_name": "Patricia Cairola", + "author_inst": "HOSPITAL DURAND" + }, + { + "author_name": "Ismael Calandri", + "author_inst": "FLENI" + }, + { + "author_name": "Juan Martin Cardozo Oliver", + "author_inst": "SANATORIO FINOCHIETTO, IADIN" + }, + { + "author_name": "Maria Emilia Clement", + "author_inst": "HOSPITAL PRIVADO DE LA COMUNIDAD" + }, + { + "author_name": "Marianna Di Egidio", + "author_inst": "hospital tornu" + }, + { + "author_name": "Jose Luis Di Pace", + "author_inst": "HOSPITAL DURAND" + }, + { + "author_name": "Melina Diaconchuk", + "author_inst": "HOSPITAL SAN LUIS" + }, + { + "author_name": "Guadalupe Bruera", + "author_inst": "HOSPITAL DE ROSARIO-INSTITUTO MAX PLANCK" + }, + { + "author_name": "MARIA M ESNAOLA Y ROJAS", + "author_inst": "INSTITUTO MILSTEIN" + }, + { + "author_name": "MABEL LASERNA", + "author_inst": "Universidad Provincial del Sudoeste" + }, + { + "author_name": "Julian Fernandez Boccazzi", + "author_inst": "sanatorio Trinidad Mitre" + }, + { + "author_name": "Andrea Fabiana Franco", + "author_inst": "HOSPITAL RAMOS MEJIA" + }, + { + "author_name": "Gisella Gargiulo", + "author_inst": "CEMIC-CONICET" + }, + { + "author_name": "Daniela Laura Giardino", + "author_inst": "CEMIC" + }, + { + "author_name": "Cesar Gomez", + "author_inst": "MUTUAL RURAL ART- UNIVERSIDAD DE BUENOS AIRES" + }, + { + "author_name": "Ana Karina Guevara", + "author_inst": "HOSPITAL VERA BARROS" + }, + { + "author_name": "Natalia Gutierrez", + "author_inst": "SANATORIO MENDEZ" + }, + { + "author_name": "Javier Hryb", + "author_inst": "HOSPITAL DURAND" + }, + { + "author_name": "Ibarra Viviana", + "author_inst": "SANATORIO MENDEZ" + }, + { + "author_name": "Franco Janota", + "author_inst": "HOSPITAL MUNIZ" + }, + { + "author_name": "Luis Alfredo Larcher", + "author_inst": "Sanatorio del Norte" + }, + { + "author_name": "Fernando Leone", + "author_inst": "CENTRO MEDICO ROCA" + }, + { + "author_name": "Geraldine Luetic", + "author_inst": "INSTITUTO DE NEUROCIENCIAS DE ROSARIO" + }, + { + "author_name": "Claudia Andrea Medina", + "author_inst": "SANATORIO LAS LOMAS" + }, + { + "author_name": "Maria L Menichini", + "author_inst": "INSTITUTO DE NEUROCIENCIAS DE ROSARIO" + }, + { + "author_name": "Gonzalo P Nieto", + "author_inst": "HOSPITAL RIVADAVIA" + }, + { + "author_name": "Maria F Paez", + "author_inst": "HOSPITAL FERNANDEZ" + }, + { + "author_name": "Francisco Penalver", + "author_inst": "Hospital Luis C. Lagomaggiore/Fundacion Cerebro y Mente" + }, + { + "author_name": "Monica Perassolo", + "author_inst": "HOSPITAL DURAND" + }, + { + "author_name": "Gabriel Persi", + "author_inst": "sanatorio trinidad mitre" + }, + { + "author_name": "Claudia Pestchanker", + "author_inst": "hospital san luis" + }, + { + "author_name": "Oscar Porta", + "author_inst": "HOSPITAL DURAND" + }, + { + "author_name": "Gabriel E Rodriguez", + "author_inst": "HOSPITAL RAMOS MEJIA" + }, + { + "author_name": "Marina Romano", + "author_inst": "CEMIC" + }, + { + "author_name": "Patricia Saidon", + "author_inst": "HOSPITAL RAMOS MEJIA" + }, + { + "author_name": "Maria F Sica", + "author_inst": "HOSPITAL PRIVADO DE LA COMUNIDAD" + }, + { + "author_name": "Erica Stankievich", + "author_inst": "CENTRO M-A.MOLTEDO" + }, + { + "author_name": "guillermo zalazar", + "author_inst": "HOSPITAL SAN LUIS" + }, + { + "author_name": "Adriana Tarulla", + "author_inst": "HOSPITAL PINERO" + }, + { + "author_name": "Roberto D rey", + "author_inst": "IADIN-SANATORIO FINOCHIETTO-UNIVERSIDAD DE BUENOS AIRES" + }, + { + "author_name": "Marcelo Rugiero", + "author_inst": "HOSPITAL ITALIANO DE BUENOS AIRES" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.03.20.21253414", "rel_title": "Functional and microstructural brain abnormalities, fatigue, and cognitive dysfunction after mild COVID-19", @@ -865940,53 +867656,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.11.21253231", - "rel_title": "Emergence of the E484K Mutation in SARS-CoV-2 Lineage B.1.1.220 in Upstate New York", - "rel_date": "2021-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253231", - "rel_abs": "Ongoing surveillance detected a SARS-CoV-2 B.1.1.220 variant carrying the E484K substitution in four patients from a hospital network in upstate New York. Patients reported no travel history and shared no obvious epidemiological linkage. A search of online databases identified 12 additional B.1.1.220 with E484K, all of which were detected in New York since December 2020. Detailed genomic analyses suggests that the mutation has emerged independently in at least two different B.1.1.220 strains in this region.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Emil Lesho", - "author_inst": "Rochester General Hospital" - }, - { - "author_name": "Brendan Corey", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Francois Lebreton", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Ana Ong", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Brett Swierczewski", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Jason Bennett", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Edward Walsh", - "author_inst": "University of Rochester School of Medicine" - }, - { - "author_name": "Patrick McGann", - "author_inst": "Walter Reed Army Institute of Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.23.436564", "rel_title": "Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527", @@ -866354,6 +868023,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.23.436613", + "rel_title": "Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers", + "rel_date": "2021-03-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.23.436613", + "rel_abs": "As the COVID-19 pandemic continues to spread, hundreds of new initiatives including studies on existing medicines are running to fight the disease. To deliver a potentially immediate and lasting treatment to current and emerging SARS-CoV-2 variants, new collaborations and ways of sharing are required to create as many paths forward as possible. Here we leverage our expertise in computational antibody engineering to rationally design/optimize three previously reported SARS-CoV neutralizing antibodies and share our proposal towards anti-SARS-CoV-2 biologics therapeutics. SARS-CoV neutralizing antibodies, m396, 80R, and CR-3022 were chosen as templates due to their diversified epitopes and confirmed neutralization potency against SARS. Structures of variable fragment (Fv) in complex with receptor binding domain (RBD) from SARS-CoV or SARS-CoV2 were subjected to our established in silico antibody engineering platform to improve their binding affinity to SARS-CoV2 and developability profiles. The selected top mutations were ensembled into a focused library for each antibody for further screening. In addition, we convert the selected binders with different epitopes into the trispecific format, aiming to increase potency and to prevent mutational escape. Lastly, to avoid antibody induced virus activation or enhancement, we applied NNAS and DQ mutations to the Fc region to eliminate effector functions and extend half-life.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Saleh Riahi", + "author_inst": "Sanofi" + }, + { + "author_name": "Jae Hyeon Lee", + "author_inst": "Sanofi" + }, + { + "author_name": "Shuai Wei", + "author_inst": "Sanofi" + }, + { + "author_name": "Robert Cost", + "author_inst": "Sanofi" + }, + { + "author_name": "Alessandro Masiero", + "author_inst": "Sanofi" + }, + { + "author_name": "Catherine Prades", + "author_inst": "Sanofi" + }, + { + "author_name": "Reza Olfati-Saber", + "author_inst": "Sanofi" + }, + { + "author_name": "Maria Wendt", + "author_inst": "Sanofi" + }, + { + "author_name": "Anna Park", + "author_inst": "Sanofi" + }, + { + "author_name": "Yu Qiu", + "author_inst": "Sanofi" + }, + { + "author_name": "Yanfeng Zhou", + "author_inst": "Sanofi" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.03.23.436573", "rel_title": "Identification, crystallization and epitope determination of public TCR shared and expanded in COVID-19 patients", @@ -867810,97 +869538,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.03.20.21254040", - "rel_title": "Symptoms of COVID-19 in a population-based cohort study", - "rel_date": "2021-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21254040", - "rel_abs": "Accurate diagnosis of potential SARS-CoV-2 infections by symptoms is one strategy for continuing global surveillance, particularly in low-resource communities. We conducted a prospective, population-based cohort study, the Arizona CoVHORT, among Arizona residents to elucidate the symptom profile of laboratory-confirmed COVID-19 participants(16.2%) compared to laboratory-confirmed negative(22.4%) and untested general population participants(61.4%). Among the 1514 study participants, those who were COVID-19 positive were more likely to be Hispanic(33.5%) and more likely to report obesity > 30 kg/m2(34.7%) compared to COVID-19 negative participants(19.2%; 31.0%) and untested CoVHORT participants(13.8%; 23.8%). Of the 245 laboratory-confirmed COVID-19 cases, 15.0% reported having had no symptoms. Of those that did report symptoms, the most commonly-reported first symptoms were sore throat(19.0%), headache(15.5%), cough(12.7%), runny nose/cold-like symptoms(12.1%), and fatigue(12.0%). In adjusted logistic regression models, COVID-19 positive participants were more likely than negative participants to experience loss of taste and smell(OR:35.7; 95% CI 18.4-69.5); bone or nerve pain(OR:17.9; 95% CI 6.7-47.4), vomiting(OR:10.8; 95% CI 3.1-37.5), nausea(OR:10.5; 95% CI 5.5-19.9), and headache(OR:8.4; 95% CI 5.6-12.8). When comparing confirmed COVID-19 cases with confirmed negative or untested participants, the pattern of symptoms that discriminates SARS-CoV-2 infection from those arising from other potential circulating pathogens may differ from general reports of symptoms among cases alone.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Sana M Khan", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Leslie V Farland", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Erika Austhof", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Melanie L Bell", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Collin J Catalfamo", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Zhao Chen", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Felina Cordova-Marks", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Kacey C Ernst", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Pamela Garcia-Filion", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Kelly M Heslin", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Joshua Hoskinson", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Megan L Jehn", - "author_inst": "Arizona State University" - }, - { - "author_name": "Emily C.S. Joseph", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Connor P Kelley", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Yann Klimentidis", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Stephanie Carrol", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Lindsay N Kohler", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Kristen Pogreba-Brown", - "author_inst": "The University of Arizona" - }, - { - "author_name": "Elizabeth T Jacobs", - "author_inst": "The University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.21.21253754", "rel_title": "Role of Combining Anticoagulant and Antiplatelet Agents in COVID-19 Treatment: A Rapid Review", @@ -868244,6 +869881,69 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.03.21.436312", + "rel_title": "Predicting hosts based on early SARS-CoV-2 samples and analyzing later world-wide pandemic in 2020", + "rel_date": "2021-03-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.21.436312", + "rel_abs": "The SARS-CoV-2 pandemic has raised the concern for identifying hosts of the virus since the early-stage outbreak. To address this problem, we proposed a deep learning method, DeepHoF, based on extracting the viral genomic features automatically, to predict host likelihood scores on five host types, including plant, germ, invertebrate, non-human vertebrate and human, for novel viruses. DeepHoF made up for the lack of an accurate tool applicable to any novel virus and overcame the limitation of the sequence similarity-based methods, reaching a satisfactory AUC of 0.987 on the five-classification. Additionally, to fill the gap in the efficient inference of host species for SARS-CoV-2 using existed tools, we conducted a deep analysis on the host likelihood profile calculated by DeepHoF. Using the isolates sequenced in the earliest stage of COVID-19, we inferred minks, bats, dogs and cats were potential hosts of SARS-CoV-2, while minks might be one of the most noteworthy hosts. Several genes of SARS-CoV-2 demonstrated their significance in determining the host range. Furthermore, the large-scale genome analysis, based on DeepHoFs computation for the later world-wide pandemic in 2020, disclosed the uniformity of host range among SARS-CoV-2 samples and the strong association of SARS-CoV-2 between humans and minks.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Qian Guo", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, Peki" + }, + { + "author_name": "Mo Li", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and " + }, + { + "author_name": "Chunhui Wang", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and " + }, + { + "author_name": "Jinyuan Guo", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, Peki" + }, + { + "author_name": "Xiaoqing Jiang", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and " + }, + { + "author_name": "Jie Tan", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and " + }, + { + "author_name": "Shufang Wu", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and " + }, + { + "author_name": "Peihong Wang", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and " + }, + { + "author_name": "Tingting Xiao", + "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 31005" + }, + { + "author_name": "Zhencheng Fang", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and " + }, + { + "author_name": "Yonghong Xiao", + "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 31005" + }, + { + "author_name": "Huaiqiu Zhu", + "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and " + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.03.22.436337", "rel_title": "Live imaging of SARS-CoV-2 infection in mice reveals neutralizing antibodies require Fc function for optimal efficacy", @@ -869948,41 +871648,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.19.21253945", - "rel_title": "Sarcopenic obesity and the risk of hospitalisation or death from COVID-19: findings from UK Biobank", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253945", - "rel_abs": "BackgroundCoronavirus disease{square}2019 (COVID{square}19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS{square}CoV{square}2 virus). The role of skeletal muscle mass in modulating immune response is well documented. Whilst obesity is well-established as a key factor in COVID-19 infection and outcome, no study has examined the influence of both sarcopenia (low muscle mass) and obesity, termed sarcopenic obesity on COVID-19 risk.\n\nMethodsThis study uses data from UK Biobank. Probable sarcopenia was defined as low handgrip strength. Sarcopenic obesity was mutually exclusively defined as the presence of obesity and low muscle mass (based on two established criteria: appendicular lean mass (ALM) adjusted for either: 1) height and 2) body mass index (BMI)). Severe COVID-19 was defined by a positive test result in a hospital setting or death with a primary cause reported as COVID-19. Fully adjusted logistic regression models were used to analyse the associations between sarcopenic status and severe COVID-19. This work was conducted under UK Biobank application number 52553.\n\nResultsWe analysed data from 490,301 UK Biobank participants. 2203 (0.4%) had severe COVID-19 infection. Individuals with probable sarcopenia were 64% more likely to have had severe COVID-19 infection (odds ratio (OR) 1.638; P<.001). Obesity increased the likelihood of severe COVID-19 infection by 76% (P<.001). Using either ALM index and ALM/BMI index to define low muscle mass, those with sarcopenic obesity were 2.6 times more likely to have severe COVID-19 (OR: 2.619; P<.001). Sarcopenia alone did not increase the risk of COVID-19.\n\nConclusionsSarcopenic obesity may increase the risk of severe COVID-19 infection, over that of obesity alone. The mechanisms for this are complex but could be a result of a reduction in respiratory functioning, immune response, and ability to respond to metabolic stress.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Thomas Wilkinson", - "author_inst": "University of Leicester" - }, - { - "author_name": "Thomas Yates", - "author_inst": "Leicester NIHR Biomedical Research Centre" - }, - { - "author_name": "Luke A Baker", - "author_inst": "University of Leicester" - }, - { - "author_name": "Francesco Zaccardi", - "author_inst": "Leicester Diabetes Research Centre" - }, - { - "author_name": "Alice C Smith", - "author_inst": "University of Leicester" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.18.21253887", "rel_title": "Effect of Increased Alcohol Consumption During COVID-19 Pandemic on Alcohol-related Liver Disease: A Modelling Study", @@ -870346,6 +872011,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.18.21253874", + "rel_title": "Diagnostic accuracy of rapid antigen tests in pre-/asymptomatic close contacts of individuals with a confirmed SARS-CoV-2 infection", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253874", + "rel_abs": "BackgroundPre-/asymptomatic close contacts of SARS-CoV-2 infected individuals were tested at day 5 after contact by real-time reverse transcriptase polymerase chain reaction (RT-PCR). Diagnostic accuracy of antigen-detecting rapid diagnostic tests (Ag-RDT) in pre-/asymptomatic close contacts was up till now unknown.\n\nMethodsWe performed a prospective cross-sectional diagnostic test accuracy study. Close contacts (e.g. selected via the test-and-trace program or contact tracing app) aged [≥]16 years and asymptomatic when requesting a test, were included consecutively and tested at day 5 at four Dutch public health service test sites. We evaluated two Ag-RDTs (BD Veritor System Ag-RDT (BD), and Roche/SD Biosensor Ag-RDT (SD-B)) with RT-PCR as the reference standard. Virus culture was performed in RT-PCR positive individuals to determine the viral load cut-off above which 95% was culture positive, as a proxy of infectiousness.\n\nResultsOf 2,678 BD-tested individuals, 233 (8.7%) were RT-PCR positive and BD detected 149 (sensitivity 63.9%; 95% confidence interval 57.4%-70.1%). Out of 1,596 SD-B-tested individuals, 132 (8.3%) were RT-PCR positive and SD-B detected 83 (sensitivity 62.9%; 54.0%-71.1%). When applying an infectiousness viral load cut-off [≥] 5.2 log10 gene copies/mL, the sensitivity was 90.1% (84.2%-94.4%) for BD, 86.8% (78.1% to 93.0%) for SD-B overall, and 88.1% (80.5%-93.5%) for BD, 85.1% (74.3%-92.6%) for SD-B for those still asymptomatic at the actual time of sampling. Specificity was >99% for both Ag-RDTs in all analyses.\n\nConclusionsThe sensitivity for detecting SARS-CoV-2 of both Ag-RDTs in pre-/asymptomatic close contacts is over 60%, increasing to over 85% after applying an infectiousness viral load cut-off.\n\nTrial registration numberNot applicable. A study protocol is available upon request.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Ewoud Schuit", + "author_inst": "University Medical Center Utrecht" + }, + { + "author_name": "Irene Veldhuijzen", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Roderick Venekamp", + "author_inst": "University Medical Center Utrecht" + }, + { + "author_name": "Wouter Bijllaardt", + "author_inst": "Amphia Hospital" + }, + { + "author_name": "Susan Pas", + "author_inst": "Amphia Hospital" + }, + { + "author_name": "Esther Lodder", + "author_inst": "Public Health Service West-Brabant" + }, + { + "author_name": "Richard Molenkamp", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Corine GeurtsvanKessel", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Jans Velzing", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Robin Huisman", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Lieke Brouwer", + "author_inst": "Public Health Service Rotterdam-Rijnmond" + }, + { + "author_name": "Timo Boelsums", + "author_inst": "Public Health Service Rotterdam-Rijnmond" + }, + { + "author_name": "Gregorius Sips", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Kim Benschop", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Lotty Hooft", + "author_inst": "University Medical Center Utrecht" + }, + { + "author_name": "Janneke van de Wijgert", + "author_inst": "University Medical Center Utrecht" + }, + { + "author_name": "Susan van den Hof", + "author_inst": "RIVM" + }, + { + "author_name": "Karel Moons", + "author_inst": "University Medical Center Utrecht" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.18.21253869", "rel_title": "Generation of Inhibitory Autoantibodies to ADAMTS13 in Coronavirus Disease 2019", @@ -872238,101 +873990,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21253960", - "rel_title": "Within-country age-based prioritisation, global allocation, and public health impact of a vaccine against SARS-CoV-2: a mathematical modelling analysis", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253960", - "rel_abs": "The worldwide endeavour to develop safe and effective COVID-19 vaccines has been extraordinary, and vaccination is now underway in many countries. However, the doses available in 2021 are likely to be limited. We extended a mathematical model of SARS-CoV-2 transmission across different country settings to evaluate the public health impact of potential vaccines using WHO-developed target product profiles. We identified optimal vaccine allocation strategies within- and between-countries to maximise averted deaths under constraints on dose supply. We found that the health impact of SARS-CoV-2 vaccination depends on the cumulative population-level infection incidence when vaccination begins, the duration of natural immunity, the trajectory of the epidemic prior to vaccination, and the level of healthcare available to effectively treat those with disease. Within a country we find that for a limited supply (doses for <20% of the population) the optimal strategy is to target the elderly. However, with a larger supply, if vaccination can occur while other interventions are maintained, the optimal strategy switches to targeting key transmitters to indirectly protect the vulnerable. As supply increases, vaccines that reduce or block infection have a greater impact than those that prevent disease alone due to the indirect protection provided to high-risk groups. Given a 2 billion global dose supply in 2021, we find that a strategy in which doses are allocated to countries proportional to population size is close to optimal in averting deaths and aligns with the ethical principles agreed in pandemic preparedness planning.\n\nHighlightsO_LIThe global dose supply of COVID-19 vaccines will be constrained in 2021\nC_LIO_LIWithin a country, prioritising doses to protect those at highest mortality risk is efficient\nC_LIO_LIFor a 2 billion dose supply in 2021, allocating to countries according to population size is efficient and equitable\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Alexandra B Hogan", - "author_inst": "Imperial College London" - }, - { - "author_name": "Peter Winskill", - "author_inst": "Imperial College London" - }, - { - "author_name": "Oliver J Watson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Patrick G T Walker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Charles Whittaker", - "author_inst": "Imperial College, London" - }, - { - "author_name": "Marc Baguelin", - "author_inst": "Imperial College London" - }, - { - "author_name": "Nicholas F Brazeau", - "author_inst": "Imperial College London" - }, - { - "author_name": "Giovanni D Charles", - "author_inst": "Imperial College London" - }, - { - "author_name": "Katy A M Gaythorpe", - "author_inst": "Imperial College London" - }, - { - "author_name": "Arran Hamlet", - "author_inst": "Imperial College London" - }, - { - "author_name": "Edward Knock", - "author_inst": "Imperial College London" - }, - { - "author_name": "Daniel J Laydon", - "author_inst": "Imperial College London" - }, - { - "author_name": "John A Lees", - "author_inst": "Imperial College London" - }, - { - "author_name": "Alessandra L\u00f8chen", - "author_inst": "Imperial College London" - }, - { - "author_name": "Robert Verity", - "author_inst": "Imperial College London" - }, - { - "author_name": "Lilith K Whittles", - "author_inst": "Imperial College London" - }, - { - "author_name": "Farzana Muhib", - "author_inst": "PATH" - }, - { - "author_name": "Katharina Hauck", - "author_inst": "Imperial College London" - }, - { - "author_name": "Neil M Ferguson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Azra C Ghani", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.19.21253889", "rel_title": "Risk of reinfection after seroconversion to SARS-CoV-2: A population-based propensity-score matched cohort study", @@ -872564,6 +874221,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2021.03.17.21253805", + "rel_title": "The effect of Covid-19 isolation measures on the cognition and mental health of people living with dementia: a rapid systematic review of one year of evidence.", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253805", + "rel_abs": "BackgroundCovid-19 control policies have entailed lockdowns and confinement. Although these isolation measures are thought to be particularly hard and possibly harmful to people with dementia, their specific impact during the pandemic has not yet been synthesised. We aimed to examine and summarise the global research evidence describing the effect of Covid-19 isolation measures on the health of people living with dementia.\n\nMethodWe searched Pubmed, PsycINFO and CINAHL up to February 2021 for peer-reviewed quantitative studies of the effects of isolation measures during Covid-19 on cognitive, psychological and functional symptoms of people with any kind of dementia or mild cognitive impairment. We summarised the findings of included papers following current guidelines for rapid reviews.\n\nResultsWe identified 15 eligible papers, examining a total of 6,442 people with dementia. 13/15 were conducted in people living in the community and 2 in care homes. 60% (9/15) studies reported changes in cognition with 77% (7/9) of them describing declined cognition by >50% of respondents. 93% (14/15) of studies reported worsening or new onset of behavioural and psychological symptoms. 46% (7/15) studies reported changes in daily function, 6 of them reporting a functional decline in a variable proportion of the population studied.\n\nConclusionLockdowns and confinement measures brought about by the pandemic have damaged the cognitive and psychological health and functional abilities of people with dementia across the world. It is urgent that infection control measures applied to people with dementia are balanced against the principles of non-maleficence. This systematic review makes 4 specific calls for action.\n\nKey PointsO_LINeuropsychiatric symptoms of people with dementia (e.g., anxiety, depressive symptoms, apathy, agitation) were found to worsen during lockdown in the majority of studies.\nC_LIO_LICognitive decline affecting memory, orientation concentration and communication was observed by caregivers within few weeks after lockdown.\nC_LIO_LIThe deterioration reported occurred in a short window of time (between 1 and 4 months) and it is unlikely to be attributable to the natural variation of the course of dementia.\nC_LIO_LIThere is little research conducted in care home residents with dementia (only 2 papers found).\nC_LIO_LIIncrease consumption of antipsychotics and benzodiazepines has occurred in people with dementia during lockdown.\nC_LIO_LIEvidence indicates that isolation measures quickly damaged peoples with dementia cognitive and mental health and probably accelerated overall decline.\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Aida Suarez-Gonzalez", + "author_inst": "UCL" + }, + { + "author_name": "Jayeeta Rajagopalan", + "author_inst": "National Institute of Mental Health and Neurosciences, Bangalore, India" + }, + { + "author_name": "Gill Livingston", + "author_inst": "Division of Psychiatry, Maple House, University College London" + }, + { + "author_name": "Suvarna Alladi", + "author_inst": "Department of Neurology, National Institute of Mental Health and Neurosciences Bangalore, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.03.17.21253816", "rel_title": "PREDICTIVE IMMUNOLOGICAL, VIROLOGICAL, AND ROUTINE LABORATORY MARKERS FOR CRITICAL COVID-19 ON ADMISSION.Immunocovid study", @@ -873884,65 +875572,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.19.435806", - "rel_title": "Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir", - "rel_date": "2021-03-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.19.435806", - "rel_abs": "Rapid repurposing of existing drugs as new therapeutics for COVID-19 has been an important strategy in the management of disease severity during the ongoing SARS-CoV-2 pandemic. Here, we used high-throughput docking to screen 6000 compounds within the DrugBank library for their potential to bind and inhibit the SARS-CoV-2 3CL main protease, a chymotrypsin-like enzyme that is essential for viral replication. For 19 candidate hits, parallel in vitro fluorescence-based protease-inhibition assays and Vero-CCL81 cell-based SARS-CoV-2 replication-inhibition assays were performed. One hit, diclazuril (an investigational anti-protozoal compound), was validated as a SARS-CoV-2 3CL main protease inhibitor in vitro (IC50 value of 29 {micro}M) and modestly inhibited SARS-CoV-2 replication in Vero-CCL81 cells. Another hit, lenvatinib (approved for use in humans as an anti-cancer treatment), could not be validated as a SARS-CoV-2 3CL main protease inhibitor in vitro, but serendipitously exhibited a striking functional synergy with the approved nucleoside analogue remdesivir to inhibit SARS-CoV-2 replication, albeit this was specific to Vero-CCL81 cells. Lenvatinib is a broadly-acting host receptor tyrosine kinase (RTK) inhibitor, but the synergistic effect with remdesivir was not observed with other approved RTK inhibitors (such as pazopanib or sunitinib), suggesting that the mechanism-of-action is independent of host RTKs. Furthermore, time-of-addition studies revealed that lenvatinib/remdesivir synergy probably targets SARS-CoV-2 replication subsequent to host-cell entry. Our work shows that combining computational and cellular screening is a means to identify existing drugs with repurposing potential as antiviral compounds. Future studies could be aimed at understanding and optimizing the lenvatinib/remdesivir synergistic mechanism as a therapeutic option.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Marie O. Pohl", - "author_inst": "University of Zurich" - }, - { - "author_name": "Idoia Busnadiego", - "author_inst": "University of Zurich" - }, - { - "author_name": "Francesco Marrafino", - "author_inst": "University of Salerno" - }, - { - "author_name": "Lars Wiedmer", - "author_inst": "University of Zurich" - }, - { - "author_name": "Annika Hunziker", - "author_inst": "University of Zurich" - }, - { - "author_name": "Sonja Fernbach", - "author_inst": "University of Zurich" - }, - { - "author_name": "Irina Glas", - "author_inst": "University of Zurich" - }, - { - "author_name": "Elena V. Moroz-Omori", - "author_inst": "University of Zurich" - }, - { - "author_name": "Benjamin G Hale", - "author_inst": "University of Zurich" - }, - { - "author_name": "Amedeo Caflisch", - "author_inst": "University of Zurich" - }, - { - "author_name": "Silke Stertz", - "author_inst": "University of Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.19.435740", "rel_title": "The inhibitory effects of toothpaste and mouthwash ingredients on the interaction between the SARS-CoV-2 spike protein and ACE2, and the protease activity of TMPRSS2, in vitro", @@ -874310,6 +875939,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.17.435863", + "rel_title": "Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies", + "rel_date": "2021-03-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.17.435863", + "rel_abs": "Monoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the viral spike receptor-binding domain (RBD) that escape binding by representatives of three potently neutralizing classes of anti-RBD antibodies with high-resolution structures. We compare the antibody-escape maps to similar maps for convalescent polyclonal plasma, including plasma from individuals from whom some of the antibodies were isolated. The plasma-escape maps most closely resemble those of a single class of antibodies that target an epitope on the RBD that includes site E484. Therefore, although the human immune system can produce antibodies that target diverse RBD epitopes, in practice the polyclonal response to infection is dominated by a single class of antibodies targeting an epitope that is already undergoing rapid evolution.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Allison J Greaney", + "author_inst": "University of Washington" + }, + { + "author_name": "Tyler N Starr", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Christopher O Barnes", + "author_inst": "Caltech" + }, + { + "author_name": "Yiska Weisblum", + "author_inst": "Rockefeller" + }, + { + "author_name": "Fabian Schmidt", + "author_inst": "Rockefeller" + }, + { + "author_name": "Marina Caskey", + "author_inst": "Rockefeller" + }, + { + "author_name": "Christian Gaebler", + "author_inst": "Rockefeller" + }, + { + "author_name": "Marianna Agudelo", + "author_inst": "Rockefeller" + }, + { + "author_name": "Shlomo Finkin", + "author_inst": "Rockefeller" + }, + { + "author_name": "Zijun Wang", + "author_inst": "Rockefeller" + }, + { + "author_name": "Daniel Poston", + "author_inst": "Rockefeller" + }, + { + "author_name": "Frauke Muecksch", + "author_inst": "Rockefeller" + }, + { + "author_name": "Theodora Hatziioannou", + "author_inst": "Rockefeller" + }, + { + "author_name": "Paul D Bieniasz", + "author_inst": "Rockefeller" + }, + { + "author_name": "Davide F Robbiani", + "author_inst": "Rockefeller" + }, + { + "author_name": "Michel C Nussenzweig", + "author_inst": "Rockefeller" + }, + { + "author_name": "Pamela J Bjorkman", + "author_inst": "Caltech" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.17.435823", "rel_title": "A novel SARS-CoV-2 related virus with complex recombination isolated from bats in Yunnan province, China", @@ -875686,37 +877402,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.03.15.21253566", - "rel_title": "Understanding Convergence Between Non-Hispanic Black and White COVID-19 Mortality: A County-Level Approach", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253566", - "rel_abs": "BackgroundNon-Hispanic Black populations have suffered greater per capita COVID-19 mortality at more than 1.5 times that of White populations. Previous work has established that, over time, rates of Black and White mortality have converged; however, some studies suggest that regional shifts in COVID-19 prevalence may play a role in the relative change between racial groups. This studys objective was to investigate changes in Black and White COVID-19 mortality over time and uncover potential mechanisms driving these changes.\n\nMethods and FindingsUsing county-level COVID-19 mortality data stratified by race, we investigate the trajectory of non-Hispanic Black mortality, White mortality, and the Black/White per capita mortality ratio from June 2020-January 2021. Over this period, in the counties studied, cumulative mortality rose by 56.7% and 82.8% for Black and White populations respectively, resulting in a decrease in mortality ratio of 0.369 (23.8%). These trends persisted even when a county-level fixed-effects model was used to estimate changes over time within counties (controlling for all time-invariant county level characteristics and removing the effects of changes in regional distribution of COVID-19). Next, we leverage county-level variation over time in COVID-19 prevalence to show that the decline in the Black/White mortality ratio can be explained by changes in COVID-19 prevalence. Finally, we study heterogeneity in the time trend, finding that convergence occurs most significantly in younger populations, areas with less dense populations, and outside of the Northeast. Limitations include suppressed data in counties with fewer than 10 deaths in a racial category, and the use of provisional COVID-19 death data that may be incomplete.\n\nConclusionsThe results of this study suggest that convergence in Black/White mortality is not driven by county-level characteristics or changes in the regional dispersion of COVID-19, but instead by changes within counties. Further, declines in the Black/White mortality ratio appear strongly linked to changes in COVID-19 prevalence, rather than a time-specific effect. Further studies on changes in exposure by race over time, or on the vulnerability of individuals who died at different points in the pandemic, may provide crucial insight on mechanisms and strategies to further reduce COVID-19 mortality disparities.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ralph Ignacio Lawton", - "author_inst": "Duke University" - }, - { - "author_name": "Kevin Z Zheng", - "author_inst": "Duke University" - }, - { - "author_name": "Daniel Zheng", - "author_inst": "University of Maryland, Baltimore County" - }, - { - "author_name": "Erich S Huang", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.03.15.21253581", "rel_title": "Tocilizumab Effect in COVID-19 Hospitalized Patients: A Systematic Review and Meta-Analysis of Randomized Control Trials", @@ -875968,6 +877653,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.16.21253717", + "rel_title": "Patterns of compliance with COVID-19 preventive behaviours: a latent class analysis of 20,000 UK adults", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253717", + "rel_abs": "BackgroundGovernments have implemented a range of measure to tackle COVID-19, primarily focusing on changing citizens behaviours in order to lower transmission of the virus. Few studies have looked at the patterns of compliance with different measures within individuals: whether people comply with all measures or selectively choose some but not others. Such research is important for designing interventions to increase compliance.\n\nMethodsWe used cross-sectional data from 20,947 UK adults in the COVID-19 Social Study collected 17 November - 23 December 2020. Self-report compliance was assessed with six behaviours: mask wearing, hand washing, indoor household mixing, outdoor household mixing, social distancing, and compliance with other guidelines. Patterns of compliance behaviour were identified using latent class analysis, and multinomial logistic regression was used to assess demographic, socioeconomic and personality predictors of behaviour patterns.\n\nResultsWe selected a four latent class solution. Most individuals reported similar levels of compliance across the six behaviour measures. High levels of compliance was the modal response. Lower self-reported compliance was related to young age, high risk-taking behaviour, low confidence in government, and low empathy, among other factors. Looking at individual behaviours, mask wearing had the highest level of compliance whilst compliance with social distancing was relatively low.\n\nConclusionResults suggest that individuals choose to comply with all guidelines, rather than some but not others. Strategies to increase compliance should focus on increasing general motivations to comply alongside specifically encouraging social distancing.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Liam Wright", + "author_inst": "University College London" + }, + { + "author_name": "Andrew Steptoe", + "author_inst": "University College London" + }, + { + "author_name": "Daisy Fancourt", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.15.21253227", "rel_title": "SARS-CoV-2 Epidemiology on a Public University Campus in Washington State", @@ -877588,185 +879300,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.03.17.21253131", - "rel_title": "Interim results of the safety and immune-efficacy of 1 versus 2 doses of COVID-19 vaccine BNT162b2 for cancer patients in the context of the UK vaccine priority guidelines", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253131", - "rel_abs": "BackgroundThe efficacy and safety profile of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have not been definitively established in immunocompromised patient populations. Patients with a known cancer diagnosis were hitherto excluded from trials of the vaccines currently in clinical use.\n\nMethodsThis study presents data on the safety and immune efficacy of the BNT162b2 (Pfizer-BioNTech) vaccine in 54 healthy controls and 151 mostly elderly patients with solid and haematological malignancies, respectively, and compares results for patients who were boosted with BNT162b2 at 3 weeks versus those who were not. Immune efficacy was measured as antibody seroconversion, T cell responses, and neutralisation of SARS-CoV-2 Wuhan strain and of a variant of concern (VOC) (B.1.1.7). We also collected safety data for the BNT162b2 vaccine up to 5 weeks following first dose.\n\nFindingsThe vaccine was largely well tolerated. However, in contrast to its very high performance in healthy controls (>90% efficacious), immune efficacy of a single inoculum in solid cancer patients was strikingly low (below 40%) and very low in haematological cancer patients (below 15%). Of note, efficacy in solid cancer patients was greatly and rapidly increased by boosting at 21-days (95% within 2 weeks of boost). Too few haematological cancer patients were boosted for clear conclusions to be drawn.\n\nConclusionsDelayed boosting potentially leaves most solid and haematological cancer patients wholly or partially unprotected, with implications for their own health; their environment and the evolution of VOC strains. Prompt boosting of solid cancer patients quickly overcomes the poor efficacy of the primary inoculum in solid cancer patients.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSSome cancer patients have been shown to exhibit sustained immune dysregulation, inefficient seroconversion and prolonged viral shedding as a consequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Consequently, their exclusion and, in particular, the exclusion of patients receiving systemic anti-cancer therapies, from the registry trials of the 5 approved COVID-19 vaccines raises questions about the efficacy and safety of SARS-CoV-2 vaccination in this patient population. In addition, whilst the change in the UKs dosing interval to 12-weeks aimed to maximise population coverage, it is unclear whether this strategy is appropriate for cancer patients and those on systemic anti-cancer therapies.\n\nAdded value of this studyWe report that the RNA-based SARS-CoV-2 BNT162b2 vaccine administered in cancer patients was well tolerated, and we provide first insights into both antibody and T cell responses to the vaccine in an immunocompromised patient population.\n\nImplications of all the available evidenceIn cancer patients, one dose of 30ug of BNT162b2 yields poor vaccine efficacy, as measured by seroconversion rates, viral neutralisation capacity and T cell responses, at 3- and 5-weeks following the first inoculum. Patients with solid cancers exhibited a significantly greater response following a booster at 21-days. These data support prioritisation of cancer patients for an early (21-day) second dose of the BNT162b2 vaccine. Given the globally poor responses to vaccination in patients with haematological cancers, post-vaccination serological testing, creation of herd immunity around these patients using a strategy of ring vaccination, and careful follow-up should be prioritised.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Leticia Monin-Aldama", - "author_inst": "The Francis Crick Institute, London, UK." - }, - { - "author_name": "Adam G. Laing", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Miguel Munoz-Ruiz", - "author_inst": "The Francis Crick Institute, London, UK." - }, - { - "author_name": "Duncan R. McKenzie", - "author_inst": "The Francis Crick Institute, London, UK." - }, - { - "author_name": "Irene del Molino del Barrio", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, UK / UCL Cancer Institute, University College " - }, - { - "author_name": "Thanussuyah Alaguthurai", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK / Breast Cancer Now Research Unit, Kings College Londo" - }, - { - "author_name": "Clara Domingo Vila", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Thomas S. Hayday", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Carl Graham", - "author_inst": "Department of Infectious Diseases, School of Immunology & Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Jeffrey Seow", - "author_inst": "Department of Infectious Diseases, School of Immunology & Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Sultan Abdul-Jawad", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Shraddha Kamdar", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK / UCL Cancer Institute, University Colleg" - }, - { - "author_name": "Elizabeth Harvey-Jones", - "author_inst": "Breast Cancer Now Research Unit, Kings College London, London, UK" - }, - { - "author_name": "Rosalind Graham", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Jack Cooper", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Muhammad Khan", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Jennifer Vidler", - "author_inst": "Department of Haematological Medicine, Kings College Hospital, London, UK" - }, - { - "author_name": "Helen Kakkassery", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Shubhankar Sinha", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Richard Davis", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK / UCL Cancer Institute, University Colleg" - }, - { - "author_name": "Liane Dupont", - "author_inst": "Breast Cancer Now Research Unit, Kings College London, London, UK" - }, - { - "author_name": "Isaac Francos Quijorna", - "author_inst": "Regeneration Group, Wolfson Centre for Age-Related Diseases, IoPPN, Kings College London, London, UK." - }, - { - "author_name": "Puay Lee", - "author_inst": "The Francis Crick Institute, London, UK." - }, - { - "author_name": "Josephine Eum", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Maria Conde Poole", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Magdalene Joseph", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Daniel Davies", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Yin Wu", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK / Comprehensive Cancer Centre, School of" - }, - { - "author_name": "Ana Montes", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Mark Harries", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Anne Rigg", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "James Spicer", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "Michael H. Malim", - "author_inst": "Department of Infectious Diseases, School of Immunology & Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Paul Fields", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK / Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Piers Patten", - "author_inst": "The Francis Crick Institute, London, UK / Department of Haematological Medicine, Kings College Hospital, London, UK" - }, - { - "author_name": "Francesca Di Rosa", - "author_inst": "Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy." - }, - { - "author_name": "Sophie Papa", - "author_inst": "Guys and St Thomas NHS Foundation Trust, London, UK / Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK." - }, - { - "author_name": "Tim Tree", - "author_inst": "Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK." - }, - { - "author_name": "Katie Doores", - "author_inst": "Department of Infectious Diseases, School of Immunology & Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Adrian C. Hayday", - "author_inst": "The Francis Crick Institute, London, UK / Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK" - }, - { - "author_name": "Sheeba Irshad", - "author_inst": "Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Kings College London, London, UK / Breast Cancer Now Research Unit, Kings College Londo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2021.03.15.21253598", "rel_title": "U.S. adolescents' mental health and COVID-19-related changes in technology use, Fall 2020", @@ -878162,6 +879695,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.16.435654", + "rel_title": "DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing", + "rel_date": "2021-03-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.16.435654", + "rel_abs": "The rapid global spread and continued evolution of SARS-CoV-2 has highlighted an unprecedented need for viral genomic surveillance and clinical viral sequencing. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine lab processes and results. This challenge will only increase with expanding global production of sequences by diverse research groups for epidemiological and clinical interpretation. We present an approach which uses synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination through a sequencing workflow. Applying this approach to the ARTIC Consortiums amplicon design, we define a series of best practices for Illumina-based sequencing and provide a detailed characterization of approaches to increase sensitivity for low-viral load samples incorporating the SDSIs. We demonstrate the utility and efficiency of the SDSI method amidst a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Kim A. Lagerborg", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Erica Normandin", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Matthew R. Bauer", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Gordon Adams", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Katherine Figueroa", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Christine Loreth", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Adrianne Gladden-Young", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Bennett Shaw", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Leah Pearlman", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Erica S. Shenoy", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA." + }, + { + "author_name": "David Hooper", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA." + }, + { + "author_name": "Virginia M. Pierce", + "author_inst": "Department of Pathology, Massachusetts General Hospital, Boston, MA, USA." + }, + { + "author_name": "Kimon C. Zachary", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA." + }, + { + "author_name": "Daniel J. Park", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Bronwyn L. MacInnis", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Jacob E. Lemieux", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Pardis C. Sabeti", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Steven K. Reilly", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + }, + { + "author_name": "Katherine J. Siddle", + "author_inst": "Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.03.14.435295", "rel_title": "3D genomic capture of regulatory immuno-genetic profiles in COVID-19 patients for prognosis of severe COVID disease outcome", @@ -879858,65 +881482,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.03.15.435309", - "rel_title": "One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening", - "rel_date": "2021-03-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.15.435309", - "rel_abs": "The potential emergence of SARS-CoV-2 Spike (S) escape mutants is a threat to reduce the efficacy of existing vaccines and neutralizing antibody (nAb) therapies. An understanding of the antibody/S escape mutations landscape is urgently needed to preemptively address this threat. Here we describe a rapid method to identify escape mutants for nAbs targeting the S receptor binding site. We identified escape mutants for five nAbs, including three from the public germline class VH3-53 elicited by natural COVID-19 infection. Escape mutations predominantly mapped to the periphery of the ACE2 recognition site on the RBD with K417, D420, Y421, F486, and Q493 as notable hotspots. We provide libraries, methods, and software as an openly available community resource to accelerate new therapeutic strategies against SARS-CoV-2.\n\nOne Sentence SummaryWe present a facile method to identify antibody escape mutants on SARS-CoV-2 S RBD.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Irene Francino Urdaniz", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Paul J Steiner", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Monica Kirby", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Fangzhu Zhao", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Cyrus M Haas", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Shawn Barman", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Emily R Rhodes", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Linghang Peng", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Kayla Sprenger", - "author_inst": "University of Colorado, Boulder" - }, - { - "author_name": "Joseph Jardine", - "author_inst": "International AIDS Vaccine Initiative" - }, - { - "author_name": "Timothy A Whitehead", - "author_inst": "University of Colorado, Boulder" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.03.14.435322", "rel_title": "Effects of Mutations in the Receptor-Binding Domain of SARS-CoV-2 Spike on its Binding Affinity to ACE2 and Neutralizing Antibodies Revealed by Computational Analysis", @@ -880368,6 +881933,185 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.03.12.21253373", + "rel_title": "A randomized, double-blind, controlled trial of convalescent plasma in adults with severe COVID-19", + "rel_date": "2021-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253373", + "rel_abs": "BackgroundAlthough convalescent plasma has been widely used to treat severe coronavirus disease 2019 (COVID-19), data from randomized controlled trials that support its efficacy are limited.\n\nObjectiveTo evaluate the clinical efficacy and safety of convalescent plasma among adults hospitalized with severe and critical COVID-19.\n\nDesignRandomized, double-blind, controlled, multicenter, phase 2 trial conducted from April 21st to November 27th, 2020.\n\nSettingFive hospitals in New York City (NY, USA) and Rio de Janeiro (Brazil).\n\nParticipantsHospitalized patients aged [≥]18 years with laboratory-confirmed COVID-19, infiltrates on chest imaging and oxygen saturation [≤] 94% on room air or requirement for supplemental oxygen, invasive mechanical ventilation, or extracorporeal membrane oxygenation.\n\nInterventionParticipants were randomized 2:1 to a single transfusion of either 1 unit of convalescent or normal control plasma.\n\nMeasurementsThe primary outcome was clinical status at 28 days, measured using an ordinal scale and analyzed using a proportional odds model in the intention-to-treat population.\n\nResultsOf 223 participants enrolled, 150 were randomized to receive convalescent plasma and 73 to normal control plasma. At 28 days, no significant improvement in clinical status was observed in participants randomized to convalescent plasma (with an odds ratio (OR) of a 1-point improvement in the scale: 1.50, 95% confidence interval (CI) 0.83-2.68, p=0.180).\n\nHowever, 28-day mortality was significantly lower in participants randomized to convalescent plasma versus control plasma (19/150 [12.6%] versus 18/73 [24.6%], OR 0.44, 95% CI 0.22-0.91, p=0.034). The median titer of anti-SARS-CoV-2 neutralizing antibody in infused convalescent plasma units was 1:160 (IQR 1:80-1:320). In a subset of nasopharyngeal swab samples (n=40) from Brazil that underwent genomic sequencing, no evidence of neutralization-escape mutants was detected. Serious adverse events occurred in 39/147 (27%) participants who received convalescent plasma and 26/72 (36%) participants who received control plasma.\n\nLimitationsSome participants did not receive high-titer convalescent plasma.\n\nConclusionIn adults hospitalized with severe COVID-19, use of convalescent plasma was not associated with significant improvement in 28 days clinical status. The significant reduction in mortality associated with convalescent plasma, however, may warrant further evaluation.\n\nRegistrationClinicalTrials.gov, NCT04359810\n\nFundingAmazon Foundation\n\nClinical Trial RegistrationClinicalTrials.gov Identifier: NCT04359810", + "rel_num_authors": 41, + "rel_authors": [ + { + "author_name": "Max O'Donnell", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Beatriz Grinsztejn", + "author_inst": "Instituto Nacional de Infectologia Evandro Chagas" + }, + { + "author_name": "Matthew Cummings", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Jessica Justman", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Matt Lamb", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Christina Eckhardt", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Neena Phillip", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Kenneth Cheung", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Darryl Abrams", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Vinay Gupta", + "author_inst": "University of Washington" + }, + { + "author_name": "Maria Pia Diniz", + "author_inst": "Instituto Nacional de Infectologia Evandro Chagas" + }, + { + "author_name": "Sandra Wagner Cardoso", + "author_inst": "Instituto Nacional de Infectologia Evandro Chagas" + }, + { + "author_name": "Kartik Rajagopalan", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Sarah Borden", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Allison Wolf", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Zachary Bitan", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Benjamin Meyer", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Samuel Jacobson", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Alex Kantor", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Nischay Mishra", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Eldad Hod", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Thomas Briese", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Leon Claude Sidi", + "author_inst": "Hospital Federal dos Servidores do Estado" + }, + { + "author_name": "Sandeep Wontakal", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Krystalyn Hudson", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Brie Stotler", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Wen-Hsuan Lin", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Jose Henrique Pilotto", + "author_inst": "Instituto Oswaldo Cruz Fiocruz" + }, + { + "author_name": "Esau Joao", + "author_inst": "Hospital Federal dos Servidores do Estado" + }, + { + "author_name": "Lokendra Chauhan", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Valdilea Veloso", + "author_inst": "Instituto Nacional de Infectologia Evandro Chagas" + }, + { + "author_name": "Joseph Schwartz", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Elizabeth Stone", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Flavia Dei Zotti", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Francesca La Carpia", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Beth Shaz", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Stephen Ferrara", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Alexandre Vizzoni", + "author_inst": "Instituto Oswaldo Cruz Fiocruz" + }, + { + "author_name": "Steven Spitalnick", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Andrew Eisenberger", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "W. Ian Lipin", + "author_inst": "Columbia University Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.11.21253419", "rel_title": "COVID-19 Vaccine Acceptance and Hesitancy in Low and Middle Income Countries, and Implications for Messaging", @@ -882180,49 +883924,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.03.09.21253186", - "rel_title": "Forecasting the COVID-19 epidemic integrating symptom search behavior: an infodemiology study", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253186", - "rel_abs": "BackgroundPrevious studies have suggested associations between trends of web searches and COVID-19 traditional metrics. It remains unclear whether models incorporating trends of digital searches lead to better predictions.\n\nMethodsAn open-access web application was developed to evaluate Google Trends and traditional COVID-19 metrics via an interactive framework based on principal components analysis (PCA) and time series modelling. The app facilitates the analysis of symptom search behavior associated with COVID-19 disease in 188 countries. In this study, we selected data of eight countries as case studies to represent all continents. PCA was used to perform data dimensionality reduction, and three different time series models (Error Trend Seasonality, Autoregressive integrated moving average, and feed-forward neural network autoregression) were used to predict COVID-19 metrics in the upcoming 14 days. The models were compared in terms of prediction ability using the root-mean-square error (RMSE) of the first principal component (PC1). Predictive ability of models generated with both Google Trends data and conventional COVID-19 metrics were compared with those fitted with conventional COVID-19 metrics only.\n\nFindingsThe degree of correlation and the best time-lag varied as a function of the selected country and topic searched; in general, the optimal time-lag was within 15 days. Overall, predictions of PC1 based on both searched termed and COVID-19 traditional metrics performed better than those not including Google searches (median [IQR]: 1.43 [0.74-2.36] vs. 1.78 [0.95-2.88], respectively), but the improvement in prediction varied as a function of the selected country and timeframe. The best model varied as a function of country, time range, and period of time selected. Models based on a 7-day moving average led to considerably smaller RMSE values as opposed to those calculated with raw data (median [IQR]: 0.74 [0.47-1.22] vs. 2.15 [1.55-3.89], respectively).\n\nInterpretationThe inclusion of digital online searches in statistical models may improve the prediction of the COVID-19 epidemic.\n\nFundingEOSCsecretariat.eu has received funding from the European Unions Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alessandro Rabiolo", - "author_inst": "Gloucestershire Hospitals NHS Foundation Trust, Cheltenham, United Kingdom" - }, - { - "author_name": "Eugenio Alladio", - "author_inst": "Department of Chemistry, University of Turin, Turin, Italy" - }, - { - "author_name": "Esteban Morales", - "author_inst": "Jules Stein Eye Institute, David Geffen School of Medicine, UCLA, Los Angeles, USA" - }, - { - "author_name": "Andrew Ian McNaught", - "author_inst": "Gloucestershire Hospitals NHS Foundation Trust, Cheltenham, United Kingdom" - }, - { - "author_name": "Francesco Bandello", - "author_inst": "(5)\tDepartment of Ophthalmology, Vita-Salute University, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy" - }, - { - "author_name": "Abdelmonem A Afifi", - "author_inst": "Department of Biostatistics, Fielding School of Public Health, UCLA, Los Angeles, USA" - }, - { - "author_name": "Alessandro Marchese", - "author_inst": "Department of Ophthalmology, Vita-Salute University, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.03.08.21252883", "rel_title": "Outcome of Different Therapeutic Interventions in Mild COVID-19 Patients in a Single OPD Clinic of West Bengal: A Retrospective study", @@ -882558,6 +884259,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.08.21252788", + "rel_title": "SARS-CoV-2 antibody prevalence and determinants of six ethnic groups living in Amsterdam, the Netherlands: a population-based cross-sectional study, June-October 2020", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252788", + "rel_abs": "BackgroundEthnic minorities have higher rates of SARS-CoV-2 diagnoses, but little is known about ethnic differences in past exposure. We aimed to determine whether prevalence and determinants of SARS-CoV-2 exposure varied between six ethnic groups in Amsterdam, the Netherlands.\n\nMethodsParticipants aged 25-79 years enrolled in a population-based prospective cohort were randomly selected within ethnic groups and invited to test for SARS-CoV-2-specific antibodies and answer COVID-19 related questions. We estimated prevalence and determinants of SARS-CoV-2 exposure within ethnic groups using survey-weighted logistic regression adjusting for age, sex and calendar time.\n\nResultsBetween June 24-October 9, 2020, we included 2497 participants. Adjusted SARS-CoV-2 seroprevalence was comparable between ethnic-Dutch (25/498; 5.5%, 95%CI=3.2-7.9), South-Asian Surinamese (22/451; 4.8%, 95%CI=2.1-7.5), African Surinamese (22/400; 8.2%, 95%CI=3.0-13.4), Turkish (30/408; 7.8%, 95%CI=4.3-11.2) and Moroccan (32/391; 7.0%, 95%CI=4.0-9.9) participants, but higher among Ghanaians (95/327; 26.5%, 95%CI=18.7-34.4). 57.1% of SARS-CoV-2-positive participants did not suspect or were unsure of being infected, which was lowest in African Surinamese (18.2%) and highest in Ghanaians (90.5%). Determinants of SARS-CoV-2 exposure varied across ethnic groups, while the most common determinant was having a household member suspected of infection. In Ghanaians, seropositivity was associated with older age, larger household sizes, living with small children, leaving home to work and attending religious services.\n\nConclusionsNo remarkable differences in SARS-CoV-2 seroprevalence were observed between the largest ethnic groups in Amsterdam after the first wave of infections. The higher infection seroprevalence observed among Ghanaians, which passed mostly unnoticed, warrants wider prevention efforts and opportunities for non-symptom-based testing.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Liza Coyer", + "author_inst": "Public Health Service of Amsterdam; Amsterdam UMC, location AMC" + }, + { + "author_name": "Anders Boyd", + "author_inst": "Public Health Service of Amsterdam; Stichting HIV Monitoring" + }, + { + "author_name": "Janke Schinkel", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Charles Agyemang", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Henrike Galenkamp", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Anitra D. M. Koopman", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Tjalling Leenstra", + "author_inst": "Public Health Service of Amsterdam" + }, + { + "author_name": "Eric P. Moll van Charante", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Bert-Jan H. van den Born", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Anja Lok", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Arnoud Verhoeff", + "author_inst": "Public Health Service of Amsterdam; University of Amsterdam" + }, + { + "author_name": "Aeilko H. Zwinderman", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Suzanne Jurriaans", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Lonneke A. van Vught", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Karien Stronks", + "author_inst": "Amsterdam UMC, location AMC" + }, + { + "author_name": "Maria Prins", + "author_inst": "Public Health Service of Amsterdam; Amsterdam UMC, location AMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.05.21251577", "rel_title": "Universal Rule for Covid 19 and Herd Immunity in the US", @@ -884006,53 +885786,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.09.21253242", - "rel_title": "Environmental drivers of SARS-CoV-2 lineage B.1.1.7 transmission in England, October to December 2020", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253242", - "rel_abs": "Previous work has shown that environment affects SARS-CoV-2 transmission, but it is unclear whether emerging strains show similar responses. Here we show that, like other SARS-CoV-2 strains, lineage B.1.1.7 spread with greater transmission in colder and more densely populated parts of England. However, we also find evidence of B.1.1.7 having a transmission advantage at warmer temperatures compared to other strains. This implies that spring and summer conditions are unlikely to slow B.1.1.7s invasion in Europe and across the Northern hemisphere - an important consideration for public health interventions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Thomas P Smith", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ilaria Dorigatti", - "author_inst": "Imperial College London" - }, - { - "author_name": "Swapnil Mishra", - "author_inst": "Imperial College London" - }, - { - "author_name": "Erik Volz", - "author_inst": "Imperial College London" - }, - { - "author_name": "Patrick G T Walker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Manon Ragonnet-Cronin", - "author_inst": "Imperial College London" - }, - { - "author_name": "Michael Tristem", - "author_inst": "Imperial College London" - }, - { - "author_name": "William D Pearse", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.09.21252822", "rel_title": "Genomic epidemiology of SARS-CoV-2 in the United Arab Emirates reveals novel virus mutation, patterns of co-infection and tissue specific host responses", @@ -884404,6 +886137,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.10.21252748", + "rel_title": "An Extended COVID-19 Epidemiological Model with Vaccination and Multiple Interventions for Controlling COVID-19 Outbreaks in the UK", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21252748", + "rel_abs": "For controlling the first wave of the UK COVID-19 pandemic in 2020, a plethora of hypothetical COVID-19 models has been developed for simulating how diseases spread under different non-pharmaceutical interventions like suppression and mitigation and providing useful guidance to UK policymakers. While many models demonstrate their effectiveness on predicting and controlling the spread of COVID-19, they rarely consider consequence of incorporating the effects of potential SARS-CoV-2 variants and implementing vaccine interventions in large-scale. By December 2020, the second wave in the UK appeared to be much more aggressive with many more cases as one potentially more contagious SARS-CoV-2 variant was detected in the UK since September 2020. Meanwhile, UK has begun their first mass vaccination campaign on 8 December 2020, where three vaccines were in use including Pfizer, BioNTech and Moderna. Thus, these new issues pose an emergent need to build up advanced models for accessing effectiveness of taking both vaccination and multiple interventions for controlling COVID-19 outbreaks and balancing healthcare demands. Targeting at this problem, we conducted a feasibility study by defining a new mathematical model SEMCVRD (Susceptible [S], Exposed [E] (infected but asymptomatic), Mild [M] and Critical [C] (mild cases, severe and critical cases), [V] (vaccinated), Recovered [R] and Deceased [D]), containing two importantly new features: the combined infection of the mutant strain and the original strain and the addition of a new group who have been vaccinated. The model was fitted and evaluated with a public COVID-19 dataset including daily new infections, new deaths and daily vaccination in the UK from February 2020 to February 2021. Based on the simulation results, 1) we find under the assumption that the vaccine is equivalently effective against both the original strain and new variants of COVID-19, if the UK government implements insensitive suppression intervention for 13 weeks, COVID-19 epidemic will be controlled by the first week of April 2021 and nearly ended by the first week of May 2021. It shows that taking both vaccine and suppression interventions can effectively inhibit the spread and infection of the new mutant virus. 2) we suggest implementing a 3-weeks phased and progressive lifting intervention strategy up to a low intensity mitigation level for effectively controlling COVID-19 outbreaks in the UK. By implementing this strategy, the total number of infections in the UK will be limited to 4.2 million and the total number of deaths in the UK is 135 thousand, by the end of June 2021. The epidemic will nearly end in the early of June 2021, and the UK will not experience a shortage of medical resources. 3) On the assumption that UK has a capability of providing 600 thousand vaccinations every day, a 3-weeks phased and progressive lifting intervention strategy up to a moderate intensity mitigation level can end the epidemic by the end of May 2021. This strategy would reduce the overall infections and deaths of COVID-19 outbreaks, and balance healthcare demand in the UK.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Shuhao Zhang", + "author_inst": "Yunnan University" + }, + { + "author_name": "Gaoshan Bi", + "author_inst": "Yunnan University" + }, + { + "author_name": "Yun Yang", + "author_inst": "Yunnan University" + }, + { + "author_name": "Jun Qi", + "author_inst": "Xi An JiaoTong-Liverpool University" + }, + { + "author_name": "Shujun Li", + "author_inst": "Kent University" + }, + { + "author_name": "Xuxin Mao", + "author_inst": "National Institute of Economic and Social Research" + }, + { + "author_name": "Ruoling Peng", + "author_inst": "The University of Sheffield" + }, + { + "author_name": "Po Yang", + "author_inst": "The University of Sheffield" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.09.21252944", "rel_title": "A phase 2 study of the inhaled pan-JAK inhibitor TD-0903 in severe COVID-19: Part 1", @@ -885644,41 +887424,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.11.21252969", - "rel_title": "Reducing the Cost of Rapid Antigen Tests through Swab Pooling and Extraction in a Device", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21252969", - "rel_abs": "The COVID-19 pandemic places a significant stress on the viral testing capabilities of many countries. The value of rapid point-of-care (PoC) antigen tests is becoming increasingly clear, but implementing frequent large scale testing is costly. We have developed an inexpensive device for pooling swabs, extracting specimens, and detecting viral antigens with a commercial lateral flow assay detecting the nucleocapsid protein of SARS-CoV-2 as antigen. The holder of the device can be produced locally through 3D printing. The extraction and the elution can be performed with the entire set-up encapsulated in a transparent bag, minimizing the risk of infection for the operator. With 6 swabs holding approx. 0.1 mL specimen each and 0.35 mL extraction buffer, 43{+/-}6 % (n= 8) of the signal for an individual extraction of a positive control standard was obtained. Image analysis still showed a signal-to-noise ratio of [≥] 7 upon further eight-fold dilution. Our current total cost of materials is below $ 2 per tested person or 20% of our cost for an individual PoC test. These findings suggest that pooling can make frequent testing more affordable for schools, universities and other institutions, without decreasing sensitivity to an unacceptable level. Further validation of the method is required.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Tim Berking", - "author_inst": "Institute of Organic Chemistry, University of Stuttgart" - }, - { - "author_name": "Sabrina G Lorenz", - "author_inst": "Institute of Organic Chemistry, University of Stuttgart" - }, - { - "author_name": "Alexander Ulrich", - "author_inst": "Institute of Organic Chemistry, University of Stuttgart" - }, - { - "author_name": "Joachim Greiner", - "author_inst": "Institute of Aircraft Design, University of Stuttgart" - }, - { - "author_name": "Clemens Richert", - "author_inst": "University of Stuttgart" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.11.21253226", "rel_title": "Analysis of Accumulated SARS-CoV-2 Seroconversion in North Carolina: The COVID-19 Community Research Partnership", @@ -886006,6 +887751,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253064", + "rel_title": "Evaluation of anti-SARS-CoV-2 antibody testing in asymptomatic or mild COVID-19 patients in outbreak on a cruise ship", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253064", + "rel_abs": "BackgroundA few studies on antibody testing have focused on asymptomatic or mild coronavirus disease 2019 (COVID-19) patients with low initial anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody responses. Anti-SARS-CoV-2 antibody-testing performance was evaluated using blood samples from asymptomatic or mild COVID-19 patients.\n\nMethodsBlood samples were collected from 143 COVID-19 patients during an outbreak on a cruise ship 3 weeks after diagnosis. Simultaneously, a second SARS-CoV-2 genetic test was performed. Samples stored before the COVID-19 pandemic were also used to evaluate the lateral flow immunochromatographic assay (LFA) and electrochemiluminescence immunoassay (ECLIA). Titers of anti-SARS-CoV-2 IgM and IgG antibodies against the nucleocapsid and spike proteins were measured using the enzyme-linked immunosorbent assay to compare false-negative-with positive-result samples.\n\nResultsSensitivity, specificity, positive-predictive, and negative-predictive values of LFA-detected IgM antibodies were 0.231, 1.000, 1.000, and 0.613, respectively; those of LFA-detected IgG antibodies were 0.483, 0.989, 0.972, and 0.601, respectively; and those of ECLIA-detected total antibodies were 0.783, 1.000, 1.000, and 0.848, respectively. IgM-, IgG-, and total-antibody positivity rates in the patients with negative results from the second genetic testing were 22.9%, 47.6%, and 72.4%, respectively. All antibody titers, especially those of the IgG antibody against nucleocapsid protein, were significantly lower in blood samples with false-negative results than in those with positive results.\n\nConclusionsThese findings suggest that anti-SARS-CoV-2 antibody testing has lower performance in asymptomatic or mild COVID-19 patients than required in the guidelines, and situations in which it is useful are limited.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Norihito Kaku", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Fumitaka Nishimura", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Yui Shigeishi", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Rina Tachiki", + "author_inst": "Nagasaki Univerisity" + }, + { + "author_name": "Hironori Sakai", + "author_inst": "Cellspect Co., Ltd" + }, + { + "author_name": "Daisuke Sasaki", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kenji Ota", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kei Sakamoto", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kosuke Kosai", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Hiroo Hasegawa", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Koichi Izumikawa", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Koya Ariyoshi", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Hiroshi Mukae", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Jiro Yasuda", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kouichi Morita", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Shigeru Kohno", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Katsunori Yanagihara", + "author_inst": "Nagasaki University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.11.21253202", "rel_title": "A novel whole-blood stimulation assay to detect and quantify memory T-cells in COVID-19 patients", @@ -887386,37 +889214,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.10.21253324", - "rel_title": "Dynamic versus Continuous Interventions: Optimizing Lockdown Policies for COVID-19", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253324", - "rel_abs": "In the context of the ongoing COVID-19 pandemic, while millions of people await the administration of a vaccine, social distancing remains the leading approach towards the effect commonly known as \"flattening the curve\" of infections. Over the last year, governmental administrations throughout the globe have implemented various lockdown policies in hopes of slowing down the transmission of the disease. However, the current lack of consensus on when and how these policies should be implemented reflects the need for further studies regarding these questions. In this paper, we tackle the issue of lockdown policy management, in particular in terms of lockdown placement (how often, when, and how long these periods should be), in order to minimize the peak of infections in a specific population. We introduce a novel combination of classic mathematical disease modelling using the equation-based SEIR model, and Evolutionary Strategies (ES) for optimizing the peak of infections. The method is evaluated using data collected in different countries, and a particular focus is placed on the study of the effect of specific model parameters on lockdown optimization, such as the transmission rate ({beta}), of which 4 alternative modelling functions have been proposed and analyzed. Our results indicate that this transmission rate parameter significantly influences the resulting optimal strategies. In particular, the presence of a gradual decay of the rate of transmission during lockdown leads to longer, more sparsely placed confinement periods while an abrupt, instantaneous drop in the amount of contacts per person favors shorter but more frequent lockdowns. Although these results are limited by the scope of action provided by the simplicity of the SEIR model, they suggest that the influence of the evolution of the rate of transmission along the disease should be assessed in further studies with alternative optimization strategies (agent-based) and models (SEIRSHUD).", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kaan Akinci", - "author_inst": "Cross Labs" - }, - { - "author_name": "Javier Fdez", - "author_inst": "Cross Labs" - }, - { - "author_name": "Elena Pena-Tapia", - "author_inst": "Cross Labs" - }, - { - "author_name": "Olaf Witkowski", - "author_inst": "Cross Labs" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.11.21253364", "rel_title": "Analysis of severe outcomes associated with the SARS-CoV-2 Variant of Concern 202012/01 in England using ICNARC Case Mix Programme and QResearch databases.", @@ -887628,6 +889425,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.03.12.21253440", + "rel_title": "Negative SARS-CoV-2 PCR or rapid antigen test result and the subsequent risk of being infectious: a mathematical simulation study", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253440", + "rel_abs": "BackgroundA considerable proportion of SARS-CoV-2 transmission occurs from asymptomatic and pre-symptomatic cases. Therefore, different polymerase chain reaction (PCR)- or rapid antigen test (RAT)-based approaches are being discussed and applied to identify infectious cases that would have gone undetected (e.g., in nursing homes). In this article, we provide a framework to estimate the time-dependent risk of being infectious after a negative SARS-CoV-2 test and we simulate the number of expected cases over time in populations of individuals who initially tested negative.\n\nMethodsA Monte Carlo approach is used to simulate infections that occurred over a one-week period in populations with 1,000 individuals following a negative SARS-Cov-2 test. Parameters representing the application of PCR tests or RATs are utilized, and SARS-CoV-2 7-day incidences between 25 and 200 per 100,000 people are considered. Simulation results are compared to case numbers predicted via a mathematical equation.\n\nResultsThe simulations showed a linear increase in cases over time in populations of individuals who initially tested SARS-CoV-2 negative. The different false negative rates of PCR tests and RATs have a strong impact on the number of simulated cases. The simulated and the mathematically predicted case numbers were comparable. However, Monte Carlo simulations highlight that, due to random effects, infectious cases can exceed predicted case numbers even shortly after a test was conducted.\n\nConclusionsThe analysis demonstrates that the number of infectious cases in a population can be effectively reduced by the screening of asymptomatic individuals. However, the time since the negative test and the underlying SARS-CoV-2 incidence are critical parameters in determining the observed subsequent number of cases in tested populations.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ralf Krumkamp", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine" + }, + { + "author_name": "Benno Kreuels", + "author_inst": "University Medical Center Hamburg-Eppendorf" + }, + { + "author_name": "Veronika K Jaeger", + "author_inst": "University of Muenster" + }, + { + "author_name": "Juergen May", + "author_inst": "Bernhard Nocht Institute for Tropical Medicine" + }, + { + "author_name": "Rafael Mikolajczyk", + "author_inst": "Martin Luther University Halle-Wittenberg" + }, + { + "author_name": "Andre Karch", + "author_inst": "University of Muenster" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.12.21253435", "rel_title": "A simplified SARS-CoV-2 pseudovirus neutralization assay", @@ -888955,45 +890791,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2021.03.09.21253212", - "rel_title": "Exploring the short-term role of particulate matter in the COVID-19 outbreak in USA cities", - "rel_date": "2021-03-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253212", - "rel_abs": "The role of particulate matter (PM) in the COVID-19 pandemic is currently being discussed by the scientific community. Long-term (years) exposure to PM is known to affect human health by increasing susceptibility to viral infections as well as to the development of respiratory and cardiovascular symptoms. In the short-term (days to months), PM has been suggested to assist airborne viral transmission. However, confounding factors such as urban mobility prevent causal conclusions. In this study, we explore short-term relationships between PM concentrations and the evolution of COVID-19 cases in a number of cities in the United States of America. We focus on the role of PM in facilitating viral transmission in early stages of the pandemic. We analyzed PM concentrations in two particle size ranges, < 2.5 {micro}m, and between 10 and 2.5 {micro}m (PM2.5 and PM10 respectively) as well as carbon monoxide (CO) and nitrogen dioxide (NO2). Granger causality analysis was employed to identify instantaneous and lagged effects of pollution in peaks of COVID-19 new daily cases in each location. The effect of pollution in shaping the disease spread was evaluated by correlating the logistic growth rate of accumulated cases with pollutants concentrations for a range of time lags and accumulation windows. PM2.5 shows the most significant results in Granger causality tests in comparison with the other pollutants. We found a strong and significant association between PM2.5 concentrations and the growth rate of accumulated cases between the 1st and 18th days after the report of the infection, peaking at the 8th day. By comparing results of PM2.5 with PM10, CO and NO2 we rule out confounding effects associated with mobility. We conclude that PM2.5 is not a first order effect in the cities considered; however, it plays a significant role in facilitating the COVID-19 transmission. We estimate that the growth rate of COVID-19 cases would be risen by 12.5% if PM2.5 is increased from 25 to 35 {micro}g m-3.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Leonardo Yoshiaki Kamigauti", - "author_inst": "Department of Atmospheric Sciences, University of Sao Paulo, Brazil" - }, - { - "author_name": "Gabriel Martins Palma Perez", - "author_inst": "Department of Meteorology, University of Reading, United Kingdom" - }, - { - "author_name": "Carlos Eduardo Souto-Oliveira", - "author_inst": "Department of Atmospheric Sciences, Univeristy of Sao Paulo, Brazil" - }, - { - "author_name": "Elizabeth Cowdery", - "author_inst": "Department of Earth and Environment, University of Boston, United States of America" - }, - { - "author_name": "Paulo Hilario Nascimento Saldiva", - "author_inst": "Department of Pathology, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Maria de Fatima Andrade", - "author_inst": "Department of Atmospheric Sciences, University of Sao Paulo, Sao Paulo, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.09.21253155", "rel_title": "High-resolution epigenome analysis in nasal samples derived from children with respiratory viral infections reveals striking changes upon SARS-CoV-2 infection", @@ -889229,6 +891026,53 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.03.11.434968", + "rel_title": "Low ozone concentration and negative ions for rapid SARS-CoV-2 inactivation", + "rel_date": "2021-03-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.11.434968", + "rel_abs": "Ozone is a powerful anti-bacterial, anti-fungal and anti-viral agent, yet exposure to high levels of ozone can pose risks to human/animal health and, in the long term, corrode certain objects. In order to overcome these risks, we evaluated the potential of using a relatively short exposure of a low concentration of ozone to disinfect an indoor environment in the absence of individuals and animals. ICON3 by O3ZONO/M2L, a new disinfection device generating both ozone and negative ions, was selected to assess the potential of this strategy to inactivate different viral isolates of SARS-CoV-2.\n\nTests under controlled laboratory conditions were performed in a system consisting of an ozone-proof airtight plastic box inside a biological safety cabinet, where suspensions of two strains of SARS-CoV-2 were exposed to ozone and negative ions and virucidal activity was measured by means of two complementary methodologies: viral replication capacity and viral titer determination.\n\nThese studies revealed that low concentration ozone (average 3.18 ppm after the peak) inactivated up to >99% of SARS-CoV-2 within 20 minutes of exposure. Under controlled conditions, similar ozone exposure was recreated with ICON3 in different volume rooms (15, 30, 60 m3) where a linear relationship was observed between the room volume and the time of continuous ozone/ions flow required to reach and maintain the desired ozone levels used in the laboratory studies.\n\nThese studies suggest that ICON3 may have the potential for use in the disinfection of SARS-CoV-2 in indoor environments in the absence of individuals and animals, under properly controlled and monitored safety conditions.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Davide De Forni", + "author_inst": "ViroStatics s.r.l., Sassari (SS), Italy" + }, + { + "author_name": "Barbara Poddesu", + "author_inst": "ViroStatics s.r.l., Sassari (SS), Italy" + }, + { + "author_name": "Giulia Cugia", + "author_inst": "ViroStatics s.r.l., Sassari (SS), Italy" + }, + { + "author_name": "Giovanni Gallizia", + "author_inst": "M2L s.r.l., Vicenza (VI), Italy" + }, + { + "author_name": "Massimo La Licata", + "author_inst": "M2L s.r.l., Vicenza (VI), Italy" + }, + { + "author_name": "Julianna Lisziewicz", + "author_inst": "Research Institute for Genetic and Human Therapy, Colorado Springs (CO), USA" + }, + { + "author_name": "James Chafouleas", + "author_inst": "Sonnet Pharma Consulting Inc., Quebec, Canada; ViroStatics s.r.l., Sassari (SS), Italy" + }, + { + "author_name": "Franco Lori", + "author_inst": "ViroStatics s.r.l., Sassari (SS), Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.10.434834", "rel_title": "In vitro and in vivo preclinical studies predict REGEN-COV protection against emergence of viral escape in humans", @@ -891072,73 +892916,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.09.434592", - "rel_title": "Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes", - "rel_date": "2021-03-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.09.434592", - "rel_abs": "There is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel aerosolization route to treat SARS-CoV-2 infections efficiently. However, it remains unknown if they possess broadly neutralizing activities against the prevalent circulating strains. We found that potent neutralizing Nbs are highly resistant to the convergent variants of concern that evade a large panel of neutralizing antibodies (Abs) and significantly reduce the activities of convalescent or vaccine-elicited sera. Subsequent determination of 9 high-resolution structures involving 6 potent neutralizing Nbs by cryoelectron microscopy reveals conserved and novel epitopes on virus spike inaccessible to Abs. Systematic structural comparison of neutralizing Abs and Nbs provides critical insights into how Nbs uniquely target the spike to achieve high-affinity and broadly neutralizing activity against the evolving virus. Our study will inform the rational design of novel pan-coronavirus vaccines and therapeutics.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Dapeng Sun", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Zhe Sang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Jeff Kim", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Yufei Xiang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Tomer Cohen", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Anna K Belford", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Alexis Huet", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "James F Conway", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Ji Sun", - "author_inst": "St Jude Childrens Research Hospital" - }, - { - "author_name": "Derek Taylor", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Cheng Zhang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Wei Huang", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Yi Shi", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.03.09.434030", "rel_title": "Development of Equine Immunoglobulin Fragment F(ab')2 with High Neutralizing Capability against SARS-CoV-2", @@ -891730,6 +893507,229 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.05.21252520", + "rel_title": "Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland", + "rel_date": "2021-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21252520", + "rel_abs": "BackgroundIn December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from the UK and later data from other countries, this variant was estimated to have a transmission fitness advantage of around 40-80% [1, 2, 3].\n\nAimThis study aims to estimate the transmission fitness advantage and the effective reproductive number of B.1.1.7 through time based on data from Switzerland.\n\nMethodsWe generated whole genome sequences from 11.8% of all confirmed SARS-CoV-2 cases in Switzerland between 14 December 2020 and 11 March 2021. Based on these data, we determine the daily frequency of the B.1.1.7 variant and quantify the variants transmission fitness advantage on a national and a regional scale.\n\nResultsWe estimate B.1.1.7 had a transmission fitness advantage of 43-52% compared to the other variants circulating in Switzerland during the study period. Further, we estimate B.1.1.7 had a reproductive number above 1 from 01 January 2021 until the end of the study period, compared to below 1 for the other variants. Specifically, we estimate the reproductive number for B.1.1.7 was 1.24 [1.07-1.41] from 01 January until 17 January 2021 and 1.18 [1.06-1.30] from 18 January until 01 March 2021 based on the whole genome sequencing data. From 10 March to 16 March 2021, once B.1.1.7 was dominant, we estimate the reproductive number was 1.14 [1.00-1.26] based on all confirmed cases. For reference, Switzerland applied more non-pharmaceutical interventions to combat SARS-CoV-2 on 18 January 2021 and lifted some measures again on 01 March 2021.\n\nConclusionThe observed increase in B.1.1.7 frequency in Switzerland during the study period is as expected based on observations in the UK. In absolute numbers, B.1.1.7 increased exponentially with an estimated doubling time of around 2-3.5 weeks. To monitor the ongoing spread of B.1.1.7, our plots are available online.", + "rel_num_authors": 52, + "rel_authors": [ + { + "author_name": "Chaoran Chen", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + }, + { + "author_name": "Sarah Ann Nadeau", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + }, + { + "author_name": "Ivan Topolsky", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + }, + { + "author_name": "Marc Manceau", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + }, + { + "author_name": "Jana S. Huisman", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland; Department of Environmental Sy" + }, + { + "author_name": "Kim Philipp Jablonski", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + }, + { + "author_name": "Lara Fuhrmann", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + }, + { + "author_name": "David Dreifuss", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + }, + { + "author_name": "Katharina Jahn", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + }, + { + "author_name": "Christiane Beckmann", + "author_inst": "Viollier AG, Allschwil, Switzerland" + }, + { + "author_name": "Maurice Redondo", + "author_inst": "Viollier AG, Allschwil, Switzerland" + }, + { + "author_name": "Christoph Noppen", + "author_inst": "Viollier AG, Allschwil, Switzerland" + }, + { + "author_name": "Lorenz Risch", + "author_inst": "Dr Risch, Labormedizinisches Zentrum, Switzerland" + }, + { + "author_name": "Martin Risch", + "author_inst": "Dr Risch, Labormedizinisches Zentrum, Switzerland" + }, + { + "author_name": "Nadia Wohlwend", + "author_inst": "Dr Risch, Labormedizinisches Zentrum, Switzerland" + }, + { + "author_name": "Sinem Kas", + "author_inst": "Dr Risch, Labormedizinisches Zentrum, Switzerland" + }, + { + "author_name": "Thomas Bodmer", + "author_inst": "Dr Risch, Labormedizinisches Zentrum, Switzerland" + }, + { + "author_name": "Tim Roloff", + "author_inst": "Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research" + }, + { + "author_name": "Madlen Stange", + "author_inst": "Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research" + }, + { + "author_name": "Adrian Egli", + "author_inst": "Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel" + }, + { + "author_name": "Isabella Eckerle", + "author_inst": "Geneva Centre for Emerging Viral Diseases, Infectious Disease Division, Geneva University Hospitals & Department of Microbiology and Molecular Medicine, Univers" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Rebecca Denes", + "author_inst": "Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" + }, + { + "author_name": "Mirjam Feldkamp", + "author_inst": "Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" + }, + { + "author_name": "Ina Nissen", + "author_inst": "Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" + }, + { + "author_name": "Natascha Santacroce", + "author_inst": "Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" + }, + { + "author_name": "Elodie Burcklen", + "author_inst": "Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" + }, + { + "author_name": "Catharine Aquino", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Andreia Cabral de Gouvea", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Maria Domenica Moccia", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Simon Gruter", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Timothy Sykes", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Lennart Opitz", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Griffin White", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Laura Neff", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Doris Popovic", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Andrea Patrignani", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Jay Tracy", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Ralph Schlapbach", + "author_inst": "Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Emmanouil T. Dermitzakis", + "author_inst": "Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland" + }, + { + "author_name": "Keith Harshman", + "author_inst": "Health 2030 Genome Center, Geneva, Switzerland" + }, + { + "author_name": "Ioannis Xenarios", + "author_inst": "Health 2030 Genome Center, Geneva, Switzerland" + }, + { + "author_name": "Henri Pegeot", + "author_inst": "Health 2030 Genome Center, Geneva, Switzerland" + }, + { + "author_name": "Lorenzo Cerutti", + "author_inst": "Health 2030 Genome Center, Geneva, Switzerland" + }, + { + "author_name": "Deborah Penet", + "author_inst": "Health 2030 Genome Center, Geneva, Switzerland" + }, + { + "author_name": "Anthony Blin", + "author_inst": "Health 2030 Genome Center, Geneva, Switzerland" + }, + { + "author_name": "Melyssa Elies", + "author_inst": "Health 2030 Genome Center, Geneva, Switzerland" + }, + { + "author_name": "Christian L. Althaus", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Christian Beisel", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland" + }, + { + "author_name": "Niko Beerenwinkel", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + }, + { + "author_name": "Martin Ackermann", + "author_inst": "Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland; Department of Environmental Microbiology, E" + }, + { + "author_name": "Tanja Stadler", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.07.21253082", "rel_title": "A Comparative Analysis of Clinical Stage 3 COVID-19 Vaccines using Knowledge Representation", @@ -893410,33 +895410,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.03.05.433897", - "rel_title": "COVIDrugNet: a network-based web tool to investigate the drugs currently in clinical trial to contrast COVID-19", - "rel_date": "2021-03-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.05.433897", - "rel_abs": "The COVID-19 pandemic poses a huge problem of public health that requires the implementation of all available means to contrast it, and drugs are one of them. In this context, we observed an unmet need of depicting the continuously evolving scenario of the ongoing drug clinical trials through an easy-to-use, freely accessible online tool. Starting from this consideration, we developed COVIDrugNet (http://compmedchem.unibo.it/covidrugnet), a web application that allows users to capture a holistic view and keep up to date on how the clinical drug research is responding to the SARS-CoV-2 infection.\n\nHere, we describe the web app and show through some examples how one can explore the whole landscape of medicines in clinical trial for the treatment of COVID-19 and try to probe the consistency of the current approaches with the available biological and pharmacological evidence. We conclude that careful analyses of the COVID-19 drug-target system based on COVIDrugNet can help to understand the biological implications of the proposed drug options, and eventually improve the search for more effective therapies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Luca Menestrina", - "author_inst": "Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna 40126 Bologna, Italy" - }, - { - "author_name": "Chiara Cabrelle", - "author_inst": "Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna 40126 Bologna, Italy" - }, - { - "author_name": "Maurizio Recanatini", - "author_inst": "Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna 40126 Bologna, Italy" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.03.09.434219", "rel_title": "The FDA-approved drug cobicistat synergizes with remdesivir to inhibit SARS-CoV-2 replication", @@ -893812,6 +895785,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.03.06.21252796", + "rel_title": "SARS-CoV-2 infects blood monocytes to activate NLRP3 and AIM2 inflammasomes, pyroptosis and cytokine release", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.06.21252796", + "rel_abs": "SARS-CoV-2 causes acute respiratory distress that can progress to multiorgan failure and death in some patients. Although severe COVID-19 disease is linked to exuberant inflammation, how SARS-CoV-2 triggers inflammation is not understood. Monocytes are sentinel blood cells that sense invasive infection to form inflammasomes that activate caspase-1 and gasdermin D (GSDMD) pores, leading to inflammatory death (pyroptosis) and processing and release of IL-1 family cytokines, potent inflammatory mediators. Here we show that ~10% of blood monocytes in COVID-19 patients are dying and infected with SARS-CoV-2. Monocyte infection, which depends on antiviral antibodies, activates NLRP3 and AIM2 inflammasomes, caspase-1 and GSDMD cleavage and relocalization. Signs of pyroptosis (IL-1 family cytokines, LDH) in the plasma correlate with development of severe disease. Moreover, expression quantitative trait loci (eQTLs) linked to higher GSDMD expression increase the risk of severe COVID-19 disease (odds ratio, 1.3, p<0.005). These findings taken together suggest that antibody-mediated SARS-CoV-2 infection of monocytes triggers inflammation that contributes to severe COVID-19 disease pathogenesis.\n\nOne sentence summaryAntibody-mediated SARS-CoV-2 infection of monocytes activates inflammation and cytokine release.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Caroline Junqueira", + "author_inst": "Instituto Rene Rachou, FIOCRUZ" + }, + { + "author_name": "Angela Crespo", + "author_inst": "Boston Children's Hospital, Harvard Medical School" + }, + { + "author_name": "Shahin Ranjbar", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Jacob Ingber", + "author_inst": "Boston Children's Hospital, Harvard medical School" + }, + { + "author_name": "Blair Parry", + "author_inst": "Massachusetts General Hospital Institute for Patient Care" + }, + { + "author_name": "Sagi David", + "author_inst": "Boston Children's Hospital, Harvard Medical School" + }, + { + "author_name": "Luna B de Lacerda", + "author_inst": "Instituto Rene Rachou, Fiocruz" + }, + { + "author_name": "Mercedes Lewandrowski", + "author_inst": "Boston Children's Hospital, Harvard Medical School" + }, + { + "author_name": "Sarah Alden Clark", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Felicia Ho", + "author_inst": "Boston Children's Hospital, Harvard Medical School" + }, + { + "author_name": "Setu Vora", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Valerie Leger", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Caroline Beackes", + "author_inst": "Massachusetts General Hospital Institute for Patient Care" + }, + { + "author_name": "Justin Margolin", + "author_inst": "Massachusetts General Hospital Institute for Patient Care" + }, + { + "author_name": "Nicole Russell", + "author_inst": "Massachusetts General Hospital Institute for Patient Care" + }, + { + "author_name": "Lee Gehrke", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Upasana Das Adhikari", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Lauren Henderson", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Erin Janssen", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Douglas Kwon", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Chris Sander", + "author_inst": "Dana Farber Cancer Center" + }, + { + "author_name": "Jonathan Abraham", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Michael Filbin", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Marcia B. Goldberg", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Hao Wu", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Mehta Gautam", + "author_inst": "University College London" + }, + { + "author_name": "Steven Bell", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Anne Goldfeld", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Judy Lieberman", + "author_inst": "Boston Children's Hospital, Harvard Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.06.21253051", "rel_title": "A 1 to 1000 SARS-CoV-2 reinfection proportion in members of a large healthcare provider in Israel: a preliminary report", @@ -895420,65 +897524,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.04.21252913", - "rel_title": "Comparison of IgG and neutralizing antibody responses after one or two doses of COVID-19 mRNA vaccine in previously infected and uninfected persons", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252913", - "rel_abs": "ObjectiveTo compare anti-SARS-CoV-2 spike receptor binding domain (RBD) IgG antibody concentrations and antibody-mediated neutralization of spike-ACE2 receptor binding in vitro following vaccination of non-hospitalized participants by sero-status and acute virus diagnosis history.\n\nMethodsParticipants were studied before and after mRNA vaccination in a community-based, home-collected, longitudinal serosurvey; none reported hospitalization for COVID-19. Prior to vaccination, some reported prior positive acute viral diagnostic testing and were seropositive (COVID-19+). Participants who did not report acute viral diagnostic testing were categorized as seropositive or seronegative based on anti-spike RBD IgG test results. Primary measures were anti-spike RBD IgG concentration and percent antibody-mediated neutralization of spike protein-ACE2 interaction prior to vaccination, and after one or two doses of vaccine.\n\nResultsOf 290 unique vaccine recipients, 42 reported a prior COVID-19 diagnosis and were seropositive (COVID-19+). Of the 248 with no history of acute viral diagnostic testing, 105 were seropositive and 143 seronegative before vaccination. The median age was 38yrs (range 21-83) with 65% female and 35% male; 40% were non-white. Responses were evaluated after one (n=140) or two (n=170) doses of BNT162b2/Pfizer or mRNA-1273/Moderna vaccine. After one dose, median post-vaccine IgG concentration and percent neutralization were each significantly higher among the COVID-19+ group (median 47.7 {micro}g/ml, IgG; >99.9% neutralization) compared to the seropositives (3.4 {micro}g /ml IgG; 62.8% neutralization) and seronegatives (2.2 {micro}g /ml IgG; 39.5% neutralization). The latter two groups reached >95% neutralization after the second vaccine dose.\n\nConclusionsA prior outpatient COVID-19 diagnosis was associated with strong anti-spike RBD IgG and in vitro neutralizing responses after one vaccine dose. Persons seropositive for anti-spike RBD IgG in the absence of acute viral diagnostic testing, and those who were seronegative, required two doses to achieve equivalently high levels of IgG and neutralization activity. One mRNA vaccine dose is not sufficient to generate in vitro evidence of strong protection against COVID-19 among most persons previously infected with SARS-CoV-2, nor among seronegative persons.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alexis R. Demonbreun", - "author_inst": "Northwestern University" - }, - { - "author_name": "Amelia Sancilio", - "author_inst": "Northwestern University" - }, - { - "author_name": "Matt E. Velez", - "author_inst": "Northwestern University" - }, - { - "author_name": "Daniel T. Ryan", - "author_inst": "Northwestern University" - }, - { - "author_name": "Rana Saber", - "author_inst": "Northwestern University" - }, - { - "author_name": "Lauren A. Vaught", - "author_inst": "Northwestern University" - }, - { - "author_name": "Nina L. Reiser", - "author_inst": "Northwestern University" - }, - { - "author_name": "Richard T. D'Aquila", - "author_inst": "Northwestern University" - }, - { - "author_name": "Brian Mustanski", - "author_inst": "Northwestern University" - }, - { - "author_name": "Elizabeth M. McNally", - "author_inst": "Northwestern University" - }, - { - "author_name": "Thomas W. McDade", - "author_inst": "Northwestern University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.04.21252880", "rel_title": "Estimation and optimal control of the multi-scale dynamics of the Covid-19", @@ -895714,6 +897759,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.04.21252921", + "rel_title": "A systematic review and meta-analysis of longitudinal cohort studies comparing mental health before versus during the COVID-19 pandemic", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252921", + "rel_abs": "BackgroundIncreases in mental health problems have been observed in some studies during the COVID-19 pandemic. It is unclear whether changes have been large and experienced by most population sub-groups, persisted over time or been symptom specific.\n\nMethodsWe systematically reviewed and meta-analysed longitudinal cohort studies that examined changes in mental health among the same group of participants before and during the pandemic (PROSPERO: CRD42021231256). Searches for published and unpublished studies were conducted in January 2021. Changes in mental health (standardised mean change; SMC) were examined using meta-analyses.\n\nFindingsSixty-five studies were included. There was an overall increase in mental health symptoms that was most pronounced during March-April 2020 (SMC = .102 [95% CI: .026 to .192], p = 0.03) before significantly declining over time (May-July SMC = .067 [95% CI: -.022 to .157], p = .141). Compared to measures of anxiety (SMC = 0.13, p = 0.02) and general mental health (SMC = -.03, p = 0.65), increases in depression and mood disorder symptoms tended to be larger (SMC = 0.22, p < .001) and reductions over time appeared less pronounced. Increased mental health symptoms were observed across most population subgroups examined but there was no evidence of any change in symptoms among samples with a pre-existing mental health condition.\n\nInterpretationThere was a small increase in mental health symptoms soon after the outbreak of the COVID-19 pandemic that decreased and was comparable to pre-pandemic levels by mid-2020 among most population sub-groups and symptom types.\n\nFundingN/A\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThere have been reported increases in mental health problems during the outbreak of the COVID-19 pandemic. However, it is unclear whether changes in mental health problems have been symptom specific, how changes have differed across populations and whether increased mental health problems have persisted over time. We systematically reviewed and meta-analysed longitudinal cohort studies that examined mental health among the same participants prior to and during the pandemic in 2020. This approach allowed us to quantify the mental health burden associated with the outbreak of the pandemic and how it has changed over time. We searched Pubmed, SCOPUS, Web of Science and PsychInfo from January 2020 to January 11, 2021 and identified eligible unpublished articles available on pre-print servers.\n\nAdded value of this studyWe identified 65 eligible articles that reported 201 comparisons of mental health pre vs. post pandemic outbreak. Meta-analysis indicated that longitudinal cohort studies that examined mental health prior to and during the COVID-19 pandemic in 2020 showed a significant but statistically small increase in mental health symptoms. The overall increase in mental health symptoms was most pronounced during the early stages of the pandemic (March-April), before decreasing and being generally comparable to pre-pandemic levels by mid-2020.\n\nCompared to anxiety and general measures of mental health functioning, increases tended to be larger in depressive symptoms and although statistically small, remained elevated past the early stages of the pandemic. Increases in mental health symptoms were observed across most population sub-groups, but there was no evidence of a change in mental health symptoms among samples of participants with a pre-existing mental health condition.\n\nImplications of all the available evidenceFindings confirm that the initial outbreak of the pandemic was associated with a significant but statistically small increase in mental health symptoms. Given that small effects may have meaningful cumulative consequences at the population level, there is a need for continued mental health provision and monitoring particularly during periods of the pandemic when infection rates and deaths are high. Further into the pandemic, mental health problems decreased significantly, which indicated recovery and resilience in overall mental health. Contrary to predictions made early in the pandemic, there was also no evidence of a worsening of mental health symptoms among samples of participants with a pre-existing mental health condition. Overall the results of the present analyses suggest that the pandemic may not have caused an unprecedented and long lasting mental health crisis, instead there appears to have been resilience in mental health.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eric Robinson", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Angelina R Sutin", + "author_inst": "Florida State University" + }, + { + "author_name": "Michael Daly", + "author_inst": "Maynooth University" + }, + { + "author_name": "Andrew Jones", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.03.04.21252918", "rel_title": "An increase in willingness to vaccinate against COVID-19 in the US between October 2020 and February 2021: longitudinal evidence from the Understanding America Study", @@ -897214,49 +899290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.05.21253022", - "rel_title": "Non-uniform UV-C dose across N95 facepieces can cause 2.9-log variation in SARS-CoV-2 inactivation", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21253022", - "rel_abs": "During public health crises like the COVID-19 pandemic, ultraviolet-C (UV-C) decontamination of N95 respirators for emergency reuse has been implemented to mitigate shortages. However, decontamination efficacy across N95s is poorly understood, due to the dependence on received UV-C dose, which varies across the complex three-dimensional N95 shape. Robust quantification of UV-C dose across N95 facepieces presents challenges, as few UV-C measurement tools have sufficient 1) small, flexible form factor, and 2) angular response. To address this gap, we combine optical modeling and quantitative photochromic indicator (PCI) dosimetry with viral inactivation assays to generate high-resolution maps of \"on-N95\" UV-C dose and concomitant SARS-CoV-2 viral inactivation across N95 facepieces within a commercial decontamination chamber. Using modeling to rapidly identify on-N95 locations of interest, in-situ measurements report a 17.4 {+/-} 5.0-fold dose difference across N95 facepieces in the chamber, yielding 2.9 {+/-} 0.2-log variation in SARS-CoV-2 inactivation. UV-C dose at several on-N95 locations was lower than the lowest-dose locations on the chamber floor, highlighting the importance of on-N95 dose validation. Overall, we couple optical simulation with in-situ PCI dosimetry to relate UV-C dose and viral inactivation at specific on-N95 locations, informing the design of safe and effective decontamination protocols.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alisha Geldert", - "author_inst": "UC Berkeley/UCSF Graduate Program in Bioengineering" - }, - { - "author_name": "Alison Su", - "author_inst": "UC Berkeley/UCSF Graduate Program in Bioengineering" - }, - { - "author_name": "Allison W. Roberts", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley" - }, - { - "author_name": "Guillaume Golovkine", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley" - }, - { - "author_name": "Samantha M. Grist", - "author_inst": "Department of Bioengineering, University of California, Berkeley" - }, - { - "author_name": "Sarah A. Stanley", - "author_inst": "Department of Molecular and Cell Biology & School of Public Health, University of California, Berkeley" - }, - { - "author_name": "Amy E. Herr", - "author_inst": "Department of Bioengineering, University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.03.06.21251482", "rel_title": "A Rapid Method to Evaluate Pre-Travel Testing Programs for COVID-19: A Study in Hawaii", @@ -897496,6 +899529,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.05.21252707", + "rel_title": "Centenarians and extremely old people living with frailty can elicit durable SARS-CoV-2 spike specific IgG antibodies with virus neutralization functions following virus infection", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21252707", + "rel_abs": "BackgroundThe SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2) has led to more than 114 million COVID-19 cases and >2.5 million deaths worldwide. Epidemiological analysis has revealed that the risk of developing severe COVID-19 increases with age. Despite a disproportionate number of older individuals and long-term care facilities being affected by SARS-CoV-2 and COVID-19, very little is understood about the immune responses and development of humoral immunity in the extremely old person after SARS-CoV-2 infection. Here we investigated the development of humoral immunity in centenarians following a SARS-CoV-2 outbreak in a long-term care facility.\n\nMethodsExtreme aged individuals and centenarians who were residents in a long-term care facility and infected with or exposed to SARS-CoV-2 were investigated for the development of antibodies to SARS-CoV-2. Blood samples were collected from positive and bystander individuals 30 and 60 days after original diagnosis of SARS-CoV-2 infection. Plasma was used to quantify IgG, IgA, and IgM isotypes and subsequent subclasses of antibodies specific for SARS-CoV-2 spike protein. The function of anti-spike was then assessed by virus neutralization assays against the native SARS-CoV-2 virus.\n\nFindingsFifteen long-term care residents were investigated for SARS-CoV-2 infection. All individuals had a Clinical Frailty scale score [≥]5 and were of extreme older age or were centenarians. Six women with a median age of 98.8 years tested positive for SARS-CoV-2. Anti-spike IgG antibody titers were the highest titers observed in our cohort with all IgG positive individuals having virus neutralization ability. Additionally, 5 out of the 6 positive participants had a robust IgA anti-SARS-CoV-2 response. In all 5, antibodies were detected after 60 days from initial diagnosis.\n\nInterpretationExtreme older frail individuals and centenarians were able to elicit robust IgG and IgA antibodies directed toward SARS-CoV-2 spike protein. The antibodies were able to neutralize the virus. Humoral responses were still detectable after 60 days from initial diagnosis. Together, these data suggest that recovered participants who are of extreme old age would be protected if re-exposed to the same SARS-CoV-2 viral variant. Considering the threat of SARS-CoV-2 and COVID-19 to older age groups and long-term care facilities, the humoral responses to SARS-CoV-2 in older age groups is of public health importance and has implications to vaccine responses.\n\nFundingCanadian Institutes of Health Research (CIHR), NIH/NIAID, Genome Atlantic. VIDO receives operational funding from the Canada Foundation for Innovation through the Major Science Initiatives Fund and by Government of Saskatchewan through Innovation Saskatchewan.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Mary K Foley", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Samuel D Searle", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Ali Toloue", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Ryan Booth", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Alec Falkenham", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Darryl Falzarano", + "author_inst": "VIDO (Vaccine and Infectious Disease Organization)" + }, + { + "author_name": "Salvatore Rubino", + "author_inst": "University of Sassari" + }, + { + "author_name": "Magen Francis", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Mara McNeil", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Christopher Richardson", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Jason J LeBlanc", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Sharon Oldford", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Volker Gerdts", + "author_inst": "VIDO (Vaccine and Infectious Disease Organization)" + }, + { + "author_name": "Melissa K Andrew", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Shelly McNeil", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Barry Clarke", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Kenneth Rockwood", + "author_inst": "Dalhousie University" + }, + { + "author_name": "David J Kelvin", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Alyson A Kelvin", + "author_inst": "VIDO (Vaccine and Infectious Disease Organization)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.05.21252977", "rel_title": "Anti-Spike protein assays to determine post-vaccination antibody levels: a head-to-head comparison of five quantitative assays", @@ -898892,129 +901016,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.06.434193", - "rel_title": "SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies", - "rel_date": "2021-03-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.06.434193", - "rel_abs": "Neutralization escape by SARS-CoV-2 variants, as has been observed in the 501Y.V2 (B.1.351) variant, has impacted the efficacy of first generation COVID-19 vaccines. Here, the antibody response to the 501Y.V2 variant was examined in a cohort of patients hospitalized with COVID-19 in early 2021 - when over 90% of infections in South Africa were attributed to 501Y.V2. Robust binding and neutralizing antibody titers to the 501Y.V2 variant were detected and these binding antibodies showed high levels of cross-reactivity for the original variant, from the first wave. In contrast to an earlier study where sera from individuals infected with the original variant showed dramatically reduced potency against 501Y.V2, sera from 501Y.V2-infected patients maintained good cross-reactivity against viruses from the first wave. Furthermore, sera from 501Y.V2-infected patients also neutralized the 501Y.V3 (P.1) variant first described in Brazil, and now circulating globally. Collectively these data suggest that the antibody response in patients infected with 501Y.V2 has a broad specificity and that vaccines designed with the 501Y.V2 sequence may elicit more cross-reactive responses.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Thandeka Moyo-Gwete", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Mashudu Madzivhandila", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Zanele Makhado", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Frances Ayres", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Donald Mhlanga", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Brent Oosthuysen", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Bronwen Lambson", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Prudence Kgagudi", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, So" - }, - { - "author_name": "Arash Iranzadeh", - "author_inst": "nstitute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Deelan Doolabh", - "author_inst": "nstitute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Lynn Tyers", - "author_inst": "Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Lionel Chinhoyi", - "author_inst": "Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Afric" - }, - { - "author_name": "Mathilda Mennen", - "author_inst": "Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Afric" - }, - { - "author_name": "Sango Skelem", - "author_inst": "Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Afric" - }, - { - "author_name": "Gert Marais", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Constantinos Kurt Wibmer", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Jinal Bhiman", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Veronica Ueckermann", - "author_inst": "Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa" - }, - { - "author_name": "Theresa Rossouw", - "author_inst": "Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa." - }, - { - "author_name": "Michael Boswell", - "author_inst": "Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "University of KwaZulu-Natal" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Wendy Burgers", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Ntobeko Ntusi", - "author_inst": "Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Lynn Morris", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Penny Moore", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.03.21252838", "rel_title": "SARS-CoV-2 transmission in intercollegiate athletics not fully mitigated with daily antigen testing", @@ -899418,6 +901419,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.03.21252856", + "rel_title": "REACT-1 round 9 final report: Continued but slowing decline of prevalence of SARS-CoV-2 during national lockdown in England in February 2021", + "rel_date": "2021-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252856", + "rel_abs": "BackgroundEngland will start to exit its third national lockdown in response to the COVID-19 pandemic on 8th March 2021, with safe effective vaccines being rolled out rapidly against a background of emerging transmissible and immunologically novel variants of SARS-CoV-2. A subsequent increase in community prevalence of infection could delay further relaxation of lockdown if vaccine uptake and efficacy are not sufficiently high to prevent increased pressure on healthcare services.\n\nMethodsThe PCR self-swab arm of the REal-time Assessment of Community Transmission Study (REACT-1) estimates community prevalence of SARS-CoV-2 infection in England based on random cross-sections of the population ages five and over. Here, we present results from the complete round 9 of REACT-1 comprising round 9a in which swabs were collected from 4th to 12th February 2021 and round 9b from 13th to 23rd February 2021. We also compare the results of REACT-1 round 9 to round 8, in which swabs were collected mainly from 6th January to 22nd January 2021.\n\nResultsOut of 165,456 results for round 9 overall, 689 were positive. Overall weighted prevalence of infection in the community in England was 0.49% (0.44%, 0.55%), representing a fall of over two thirds from round 8. However the rate of decline of the epidemic has slowed from 15 (13, 17) days, estimated for the period from the end of round 8 to the start of round 9, to 31 days estimated using data from round 9 alone (lower confidence limit 17 days). When comparing round 9a to 9b there were apparent falls in four regions, no apparent change in one region and apparent rises in four regions, including London where there was a suggestion of sub-regional heterogeneity in growth and decline. Smoothed prevalence maps suggest large contiguous areas of growth and decline that do not align with administrative regions.\n\nPrevalence fell by 50% or more across all age groups in round 9 compared to round 8, with prevalence (round 9) ranging from 0.21% in those aged 65 and over to 0.71% in those aged 13 to 17 years. Round 9 prevalence was highest among Pakistani participants at 2.1% compared to white participants at 0.45% and Black participants at 0.83%. There were higher adjusted odds of infection for healthcare and care home workers, for those working in public transport and those working in education, school, nursery or childcare and lower adjusted odds for those not required to work outside the home.\n\nConclusionsCommunity prevalence of swab-positivity has declined markedly between January and February 2021 during lockdown in England, but remains high; the rate of decline has slowed in the most recent period, with a suggestion of pockets of growth. Continued adherence to social distancing and public health measures is required so that infection rates fall to much lower levels. This will help to ensure that the benefits of the vaccination roll-out programme in England are fully realised.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Steven Riley", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Caroline E. Walters", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Haowei Wang", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Oliver Eales", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "David Haw", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Kylie E. C. Ainslie", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Christina Atchinson", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Claudio Fronterre", + "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" + }, + { + "author_name": "Peter J. Diggle", + "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Helen Ward", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a" + }, + { + "author_name": "Paul Elliott", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.03.21251639", "rel_title": "SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay", @@ -900986,65 +903066,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.03.21252509", - "rel_title": "Efficacy of Nitazoxanide in reducing the viral load in COVID-19 patients. Randomized, placebo-controlled, single-blinded, parallel group, pilot study.", - "rel_date": "2021-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252509", - "rel_abs": "The fast spread of COVID-19 has overcrowded Public Health Systems facilities in major countries due to the large number of seriously ill patients, particularly those requiring admission to intensive care units. Reducing viral load, along with other recommended epidemiological measures, such as social distancing and home confinement, can in time significantly help to reduce the infection R0 (Basic Reproductive Rate) and then mitigate disease burden. Early negativization or otherwise reduction of the viral load can potentially diminish disease severity, resulting in a better-controlled public health response, avoiding collapse of healthcare systems. Nitazoxanide, a widely used thiazolide approved by the FDA as an antiparasitic drug, also approved in Brazil for Norovirus and Rotavirus treatments, has an excellent safety record for a variety of indications. Nitazoxanide exhibits activity in vitro against MERS-CoV and other coronaviruses; and a specific antiviral effect (in micro molar doses) against SARS-CoV-2. The objective of this study was to evaluate the efficacy and safety of Nitazoxanide in reducing the SARS-COV 2 viral load within 7 days of treatment in respiratory samples from COVID-19-infected patients with mild to moderate disease, compared to placebo. An interim analysis showed that the ratio of patients with a viral load reduction [≥] 35% from baseline up to day 7 of treatment was significantly greater for Nitazoxanide compared to placebo (47.8% vs. 15.4%; {Delta} 34.6%; 95% CI: 64.7; 4.6: p = 0.037).\n\nKEY POINTSO_ST_ABSState of the ArtC_ST_ABSO_LIDifferent studies conclude that viral load (VL) would correlate with morbidity, mortality and contagiousness of COVID-19.\nC_LIO_LIEarly negativization or reduction of the viral load can potentially reduce the severity of this disease.\nC_LIO_LIIn vitro data demonstrated a specific antiviral effect of Nitazoxanide for SARS-CoV-2.\nC_LI\n\nArticle contributionO_LINitazoxanide showed a statistically significant difference versus placebo in the number of patients who had their viral load reduced by at least 35% in mild to moderate COVID-19 disease.\nC_LIO_LIThe observed antiviral effect in vitro would seems to be verified in patients with mild to moderate COVID-19 infection, which should be confirmed by studies with a larger cohort of patients.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Marcelo Silva", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Andres Espejo", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Maria Laura Pereyra", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Martin Lynch", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Marcos Thompson", - "author_inst": "Unidad de Hepatologia y Trasplante Hepatico, Hospital Universitario Austral, Pilar, Argentina." - }, - { - "author_name": "Hernan Taconelli", - "author_inst": "Sanatorio Nuestra Senora del Pilar, Ciudadela, Argentina." - }, - { - "author_name": "Patricia Bare", - "author_inst": "IIHEMA, IMEX-CONICET, Academia Nacional de Medicina" - }, - { - "author_name": "Matias Pereson", - "author_inst": "IIHEMA, IMEX-CONICET, Academia Nacional de Medicina." - }, - { - "author_name": "Marcelo Garbini", - "author_inst": "Roemmers" - }, - { - "author_name": "Pablo Crucci", - "author_inst": "Departamento de Investigacon Clinica, Laboratorios Roemmers" - }, - { - "author_name": "Diego Enriquez", - "author_inst": "Departamento de Investigacon Clinica, Laboratorios Roemmers" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.02.21252746", "rel_title": "Providing a safe, in-person, residential college experience during the COVID-19 pandemic", @@ -901456,6 +903477,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.03.21252425", + "rel_title": "Diagnostic Performance and Characteristics of Anterior Nasal Collection for the SARS-CoV-2 Antigen Test: A Prospective Study in Japan", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252425", + "rel_abs": "We conducted a prospective study in Japan to evaluate the diagnostic performance of the antigen test QuickNavi-COVID19 Ag using anterior nasal samples and to compare the degrees of coughs or sneezes induction and the severity of pain between anterior nasal collection and nasopharyngeal collection. A total of 862 participants were included in the analysis. In comparison to the findings of reverse transcription PCR using nasopharyngeal samples, the antigen test using anterior nasal samples showed 72.5% sensitivity (95% confidence interval [CI]: 58.3%-84.1%) and 100% specificity (95% CI: 99.3%-100%). Anterior nasal collection was associated with a significantly lower degree of coughs or sneezes induction and the severity of pain in comparison to nasopharyngeal collection (p < 0.001). The antigen test using anterior nasal samples showed moderate sensitivity but was less painful and induced fewer coughs or sneezes.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yuto Takeuchi", + "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital, 2-1-1 Amakubo, Tsukuba, Ibaraki 305-8576, Japan" + }, + { + "author_name": "Yusaku Akashi", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, 1-3-1 Amakubo Tsukuba, Ibaraki 305-8558, Japan" + }, + { + "author_name": "Daisuke Kato", + "author_inst": "Denka Co., Ltd. Gosen site, Reaserch & Development Division, Reagent R&D Depertment, 1-2-2 Minami-hon-cho, Gosen-shi, Niigata 959-1695, Japan" + }, + { + "author_name": "Miwa Kuwahara", + "author_inst": "Denka Co., Ltd. Gosen site, Reaserch & Development Division, Reagent R&D Depertment, 1-2-2 Minami-hon-cho, Gosen-shi, Niigata 959-1695, Japan" + }, + { + "author_name": "Shino Muramatsu", + "author_inst": "Denka Co., Ltd. Gosen site, Reaserch & Development Division, Reagent R&D Depertment, 1-2-2 Minami-hon-cho, Gosen-shi, Niigata 959-1695, Japan" + }, + { + "author_name": "Atsuo Ueda", + "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital, 1-3-1 Amakubo, Tsukuba, Ibaraki 305-8558, Japan" + }, + { + "author_name": "Shigeyuki Notake", + "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital, 1-3-1 Amakubo, Tsukuba, Ibaraki 305-8558, Japan" + }, + { + "author_name": "Hiroichi Ishikawa", + "author_inst": "Department of Respiratory Medicine, Tsukuba Medical Center Hospital, 1-3-1 Amakubo, Tsukuba, Ibaraki 305-8558, Japan" + }, + { + "author_name": "Hiromichi Suzuki", + "author_inst": "Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.02.21252400", "rel_title": "Real World Performance of SARS-CoV-2 Antigen Rapid Diagnostic Tests in Various Clinical Settings", @@ -902888,37 +904960,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.04.433846", - "rel_title": "SARS-CoV-2 viability in time on experimental surfaces", - "rel_date": "2021-03-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.04.433846", - "rel_abs": "We evaluated the SARS-CoV-2 viability preservation on different model surfaces over time. It was found that the SARS-CoV-2 RNA was detected on all studied surfaces for 360 minutes, while the viability of the virus was completely lost after 120 minutes. Type of experimental surface significantly affects viability preservation.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maria Nikiforova", - "author_inst": "N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia" - }, - { - "author_name": "Andrei Siniavin", - "author_inst": "N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia" - }, - { - "author_name": "Elena Shidlovskaya", - "author_inst": "N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia" - }, - { - "author_name": "Nadezhda Kuznetsova", - "author_inst": "N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.04.433849", "rel_title": "Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation", @@ -903190,6 +905231,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.03.433579", + "rel_title": "T-cell Repertoire Characteristics of Asymptomatic and Re-detectable Positive COVID-19 Patients", + "rel_date": "2021-03-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.03.433579", + "rel_abs": "BackgroundThe prevention of COVID-19 pandemic is highly complicated by the prevalence of asymptomatic and recurrent infection. Many previous immunological studies have focused on symptomatic and convalescent patients, while the immune responses in asymptomatic patients and re-detectable positive cases remain unclear.\n\nMethodsHere we comprehensively analyzed the peripheral T-cell receptor (TCR) repertoire of 54 COVID-19 patients in different phases, including asymptomatic, symptomatic, convalescent and re-detectable positive cases.\n\nResultsWe found progressed immune responses from asymptomatic to symptomatic phase. Furthermore, the TCR profiles of re-detectable positive cases were highly similar to those of asymptomatic patients, which could predict the risk of recurrent infection.\n\nConclusionTherefore, TCR repertoire surveillance has the potential to strengthen the clinical management and the immunotherapy development for COVID-19.\n\nFundingThe Science and Technology Innovation Project of Foshan Municipality (2020001000431) and the National Key Research and Development Project (2020YFA0708001).", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jianhua Xu", + "author_inst": "ShunDe Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Yongsi Wang", + "author_inst": "Guangzhou Huayin Medical Laboratory Center.Ltd" + }, + { + "author_name": "Yuntao Liu", + "author_inst": "The Second Affiliated Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Jiaqi Zhang", + "author_inst": "ShunDe Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Wei Hu", + "author_inst": "ShunDe Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Wentao Fan", + "author_inst": "Guangzhou Huayin Medical Laboratory Center.Ltd" + }, + { + "author_name": "Linlin Li", + "author_inst": "Guangzhou Huayin Medical Laboratory Center Co.Ltd." + }, + { + "author_name": "Hai Lan", + "author_inst": "ShunDe Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Kejian Wang", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Dawei Wang", + "author_inst": "ShunDe Hospital of Guangzhou University of Chinese Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.03.433725", "rel_title": "Disinfection of SARS-CoV-2 contaminated surfaces of personal items with UVC-LED disinfection boxes", @@ -904842,125 +906938,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.09.21251168", - "rel_title": "A novel, multiplexed RT-qPCR assay to distinguish lineage B.1.1.7 from the remaining SARS-CoV-2 lineages", - "rel_date": "2021-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251168", - "rel_abs": "The emergence of a novel SARS-CoV-2 variant called lineage B.1.1.7 sparked global alarm due to evidence of increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating efforts to detect and track the variant. Current approaches to detect lineage B.1.1.7 include sequencing and RT-qPCR tests containing a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack robust genomic surveillance programs and failed assays detect multiple unrelated variants containing similar mutations as B.1.1.7, we sought to develop an RT-qPCR test that can accurately and rapidly differentiate the B.1.1.7 variant from other SARS-CoV-2 variants. We used bioinformatics, allele-specific PCR, and judicious placement of LNA-modified nucleotides to develop a test that differentiates B.1.1.7 from other SARS-CoV-2 variants. We validated the test on 106 clinical samples with lineage status confirmed by sequencing. Our room temperature-stable, multiplexed RT-qPCR test consists of two assays that target either the common SARS-CoV-2 spike gene or spike gene deletions specific to lineage B.1.1.7. A simple relative comparison of the Ct values of the two assays permits not only identification of the B.1.1.7 variant but also its differentiation from other variants that harbor only the {Delta}H69/{Delta}V70 deletion.The test showed 97% clinical sensitivity at detecting lineage B.1.1.7. This test can easily be implemented in labs to rapidly scale B.1.1.7 surveillance efforts and is particularly useful in countries with high prevalence of variants possessing only the {Delta}H69/{Delta}V70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Viera Kovacova", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Krist\u00edna Bor\u0161ov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia; Department of Microbiology and Virology, Faculty of Natural" - }, - { - "author_name": "Evan D Paul", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Monika Radvanszka", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Roman Hajdu", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Vikt\u00f3ria \u010cabanov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - }, - { - "author_name": "Monika Sl\u00e1vikov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - }, - { - "author_name": "Martina Li\u010dkov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - }, - { - "author_name": "\u013dubom\u00edra Luk\u00e1\u010dikov\u00e1", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - }, - { - "author_name": "Andrej Belak", - "author_inst": "Institute of Ethnology and Social Anthropology, Slovak Academy of Sciences, Bratislava, Slovakia; Intervention team, Ministry of Health, Slovakia" - }, - { - "author_name": "Lucia Roussier", - "author_inst": "Intervention team, Ministry of Health, Slovakia" - }, - { - "author_name": "Michaela Kosti\u010dov\u00e1", - "author_inst": "Intervention team, Ministry of Health, Slovakia; Institute of Social Medicine and Medical Ethics, Faculty of Medicine, Comenius University in Bratislava, Bratis" - }, - { - "author_name": "Anna L\u00ed\u0161kov\u00e1", - "author_inst": "Nitra Faculty Hospital, Department of Clinical Microbiology, Nitra, Slovakia" - }, - { - "author_name": "Lucia Ma\u010farov\u00e1", - "author_inst": "Regional Authority of Public Health, Banska Bystrica, Slovakia" - }, - { - "author_name": "M\u00e1ria \u0160tefkovi\u010dov\u00e1", - "author_inst": "Regional Authority of Public Health, Trencin, Slovakia; Faculty of Healthcare, Alexander Dubcek University of Trencin, Slovakia" - }, - { - "author_name": "Lenka Reizigov\u00e1", - "author_inst": "Regional Authority of Public Health, Trencin, Slovakia; Department of Laboratory Medicine, Faculty of Healthcare and Social Work, Trnava University, Trnava, Slo" - }, - { - "author_name": "Elena Nov\u00e1kov\u00e1", - "author_inst": "Department of Microbiology and Immunology, Comenius University in Bratislava, Jessenius Faculty of Medicine, Martin, Slovakia" - }, - { - "author_name": "Peter Sabaka", - "author_inst": "Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Alena Ko\u0161\u010d\u00e1lov\u00e1", - "author_inst": "Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia; Department of Infectious Dise" - }, - { - "author_name": "Bro\u0148a Brejov\u00e1", - "author_inst": "Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Edita Staro\u0148ov\u00e1", - "author_inst": "National Influenza Centre, National Public Health Authority of Slovak Republic in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Matej Mi\u0161\u00edk", - "author_inst": "Institute for Healthcare Analyses, Ministry of Health, Slovakia" - }, - { - "author_name": "Tomas Vinar", - "author_inst": "Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Jozef Nosek", - "author_inst": "Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia" - }, - { - "author_name": "Pavol Cekan", - "author_inst": "MultiplexDX, Inc., Comenius University Science Park, Bratislava, Slovakia" - }, - { - "author_name": "Boris Klempa", - "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" - } - ], - "version": "2", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.02.21250607", "rel_title": "Modeling University Reopening in Low Risk Countries During COVID-19", @@ -905200,6 +907177,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.03.433704", + "rel_title": "Low-dose lung radiotherapy for COVID-19 lung disease: a pre-clinical efficacy study in a bleomycin model of pneumonitis.", + "rel_date": "2021-03-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.03.433704", + "rel_abs": "PurposeLow-dose whole lung radiotherapy (LDLR) has been proposed as a treatment for patients with acute respiratory distress syndrome associated with SARS-CoV-2 infection and clinical trials are underway. There is an urgent need for preclinical evidence to justify this approach and inform dose, scheduling and mechanisms of action.\n\nMaterials and methodsFemale C57BL/6 mice were treated with intranasal bleomycin sulphate (7.5 or 11.25 units/kg, day 0), then exposed to whole lung radiation therapy (0.5, 1.0, 1.5 Gy or sham, day 3). Bodyweight was measured daily and lung tissue harvested for histology and flow cytometry on day 10. Computed tomography (CT) lung imaging was performed pre-radiation (day 3) and pre-endpoint (day 10).\n\nResultsBleomycin caused pneumonitis of variable severity which correlated with weight loss. LDLR at 1.0 Gy was associated with a significant increase in the proportion of mice recovering to 98% of initial bodyweight and a proportion of these mice exhibited less severe histopathological lung changes. Mice experiencing moderate initial weight loss were more likely to respond to LDLR than those experiencing severe initial weight loss. Additionally, LDLR (1.0 Gy) significantly reduced bleomycin-induced increases in interstitial macrophages, CD103+ dendritic cells and neutrophil-DC hybrids. Overall,bleomycin-treated mice exhibited significantly higher percentages of non-aerated lung in left than right lungs and LDLR (1.0 Gy) prevented further reductions in aerated lung volume in right but not left lungs. LDLR at 0.5 and 1.5 Gy did not modulate bodyweight or flow cytometric readouts of bleomycin-induced pneumonitis.\n\nConclusionsOur data support the concept that LDLR can ameliorate acute inflammatory lung injury, identify 1.0 Gy as the most effective dose and provide preliminary evidence that it is more effective in the context of moderate than severe pneumonitis. Mechanistically, LDLR at 1.0 Gy significantly suppressed bleomycin-induced accumulation of pulmonary interstitial macrophages, CD103+ dendritic cells and neutrophil-DC hybrids.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mark R Jackson", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Katrina Stevenson", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Sandeep K Chahal", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Emer Curley", + "author_inst": "CRUK Beatson Institute" + }, + { + "author_name": "George Finney", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Rodrigo Gutierrez-Quintana", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Evarest Onwubiko", + "author_inst": "CRUK Beatson Institute" + }, + { + "author_name": "Angelika F Rupp", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Karen Strathdee", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Megan KL MacLeod", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Charles McSharry", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Anthony J Chalmers", + "author_inst": "University of Glasgow" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.02.433156", "rel_title": "Altered Sub-Genomic RNA Expression in SARS-CoV-2 B.1.1.7 Infections", @@ -907028,61 +909068,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.28.21252633", - "rel_title": "A new accessible adaptable COVID-19 model", - "rel_date": "2021-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252633", - "rel_abs": "ObjectivesSophisticated epidemic models have been created to help governments and large healthcare organisations plan the necessary resources to manage the COVID-19 pandemic. Whilst helpful, current modelling systems are not widely accessible or easily adapted to different populations and circumstances. Our objective was to develop a widely applicable, easily accessible, adaptable model for projecting new COVID-19 infections and deaths that requires minimal expertise or resources to use. The model should be adaptable to different populations and able to accommodate social and pharmaceutical interventions as well as changes in the disease.\n\nDesignA Susceptible, Infected and Removed (SIR) infectious disease model was created using widely available Microsoft Excel(C) software. The model is deterministic, generating projections based on the available data and assumptions made. It uses a process of Monitored Forecasting through Visual Matching of predicated vs observed curves to improve accuracy and facilitate adaptability. A review of the COVID-19 literature was performed in order to produce an initial set of adjustable parameters on which to base the output of the model.\n\nSettingThis model can be adapted to different regions or countries for which the requisite input data (population size and number of deaths due to the disease) are available. This model has been successfully used with data from England, Sudan and Saudi Arabia. Data from NHS England were used for producing the illustrative results presented here. The model is a generic infectious disease forecast model which may be adapted to other epidemics.\n\nInterventionGovernments, public health organisations, pharmaceutical companies and other public institutions may introduce interventions that affect disease transmission or severity. Other unknown factors such as new variants of the infective agent may do the same. The effects of changes in disease transmission are identified by the model when predicted and observed curves deviate. By aligning the curves an evaluation of the effect of the changes can be made.\n\nOutcome MeasuresThe model graphically demonstrates projections for daily deaths, cumulative deaths, case mix (asymptomatic, symptomatic and severe infections requiring admission), hospital admissions and bed occupancy (ICU, general medical and total).\n\nResultsThe model successfully produced projections for the outcome measures using NHS England data. Users can adapt and continuously update the model correcting its projections as further local data becomes available. The Microsoft Excel platform allows the model to be used without expensive health information systems or computing infrastructure.\n\nConclusionWe present an SIR epidemic model that projects COVID-19 disease progression, is widely accessible, adaptable to different populations and environments as the disease progresses and is likely to be of benefit for identifying changing population healthcare needs.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael G Baker", - "author_inst": "epidemic projections.org, Surrey, England." - }, - { - "author_name": "Maximilian de Courten", - "author_inst": "Mitchell Institute, Victoria University, Melbourne, Australia." - }, - { - "author_name": "David A Sidloff", - "author_inst": "Nottingham University Hospitals, Nottingham, England." - }, - { - "author_name": "Alexander DL Baker", - "author_inst": "Lancashire Teaching Hospitals NHS Foundation Trust, Lancashire, England." - }, - { - "author_name": "Walid S El Sayes", - "author_inst": "King Saud Medical City, Riyadh, Saudi Arabia." - }, - { - "author_name": "Faisal A Alaklobi", - "author_inst": "King Saud Medical City, Riyadh, Saudi Arabia." - }, - { - "author_name": "Abdulrahman S Alqahtani", - "author_inst": "Ministry of Health, Riyadh, Saudi Arabia." - }, - { - "author_name": "Edward Fraser", - "author_inst": "First Riyadh Health Cluster, Saudi Arabia." - }, - { - "author_name": "Charles R Cohen", - "author_inst": "Projection Modeller, Riyadh, Saudi Arabia" - }, - { - "author_name": "Isam SM Osman", - "author_inst": "King Saud Medical City, Riyadh, Saudi Arabia." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.28.21252648", "rel_title": "Shifting research priorities in maternal and child health in the COVID-19 pandemic era in India: a renewed focus on systems strengthening", @@ -907330,6 +909315,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.28.21252644", + "rel_title": "Optimal mobility restriction minimizing COVID-19 and excess suicide deaths in Japan", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252644", + "rel_abs": "BackgroundStrict countermeasures for COVID-19 outbreak such as lockdowns and voluntary restrictions against going out might have reduced mortality because of COVID-19 directly, but might have raised suicide rates.\n\nObjectWe examined best policies for minimizing overall mortality attributable to COVID-19 directly, and excess mortality by suicide because of COVID-19.\n\nMethodWe regressed the estimated excess mortality attributable to suicide deaths against mobility-restrictive measures. Mortality attributable to COVID-19 directly was estimated through association between the effective reproduction number and mobility. We sought the best mobility restriction for minimizing overall deaths.\n\nResultsSignificant association was found between mobility and suicide, but the data were very few. Results showed the best mobility level as 65.5, which represents a 34.5% reduction in mobility from the normal level.\n\nDiscussion and ConclusionAn overly restrictive policy inducing lower than optimal mobility led to higher total mortality.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Junko Kurita", + "author_inst": "Tokiwa University, Ibaraki, Japan" + }, + { + "author_name": "Tamie Sugawara", + "author_inst": "Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan" + }, + { + "author_name": "Yoshiyuki Sugishita", + "author_inst": "Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.01.21252602", "rel_title": "The impact of COVID-19 on primary health care and antibiotic prescribing in rural China: qualitative study", @@ -908942,61 +910958,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.26.21252504", - "rel_title": "Opening schools and trends in SARS-CoV-2 transmission in European countries", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252504", - "rel_abs": "BackgroundIt is important to understand the role of schools in the community transmission of SARS-CoV-2, bearing in mind that children and adolescents can spread the infection within families, even when their own symptoms are mild. The aim of this study was to examine the trends of contagion before and after schools reopened across 27 countries in the European Union.\n\nMethodsAll data on the number of people testing positive for COVID-19 in each European country were collected from 20 days before schools reopened to 45 days afterwards. The Joinpoint regression method was used to detect single change points on the trend of contagion. The Bayesian Information Criterion (BIC) was used for model selection purposes.\n\nResultsWe calculated 27 linear regression models for the daily case numbers of SARS-CoV-2 infection in the 27 countries from 20 days before schools reopened to 45 days afterwards. A significant increase in the number of daily infections was seen for 21 countries after a change point in the linear regression lines. The change points in different countries varied, ranging from 10 to 42 days after schools reopened, with the majority occurring beyond the 21st day.\n\nConclusionThis study analysed the trend of SARS-CoV-2 transmission before and after schools reopened in Europe. We observed a significant increase in the number of new daily cases in most countries. This issue poses a public health problem that needs to be taken into account in deciding strategies to contain the spread of COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alessandra Buja", - "author_inst": "University of Padova" - }, - { - "author_name": "Matteo Paganini", - "author_inst": "University of Padova" - }, - { - "author_name": "Vittorio Cristofori", - "author_inst": "University of Padova" - }, - { - "author_name": "Tatjana Baldovin", - "author_inst": "University of Padova" - }, - { - "author_name": "Riccardo Fusinato", - "author_inst": "University of Padova" - }, - { - "author_name": "Giovanna Boccuzzo", - "author_inst": "University of Padova" - }, - { - "author_name": "Silvia Cocchio", - "author_inst": "University of Padova" - }, - { - "author_name": "Silvia Coretti", - "author_inst": "University of Padova" - }, - { - "author_name": "Vincenzo Rebba", - "author_inst": "University of Padova" - }, - { - "author_name": "Maria Parpinel", - "author_inst": "University of Udine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.27.21252593", "rel_title": "Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study", @@ -909224,6 +911185,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.25.21252488", + "rel_title": "Povidone iodine, hydrogen peroxide and chlorhexidine mouthwashes reduce SARS-CoV2 burden in whole mouth fluid and respiratory droplets", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252488", + "rel_abs": "SARS-CoV2 is transmitted primarily through oral mouth secretions and respiratory droplets. Commercial mouthwashes, povidone iodine (PI), hydrogen peroxide (HP) and chlorhexidine (CHX) have been tested in cell culture and RT-PCR studies for their efficacy to reduce SARS-CoV2 burden. Here, we evaluated SARS-CoV2 burden in whole mouth fluid (WMF) and respiratory droplets (RD) samples before and after the use of PI, HP or CHX mouthwashes in hospitalized COVID-19 patients using RT-PCR and rapid antigen test (RAT). Thirty-six SARS-CoV2 RT-PCR-positive in-patients were randomly assigned to one of the four groups: 20 and 60 minutes after 1% w/v PI or 1.5% HP; 90 and 180 minutes after 1.5% HP or 0.2% w/v CHX. WMF and RD samples were collected concurrently at baseline and after the two different time points. RD (92%) showed a higher reduction in SARS-CoV2 burden than WMF samples (50%; p=0.008). SARS-CoV2 burden was statistically lower at both 20 minutes (p=0.02) and 60 minutes (p=0.03) with PI; at 20 minutes with HP (p=0.0001); and 90 minutes with CHX (p=0.04). The overall and individual mean logarithmic reductions in the WMF and RD samples were greater than 1.0 at 20, 60 and 90 minutes after PI, HP or CHX. RAT-positive patients at 90 minutes post-treatment (n=3) demonstrated a one log increase in virus copies. Among the three RAT-negative post-treatment patients, SARS-CoV2 burden declined by one log in two while the third patient had a slight increase in RNA copies. In conclusion, we have shown for the first time that the mouthwashes, PI, HP and CHX can reduce the SARS-CoV2 burden in the concurrently collected RD and WMF samples. RAT is more appropriate than RT-PCR to evaluate the efficacy of the mouthwashes.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Bagavad Gita Jayaraman", + "author_inst": "Chennai Dental Research Foundation, Chennai" + }, + { + "author_name": "Gunaseelan Rajan", + "author_inst": "Chennai Dental Research Foundation, Chennai" + }, + { + "author_name": "Priya Kannian", + "author_inst": "The Voluntary Health Services Hospital" + }, + { + "author_name": "Chandra Lavanya", + "author_inst": "Ragas Dental College and Hospital, Chennai" + }, + { + "author_name": "Krittika Ravichandran", + "author_inst": "Chennai Dental Research Foundation, Chennai" + }, + { + "author_name": "Nagalingeswaran Kumarasamy", + "author_inst": "The Voluntary Health Services Hospital, Chennai" + }, + { + "author_name": "Kannan Ranganathan", + "author_inst": "Ragas Dental College and Hospital, Chennai" + }, + { + "author_name": "Veeraraghavan Ashwini", + "author_inst": "The Voluntary Health Services Hospital, Chennai" + }, + { + "author_name": "Pasuvaraj Mahanathi", + "author_inst": "The Voluntary Health Services Hospital, Chennai" + }, + { + "author_name": "Stephen J Challacombe", + "author_inst": "King's College, London" + }, + { + "author_name": "Jennifer Webster-Cyriaque", + "author_inst": "University of North Carolina, Chapel Hill" + }, + { + "author_name": "Newell W Johnson", + "author_inst": "Menzies Health Institute Queensland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.26.21252512", "rel_title": "REACT-2 Round 5: increasing prevalence of SARS-CoV-2 antibodies demonstrate impact of the second wave and of vaccine roll-out in England", @@ -910796,33 +912820,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.03.01.433379", - "rel_title": "Meta-Research: Citation needed? Wikipedia and the COVID-19 pandemic", - "rel_date": "2021-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433379", - "rel_abs": "BackgroundWith the COVID-19 pandemics outbreak, millions flocked to Wikipedia for updated information. Amid growing concerns regarding an \"infodemic\", ensuring the quality of information is a crucial vector of public health. Investigating if and how Wikipedia remained up to date and in line with science is key to formulating strategies to counter misinformation. Using citation analyses, we asked: which sources informed Wikipedias COVID-19-related articles before and during the pandemics first wave (January-May 2020).\n\nResultsWe found that coronavirus-related articles referenced trusted media sources and high-quality academic research. Moreover, despite a surge in COVID-19 preprints, Wikipedia had a clear preference for open-access studies published in respected journals and made little use of preprints. Building a timeline of English COVID-19 articles from 2001-2020 revealed a nuanced trade-off between quality and timeliness. It further showed how preexisting articles on key topics related to the virus created a framework for integrating new knowledge. Supported by a rigid sourcing policy, this \"scientific infrastructure\" facilitated contextualization and regulated the influx of new information. Lastly, we constructed a network of DOI-Wikipedia articles, which showed the shifting landscape of pandemic-related knowledge on Wikipedia and how academic citations create a web of shared knowledge supporting topics like COVID-19 vaccine development.\n\nConclusionsUnderstanding how scientific research interacts with the digital knowledge-sphere during the pandemic provides insight into how Wikipedia can facilitate access to science. It also reveals how, aided by what we term its \"citizen encyclopedists\", it successfully fended off COVID-19 disinformation and how this unique model may be deployed in other contexts.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Omer Benjakob", - "author_inst": "The Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Rona Aviram", - "author_inst": "Weizmann Institute of Science, Rehovot, Israel" - }, - { - "author_name": "Jonathan Aryeh Sobel", - "author_inst": "Technion" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2021.02.27.21252577", "rel_title": "Nationwide rollout reveals efficacy of epidemic control through digital contact tracing", @@ -911062,6 +913059,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.02.24.21252390", + "rel_title": "Graphical Models of Pandemic", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252390", + "rel_abs": "Both COVID-19 and novel pandemics challenge those of us within the modeling community, specifically in establishing suitable relations between lifecycles, scales, and existing methods. Herein we demonstrate transitions between models in space/time, individual-to-community, county-to-city, along with models for the trace beginning with exposure, then to symptom manifest, then to community transmission. To that end, we leverage publicly available data to compose a chain of Graphical Models (GMs) for predicting infection rates across communities, space, and time. Well anchor our GMs against the more expensive yet state-of-the-art Agent-Based Models (ABMs). Insight obtained from designing novel GMs calibrated to ABMs furnishes reduced, yet reliable surrogates for the end-to-end public health challenge of community contact tracing and transmission. Further, this novel research transcends and synergizes information integration and informatics, leading to an advance in the science of GMs. Cognizance into the data lifecycle using properly coarse-grained modeling will broaden the toolkit available to public health specialists, and hopefully empower governments and health agencies, here and abroad, in addressing the profound challenges in disease and vaccination campaigns confronting us by COVID and future pandemics.\n\nIn this proof of principle study, focusing on the GM methodology development, we show, first, how static GM of the Ising model type (characterized by pair-wise interaction between nodes related to traffic and communications between nodes representing communities, or census tracts within a given city, and with local infection bias) emerge from a dynamic GM of the Independent Cascade type, introduced and studied in Computer and Networks sciences mainly in the context of the spread of social influences. Second, we formulate the problem of inference in epidemiology as inference problems in the Ising model setting. Specifically, we pose the challenge of computing Conditional A-posteriori Level of Infection (CALI), which provides a quantitative answer to the questions: What is the probability that a given node in the GM (given census tract within the city) becomes infected in the result of injection of the infection at another node, e.g. due to arrival of a super-spreader agent or occurence of the super-spreader event in the area. To answer the question exactly is not feasible for any realistic size (larger than 30-50 nodes) model. We therefore adopt and develop approximate inference techniques, of the variational and variable elimination types, developed in the GM literature. To demonstrate utility of the methodology, which seems new for the public health application, we build a 123-node model of Seattle, as well as its 10-node and 20-node coarsegrained variants, and then conduct the proof of principles experimental studies. The experiments on the coarse-grained models have helped us to validate the approximate inference by juxtaposing it to the exact inference. The experiments also lead to discovery of interesting and most probably universal phenomena. In particular, we observe (a) a strong sensitivity of CALI to the location of the initial infection, and (b) strong alignment of the resulting infection probability (values of CALI) observed at different nodes in the regimes of moderate interaction between the nodes. We then speculate how these, and other observations drawn from the synthetic experiments, can be extended to a more realistic, data driven setting of actual operation importance. We conclude the manuscript with an extensive discussion of how the methodology should be developed further, both at the level of devising realistic GMs from observational data (and also enhancing it with microscopic ABM modeling and simulations) and also regarding utilization of the GM inference methodology for more complex problems of the pandemic mitigation and control.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Michael Chertkov", + "author_inst": "University of Arizona" + }, + { + "author_name": "Ruby Abrams", + "author_inst": "University of Arizona" + }, + { + "author_name": "Amir Mohammad Esmaieeli Sikaroudi", + "author_inst": "University of Arizona" + }, + { + "author_name": "Mikhail Krechetov", + "author_inst": "Skolkovo Institute of Technology" + }, + { + "author_name": "Conrad NP Slagle", + "author_inst": "University of Arizona" + }, + { + "author_name": "Alon Efrat", + "author_inst": "University of Arizona" + }, + { + "author_name": "Radoslav Fulek", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Eyal Oren", + "author_inst": "San Diego State University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.24.21252394", "rel_title": "HYPER: Group testing via hypergraph factorization applied to COVID-19", @@ -912378,41 +914422,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.26.21252336", - "rel_title": "What is the effect of lockdown upon hospitalisation due to COVID-19 amongst patients from a heart failure registry?", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252336", - "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) is associated with a high risk of mortality especially in patients with cardiovascular conditions such as heart failure. The UK government announced a national lockdown last year to curb the spread of the virus. We conducted this study primarily to ascertain the impact of lockdown upon the incidence of COVID-19 hospitalisation amongst patients with a known diagnosis of heart failure (HF)\n\nMethodsThis was a retrospective cohort study of 1097 patients from our HF registry who had presented with acute decompensated HF in 2018 and 2019. Incidence and outcomes of hospitalisation due to COVID-19 were analysed in this cohort both during the 1st UK lockdown as well as after the lockdown period. Co-morbidities, frailty index, clinical features, blood results, and heart failure treatments were compared between the 2 groups (COVID versus no-COVID) and between the group of patients who died versus survivors.\n\nResults50 out of 801 surviving (6.2%) HF patients required hospitalisation due to COVID-19 from March to November 2020; 24 patients (3.1%) during the first lockdown and 26 (3.5%) in the post-lockdown period; p=0.7. In comparison to patients not hospitalised with COVID-19 (\"no-COVID group), there was a significantly higher prevalence of co-morbidities amongst HF patients who were hospitalised with COVID-19, such as hypertension (p<0.001), diabetes (p=0.005), ischaemic heart disease (p=0.01) and increased body mass index. 30 day mortality amongst HF patients hospitalised due to COVID-19 was 52%. Rockwood Frailty Score [≥]6 (OR 6.530695 % CI:1.8958 to 22.4961; p=0.003) and diabetes (OR 3.82;95% CI 1.13 to 12.95; p=0.03) were independent predictors of 30 day mortality.\n\nConclusionOur data suggests that the incidence of hospitalisation due to COVID-19 was similar both during as well as post lockdown amongst patients from our HF registry. HF patients with cardiovascular co-morbidities such as obesity, hypertension, diabetes and ischaemic heart disease have a higher risk of hospitalisation due to COVID-19. Diabetes and Rockwood Frailty score are independent predictors of short term mortality. Co-morbidity and frailty scores should be incorporated during initial assessment to help risk-prediction.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "hani abobakr essa", - "author_inst": "Aintree university hospital" - }, - { - "author_name": "Sophia brousas", - "author_inst": "Aintree university hospital" - }, - { - "author_name": "Isabel whybrow-huppatz", - "author_inst": "Aintree university hospital" - }, - { - "author_name": "thomas salmon", - "author_inst": "Aintree university hospital" - }, - { - "author_name": "rajiv sankaranarayanan", - "author_inst": "Aintree university hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.02.26.21252553", "rel_title": "Vaccination and herd immunity thresholds in heterogeneous populations", @@ -912604,6 +914613,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.25.21252481", + "rel_title": "Excess deaths reveal the true spatial, temporal, and demographic impact of COVID-19 on mortality in Ecuador", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252481", + "rel_abs": "BackgroundIn early 2020, Ecuador reported one of the highest surges of per capita deaths across the globe.\n\nMethodsWe collected a comprehensive dataset containing individual death records between 2015 and 2020 from the Ecuadorian National Institute of Statistics and Census and the Ecuadorian Ministry of Government. We computed the number of excess deaths across time, geographical locations and demographic groups using Poisson regression methods.\n\nResultsBetween January 1st and September 23rd, 2020, the number of excess deaths in Ecuador is 36,402 (95% CI: 35,762-36,827) or 208 per 105 population, which is 171% of the expected deaths in that period in a typical year. Only 20% of the excess deaths are attributable to confirmed COVID-19 deaths. Strikingly, in provinces that were most affected by COVID-19, such as Guayas and Santa Elena, the all-cause deaths are more than double the expected number of deaths that would have occurred in a normal year. The extent of excess deaths in men is higher than in women, and the number of excess deaths increases with age. Indigenous populations had the highest level of excess deaths among all ethnic groups.\n\nConclusionsOverall, the exceptionally high level of excess deaths in Ecuador highlights the enormous burden and heterogeneous impact of COVID-19 on mortality especially in older age groups and indigenous populations in Ecuador that was not fully revealed by COVID-19 death counts. Together with the limited testing in Ecuador, our results suggest that the majority of the excess deaths were likely to be undocumented COVID-19 deaths.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Leticia Cu\u00e9llar", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Irene Torres", + "author_inst": "Fundacion Octaedro" + }, + { + "author_name": "Ethan Obie Romero-Severson", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Riya Mahesh", + "author_inst": "Los Alamos National Laboratory and University of Texas, Austin, Texas" + }, + { + "author_name": "Nathaniel R. Ortega", + "author_inst": "Los Alamos National Laboratory and University of California, Santa Barbara, CA" + }, + { + "author_name": "Sarah Pungitore", + "author_inst": "Los Alamos National Laboratory and University of Arizona, Tucson, AZ" + }, + { + "author_name": "Nicolas Hengartner", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ruian Ke", + "author_inst": "Los Alamos National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.26.21252547", "rel_title": "When thinking you are better leads to feeling worse: Self-other asymmetries in prosocial behavior and increased anxiety during the Covid-19 pandemic", @@ -914080,141 +916136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.24.21252335", - "rel_title": "The neurology and neuropsychiatry of COVID-19: a systematic review and meta-analysis of the early literature reveals frequent CNS manifestations and key emerging narratives", - "rel_date": "2021-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252335", - "rel_abs": "ObjectivesThere is accumulating evidence of the neurological and neuropsychiatric features of infection with SARS-CoV-2. In this systematic review and meta-analysis, we aimed to describe the characteristics of the early literature and estimate point prevalences for neurological and neuropsychiatric manifestations.\n\nMethodsWe searched MEDLINE, Embase, PsycInfo and CINAHL up to 18 July 2020 for randomised controlled trials, cohort studies, case-control studies, cross-sectional studies and case series. Studies reporting prevalences of neurological or neuropsychiatric symptoms were synthesised into meta-analyses to estimate pooled prevalence.\n\nResults13,292 records were screened by at least two authors to identify 215 included studies, of which there were 37 cohort studies, 15 case-control studies, 80 cross-sectional studies and 83 case series from 30 countries. 147 studies were included in the meta-analysis. The symptoms with the highest prevalence were anosmia (43.1% [35.2--51.3], n=15,975, 63 studies), weakness (40.0% [27.9--53.5], n=221, 3 studies), fatigue (37.8% [31.6--44.4], n=21,101, 67 studies), dysgeusia (37.2% [30.0--45.3], n=13,686, 52 studies), myalgia (25.1% [19.8--31.3], n=66.268, 76 studies), depression (23.0 % [11.8--40.2], n=43,128, 10 studies), headache (20.7% [95% CI 16.1--26.1], n=64,613, 84 studies), anxiety (15.9% [5.6--37.7], n=42,566, 9 studies) and altered mental status (8.2% [4.4--14.8], n=49,326, 19 studies). Heterogeneity for most clinical manifestations was high.\n\nConclusionsNeurological and neuropsychiatric symptoms of COVID-19 in the pandemics early phase are varied and common. The neurological and psychiatric academic communities should develop systems to facilitate high-quality methodologies, including more rapid examination of the longitudinal course of neuropsychiatric complications of newly emerging diseases and their relationship to neuroimaging and inflammatory biomarkers.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Jonathan P Rogers", - "author_inst": "Division of Psychiatry, University College London, London, UK. South London and Maudsley NHS Foundation Trust, London, UK." - }, - { - "author_name": "Cameron Watson", - "author_inst": "Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of Medicine. Barts Health NHS Trust." - }, - { - "author_name": "James Badenoch", - "author_inst": "Medical School, University of Birmingham" - }, - { - "author_name": "Benjamin Cross", - "author_inst": "East Lancashire Hospitals NHS Trust" - }, - { - "author_name": "Matthew Butler", - "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London" - }, - { - "author_name": "Jia Song", - "author_inst": "East London NHS Foundation Trust" - }, - { - "author_name": "Danish Hafeez", - "author_inst": "School of Medical Sciences, The University of Manchester, Manchester, UK" - }, - { - "author_name": "Hamilton Morrin", - "author_inst": "Maidstone & Tunbridge Wells NHS Trust, Kent, UK" - }, - { - "author_name": "Emma Rachel Rengasamy", - "author_inst": "Cwm Taf Morgannwg University Health Board" - }, - { - "author_name": "Lucretia Thomas", - "author_inst": "College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK." - }, - { - "author_name": "Silviya Ralovska", - "author_inst": "Department of Neurology, Psychiatry, Physiotherapy and Rehabilitation, Preventive Medicine, and Public Health, Sofia University \"St. Kliment Ohridski\"" - }, - { - "author_name": "Abigail Smakowski", - "author_inst": "Neuropsychiatry Outpatients & Persistent Physical Symptoms Research and Treatment Unit, Maudsley Hospital, South London and Maudsley Hospital NHS Trust, London," - }, - { - "author_name": "Ritika Dilip Sundaram", - "author_inst": "School of Medicine, University of Glasgow, UK" - }, - { - "author_name": "Camille Kaitlyn Hunt", - "author_inst": "MS & NMO Clinical Trials Group, Division of Neurology, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, B.C., Canada" - }, - { - "author_name": "Mao Fong Lim", - "author_inst": "Cambridge University Hospital NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK" - }, - { - "author_name": "Daruj Aniwattanapong", - "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK. Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangko" - }, - { - "author_name": "Vanshika Singh", - "author_inst": "Senior Sub-Editor and Staff Writer, The Wire Science" - }, - { - "author_name": "Zain Hussain", - "author_inst": "Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK" - }, - { - "author_name": "Stuti Chakraborty", - "author_inst": "Department of Physical Medicine and Rehabilitation, Christian Medical College and Hospital, Vellore, India" - }, - { - "author_name": "Ella Burchill", - "author_inst": "King's College London, Faculty of Medicine and Life Sciences, London SE1 1UL" - }, - { - "author_name": "Katrin Jansen", - "author_inst": "Department of Psychology, University of Munster, Germany" - }, - { - "author_name": "Heinz Holling", - "author_inst": "Department of Psychology, University of Munster, Germany" - }, - { - "author_name": "Dean Walton", - "author_inst": "Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK" - }, - { - "author_name": "Thomas A Pollak", - "author_inst": "Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK" - }, - { - "author_name": "Mark Ellul", - "author_inst": "Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emergi" - }, - { - "author_name": "Ivan Koychev", - "author_inst": "Department of Psychiatry, University of Oxford, Oxford, UK; Department of Psychological Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK" - }, - { - "author_name": "Tom Solomon", - "author_inst": "National Institute for Health Research Health Protection Research Unit on Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sc" - }, - { - "author_name": "Benedict Daniel Michael", - "author_inst": "Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emergi" - }, - { - "author_name": "Timothy R Nicholson", - "author_inst": "Section of Cognitive Neuropsychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK" - }, - { - "author_name": "Alasdair G Rooney", - "author_inst": "Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.02.24.21252135", "rel_title": "Risk factors for increased COVID-19 case-fatality in the United States: A county-level analysis during the first wave", @@ -914538,6 +916459,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2021.02.23.21252323", + "rel_title": "An empirical analysis of what people learned about COVID-19 through a web search and the impacts on misinformation and attitude towards public health safety guidelines.", + "rel_date": "2021-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252323", + "rel_abs": "Several people flocked to the Internet to learn about the SARS-CoV-2 and COVID-19 after the outbreak in Wuhan, China, in December 2019. As the novel coronavirus spread rapidly worldwide and was declared a global pandemic, the public rushed to Internet platforms to learn about the outbreak through Google search, online news outlets, and social media platforms. This paper evaluates the publics web search to learn about the pandemic and the possible impacts on attitude to the public health guidelines. The results highlight four outcomes: First, a significant global population learned about the ongoing pandemic through a web search. Second, there is a direct correlation between learning SARS-CoV-2, COVID-19, and SARS-CoV and searching information on public health measures (wearing a facial mask and social distancing). Third, learning conspiracy theories or misinformation correspond with a lack of interest in gaining knowledge about public health safety guidelines. Also, the initial high interest in learning about Influenza declined as people gained information about SARS-CoV-2 and COVID-19. The results highlight the critical need to promptly sensitize the public about global health concerns using both the Internet platforms and traditional sources, adopt effective health communication strategies, and build trust.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ikpe Justice Akpan", + "author_inst": "Kent State University" + }, + { + "author_name": "Obianuju Genevieve Aguolu", + "author_inst": "Yale School of Medicine, Yale University" + }, + { + "author_name": "Asuama A. Akpan", + "author_inst": "Ibom International Center for Research and Scholarship" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.02.23.21252314", "rel_title": "Sex differences in the mortality rate for coronavirus disease 2019 compared to other causes of death", @@ -916298,61 +918246,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.02.25.432853", - "rel_title": "Pyroptosis of syncytia formed by fusion of SARS-CoV-2 Spike and ACE2 expressing cells", - "rel_date": "2021-02-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.432853", - "rel_abs": "SARS-Cov-2 infected cells fused with the ACE2-positive neighboring cells forming syncytia. However, the effect of syncytia in disease development is largely unknown. We established an in vitro cell-cell fusion system and used it to mimic the fusion of SARS-CoV-2 infected cells with ACE2-expressing cells to form syncytia. We found that Caspase-9 was activated after syncytia formation, and Caspase-3/7 was activated downstream of Caspase-9, but it triggered GSDME-dependent pyroptosis rather than apoptosis. What is more, single cell RNA-sequencing data showed that both ACE2 and GSDME were expression in alveolar type 2 cells in human lung. We propose that pyroptosis is the fate of syncytia formed by SARS-CoV-2 infected host cells and ACE2-positive cells, which indicated that lytic death of syncytia may contribute to the excessive inflammatory responses in severe COVID-19 patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Huabin Ma", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Zhoujie Zhu", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Huaipeng Lin", - "author_inst": "Xiamen University" - }, - { - "author_name": "Shanshan Wang", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Peipei Zhang", - "author_inst": "Xiamen University" - }, - { - "author_name": "Yanguo Li", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Long Li", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Jinling Wang", - "author_inst": "Department of Emergency, Zhongshan Hospital of Xiamen University" - }, - { - "author_name": "Yufen Zhao", - "author_inst": "Institute of Drug Discovery Technology, Ningbo University" - }, - { - "author_name": "Jiahuai Han", - "author_inst": "Xiamen University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.02.25.432762", "rel_title": "The type 2 asthma mediator IL-13 inhibits SARS-CoV-2 infection of bronchial epithelium", @@ -916648,6 +918541,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.23.21251866", + "rel_title": "Genetic predisposition to psychiatric disorders and risk of COVID-19", + "rel_date": "2021-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21251866", + "rel_abs": "BackgroundPre-pandemic psychiatric disorders have been associated with an increased risk of COVID-19. However, the underlying mechanisms remain unknown, e.g. to what extent genetic predisposition to psychiatric disorders contributes to the observed association.\n\nMethodsThe analytic sample consisted of white British participants of UK Biobank registered in England, with available genetic data, and alive on Jan 31, 2020 (i.e., the start of the COVID-19 outbreak in the UK) (n=346,554). We assessed individuals genetic predisposition to different psychiatric disorders, including substance misuse, depression, anxiety, and psychotic disorder, using polygenic risk score (PRS). Diagnoses of psychiatric disorders were identified through the UK Biobank hospital inpatient data. We performed a GWAS analysis for each psychiatric disorder in a randomly selected half of the study population who were free of COVID-19 (i.e., the base dataset). For the other half (i.e., the target dataset), PRS was calculated for each psychiatric disorder using the discovered genetic variants from the base dataset. We then examined the association between PRS of each psychiatric disorder and risk of COVID-19, or severe COVID-19 (i.e., hospitalization and death), using logistic regression models. The ascertainment of COVID-19 was through the Public Health England dataset, the UK Biobank hospital inpatient data and death registers, updated until July 26, 2020. For validation, we repeated the PRS analyses based on publicly available GWAS summary statistics.\n\nResults155,988 participants (including 1,451 COVID-19 cases), with a mean age of 68.50 years at COVID-19 outbreak, were included for PRS analysis. Higher genetic liability forwards psychiatric disorders was associated with increased risk of both any COVID-19 and severe COVID-19, especially genetic risk for substance misuse and depression. The adjusted odds ratios (ORs) for any COVID-19 were 1.15 (95% confidence interval [CI] 1.02-1.31) and 1.26 (1.11-1.42) among individuals with a high genetic risk (above the upper tertile of PRS) for substance misuse and depression, respectively, compared with individuals with a low genetic risk (below the lower tertile). Largely similar ORs were noted for severe COVID-19 and similar albeit slightly lower estimates using PRSs generated from GWAS summary statistics from independent samples.\n\nConclusionIn the UK Biobank, genetic predisposition to psychiatric disorders was associated with an increased risk of COVID-19, including severe course of the disease. These findings suggest the potential role of genetic factors in the observed phenotypic association between psychiatric disorders and COVID-19, underscoring the need of increased medical surveillance of for this vulnerable population during the pandemic.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Wenwen Chen", + "author_inst": "Division of Nephrology, Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China" + }, + { + "author_name": "Yu Zeng", + "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China" + }, + { + "author_name": "Chen Suo", + "author_inst": "Department of Epidemiology & Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China" + }, + { + "author_name": "Huazhen Yang", + "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China" + }, + { + "author_name": "Yilong Chen", + "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China" + }, + { + "author_name": "Can Hou", + "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China" + }, + { + "author_name": "Yao Hu", + "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China" + }, + { + "author_name": "Zhiye Ying", + "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China" + }, + { + "author_name": "Yajing Sun", + "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China" + }, + { + "author_name": "Yuanyuan Qu", + "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China" + }, + { + "author_name": "Donghao Lu", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Fang Fang", + "author_inst": "Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden" + }, + { + "author_name": "Unnur A. Valdimarsd\u00f3ttir", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Huan Song", + "author_inst": "Sichuan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.22.21250768", "rel_title": "Detection and stability of SARS-CoV-2 fragments in wastewater: Impact of storage temperature", @@ -918016,41 +919980,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.24.432721", - "rel_title": "A missense variant effect prediction and annotation resource for SARS-CoV-2", - "rel_date": "2021-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.24.432721", - "rel_abs": "The COVID19 pandemic is a global crisis severely impacting many people across the world. An important part of the response is monitoring viral variants and determining the impact they have on viral properties, such as infectivity, disease severity and interactions with drugs and vaccines. In this work we generate and make available computational variant effect predictions for all possible single amino-acid substitutions to SARS-CoV-2 in order to complement and facilitate experiments and expert analysis. The resulting dataset contains predictions from evolutionary conservation and protein and complex structural models, combined with viral phosphosites, experimental results and variant frequencies. We demonstrate predictions effectiveness by comparing them with expectations from variant frequency and prior experiments. We then identify higher frequency variants with significant predicted effects as well as finding variants measured to impact antibody binding that are least likely to impact other viral functions. A web portal is available at sars.mutfunc.com, where the dataset can be searched and downloaded.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alistair Dunham", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK" - }, - { - "author_name": "Gwendolyn M Jang", - "author_inst": "Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA" - }, - { - "author_name": "Monita Muralidharan", - "author_inst": "Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA" - }, - { - "author_name": "Danielle Swaney", - "author_inst": "Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA" - }, - { - "author_name": "Pedro Beltrao", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.02.24.432656", "rel_title": "SARS-CoV-2 ORF6 disturbs nucleocytoplasmic trafficking to advance the viral replication", @@ -918470,6 +920399,25 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2021.02.19.21252062", + "rel_title": "International travel in times of the COVID-19 pandemic: Evidence from German school breaks", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252062", + "rel_abs": "The COVID-19 pandemic has triggered severe global restrictions on international travel with the intention of limiting the spread of SARS-CoV-2 across countries. This paper studies the effects of the partial relaxation of these travel restrictions in Europe during the summer months of 2020. It exploits the staggered start of the summer school breaks across German states as an exogenous shock to the travel opportunities of the population. While the school breaks also increased mobility within Germany, the event study regressions include disaggregated and time-varying controls for domestic mobility and local COVID-19-related restrictions. The resulting intention-to-treat effects of the relaxed travel restrictions show a significant and sizable increase of the COVID-19 incidence in German counties during the later weeks of the school breaks.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Andreas Backhaus", + "author_inst": "Federal Institute for Population Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.29.21250743", "rel_title": "Reproduction as a Means of Evaluating Policy Models: A Case Study of a COVID-19 Simulation", @@ -919994,93 +921942,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.22.21252237", - "rel_title": "Group IIA Secreted Phospholipase A2 Plays a Central Role in the Pathobiology of COVID-19", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252237", - "rel_abs": "There is an urgent need to identify cellular and molecular mechanisms responsible for severe COVID-19 disease accompanied by multiple organ failure and high mortality rates. Here, we performed untargeted/targeted lipidomics and focused biochemistry on 127 patient plasma samples, and showed high levels of circulating, enzymatically active secreted phospholipase A2 Group IIA (sPLA2-IIA) in severe and fatal COVID-19 disease compared with uninfected patients or mild illness. Machine learning demonstrated that sPLA2-IIA effectively stratifies severe from fatal COVID-19 disease. We further introduce a PLA-BUN index that combines sPLA2-IIA and blood urea nitrogen (BUN) threshold levels as a critical risk factor for mitochondrial dysfunction, sustained inflammatory injury and lethal COVID-19. With the availability of clinically tested inhibitors of sPLA2-IIA, our study opens the door to a precision intervention using indices discovered here to reduce COVID-19 mortality.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Justin M Snider", - "author_inst": "University of Arizona" - }, - { - "author_name": "Jeehyun Karen You", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Xia Wang", - "author_inst": "University of Arizona" - }, - { - "author_name": "Ashley J Snider", - "author_inst": "University of Arizona" - }, - { - "author_name": "Brian Hallmark", - "author_inst": "University of Arizona" - }, - { - "author_name": "Michael C Seeds", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Susan Sergeant", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Laurel Johnstone", - "author_inst": "University of Arizona" - }, - { - "author_name": "Qiuming Wang", - "author_inst": "University of Arizona" - }, - { - "author_name": "Ryan Sprissler", - "author_inst": "University of Arizona" - }, - { - "author_name": "Hao Helen Zhang", - "author_inst": "University of Arizona" - }, - { - "author_name": "Chiara Luberto", - "author_inst": "Stony Brook University, Stony Brook Cancer Center" - }, - { - "author_name": "Richard R Kew", - "author_inst": "Stony Brook Cancer Center, Stony Brook University, Veteran Affairs Medical Center" - }, - { - "author_name": "Yusuf A Hannun", - "author_inst": "Stony Brook Cancer Center, Stony Brook University, Veteran Affairs Medical Center - Northport" - }, - { - "author_name": "Charles E McCall", - "author_inst": "Wake Forest Medical School" - }, - { - "author_name": "Guang Yao", - "author_inst": "University of Arizona, Arizona Cancer Center" - }, - { - "author_name": "Maurizio Del Poeta", - "author_inst": "Stony Brook University, Veteran Affairs Medical Center -Northport" - }, - { - "author_name": "Floyd H Chilton", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.22.21251534", "rel_title": "The spatio-temporal distribution of COVID-19 infection in England between January and June 2020.", @@ -920324,6 +922185,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.18.21251422", + "rel_title": "Smelling Household-Odorants Effectively Screens for COVID-19", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251422", + "rel_abs": "Key to curtailing the COVID-19 pandemic are wide-scale testing strategies1,2. An ideal test is one that would not rely on transporting, distributing, and collecting physical specimens. Given the olfactory impairment associated with COVID-193-7, we developed a novel measure of olfactory perception that relies on smelling household odorants and rating them online. We tested the performance of this real-time tool in 12,020 participants from 134 countries who provided 171,500 perceptual ratings of 60 different household odorants. We observed that olfactory ratings were indicative of COVID-19 status in a country, significantly correlating with national infection rates over time. More importantly, we observed remarkable indicative power at the individual level (90% sensitivity and 80% specificity). Critically, olfactory testing remained highly effective in participants with COVID-19 but without symptoms, and in participants with symptoms but without COVID-19. In this, the current odorant-based olfactory test stands apart from symptom-checkers (including olfactory symptom-checkers)3, and even from antigen tests8, to potentially provide a first line of screening that can help halt disease progression at the population level.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "kobi snitz", + "author_inst": "weizmann institute of science" + }, + { + "author_name": "Danielle Honigstein", + "author_inst": "Weizmann institue of science" + }, + { + "author_name": "Reut Weisgross", + "author_inst": "Weizmann institute of science" + }, + { + "author_name": "Aharon Ravia", + "author_inst": "Weizmann institute of science" + }, + { + "author_name": "Eva Mishor", + "author_inst": "Weizmann institute of science" + }, + { + "author_name": "Ofer Perl", + "author_inst": "Weizmann institute of science" + }, + { + "author_name": "Shiri Karagach", + "author_inst": "Weizmann institute of science" + }, + { + "author_name": "Abebe Medhanie", + "author_inst": "Weizmann institute of science" + }, + { + "author_name": "Nir Harel", + "author_inst": "Bezalel Academy of Fine Arts and Design, Department of Fine Arts" + }, + { + "author_name": "Sagit Shushan", + "author_inst": "Weizmann institute of science" + }, + { + "author_name": "Yehudah Roth", + "author_inst": "Edith Wolfson Medical Center, Department of ENT," + }, + { + "author_name": "Behzad Iravani", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Artin Arshamian", + "author_inst": "Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden. Department of Psychology, Stockholm University," + }, + { + "author_name": "Gernot Ernst", + "author_inst": "Psychological institute, Oslo university" + }, + { + "author_name": "Masako Okamoto", + "author_inst": "Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo" + }, + { + "author_name": "Zachary Mainen", + "author_inst": "Champalimaud Research, Champalimaud Centre for the Unknown" + }, + { + "author_name": "Cindy Poo", + "author_inst": "Champalimaud Research, Champalimaud Centre for the Unknown" + }, + { + "author_name": "Niccolo Bonacchi", + "author_inst": "Champalimaud Research, Champalimaud Centre for the Unknown" + }, + { + "author_name": "Erminio Monteleone", + "author_inst": "Department of Agriculture, Food, Environment and Forestry, University of Florence" + }, + { + "author_name": "Caterina Dinnella", + "author_inst": "Department of Agriculture, Food, Environment and Forestry, University of Florence" + }, + { + "author_name": "Sara Spinelli", + "author_inst": "Department of Agriculture, Food, Environment and Forestry, University of Florence" + }, + { + "author_name": "Franklin Marino-Sanchez", + "author_inst": "Rhinology and Skull Base Surgery Unit. Otorhinolaryngology Department. Ramon y Cajal University Hospital" + }, + { + "author_name": "Camille Ferdenzi", + "author_inst": "Lyon Neuroscience Research Center, CNRS - INSERM - University Claude Bernard of Lyon" + }, + { + "author_name": "Monique Smeets", + "author_inst": "Faculty of Social and Behavioral Sciences, Utrecht University" + }, + { + "author_name": "Kazushige Touhara", + "author_inst": "Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo" + }, + { + "author_name": "Moustafa Bensafi", + "author_inst": "Lyon Neuroscience Research Center, CNRS - INSERM - University Claude Bernard of Lyon" + }, + { + "author_name": "Thomas Hummel", + "author_inst": "Smell and Taste Clinic, Department of Otorhinolaryngology, TU Dresden" + }, + { + "author_name": "Johan N Lundstrom", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Noam Sobel", + "author_inst": "Weizmann institute of science" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.18.21251973", "rel_title": "REACT-1 round 9 interim report: downward trend of SARS-CoV-2 in England inFebruary 2021 but still at high prevalence", @@ -922028,57 +924020,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.22.21252190", - "rel_title": "A cross-sectional study of socioeconomic status and treatment interruption among Japanese workers during the COVID-19 pandemic", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252190", - "rel_abs": "BackgroundThe COVID-19 pandemic has caused interruptions to chronic disease and non-emergency treatment. The purpose of this study is to examine which socioeconomic status groups are most at risk of treatment interruption.\n\nMethodsThis cross-sectional internet monitor study was conducted on December 22-26, 2020, when Japan experienced its third wave of COVID-19 infection. Out of a total of 33,302 participants in the survey, 9510 (5392 males and 4118 females) who responded that they required regular treatment or hospital visits were included in the analysis. A multilevel logistic model nested in the prefecture of residence was used to estimate the odds ratio (OR) for treatment disruption. We examined separate multivariate models for socioeconomic factors, health factors, and lifestyle factors.\n\nResultsDuring a period of rapid COVID-19 infection, about 11% of Japanese workers who required regular treatment experienced interruptions to their treatment. The OR of treatment interruption associated with not being married compared to being married was 1.44; manual labor work compared to desk work was 1.30; loss of employment when the COVID-19 pandemic started and continued unemployment compared to being employed over the entire pandemic period was 1.62 and 2.57, respectively; and feeling financially unstable was 2.92.\n\nConclusionTreatment interruption is a new health inequality brought about by COVID-19 with possible medium- and long-term effects, including excess mortality, morbidity, and productivity loss due to increased presenteeism. Efforts are needed to reduce treatment interruptions among workers who require regular treatment.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kenji Fujimoto", - "author_inst": "Occupational Health Data Science Center, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohiro Ishimaru", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hisashi Eguchi", - "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.02.22.21252207", "rel_title": "Critical COVID-19 represents an endothelial disease with high similarity to kidney disease on the molecular level", @@ -922350,6 +924291,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.23.432424", + "rel_title": "Structural and functional characterization of SARS-CoV-2 RBD domains produced in mammalian cells", + "rel_date": "2021-02-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.23.432424", + "rel_abs": "As the SARS-CoV-2 pandemic is still ongoing and dramatically influences our life, the need for recombinant proteins for diagnostics, vaccine development, and research is very high. The spike (S) protein, and particularly its receptor binding domain (RBD), mediates the interaction with the ACE2 receptor on host cells and may be modulated by its structural features. Therefore, well characterized recombinant RBDs are essential. We have performed an in-depth structural and functional characterization of RBDs expressed in Chinese hamster ovary (CHO) and human embryonic kidney (HEK293) cells. To structurally characterize the native RBDs (comprising N- and O-glycans and additional posttranslational modifications) a multilevel mass spectrometric approach was employed. Released glycan and glycopeptide analysis were integrated with intact mass analysis, glycan-enzymatic dissection and top-down sequencing for comprehensive annotation of RBD proteoforms. The data showed distinct glycosylation for CHO- and HEK293-RBD with the latter exhibiting antenna fucosylation, higher level of sialylation and a combination of core 1 and core 2 type O-glycans. Additionally, from both putative O-glycosylation sites, we could confirm that O-glycosylation was exclusively present at T323, which was previously unknown. For both RBDs, the binding to SARS-CoV-2 antibodies of positive patients and affinity to ACE2 receptor was addressed showing comparable results. This work not only offers insights into RBD structural and functional features but also provides a workflow for characterization of new RBDs and batch-to-batch comparison.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Christoph Gstoettner", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Tao Zhang", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Anja Resemann", + "author_inst": "Bruker Daltonik GmbH" + }, + { + "author_name": "Sophia Ruben", + "author_inst": "InVivo BioTech Services GmbH" + }, + { + "author_name": "Stuart Pengelley", + "author_inst": "Bruker Daltonik GmbH" + }, + { + "author_name": "Detlev Suckau", + "author_inst": "Bruker Daltonics GmbH" + }, + { + "author_name": "Tim Welsink", + "author_inst": "InVivo BioTech Services GmbH" + }, + { + "author_name": "Manfred Wuhrer", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Elena Dominguez-Vega", + "author_inst": "Leiden University Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.02.19.21251841", "rel_title": "SARS-Cov-2 testing in the United Arab Emirates: Population Attitudes and Beliefs.", @@ -923726,37 +925718,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.18.21250271", - "rel_title": "Effectiveness of Non-Pharmaceutical Interventions on Child and Staff COVID-19 Cases in US Summer Camps", - "rel_date": "2021-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21250271", - "rel_abs": "BackgroundMost camps remained closed during Summer 2020, due to concerns regarding child transmission of SARS-CoV-2 and limited information about the effectiveness of non-pharmaceutical interventions (NPIs) within child congregate settings.\n\nMethodsWe surveyed US camps about on-site operations, camper and staff demographics, COVID-19 cases amongst campers and staff, and NPI usage as related to pre-camp quarantines, facial coverings, physical distancing, cleaning, and facility modifications. For all NPIs, save quarantines, responses were provided on a 5-point Likert scale format.\n\nResultsWithin 486 on-site camps, a range of NPIs were instituted, most often related to reduced camper interactions, staff face coverings, cleaning, and hand hygiene. Camper facial coverings were less common, with campers always wearing masks at [~]34% of the camps. Approximately 15% of camps reported 1+ confirmed COVID-19 case in either campers or staff, with three camps reporting a COVID outbreak. In both single and multi-NPI analyses, the risk of COVID-19 cases was lowest when campers always wore facial coverings. While less effective, constant use of staff facial coverings and targeted physical distancing measures, but not pre-camp quarantine, also reduced COVID-19 risks.\n\nConclusionsWe found constant facial coverings, especially for campers, and targeted physical distancing measures to reduce risks of SARS-CoV-2 transmission within summer camps. Our findings provide valuable guidance for future operations of camp and other child congregate settings with regard to efficient and effective NPI usage to mitigate SARS-CoV-2 infection.\n\nWhats Known on This SubjectApproximately 82% of US overnight camps did not open during Summer 2020 due to concerns regarding childrens ability to transmit SARS-CoV-2. Camps that did operate during this time instituted varied non-pharmaceutical interventions (NPIs) to reduce SARS-CoV-2 transmission, with little information available on the effectiveness of these NPIs within child congregate settings. Large population-based studies are needed to improve our understanding of the extent of SARS-CoV-2 infection amongst children and their caregivers and to determine whether and to what degree child congregate programs can safely open during the pandemic.\n\nWhat This Study AddsOur study, the largest survey of COVID-19 cases in child congregate settings at the national level, provides new information on the relative effectiveness of NPIs on mitigating COVID cases among children and staff within camp settings. We showed COVID-19 case rates in campers and staff to be low relative to corresponding case rates in the US and found constant camper facial coverings to be the most effective risk reduction method for SARS-CoV-2 transmission within camps. While less effective, constant use of staff facial coverings and targeted physical distancing measures, but not pre-camp quarantines, were also shown to reduce COVID-19 risks. Our findings has important implications for child congregate settings, helping to guide their successful opening and operation.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Helen H Suh", - "author_inst": "Tufts University" - }, - { - "author_name": "Laura Blaisdell", - "author_inst": "Department of Pediatrics, Maine Medical Center, Portland, ME & Camp Winnebago, Fayette, ME" - }, - { - "author_name": "Julianne Meehan", - "author_inst": "Environmental Health & Engineering, Inc." - }, - { - "author_name": "Laurie Browne", - "author_inst": "American Camp Association" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.20.432081", "rel_title": "Nanoceutical Fabric Prevents COVID-19 Spread through Expelled Respiratory Droplets: A Combined Computational, Spectroscopic and Anti-microbial Study", @@ -924028,6 +925989,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.21.432184", + "rel_title": "High-Throughput, Single-Copy Sequencing Reveals SARS-CoV-2 Spike Variants Coincident with Mounting Humoral Immunity during Acute COVID-19", + "rel_date": "2021-02-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.21.432184", + "rel_abs": "Tracking evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within infected individuals will help elucidate coronavirus disease 2019 (COVID-19) pathogenesis and inform use of antiviral interventions. In this study, we developed an approach for sequencing the region encoding the SARS-CoV-2 virion surface proteins from large numbers of individual virus RNA genomes per sample. We applied this approach to the WA-1 reference clinical isolate of SARS-CoV-2 passaged in vitro and to upper respiratory samples from 7 study participants with COVID-19. SARS-CoV-2 genomes from cell culture were diverse, including 18 haplotypes with non-synonymous mutations clustered in the spike NH2-terminal domain (NTD) and furin cleavage site regions. By contrast, cross-sectional analysis of samples from participants with COVID-19 showed fewer virus variants, without structural clustering of mutations. However, longitudinal analysis in one individual revealed 4 virus haplotypes bearing 3 independent mutations in a spike NTD epitope targeted by autologous antibodies. These mutations arose coincident with a 6.2-fold rise in serum binding to spike and a transient increase in virus burden. We conclude that SARS-CoV-2 exhibits a capacity for rapid genetic adaptation that becomes detectable in vivo with the onset of humoral immunity, with the potential to contribute to delayed virologic clearance in the acute setting.\n\nAuthor SummaryMutant sequences of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) arising during any individual case of coronavirus disease 2019 (COVID-19) could theoretically enable the virus to evade immune responses or antiviral therapies that target the predominant infecting virus sequence. However, commonly used sequencing technologies are not optimally designed to detect variant virus sequences within each sample. To address this issue, we developed novel technology for sequencing large numbers of individual SARS-CoV-2 genomic RNA molecules across the region encoding the virus surface proteins. This technology revealed extensive genetic diversity in cultured viruses from a clinical isolate of SARS-CoV-2, but lower diversity in samples from 7 individuals with COVID-19. Importantly, concurrent analysis of paired serum samples in selected individuals revealed relatively low levels of antibody binding to the SARS-CoV-2 spike protein at the time of initial sequencing. With increased serum binding to spike protein, we detected multiple SARS-CoV-2 variants bearing independent mutations in a single epitope, as well as a transient increase in virus burden. These findings suggest that SARS-CoV-2 replication creates sufficient virus genetic diversity to allow immune-mediated selection of variants within the time frame of acute COVID-19. Large-scale studies of SARS-CoV-2 variation and specific immune responses will help define the contributions of intra-individual SARS-CoV-2 evolution to COVID-19 clinical outcomes and antiviral drug susceptibility.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Sung Hee Ko", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Elham Bayat Mokhtari", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Prakriti Mudvari", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Sydney Stein", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Christopher D Stringham", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Danielle Wagner", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Sabrina Ramelli", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Marcos J Ramirez-Benitez", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Jeffrey R Strich", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Richard T Davey Jr.", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Tongqing Zhou", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "John Misasi", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Peter D Kwong", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Daniel S Chertow", + "author_inst": "National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Nancy J Sullivan", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH USA" + }, + { + "author_name": "Eli A Boritz", + "author_inst": "Vaccine Research Center" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.22.432189", "rel_title": "Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants", @@ -925276,37 +927316,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.02.18.21251776", - "rel_title": "Rapid increase of SARS-CoV-2 seroprevalence during the 2020 pandemic year in the population of the city of Tirana, Albania", - "rel_date": "2021-02-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251776", - "rel_abs": "IntroductionWhile the identification of anti SARS-CoV-2 antibodies has been used to measure the hidden circulation of the COVID-19 in communities, there are few publications on the dynamics of SARS-CoV-2 seroprevalence during both waves of 2020. This study provides original data about the change in proportion of individuals showing immune response to COVID-19 between beginning of July and end of December 2020.\n\nMethodsThe study was conducted in two rounds, 27 June -3 July, and 21-28 December 2020, using two independently selected samples of individuals 20-70 years old. Study participants were randomly selected from lists of the inhabitants of the catchment communities of four primary health care centers in Tirana City. Serological testing was performed by an ELISA method which determines IgG class antibodies anti S1 protein of SARS-CoV-2 virus. The validity of the method was tested in a sample of blood donors sera of 2018.\n\nResultsThe proportion of individuals classified as seropositive during the first round, in early July was 7.5% (95% CI: 4.3% -10.7%). The proportion rose sharply in the second round, by late December 2020, reaching 48.2% (95% CI: 44.8% -51.7%). The same increasing pattern was observed in all studied categories. No statistical significance was found between men and women and between age categories. The prevalence of seropositive individuals was always significantly higher among those who reported symptoms and those who had done the molecular test.\n\nConclusionThe ratio of total infected cases over confirmed cases was estimated to be higher than 10 to 1 in Albania. The rapid increase in SARS-CoV-2 seroprevalence observed in Tirana City may have been facilitated by a number of factors, including the very low infection exposure during the period March -May 2020, and the consecutive high susceptibility in population. Despite the observed high seroprevalence, one month after the study, COVID-19 incidence continued to increase in Tirana.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Genc Sulcebe", - "author_inst": "1. Laboratory of Immunology, University of Medicine and University Hospital Center of Tirana; 2. Academy of Sciences of Albania" - }, - { - "author_name": "Alban Ylli", - "author_inst": "Institute of Public Health, Tirana, Albania; Tirana Univeresity of Medicine" - }, - { - "author_name": "Fabian Cenko", - "author_inst": "Catholic University \"Our Lady of Good Counsel\", Tirana, Albania" - }, - { - "author_name": "Margarita Kurti-Prifti", - "author_inst": "Laboratory of Immunology, University of Medicine and University Hospital Center of Tirana" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.18.21251793", "rel_title": "Accessible LAMP-Enabled Rapid Test (ALERT) for detecting SARS-CoV-2", @@ -925602,6 +927611,61 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.02.18.431919", + "rel_title": "Adequate knowledge of COVID-19 impacts good practices amongst health profession students in the Philippines", + "rel_date": "2021-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.18.431919", + "rel_abs": "BackgroundThe spread of the coronavirus disease 2019 (COVID-19) in the Philippines started with its first suspected case on January 22, 2020. The government reacted by imposing several measures including community quarantine, class suspensions, drug therapy and vaccine development, and travel restrictions. This online survey was done amongst Filipino health professions undergraduate students to uncover the relationship between their knowledge, attitude, and practice during this pandemic.\n\nMethodsCross-sectional data were obtained from an online survey done on students of medicine, dentistry, optometry, rehabilitative sciences, and pharmacy.\n\nResultsAt a response rate of 100% (n=1257), the results show that healthcare profession students in the Philippines have good knowledge (87.6%) and practices (63.6%) regarding COVID-19, yet attitude (63.6%) was just passable. This study also shows that a strong correlation exists between knowledge and practice concerning the current pandemic, r(2) = 0.08, P = 0.004.\n\nConclusionAdequate knowledge of COVID-19 impacts good practices of avoiding crowded places and misuse of steam inhalation amongst health profession students in the Philippines. Knowledge and practice pertaining to the current pandemic have been found to be good, but attitude remains low.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Junhel Dalanon", + "author_inst": "Southwestern University PHINMA" + }, + { + "author_name": "Rhomeljustein Redoble", + "author_inst": "Southwestern University PHINMA" + }, + { + "author_name": "Jo-Ann Belotindos", + "author_inst": "Southwestern University PHINMA" + }, + { + "author_name": "Cand Delos Reyes", + "author_inst": "Southwestern University PHINMA" + }, + { + "author_name": "Jaime Fabillar Jr.", + "author_inst": "Southwestern University PHINMA" + }, + { + "author_name": "Ma. Shiril Armero", + "author_inst": "Southwestern University PHINMA" + }, + { + "author_name": "Rozzano Locsin", + "author_inst": "Tokushima University Graduate School of Biomedical Sciences" + }, + { + "author_name": "Yoshitaka Suzuki", + "author_inst": "Tokushima University Graduate School of Biomedical Sciences" + }, + { + "author_name": "Kazuo Okura", + "author_inst": "Tokushima University Graduate School of Biomedical Sciences" + }, + { + "author_name": "Yoshizo Matsuka", + "author_inst": "Tokushima University Graduate School of Biomedical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.02.11.21251285", "rel_title": "A New Hematological Prognostic Index For Covid-19 Severity", @@ -926806,45 +928870,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.15.21251765", - "rel_title": "When efficacy and adherence conflict: preferences and patterns of response to public health advice during the COVID-19 pandemic", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251765", - "rel_abs": "With recurring waves of the Covid-19 pandemic, a dilemma facing public health leadership is whether to provide public advice that is medically optimal (e.g., most protective against infection if followed), but unlikely to be adhered to, or advice that is less protective but is more likely to be followed. To provide insight about this dilemma, we examined and quantified public perceptions about the tradeoff between (a) the stand-alone value of health behavior advice, and (b) the advices adherence likelihood. In a series of studies about preference for public health leadership advice, we asked 1,061 participants to choose between (1) strict advice that is medically optimal if adhered to but which is less likely to be broadly followed, and (2) relaxed advice, which is less medically effective but more likely to gain adherence - given varying infection expectancies. Participants preference was consistent with risk aversion. Offering an informed choice alternative that shifts volition to advice recipients only strengthened risk aversion, but also demonstrated that informed choice was preferred as much or more than the risk-averse strict advice.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Oded Nov", - "author_inst": "New York University Tandon School of Engineering" - }, - { - "author_name": "Graham Dove", - "author_inst": "New York University Tandon School of Engineering" - }, - { - "author_name": "Martina Balestra", - "author_inst": "New York University Tandon School of Engineering" - }, - { - "author_name": "Katharine Lawrence", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Devin Mann", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Batia Wiesenfeld", - "author_inst": "New York University Stern School of Business" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.16.21251676", "rel_title": "Incidence and Outcomes of Pulmonary embolism among hospitalized COVID-19 patients", @@ -927040,6 +929065,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.16.21251805", + "rel_title": "The detection of SARS-CoV-2 in autolysed samples from an exhumed decomposed body: Implications to virus survival, genome stability, and spatial distribution in tissues", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251805", + "rel_abs": "Here we report for the first time the SARS-CoV-2 detection in autolysed samples from an exhumed decomposed body post-thirty six days after death. Both naso-oropharyngeal swabs and visceral samples from the lung, intestine, liver, and kidney were collected from the body exhumed post-fifteen days after burial, stored in viral transport medium and in saturated salt solution respectively. Naso-oropharyngeal swabs showed the presence of the SARS-CoV-2 genome as identified by the amplification of viral E, N, RdRP, or ORF1ab genes by RT-PCR. Subsequent examination of tissues reveal the detection of the virus genome in the intestine and liver, while no detection in the kidney and lung. These results signify the genome stability and implicate the virus survival in decomposed swab samples and in tissues and thereafter in storage solution. Further results also indicate spatial distribution of the virus in tissues during the early stage of infection in the subject with no respiratory distress. Considering the presence of cool, humid, and moist location of the exhumation, the presence of virus genome might also indicate that SARS-CoV-2 can persist for more than seven days on the surface of dead bodies similar to the Ebola virus, confirming that transmission from deceased subjects is possible for an extended period after death. These results further reaffirm the robustness of the RT-PCR aiding in the detection of viruses or their genome in decomposed samples when other methods of detection could not be useful.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mahadeshwara Prasad", + "author_inst": "Senior Specialist, Department of Forensic Medicine, District Hospital, Metagalli, Mysuru- 570016." + }, + { + "author_name": "Somanna Ajjamada Nachappa", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre, CSIR-Central Food Technological Research Institute" + }, + { + "author_name": "Niveditha Anand", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre, CSIR-Central Food Technological Research Institute" + }, + { + "author_name": "Deepika Udayawara Rudresh", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre, CSIR-Central Food Technological Research Institute" + }, + { + "author_name": "Yashika Singh", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre, CSIR-Central Food Technological Research Institute." + }, + { + "author_name": "Surabhi P. Gangani", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre, CSIR-Central Food Technological Research Institute" + }, + { + "author_name": "Forum K. Bhansali", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre, CSIR-Central Food Technological Research Institute" + }, + { + "author_name": "Basista Rabina Sharma", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre, CSIR-Central Food Technological Research Institute" + }, + { + "author_name": "Deep Nithun Senathipathi", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre, CSIR-Central Food Technological Research Institute" + }, + { + "author_name": "Shashidhar H. Byrappa", + "author_inst": "Department of Pathology, Mysore Medical College & Research Institute (MMC&RI), Irvin Road, 570001" + }, + { + "author_name": "Prakash M. Halami", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre, CSIR-Central Food Technological Research Institute" + }, + { + "author_name": "Ravindra P Veeranna", + "author_inst": "CSIR-CFTRI COVID-19 Testing Centre. CSIR-Central Food Technological Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.16.21251653", "rel_title": "IMMUNO-COV\u2122 v2.0: Development and Validation of a High-Throughput Clinical Assay for Measuring SARS-CoV-2-Neutralizing Antibody Titers", @@ -928560,33 +930648,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.02.18.21251981", - "rel_title": "Assessing Age-Specific Vaccination Strategies and Post-Vaccination Reopening Policies for COVID-19 Control Using SEIR Modeling Approach", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251981", - "rel_abs": "BackgroundAs the availability of COVID-19 vaccines, it is badly needed to develop vaccination guidelines to prioritize the vaccination delivery in order to effectively stop COVID-19 epidemic and minimize the loss.\n\nMethodsWe evaluated the effect of age-specific vaccination strategies on the number of infections and deaths using an SEIR model, considering the age structure and social contact patterns for different age groups for each of different countries.\n\nResultsIn general, the vaccination priority should be given to those younger people who are active in social contacts to minimize the number of infections; while the vaccination priority should be given to the elderly to minimize the number of deaths. But this principle may not always apply when the interaction of age structure and age-specific social contact patterns is complicated. Partially reopening schools, workplaces or households, the vaccination priority may need to be adjusted accordingly.\n\nConclusionsPrematurely reopening social contacts could initiate a new outbreak or even a new pandemic out of control if the vaccination rate and the detection rate are not high enough. Our result suggests that it requires at least nine months of vaccination before fully reopening social contacts in order to avoid a new pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Xia Wang", - "author_inst": "Shaanxi Normal University" - }, - { - "author_name": "Hulin Wu", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Sanyi Tang Sr.", - "author_inst": "Shaanxi Normal University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.17.21251725", "rel_title": "Assessment of knowledge, attitude and practices among Accredited Social Health Activists (ASHAs) towards COVID-19: a descriptive cross-sectional study in Tripura, India", @@ -928758,6 +930819,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.17.21251946", + "rel_title": "Estimating the Failure Risk of Hotel-based Quarantine for Preventing COVID-19 Outbreaks in Australia and New Zealand", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251946", + "rel_abs": "ObjectivesTo identify COVID-19 outbreaks and border control failures associated with quarantine systems in Australia and New Zealand and to estimate the failure risks.\n\nDesign, setting, participantsObservational epidemiological study of travellers transiting quarantine in Australia and New Zealand up to 15 June 2021.\n\nMain outcome measuresThe incidence of COVID-19 related failures arising from quarantine, and the failure risk for those transiting quarantine, estimated both per 100,000 travellers and per 1000 SARS-CoV-2 positive cases.\n\nResultsAustralia and New Zealand had 32 COVID-19 related failures arising from quarantine systems up to 15 June 2021 (22 and 10, respectively). One resultant outbreak involved an estimated 800 deaths and quarantine failures instigated nine lockdowns. The failure risk for those transiting quarantine was estimated at 5.0 failures per 100,000 travellers and 6.1 failures (95%CI: 4.0 to 8.3) per 1000 SARS-CoV-2 positive cases. The latter risk was two-fold higher in New Zealand compared with Australia. The full vaccination of frontline border workers could likely have prevented a number of quarantine system failures.\n\nConclusionsQuarantine system failures can be costly in terms of lives and economic impacts such as lockdowns. Ongoing improvements or alternatives to hotel-based quarantine are required.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Leah M Grout", + "author_inst": "University of Otago Wellington" + }, + { + "author_name": "Ameera Katar", + "author_inst": "Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia" + }, + { + "author_name": "Driss Ait Ouakrim", + "author_inst": "Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia" + }, + { + "author_name": "Jennifer A Summers", + "author_inst": "Department of Public Health, University of Otago Wellington, New Zealand" + }, + { + "author_name": "Amanda Kvalsvig", + "author_inst": "Department of Public Health, University of Otago Wellington, New Zealand" + }, + { + "author_name": "Michael G Baker", + "author_inst": "Department of Public Health, University of Otago Wellington, New Zealand" + }, + { + "author_name": "Tony Blakely", + "author_inst": "Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia" + }, + { + "author_name": "Nick Wilson", + "author_inst": "Department of Public Health, University of Otago Wellington, New Zealand" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.17.21251907", "rel_title": "Clinical validation of the quantitative Siemens SARS-CoV-2 spike IgG assay (sCOVG) reveals improved sensitivity and a good correlation with virus neutralization titers", @@ -930306,113 +932414,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.15.21251753", - "rel_title": "Severe SARS-CoV-2 infection induces a distinct nasal cytokine profile", - "rel_date": "2021-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251753", - "rel_abs": "Although the COVID-19 pandemic has left no country untouched there has been limited research to understand clinical and immunological responses in African populations. Here we comprehensively characterise patients hospitalised with suspected or confirmed COVID-19, and healthy community controls. PCR-confirmed COVID-19 participants were more likely to receive dexamethasone and a beta-lactam antibiotic, and survive to hospital discharge than PCR-/IgG+ and PCR-/IgG-participants. PCR-/IgG+ participants exhibited a nasal and systemic cytokine signature analogous to PCR-confirmed COVID-19 participants, but increased propensity for Staphylococcus aureus and Streptococcus pneumoniae colonisation. We did not find evidence that HIV co-infection in COVID-19 participants was associated with mortality or altered cytokine responses. The nasal immune signature in PCR-/IgG+ and PCR-confirmed COVID-19 participants was distinct and predominated by chemokines and neutrophils. In addition, PCR-/IgG+ individuals with high COVID-19 clinical suspicion had inflammatory profiles analogous to PCR-confirmed disease and potentially represent a target population for COVID-19 treatment strategies.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Ben Morton", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Kayla Barnes", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, USA" - }, - { - "author_name": "Catherine Anscombe", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Khuzwayo Jere", - "author_inst": "University of Liverpool, Liverpool, United Kingdom" - }, - { - "author_name": "Comfort Brown", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "James Nyirenda", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Tamara Phiri", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Ndaziona Peter Banda", - "author_inst": "University of Malawi-College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Charlotte Van der veer", - "author_inst": "University of Liverpool, Liverpool, United Kingdom" - }, - { - "author_name": "Kwazizira Samson Mndolo", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Kelvin Mponda", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Jamie Rylance", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Chimota Phiri", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Jane Mallewa", - "author_inst": "University of Malawi-College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Mulinda Nyirenda", - "author_inst": "University of Malawi-College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Grace Katha", - "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi" - }, - { - "author_name": "Paul Kambiya", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "James Jafali", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Henry Mwandumba", - "author_inst": "Liverpool School of Tropical Medicine, Liverpool, United Kingdom" - }, - { - "author_name": "Stephen Gordon", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi" - }, - { - "author_name": "Jenifer Cornick", - "author_inst": "University of Liverpool, Liverpool, United Kingdom" - }, - { - "author_name": "Kondwani Charles Jambo", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Programme" - }, - { - "author_name": "- Blantyre COVID-19 consortium", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.02.15.21251586", "rel_title": "Epidemiology of COVID-19 infection amongst workers in Primary Healthcare in Qatar", @@ -930648,6 +932649,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.18.431835", + "rel_title": "Rotavirus as an Expression Platform of the SARS-CoV-2 Spike Protein", + "rel_date": "2021-02-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.18.431835", + "rel_abs": "Rotavirus, a segmented double-stranded RNA virus, is a major cause of acute gastroenteritis in young children. The introduction of live oral rotavirus vaccines has reduced the incidence of rotavirus disease in many countries. To explore the possibility of establishing a combined rotavirus-SARS-CoV-2 vaccine, we generated recombinant (r)SA11 rotaviruses with modified segment 7 RNAs that contained coding sequences for NSP3 and FLAG-tagged portions of the SARS-CoV-2 spike (S) protein. A 2A translational element was used to drive separate expression of NSP3 and the S product. rSA11 viruses were recovered that encoded the S-protein S1 fragment, N-terminal domain (NTD), receptor-binding domain (RBD), extended receptor-binding domain (ExRBD), and S2 core (CR) domain (rSA11/NSP3-fS1, -fNTD, -fRBD, -fExRBD, and -fCR, respectively). Generation of rSA11/fS1 required a foreign-sequence insertion of 2.2-kbp, the largest such insertion yet made into the rotavirus genome. Based on isopycnic centrifugation, rSA11 containing S sequences were denser than wildtype virus, confirming the capacity of the rotavirus to accommodate larger genomes. Immunoblotting showed that rSA11/-fNTD, -fRBD, -fExRBD, and -fCR viruses expressed S products of expected size, with fExRBD expressed at highest levels. These rSA11 viruses were genetically stable during serial passage. In contrast, rSA11/NSP3-fS1 failed to express its expected 80-kDa fS1 product, for unexplained reasons. Moreover, rSA11/NSP3-fS1 was genetically unstable, with variants lacking the S1 insertion appearing during serial passage. Nonetheless, these results emphasize the potential usefulness of rotavirus vaccines as expression vectors of portions of the SARS-CoV-2 S protein (e.g., NTD, RBD, ExRBD, and CR) with sizes smaller than the S1 fragment.\n\nImportanceAmong the vaccines administered to children in the US and many other countries are those targeting rotavirus, a segmented double-stranded RNA virus that is a major cause of severe gastroenteritis. In this study, we have examined the feasibility of modifying the rotavirus genome by reverse genetics, such that the virus could serve as an expression vector of the SARS-CoV-2 spike protein. Results were obtained showing that recombinant rotaviruses can be generated that express domains of the SARS CoV-2 spike protein, including the receptor-binding domain (RBD), a common target of neutralizing antibodies produced in individuals infected by the virus. Our findings raise the possibility of creating a combined rotavirus-COVID-19 vaccine that could be used in place of current rotavirus vaccines.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Asha A Philip", + "author_inst": "Indiana University Bloomington" + }, + { + "author_name": "John T Patton", + "author_inst": "Indiana University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.18.431825", "rel_title": "Meta-analysis of orthogonal OMICs data from COVID-19 patients unveils prognostic markers and antiviral factors.", @@ -932056,193 +934080,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.17.431492", - "rel_title": "SARS-CoV-2 vaccination induces neutralizing antibodies against pandemic and pre-emergent SARS-related coronaviruses in monkeys", - "rel_date": "2021-02-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.17.431492", - "rel_abs": "Betacoronaviruses (betaCoVs) caused the severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS) outbreaks, and now the SARS-CoV-2 pandemic. Vaccines that elicit protective immune responses against SARS-CoV-2 and betaCoVs circulating in animals have the potential to prevent future betaCoV pandemics. Here, we show that immunization of macaques with a multimeric SARS-CoV-2 receptor binding domain (RBD) nanoparticle adjuvanted with 3M-052-Alum elicited cross-neutralizing antibody responses against SARS-CoV-1, SARS-CoV-2, batCoVs and the UK B.1.1.7 SARS-CoV-2 mutant virus. Nanoparticle vaccination resulted in a SARS-CoV-2 reciprocal geometric mean neutralization titer of 47,216, and robust protection against SARS-CoV-2 in macaque upper and lower respiratory tracts. Importantly, nucleoside-modified mRNA encoding a stabilized transmembrane spike or monomeric RBD protein also induced SARS-CoV-1 and batCoV cross-neutralizing antibodies, albeit at lower titers. These results demonstrate current mRNA vaccines may provide some protection from future zoonotic betaCoV outbreaks, and provide a platform for further development of pan-betaCoV nanoparticle vaccines.", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "Kevin O Saunders", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA; Departme" - }, - { - "author_name": "Esther Lee", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Robert Parks", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "David R Martinez", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" - }, - { - "author_name": "Dapeng Li", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Haiyan Chen", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Robert J Edwards", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Sophie M. C. Gobeil", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Maggie Barr", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Katayoun Mansouri", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "S Munir Alam", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Laura L Sutherland", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Fangping Cai", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Aja Sanzone", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Madison Berry", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Kartik Manne", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Anyway B Kapingidza", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Mihai Azoitei", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Longping V Tse", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" - }, - { - "author_name": "Trevor D Scobey", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" - }, - { - "author_name": "Rachel Spreng", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "R. Wes Rountree", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "C Todd DeMarco", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" - }, - { - "author_name": "Thomas N Denny", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA" - }, - { - "author_name": "Christopher W Woods", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Elizabeth W Petzold", - "author_inst": "Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC 27710, USA" - }, - { - "author_name": "Thomas H Oguin III", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Gregory D Sempowski", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Matthew Gagne", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA" - }, - { - "author_name": "Daniel C Douek", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA" - }, - { - "author_name": "Mark A Tomai", - "author_inst": "Corporate Research Materials Lab, 3M Company, St. Paul, MN 55144, USA." - }, - { - "author_name": "Christopher B Fox", - "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beth" - }, - { - "author_name": "Robert Seder", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA" - }, - { - "author_name": "Kevin Wiehe", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - }, - { - "author_name": "Drew Weissman", - "author_inst": "Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA" - }, - { - "author_name": "Norbert Pardi", - "author_inst": "Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA" - }, - { - "author_name": "Priyamvada Acharya", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "BIOQUAL, Rockville, MD 20850, USA" - }, - { - "author_name": "Mark G Lewis", - "author_inst": "BIOQUAL, Rockville, MD 20850, USA" - }, - { - "author_name": "Ian N Moore", - "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beth" - }, - { - "author_name": "David C Montefiori", - "author_inst": "Department of Surgery, Duke University, Durham, NC 27710, USA" - }, - { - "author_name": "Ralph S Baric", - "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA" - }, - { - "author_name": "Barton F Haynes", - "author_inst": "Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC " - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.16.430500", "rel_title": "Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants", @@ -932473,6 +934310,81 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.02.17.431579", + "rel_title": "Traditional use of Cissampelos pareira L. for hormone disorder and fever provides molecular links of ESR1 modulation to viral inhibition", + "rel_date": "2021-02-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.17.431579", + "rel_abs": "Bioactive fractions or compounds obtained from medicinal plants have been used for the treatment of multiple diseases. This effect could be due to common pathways underlying these conditions that are targeted by such medicines. In this study, we explored the molecular basis of action of one such herbal formulation Cissampelos pareira, used for the treatment of female hormone disorders and fever. Genome-wide expression studies on MCF7 cell lines treated with Cipa extract were carried out using Affymetrix arrays. Transcriptome analysis revealed a downregulation of signatures of estrogen response governed by estrogen receptor (ER). Molecular docking analysis identified 38 constituent molecules in Cipa that potentially bind ({Delta}G< -7.5) with ER at the same site as estrogen. Cipa transcriptome signatures show high positive connectivity (https://clue.io/) scores with protein translation inhibitors such as emetine (score: 99.61) and knockdown signatures of genes linked to the antiviral response such as ribosomal protein RPL7 (score: 99.92), which is also an ER coactivator. Cipa exhibits antiviral activity in dengue infected MCF7 cells that is decreased upon ESR1 (estrogen receptor 1) gene knockdown. This approach reveals a novel pathway involving ESR1-RPL7 axis that could be a potential target in dengue viral infection.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Madiha Haider", + "author_inst": "Institute of Genomics and Integrative Biology" + }, + { + "author_name": "Dhwani Dholakia", + "author_inst": "Institute of Genomics and Integrative Biology" + }, + { + "author_name": "Aleksha Panwar", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "Parth Garg", + "author_inst": "Indraprastha Institute of Information Technology" + }, + { + "author_name": "Atish Prabhakar Gheware", + "author_inst": "Institute of Genomics and Integrative Biology" + }, + { + "author_name": "Khushboo Singhal", + "author_inst": "Institute of Genomics and Integrative Biology" + }, + { + "author_name": "Dayanidhi Singh", + "author_inst": "Institute of Genomics and Integrative Biology" + }, + { + "author_name": "Shaunak A Burse", + "author_inst": "Institute of Genomics and Integrative Biology" + }, + { + "author_name": "Surekha Kumari", + "author_inst": "Institute of Himalayan Bioresource Technology" + }, + { + "author_name": "Anmol Kumar", + "author_inst": "Institute of Himalayan Bioresource Technology" + }, + { + "author_name": "Arjun Ray", + "author_inst": "Indraprastha Institute of Information Technology" + }, + { + "author_name": "Guruprasad R Medigeshi", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "Upendra Sharma", + "author_inst": "Institute of Himalayan Bioresource Technology" + }, + { + "author_name": "Bhavana Prasher", + "author_inst": "Institute of Genomics and Integrative Biology" + }, + { + "author_name": "Mitali Mukerji", + "author_inst": "Institute of Genomics and Integrative Biology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.02.17.431647", "rel_title": "Potent neutralization antibodies induced by a recombinant trimeric Spike protein vaccine candidate containing PIKA adjuvant for COVID-19", @@ -933832,49 +935744,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.13.21251682", - "rel_title": "Mortality from injury, overdose and suicide during the 2020 COVID-19 pandemic, March-July, 2020", - "rel_date": "2021-02-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.13.21251682", - "rel_abs": "Introduction\n\nThe COVID-19 pandemic has been associated with substantial rates of all-cause excess mortality. The contribution of external causes of death to excess mortality including drug overdose, homicide, suicide, and unintentional injuries during the initial outbreak in the United States is less well documented.\n\nMethodsUsing public data published by the National Center for Health Statistics on February 10, 2021, we measured monthly excess mortality (the gap between observed and expected deaths) from five external causes using national-level data published by National Center for Health Statistics; assault (homicide); intentional self-harm (suicide); accidents (unintentional injuries); and motor vehicle accidents. We used seasonal autoregressive integrated moving average (sARIMA) models developed with cause-specific monthly mortality counts and US population data from 2015-2019 and estimated the contribution of individual cause-specific mortality to all-cause excess mortality from March-July 2020.\n\nResultsFrom March-July, 2020, 212,825 (95% CI 136,236-290,776) all-cause excess deaths occurred in the US). There were 8,540 excess drug overdoses (all intents) (95% CI 5,106 to 11,975), accounting for 4% of all excess mortality; 1,455 excess homicide deaths (95% CI 708 to 2202, accounting for 0.7% of excess mortality; 5,492 excess deaths due to unintentional accidents occurred (95% CI 85 to 10,899, accounting for 2.6% of excess mortality. Though a non-significantly 135 (95% CI -1361 to 1,630) more MVA deaths were recorded during the study period, a significant decrease in April (525; 95% CI -817 to -233) and significant increases in June-July (965; 95% CI 348 to 1,587) were observed. Suicide deaths were statistically lower than projected by 2,067 (95% CI 941-3,193 fewer deaths).\n\nMeaningExcess deaths from drug overdoses, homicide, and addicents occurred during the pandemic but represented a small fraction of all-cause excess mortality. The excess external causes of death, however, still represent thousands of lives lost. Notably, deaths from suicide were lower than expected and therefore did not contribute to excess mortality.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jeremy Faust", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Chengan Du", - "author_inst": "Yale University School of Medicine, Yale New Haven Hospital, Center for Outcomes Research and Evaluation New Haven, CT" - }, - { - "author_name": "Katherine Mayes", - "author_inst": "Harvard Affiliated Emergency Medicine Residency, Boston, Massachusetts" - }, - { - "author_name": "Shu-Xia Li", - "author_inst": "Yale New Haven Hospital, Center for Outcomes Research and Evaluation, New Haven, CT" - }, - { - "author_name": "Zhenqiu Lin", - "author_inst": "Yale New Haven Hospital, Center for Outcomes Research and Evaluation, New Haven, CT" - }, - { - "author_name": "Michael L Barnett", - "author_inst": "Department of Health Policy and Management, Harvard T. H. Chan School of Public Health, Boston, MA" - }, - { - "author_name": "Harlan M Krumholz", - "author_inst": "Yale University School of Medicine, Yale New Haven Hospital, Center for Outcomes Research and Evaluation, New Haven, CT" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.12.21251479", "rel_title": "Severe COVID-19 pneumonia and barotrauma: From the frying pan into the fire.", @@ -934170,6 +936039,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.12.21251419", + "rel_title": "Treatment of irritant contact dermatitis in healthcare settings during the COVID19 pandemic: The emollient Dermol 500 exhibits virucidal activity against influenza A virus and SARS-CoV-2.", + "rel_date": "2021-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.12.21251419", + "rel_abs": "ObjectivesTo investigate whether the antimicrobial emollient Dermol 500 and its active components, benzalkonium chloride (BAK) and chlorhexidine dihydrochloride (CD), exhibit virucidal activity thus informing whether Dermol 500 is a suitable soap substitute for use during the COVID19 pandemic, to combat the increased incidence of work-related contact dermatitis in clinical settings that we report here.\n\nMethodsInactivation of influenza A virus and SARS-CoV-2 by Dermol 500 and the independent and combined virucidal activity of the Dermol 500 components BAK and CD was assessed by influenza A virus and SARS-CoV-2 infectivity assays. Viruses were treated with concentrations of BAK and CD comparable to Dermol 500, and lower, and infectivity of the viruses assessed by titration.\n\nResultsDermol 500 exhibits comparable virucidal activity to alcohol-based sanitisers against influenza A virus and SARS-CoV-2. In addition, the Dermol 500 components BAK and CD exhibit independent and synergistic virucidal activity against influenza A virus and SARS-CoV-2, the causative agent of COVID19.\n\nConclusionsThe synergistic virucidal activity of the Dermol 500 components BAK and CD makes Dermol 500 suitable as a soap substitute to treat and prevent work-related contact dermatitis in healthcare settings.\n\nKEY MESSAGESO_LIWhat is already known about this subject?\nO_LIWork-related contact dermatitis is a prominent issue among healthcare workers, and likely exacerbated by the enhanced hand hygiene and personal protective equipment required to control infection during the COVID19 pandemic.\nC_LIO_LIThe antimicrobial lotion Dermol 500 is frequently prescribed as an emollient and soap substitute to help prevent and treat dermatitis, but its use during the COVID19 pandemic was not advised as its capacity to inactivate viruses was unknown.\nC_LI\nC_LIO_LIWhat are the new findings?\nO_LIIncreased incidence of irritant contact dermatitis was recorded amongst healthcare workers at Kings College Hospital NHS Foundation Trust in 2020 compared to 2019.\nC_LIO_LIDermol 500 lotion and its antimicrobial components, benzalkonium chloride (BAK) and chlorhexidine dihydrochloride (CD), exhibit virucidal activity against influenza A virus and SARS-CoV-2, the virus responsible for COVID19 pandemic.\nC_LI\nC_LIO_LIHow might this impact policy or clinical practice in the foreseeable future?\nO_LIOur results demonstrate that Dermol 500 can be safely used as a soap substitute to treat work-related contact dermatitis in clinical care settings during the COVID19 pandemic.\nC_LIO_LIEmployers can meet their obligations under COSHH to eliminate workplace exposure to a harmful substance and substitute with an alternative product for hand hygiene.\nC_LI\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Christine T Styles", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michael Vanden Oever", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jonathan Brown", + "author_inst": "Imperial College London" + }, + { + "author_name": "Sweta Rai", + "author_inst": "King's College Hospital NHS Foundation Trust" + }, + { + "author_name": "Sarah Walsh", + "author_inst": "King's College Hospital NHS Foundation Trust" + }, + { + "author_name": "Finola M Ryan", + "author_inst": "King's College Hospital NHS Foundation Trust" + }, + { + "author_name": "Wendy S Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Rachel S Edgar", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.12.21251229", "rel_title": "Comparison of SARS-CoV-2 viral load in saliva samples in symptomatic and asymptomatic cases", @@ -935642,65 +937558,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.11.21251548", - "rel_title": "Association of demographic and occupational factors with SARS-CoV-2 vaccine uptake in a multi-ethnic UK healthcare workforce: a rapid real-world analysis", - "rel_date": "2021-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251548", - "rel_abs": "BackgroundHealthcare workers (HCWs) and ethnic minority groups are at increased risk of COVID-19 infection and adverse outcome. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) vaccination is now available for frontline UK HCWs; however, demographic/occupational associations with vaccine uptake in this cohort are unknown. We sought to establish these associations in a large UK hospital workforce.\n\nMethodsWe conducted cross-sectional surveillance examining vaccine uptake amongst all staff at University Hospitals of Leicester NHS Trust. We examined proportions of vaccinated staff stratified by demographic factors, occupation and previous COVID-19 test results (serology/PCR) and used logistic regression to identify predictors of vaccination status after adjustment for confounders.\n\nFindingsWe included 19,044 HCWs; 12,278 (64.5%) had received SARS-CoV-2 vaccination. Compared to White HCWs (70.9% vaccinated), a significantly smaller proportion of ethnic minority HCWs were vaccinated (South Asian 58.5%, Black 36.8% p<0.001 for both). After adjustment, factors found to be negatively associated with vaccine uptake were; younger age, female sex, increasing deprivation and belonging to any non-White ethnic group (Black: aOR0.30, 95%CI 0.26-0.34, South Asian:0.67, 0.62-0.72). Those that had previously had confirmed COVID-19 (by PCR) were less likely to be vaccinated than those who had tested negative.\n\nInterpretationEthnic minority HCWs and those from more deprived areas as well as younger, female staff are less likely to take up SARS-CoV-2 vaccination. These findings have major implications for the delivery of SARS-CoV-2 vaccination programmes in HCWs and the wider population and should inform the national vaccination programme to prevent the disparities of the pandemic from widening.\n\nFundingNIHR, UKRI/MRC", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christopher A Martin", - "author_inst": "University of Leicester" - }, - { - "author_name": "Collette Marshall", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Prashanth Patel", - "author_inst": "University of Leicester" - }, - { - "author_name": "Charles Goss", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "David R Jenkins", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Claire Ellwood", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Linda Barton", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Arthur Price", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Nigel J Brunskill", - "author_inst": "University of Leicester" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "University of Leicester" - }, - { - "author_name": "Manish Pareek", - "author_inst": "University of Leicester" - } - ], - "version": "2", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.11.21251562", "rel_title": "Population Age-Ineligible for COVID-19 Vaccine in the United States: Implications for State, County, and Race/Ethnicity Vaccination Targets", @@ -935884,6 +937741,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.10.21251510", + "rel_title": "Identification of high-risk COVID-19 patients using machine learning", + "rel_date": "2021-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251510", + "rel_abs": "The current COVID-19 public health crisis, caused by SARSCoV-2 (severe acute respiratory syndrome coronavirus 2), has produced a devastating toll both in terms of human life loss and economic disruption. In this paper we present a machine-learning algorithm capable of identifying whether a given patient (actually infected or suspected to be infected) is more likely to survive than to die, or vice-versa. We train this algorithm with historical data, including medical history, demographic data, as well as COVID-19-related information. This is extracted from a database of confirmed and suspected COVID-19 infections in Mexico, constituting the official COVID-19 data compiled and made publicly available by the Mexican Federal Government. We demonstrate that the proposed method can detect high-risk patients with high accuracy, in each of four identified treatment stages, thus improving hospital capacity planning and timely treatment. Furthermore, we show that our method can be extended to provide optimal estimators for hypothesis-testing techniques commonly-used in biological and medical statistics. We believe that our work could be of use in the context of the current pandemic in assisting medical professionals with real-time assessments so as to determine health care priorities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mario A. Quiroz-Juarez", + "author_inst": "Universidad Autonoma Metropolitana" + }, + { + "author_name": "Armando Torres-Gomez", + "author_inst": "ABC Medical Center" + }, + { + "author_name": "Irma Hoyo-Ulloa", + "author_inst": "ABC Medical Center" + }, + { + "author_name": "Roberto de J. Leon-Montiel", + "author_inst": "Instituto de Ciencias Nucleares-UNAM" + }, + { + "author_name": "Alfred B. U'Ren", + "author_inst": "Instituto de Ciencias Nucleares-UNAM" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.09.21251436", "rel_title": "The global distribution of COVID-19 vaccine: The role of macro-socioeconomics measures", @@ -937248,69 +939140,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.12.430907", - "rel_title": "A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients", - "rel_date": "2021-02-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.430907", - "rel_abs": "COVID-19 disease outcome is highly dependent on adaptive immunity from T and B lymphocytes, which play a critical role in the control, clearance and long-term protection against SARS-CoV-2. To date, there is limited knowledge on the composition of the T and B cell immune receptor repertoires [T cell receptors (TCRs) and B cell receptors (BCRs)] and transcriptomes in convalescent COVID-19 patients of different age groups. Here, we utilize single-cell sequencing (scSeq) of lymphocyte immune repertoires and transcriptomes to quantitatively profile the adaptive immune response in COVID-19 patients of varying age. We discovered highly expanded T and B cells in multiple patients, with the most expanded clonotypes coming from the effector CD8+ T cell population. Highly expanded CD8+ and CD4+ T cell clones show elevated markers of cytotoxicity (CD8: PRF1, GZMH, GNLY; CD4: GZMA), whereas clonally expanded B cells show markers of transition into the plasma cell state and activation across patients. By comparing young and old convalescent COVID-19 patients (mean ages = 31 and 66.8 years, respectively), we found that clonally expanded B cells in young patients were predominantly of the IgA isotype and their BCRs had incurred higher levels of somatic hypermutation than elderly patients. In conclusion, our scSeq analysis defines the adaptive immune repertoire and transcriptome in convalescent COVID-19 patients and shows important age-related differences implicated in immunity against SARS-CoV-2.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Florian Bieberich", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Rodrigo Vazquez-Lombardi", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Alexander Yermanos", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Roy A Ehling", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Derek M Mason", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Bastian Wagner", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Edo Kapetanovic", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Raphael Brisset Di Roberto", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Cedric R Weber", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Miodrag Savic", - "author_inst": "University of Basel" - }, - { - "author_name": "Fabian Rudolf", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Sai T Reddy", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.12.430933", "rel_title": "Rapidly Increasing SARS-CoV-2 Neutralization by Intravenous Immunoglobulins Produced from Plasma Collected During the 2020 Pandemic", @@ -937694,6 +939523,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.12.430940", + "rel_title": "Single-cell sequencing of plasma cells from COVID-19 patients reveals highly expanded clonal lineages produce specific and neutralizing antibodies to SARS-CoV-2", + "rel_date": "2021-02-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.430940", + "rel_abs": "Isolation and characterization of antibodies in COVID-19 patients has largely focused on memory B cells, however it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in controlling and resolving SARS-CoV-2 infection. To date there is little known about the specificity of plasma cells in COVID-19 patients. This is largely because plasma cells lack surface antibody expression, which complicates their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and high-throughput mammalian display screening to interrogate the specificity of plasma cells from 16 convalescent COVID-19 patients. Single-cell sequencing allows us to profile antibody repertoire features in these patients and identify highly expanded clonal lineages. Mammalian display screening is employed to reveal that 37 antibodies (out of 132 candidates) derived from expanded plasma cell clonal lineages are specific for SARS-CoV-2 antigens, including antibodies that target the receptor binding domain (RBD) with high affinity and exhibit potent neutralization of SARS-CoV-2.\n\nOne Sentence SummarySingle-cell antibody repertoire sequencing and high-throughput screening identifies highly expanded plasma cells from convalescent COVID-19 patients that produce SARS-CoV-2-specific antibodies capable of potent neutralization.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Roy A Ehling", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Cedric R Weber", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Derek M Mason", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Simon Friedensohn", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Bastian Wagner", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Florian Bieberich", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Edo Kapetanovic", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Rodrigo Vazquez-Lombardi", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Raphael Brisset Di Roberto", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Kai-Lin Hong", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Camille Wagner", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Daniel J Sheward", + "author_inst": "Karolinksa Institutet" + }, + { + "author_name": "Ben Murrell", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Alexander Yermanos", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Andreas Cuny", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Miodrag Savic", + "author_inst": "University of Basel" + }, + { + "author_name": "Fabian Rudolf", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Sai T Reddy", + "author_inst": "ETH Zurich" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.11.430728", "rel_title": "IN VITRO ANTI-VIRAL ACTIVITY OF HEXETIDINE (BACTIDOL) ORAL MOUTHWASH AGAINST HUMAN CORONAVIRUS OC43 ANDINFLUENZA A (H1N1) VIRUS", @@ -938961,24 +940877,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.10.21251523", - "rel_title": "Decline in mitigation readiness facilitated second waves of SARS-CoV-2", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251523", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Kai W Wirtz", - "author_inst": "Helmholtz Centre Geesthacht" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.10.21251533", "rel_title": "County-Specific, Real-Time Projection of the Effect of Business Closures on the COVID-19 Pandemic", @@ -939281,6 +941179,44 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.11.21251587", + "rel_title": "Assessing the impact of secondary school reopening strategies on within-school COVID-19 transmission and absences: a modelling study", + "rel_date": "2021-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251587", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Trystan Leng", + "author_inst": "University of Warwick" + }, + { + "author_name": "Edward M Hill", + "author_inst": "University of Warwick" + }, + { + "author_name": "Robin N Thompson", + "author_inst": "University of Warwick" + }, + { + "author_name": "Michael J Tildesley", + "author_inst": "University of Warwick" + }, + { + "author_name": "Matt J Keeling", + "author_inst": "University of Warwick" + }, + { + "author_name": "Louise J Dyson", + "author_inst": "University of Warwick" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.11.21251589", "rel_title": "SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 \u2013 implementation of Swiss-wide diagnostic screening and whole genome sequencing", @@ -941260,25 +943196,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.08.21251290", - "rel_title": "Confirmed forecasts for the expansion of the COVID-19 epidemic in the S. Paulo city, Brazil", - "rel_date": "2021-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251290", - "rel_abs": "ObjectiveA SEIR compartmental model was previously selected to estimate future outcomes to the dynamics of the Covid-19 epidemic breakout in Brazil.\n\nMethodCompartments for individuals vaccinated, and prevalent SARS-Cov-2 variants were not included. A time-dependent incidence weight on the reproductive basic number accounted for Non Pharmaceutical Interventions (NPI). A first series of published data from March 1st to May 8, 2020 was used to adjust all model parameters aiming to forecast one year of evolutionary outbreak. The cohort study was set as a city population-based analysis.\n\nAnalysisThe population-based sample, 25,366 during the study period, was the number of confirmed cases on exposed individuals. The analysis was applied to predict the consequences of holding for posterior NPI releases, and indicates the appearance of a second wave starting last quarter of 2020.\n\nFindingsBy March 1st2021, the number of confirmed cases was predicted to reach 0.47Million (0.24-0.78), and fatalities would account for 21 thousand (12-33), 5 to 95% CRI. A second series of data published from May 9, 2020 to March 1st, 2021 confirms the forecasts previously reported for the evolution of infected people and fatalities.\n\nNoveltyBy March 1st 2021, the number of confirmed cases reached 527,710 (12% bellow predicted average of accumulated cases), and fatalities accounted for 18,769 (10% above the accumulated average of estimated fatalities). After March 1st, new peaks on reported numbers of daily new infected and new fatalities appeared as a combined result to the appearance of the prevalent SARS-CoV-2 P1 variant, and the increased number of vaccinated individuals.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Sergio Celaschi", - "author_inst": "CTI Renato Archer" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.08.21251352", "rel_title": "Assessment of Post SARS CoV 2 Fatigue among Physicians Working in COVID Designated Hospitals in Dhaka, Bangladesh", @@ -941574,6 +943491,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.02.08.21251358", + "rel_title": "Large-scale silane bead-based SARS-CoV-2 testing of a nursing home in Spain identifies a viral reservoir during lockdown period", + "rel_date": "2021-02-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251358", + "rel_abs": "Background: Spain is one of the countries most heavily affected by the COVID-19 pandemic. As in other countries such as UK and USA, nursing homes have been an important human reservoir for the virus and the population with the highest mortality worldwide. The presence of asymptomatic carriers within nursing homes is one of the factors that could provoke new outbreaks during the relaxing of lockdown measures. Methods: We developed a high-throughput protocol for RNA extraction of patient samples based on silane magnetic beads in multi-well plates. The sensitivity, specificity and reproducibility rates were assessed using positive and negative clinical samples from the Clinica Universidad de Navarra, Spain. We utilized the protocol to test a pilot cohort of 138 residents and 87 staff from a nursing home in Northern Navarre, Spain. Findings: Our protocol showed high sensitivity (100%), specificity (96.0%) and linear correlation with PCR cycle threshold values obtained with a standard testing kit (R2 = 0.807, p=3E-05). Testing of 225 individuals from the nursing home revealed 63 residents (46%) and 14 staff (16%) positive for SARS-CoV-2. Only 18 of the positive residents (28.6%) were symptomatic at time of testing. During follow-up, six PCR-negative symptomatic residents were retested and resulted positive. One-month mortality among positive residents was higher than in negative residents (15.9% vs 1.3%), regardless of age or comorbidities. Interpretation: Rapid silane bead-based RNA extraction expanded the testing capabilities and COVID-19 patients were promptly identified. Personal and public health measures were enacted to avoid spreading and tighten clinical surveillance. The ability to easily adapt the technical capabilities of academic research centers to large-scale testing for SARS-CoV-2 could provide an invaluable tool for ensuring a safe lifting of lockdown in countries with high numbers of cases.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Nick Weber", + "author_inst": "Vivet Therapeutics SL, Pamplona, Spain." + }, + { + "author_name": "Ainhoa Goni-Salaverri", + "author_inst": "Oncohematology Department, Cima Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "Jose A Rodriguez", + "author_inst": "Genomics Unit, Cima Universidad de Navarra, Pamplona, Spain" + }, + { + "author_name": "Juan Pablo Unfried", + "author_inst": "Centro de Investigacion Medica Aplicada" + }, + { + "author_name": "Daniel Alameda", + "author_inst": "Genomics Unit, Cima Universidad de Navarra, Pamplona, Spain" + }, + { + "author_name": "Mirian Fernandez-Alonso", + "author_inst": "Microbiology Unit. Clinica Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "Elena Saez", + "author_inst": "Medicinal Chemistry Laboratory, Department of Molecular Therapy, CIMA Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "Sheila Maestro-Galilea", + "author_inst": "Department of Gene Therapy and Regulation of Gene Expression, Cima Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "Felix Alegre", + "author_inst": "Internal Medicine Department, Clinica Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "Francisco Carmona-Torre", + "author_inst": "Infectious Diseases Division and Clinical Microbiology, Clinica Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "Marta Marin-Oto", + "author_inst": "Respiratory Medicine Department, Clinica Universidad de Navarra, Pamplona, Spain" + }, + { + "author_name": "Cristina Olague", + "author_inst": "Department of Gene Therapy and Regulation of Gene Expression, Cima Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "Leticia Odriozola", + "author_inst": "Department of Gene Therapy and Regulation of Gene Expression, Cima Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "Mar Navarro-Alonso", + "author_inst": "Oncohematology Department, Cima Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "Rafael Sanchez-Ostiz", + "author_inst": "Idea Innovacion, Cizur Menor, Navarra, Spain." + }, + { + "author_name": "Josepmaria Argemi", + "author_inst": "Liver Unit, Internal Medicine Department. Clinica Universidad de Navarra, Pamplona, Spain. Division of Medicine - Gastroenterology and Hepatology Department, Un" + }, + { + "author_name": "Jose Luis del Pozo", + "author_inst": "Microbiology Unit. Clinica Universidad de Navarra, Pamplona, Spain." + }, + { + "author_name": "DAVID LARA-ASTIASO", + "author_inst": "Cambridge Stem cell Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.09.21251402", "rel_title": "Whole-genome sequencing of SARS-CoV-2 in the Republic of Ireland during waves 1 and 2 of the pandemic", @@ -942998,93 +945002,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.07.21251281", - "rel_title": "Galectin-3 as a potential prognostic biomarker of severe COVID-19 in SARS-CoV-2 infected patients", - "rel_date": "2021-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251281", - "rel_abs": "BACKGROUNDPrognostic biomarkers are needed to identify patients at high-risk for severe COVID-19. Galectin-3 is known to drive neutrophil infiltration and release of pro-inflammatory cytokines contributing to airway inflammation.\n\nMETHODSIn this prospective cohort, we assessed galectin-3 levels in 156 hospitalized patients with confirmed COVID-19. COVID-19 patients were diagnosed as either critical (>50% lung damage) or moderate (<50% of lung damage) based on computerized tomography. Patients who required invasive mechanical ventilation (IMV) and/or died during hospitalization were categorized as having a severe outcome, and a non-severe outcome if they were discharged and none of the former occurred.\n\nRESULTSElevated serum galectin-3 was significantly higher in critical patients compared to moderate ones (35.91 {+/-} 19.37 ng/mL vs. 25 {+/-} 14.85 ng/mL, p<0.0001). Patients who progressed to a severe outcome including IMV and/or in-hospital death, presented higher galectin-3 levels (41.17 ng/mL [IQR 29.71 - 52.25] vs. 23.76 ng/mL [IQR 15.78 - 33.97] compared to those of a non-severe outcome, p<0.0001). Galectin-3 discriminated well between those with severe and non-severe outcome, with an AUC of 0.75 (95% CI 0.67 - 0.84, p<0.0001) and was found to be an independent predictor of severe outcome regardless of the percentage of lung involvement. Additionally, the combination of galectin-3, CRP and albumin, significantly improved its individual predicting ability with an AUC 0.84 (95% CI 0.77 - 0.91, p<0.0001).\n\nCONCLUSIONCirculating galectin-3 levels can be used to predict severe outcomes in COVID-19 patients, including the requirement of mechanical ventilation and/or death, regardless of the initial severity of the disease.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Eduardo Cervantes-Alvarez", - "author_inst": "PECEM, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" - }, - { - "author_name": "Nathaly Limon-de la Rosa", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Gastroenterology, Mexico City, Mexico" - }, - { - "author_name": "Moises Salgado-de la Mora", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Paola Valdez-Sandoval", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Mildred Palacios-Jimenez", - "author_inst": "Universidad Veracruzana, Veracruz, Mexico" - }, - { - "author_name": "Fatima Rodriguez-Alvarez", - "author_inst": "Universidad Veracruzana, Veracruz, Mexico" - }, - { - "author_name": "Brenda I. Vera-Maldonado", - "author_inst": "Universidad Veracruzana, Veracruz, Mexico" - }, - { - "author_name": "Eduardo Aguirre-Aguilar", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Juan Manuel Escobar-Valderrama", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Jorge Alanis-Mendizabal", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Internal Medicine, Mexico City, Mexico" - }, - { - "author_name": "Osvely Mendez-Guerrero", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Gastroenterology, Mexico City, Mexico" - }, - { - "author_name": "Farid Tejeda-Dominguez", - "author_inst": "Universidad Panamericana School of Medicine, Campus Mexico, Mexico City" - }, - { - "author_name": "Jiram Torres-Ruiz", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Immunology and Rheumatology, Mexico City, Mexico" - }, - { - "author_name": "Diana Gomez-Martin", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Immunology and Rheumatology, Mexico City, Mexico" - }, - { - "author_name": "Kathryn L. Colborn", - "author_inst": "Department of Surgery, University of Colorado Anschutz Medical Campus, Denver, CO" - }, - { - "author_name": "David Kershenobich", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico" - }, - { - "author_name": "Christene A. Huang", - "author_inst": "Department of Surgery, University of Colorado Anschutz Medical Campus, Denver, CO" - }, - { - "author_name": "Nalu Navarro-Alvarez", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Department of Gastroenterology, Mexico City, Mexico" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.08.21251070", "rel_title": "The protective association between statins use and adverse outcomes among COVID-19 patients: a systematic review and meta-analysis", @@ -943352,6 +945269,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.07.21251314", + "rel_title": "High School Sports During the CoVID-19 Pandemic: The Impact of Sport Participation on the Health of Adolescents", + "rel_date": "2021-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251314", + "rel_abs": "ContextDuring the fall of 2020, some high schools across the US allowed their students to participate in interscholastic sports while others cancelled or postponed their sport programs due to concerns regarding CoVID19 transmission. It is unknown what effect this has had on the physical and mental health of student athletes.\n\nObjectiveIdentify the impact of playing a sport during the CoVID19 pandemic on the health of student athletes.\n\nDesignCross-sectional study.\n\nSettingSample recruited via email.\n\nPatients or Other Participants559 Wisconsin high school athletes (age=15.7+1.2 yrs., female=44%) from 44 high schools completed an online survey in October 2020. A total of 171 (31%) athletes played (PLY) a fall sport, while 388 (69%) did not play (DNP).\n\nMain Outcome Measure(s)Demographics included: sex, grade and sports played. Assessments included the General Anxiety Disorder-7 Item (GAD-7) for anxiety, Patient Health Questionnaire-9 Item (PHQ-9) for depression, the Pediatric Functional Activity Brief Scale (PFABS) for physical activity, and the Pediatric Quality of Life Inventory 4.0 (PedsQL) for quality of life. Univariable comparisons between the two groups were made via t-tests or chi-square tests. Means for each continuous outcome measure were compared between the groups by ANOVA models that controlled for Age, Sex, Teaching method (Virtual, Hybrid, or In-person), and the % of students eligible for free lunch.\n\nRESULTSPLY group participants were less likely to report moderate to severe symptoms of anxiety (PLY=6.6%, DNP=44.1%, p<0.001) and depression (PLY=18.2%, DNP=40.4%, p<0.001). PLY athletes reported higher (better) PFABS scores (mean: [95%CI]), (PLY=23.2[22.0,24.5], DNP=16.4[15.0,17.8], p <0.001) and higher (better) PedsQL total scores (PLY=88.4[85.9,90.9], DNP=79.6[76.8,82.4], p <0.001).\n\nCONCLUSIONSAdolescent athletes who played a sport during the CoVID19 pandemic reported fewer symptoms of anxiety and depression, as well as higher physical activity and quality of life scores compared to adolescent athletes who did not play a sport.\n\nKey pointsO_LIHigh school students who played a sport during the CoVID-19 pandemic in the fall of 2020 were less likely to report anxiety and depression symptoms than athletes who did not play a sport.\nC_LIO_LIHigh school students who played a sport during the CoVID-19 pandemic in the fall of 2020 reported higher physical activity and quality of life scores compared to high school athletes who did not play a sport.\nC_LIO_LIParticipation in high school sports may have significant physical and mental health benefits for US adolescent athletes during the CoVID-19 pandemic.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Timothy McGuine", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Kevin Biese", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Allison Schwarz", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Claudia Reardon", + "author_inst": "University of Wisconsin- Madison" + }, + { + "author_name": "Scott Hetzel", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "M. Alison Brooks", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "David Bell", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Andrew Watson", + "author_inst": "University of Wisconsin-Madison" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.05.21250672", "rel_title": "COVID-19 in pregnancy: characteristics and outcomes of pregnant women admitted to hospital because of SARS-CoV-2 infection in the Nordic countries.", @@ -944752,45 +946716,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.02.04.21251167", - "rel_title": "A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251167", - "rel_abs": "The effective reproduction number Reff is a critical epidemiological parameter that characterizes the transmissibility of a pathogen. However, this parameter is difficult to estimate in the presence of silent transmission and/or significant temporal variation in case reporting. This variation can occur due to the lack of timely or appropriate testing, public health interventions and/or changes in human behavior during an epidemic. This is exactly the situation we are confronted with during this COVID-19 pandemic.\n\nIn this work, we propose to estimate Reff for the SARS-CoV-2 (the etiological agent of the COVID-19), based on a model of its propagation considering a time-varying transmission rate. This rate is modeled by a Brownian diffusion process embedded in a stochastic model. The model is then fitted by Bayesian inference (particle Markov Chain Monte Carlo method) using multiple well-documented hospital datasets from several regions in France and in Ireland. This mechanistic modeling framework enables us to reconstruct the temporal evolution of the transmission rate of the COVID-19 based only on the available data. Except for the specific model structure, it is non-specifically assumed that the transmission rate follows a basic stochastic process constrained by the observations. This approach allows us to follow both the course of the COVID-19 epidemic and the temporal evolution of its Reff(t). Besides, it allows to assess and to interpret the evolution of transmission with respect to the mitigation strategies implemented to control the epidemic waves in France and in Ireland. We thus can estimate a reduction of more than 80% for the first wave in all the studied regions but a smaller reduction for the second wave when the epidemic was less active. For the third wave in Ireland the reduction was again significant (>70%).\n\nAuthor SummaryIn the early stages of any new epidemic, one of the first steps to design a control strategy is to estimate pathogen transmissibility in order to provide information on its potential to spread in the population. Among the different epidemiological indicators that characterize the transmissibility of a pathogen, the effective reproduction number Reff is commonly used for measuring time-varying transmissibility. It measures how many additional people can be infected by an infected individual during the course of an epidemic. However, Reff is difficult to estimate in the presence of silent transmission and/or significant temporal variation in case reporting. This is exactly the situation we are confronted with during this COVID-19 pandemic.\n\nThe statistical methods classically used for the estimation of Reff have some shortcomings in the rigorous consideration of the transmission characteristics of SARS-CoV-2. We propose here to use an original approach based on a stochastic model whose parameters vary in time and are inferred in a Bayesian framework from reliable hospital data. This enables us to reconstruct both the COVID-19 epidemic and its Reff. The Reff time evolution allows us to get information regarding the potential effects of mitigation measures taken during and between epidemics waves.\n\nThis approach, based on a stochastic model that realistically describes the hospital multiple datasets and which overcomes many of the biases associated with Reff estimates, appears to have some advantage over previously developed methods.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bernard Cazelles", - "author_inst": "Sorbonne University" - }, - { - "author_name": "Clara Champagne", - "author_inst": "Universty of Basel" - }, - { - "author_name": "Benjamin Nguyen Van Yen", - "author_inst": "Ecole Normale Superieure" - }, - { - "author_name": "Catherine Comiskey", - "author_inst": "Trinity College Dublin, The University of Dublin" - }, - { - "author_name": "Elisabeta Vergu", - "author_inst": "INRAE" - }, - { - "author_name": "Benjamin Roche", - "author_inst": "IRD" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.04.21251171", "rel_title": "Mapping internet activity in Australian cities during COVID-19 lockdown: how occupational factors drive inequality", @@ -945078,6 +947003,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.05.21251208", + "rel_title": "The kinetic variations of anti-nucleocapsid antibody in SARS-CoV-2 infection", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.05.21251208", + "rel_abs": "The humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a pivotal role in controlling coronavirus disease 2019 (COVID-19) infections. However, little is known about the persistence of the antibody response.\n\nWe evaluated that the kinetics of anti-nucleocapsid protein antibody of SARS-CoV2 infected healthcare workers in COVID-19 cluster occurred hospital. The long-term kinetics of anti-N antibody was classified high and keep pattern, high and decay pattern, and low and keep pattern. COVID-19 contact and symptomaticity was not related to kinetic patterns.\n\nThe reason of kinetic difference was still unclear. However natural anti-SARS-CoV-2 antibody persistence was not uniform, suggesting inter-individual difference of SARS-CoV2 vaccine efficacy.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shoji Kawada", + "author_inst": "Daini Osaka Police Hospital" + }, + { + "author_name": "Atsushi Ogata", + "author_inst": "Daini Osaka Police Hospital" + }, + { + "author_name": "Yasuhiro Kato", + "author_inst": "Osaka University Graduate School of Medicine" + }, + { + "author_name": "Masashi Okamoto", + "author_inst": "Daini Osaka Police Hospital" + }, + { + "author_name": "Yuta Yamaguchi", + "author_inst": "Osaka University Graduate School of Medicine" + }, + { + "author_name": "Takayoshi Morita", + "author_inst": "Osaka University Graduate School of Medicine" + }, + { + "author_name": "Atsushi Kumanogoh", + "author_inst": "Osaka University Graduate School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.05.21251219", "rel_title": "The antibody response to SARS-CoV-2 increases over 5 months in patients with anosmia/dysgeusia", @@ -946706,85 +948674,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.06.21251246", - "rel_title": "Dynamics of neutralizing antibody responses in acute-phase COVID-19: A potential relationship between disease progression and rapid neutralizing antibody response", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.06.21251246", - "rel_abs": "IntroductionAdaptive immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) dynamics remain largely unknown. The neutralizing antibody (NAb) levels in patients with coronavirus disease 2019 (COVID-19) are helpful for understanding the pathology.\n\nPatients and MethodsUsing SARS-CoV-2 pseudotyped virus, serum sample neutralization values in symptomatic COVID-19 patients were measured using the chemiluminescence reduction neutralization test (CRNT). At least two sequential serum samples collected during hospitalization were analyzed to assess NAbs neutralizing activity dynamics at different time points.\n\nResultsOf the 11 patients, four (36.4%), six (54.5%), and one (9.1%) had moderate, severe, and critical disease, respectively. Fifty percent neutralization (N50%-CRNT) was observed upon admission in 90.9% (10/11); all patients acquired neutralizing activity 2-12 days after onset. In patients with moderate disease, neutralization was observed at earliest within two days after symptom onset. In patients with severe-to-critical disease, neutralization activity increased, plateauing 9-16 days after onset. Neutralization activity on admission was significantly higher in patients with moderate disease than in patients with severe-to-critical disease (relative % of infectivity, 6.4% vs. 41.1%; P=.0011).\n\nConclusionsNeutralization activity on admission inversely correlated with disease severity. The rapid NAb response may play a crucial role in preventing the progression of COVID-19.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Hitoshi Kawasuji", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yoshitomo Morinaga", - "author_inst": "Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Hideki Tani", - "author_inst": "Department of Virology, Toyama Institute of Health" - }, - { - "author_name": "Miyuki Kimura", - "author_inst": "Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Hiroshi Yamada", - "author_inst": "Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yoshihiro Yoshida", - "author_inst": "Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yusuke Takegoshi", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Makito Kaneda", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yushi Murai", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Kou Kimoto", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Akitoshi Ueno", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yuki Miyajima", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Koyomi Kawago", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yasutaka Fukui", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Ippei Sakamaki", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - }, - { - "author_name": "Yoshihiro Yamamoto", - "author_inst": "Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.07.21250586", "rel_title": "The impact of mobility network properties on predicted epidemic dynamics in Dhaka and Bangkok", @@ -946984,6 +948873,169 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.05.21250735", + "rel_title": "Sero-surveillance for IgG to SARS-CoV-2 at antenatal care clinics in two Kenyan referral hospitals", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.05.21250735", + "rel_abs": "The high proportion of SARS-CoV-2 infections that remain undetected presents a challenge to tracking the progress of the pandemic and implementing control measures in Kenya. We determined the prevalence of IgG to SARS-CoV-2 in residual blood samples from mothers attending antenatal care services at 2 referral hospitals in Kenya. We used a validated IgG ELISA for SARS-Cov-2 spike protein and adjusted the results for assay sensitivity and specificity. In Kenyatta National Hospital, Nairobi, seroprevalence in August 2020 was 49.9% (95% CI 42.7-58.0). In Kilifi County Hospital seroprevalence increased from 1.3% (95% CI 0.04-4.7) in September to 11.0% (95% CI 6.2-16.7) in November 2020. There has been substantial, unobserved transmission of SARS-CoV-2 in parts of Nairobi and Kilifi Counties.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "R Lucinde", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "D Mugo", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "C Bottomley", + "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London, UK" + }, + { + "author_name": "R Aziza", + "author_inst": "School of Life Sciences and the Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research (SBIDER),). University of Warwick, Coventry, Uni" + }, + { + "author_name": "J Gitonga", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "H Karanja", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "J Nyagwange", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "P Wanjiku", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "E Nzomo", + "author_inst": "Kilifi County Hospital, Ministry of Health, Government of Kenya" + }, + { + "author_name": "J Tuju", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "E Kamurie", + "author_inst": "Kenyatta National Hospital, Ministry of Health, Government of Kenya" + }, + { + "author_name": "K Thuranira", + "author_inst": "Kenyatta National Hospital, Ministry of Health, Government of Kenya" + }, + { + "author_name": "S Agunda", + "author_inst": "Kenyatta National Hospital, Ministry of Health, Government of Kenya" + }, + { + "author_name": "G M Nyutu", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "A Etyang", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "I M.O. Adetifa", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & London School of Hygiene and Tropical Medicine, Keppel Street, London, UK" + }, + { + "author_name": "E Kagucia", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "S Uyoga", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "M Otiende", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "E Otieno", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "L Ndwiga", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "C N Agoti", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "R Aman", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "M Mwangangi", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "P Amoth", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "K Kasera", + "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "A Nyaguara", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "W Ng' ang'a", + "author_inst": "Presidential Policy and Strategy Unit, The Presidency, Government of Kenya, Nairobi, Kenya" + }, + { + "author_name": "L I Ochola-Oyier", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "L B Ochola", + "author_inst": "Institute of Primate Research, Nairobi, Kenya" + }, + { + "author_name": "E Barasa", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & Nuffield Department of Medicine, Oxford University, Oxford, UK" + }, + { + "author_name": "P Bejon", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & Nuffield Department of Medicine, Oxford University, Oxford, UK" + }, + { + "author_name": "B Tsofa", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "G Warimwe", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "A Agweyu", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya." + }, + { + "author_name": "J A. G. Scott", + "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & London School of Hygiene and Tropical Medicine, Keppel Street, London, UK" + }, + { + "author_name": "Katherine E Gallagher", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.07.21251079", "rel_title": "Explaining ethnicity disparities in COVID-19 mortality: population-based, prospective cohort study", @@ -948564,61 +950616,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.01.21249903", - "rel_title": "Quantifying transmissibility of COVID-19 and impact of intervention within long-term health care facilities", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21249903", - "rel_abs": "Estimates of the basic reproduction number (R0) for Coronavirus disease 2019 (COVID-19) are particularly variable in the context of transmission within locations such as long-term health care (LTHC) facilities. We sought to characterise the heterogeneity of R0 across known outbreaks within these facilities. We used a unique comprehensive dataset of all outbreaks that have occurred within LTHC facilities in British Columbia, Canada. We estimated R0 with a Bayesian hierarchical dynamic model of susceptible, exposed, infected, and recovered individuals, that incorporates heterogeneity of R0 between facilities. We further compared these estimates to those obtained with standard methods that utilize the exponential growth rate and maximum likelihood. The total size of an outbreak varied dramatically, with a range of attack rates of 2%-86%. The Bayesian analysis provides more constrained overall estimates of R0 = 2.19 (90% CrI [credible interval] 0.19-6.69) than standard methods, with a range within facilities of 0.48-10.08. We further estimated that intervention led to 57% (47%-66%) of all cases being averted within the LTHC facilities, or 73% (63%-78%) when using a model with multi-level intervention effect. Understanding the risks and impact of intervention are essential in planning during the ongoing global pandemic, particularly in high-risk environments such as LTHC facilities.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jessica E Stockdale", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Sean C Anderson", - "author_inst": "Simon Fraser University; Pacific Biological Station, Fisheries and Oceans Canada" - }, - { - "author_name": "Andrew M Edwards", - "author_inst": "Pacific Biological Station, Fisheries and Oceans Canada; University of Victoria" - }, - { - "author_name": "Sarafa I Iyaniwura", - "author_inst": "University of British Columbia; British Columbia Centre for Disease Control" - }, - { - "author_name": "Nicola Mulberry", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Michael C Otterstatter", - "author_inst": "British Columbia Centre for Disease Control; University of British Columbia" - }, - { - "author_name": "Naveed Z Janjua", - "author_inst": "British Columbia Centre for Disease Control; University of British Columbia" - }, - { - "author_name": "Daniel Coombs", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Caroline Colijn", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Michael A Irvine", - "author_inst": "British Columbia Centre for Disease Control; British Columbia Children's Hospital Research Institute; Simon Fraser University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.02.21251042", "rel_title": "Mental Health, Substance Use, and Suicidal Ideation Among Unpaid Caregivers in the United States During the COVID-19 Pandemic: Relationships to Age, Race/Ethnicity, Employment, and Caregiver Intensity", @@ -948814,6 +950811,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.02.02.21250639", + "rel_title": "HEALTHCARE WORKERS PSYCHOLOGICAL DISTRESS At EARLY PHASE OF THE COVID-19 PANDEMIC IN MOROCCO", + "rel_date": "2021-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250639", + "rel_abs": "IntroductionThe mental being of healthcare workers with the COVID 19 pandemic is a determinant of their resilience. We investigated the psychological impact of health workers during early phase of Covid 19 pandemic in Morocco.\n\nMethodsThis was a cross-sectional study based on a survey of health workers of the Rabat University Hospital Ibn-Sina in Morocco. Data were collected during the first week of health emergency state -between 23 and 30 march-related to the covid-19 pandemic declaration in Morocco. Sociodemographic, health characteristics and professional characteristics of each health worker were collected. We also evaluated the knowledge of health workers concerning the protective measures against COVID 19. The mental health status of the health workers was investigated using the Arabic validated version of HADS 14 items, evaluating hospital anxiety and depression\n\nResultsTwo hundred eighty-seven health workers were included.The mean age was 34.4{+/-}12.18 year; and 64.5% were female, 54% have been trained regarding protection procedures, and 94.8% declared that they are aware of individual protection measures. The incidence of anxiety and depression was respectively 77.4% and 73.9%. High degree of anxiety and depression was associated with female gender. However, Higher degree of anxiety was also related to function, specialty of practice, and knowledge of the protective measures against COVID-19.\n\nConclusionWe reported the result of the first evaluation of psychological burden of health worker during early period of COVID-19 pandemic in a developing country. The study showed high frequency of anxiety and depression among Moroccan health worker in a hospital faced to COVID-19 patient management.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jihane Belayachi", + "author_inst": "Mohammed V University in Rabat," + }, + { + "author_name": "Sarah Benammi", + "author_inst": "Acute Medical Unit, Ibn Sina University Hospital, 10000, Rabat, Morocco" + }, + { + "author_name": "Hasnae CHIPPO", + "author_inst": "Hospital Administration, Ibn Sina University Hospital, 10000, Rabat, Morocco." + }, + { + "author_name": "Rhita Nechba BENNIS", + "author_inst": "Acute Medical Unit, Ibn Sina University Hospital, 10000, Rabat, Morocco" + }, + { + "author_name": "Naoufel Madani", + "author_inst": "Acute Medical Unit, Ibn Sina University Hospital, 10000, Rabat, Morocco" + }, + { + "author_name": "Abdelmalek Hrora", + "author_inst": "Surgical Departement, Ibn Sina University Hospital, 10000, Rabat, Morocco." + }, + { + "author_name": "Redouane Abouqal", + "author_inst": "Acute Medical Unit, Ibn Sina University Hospital, 10000, Rabat, Morocco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.02.03.21251075", "rel_title": "Association between Median Household Income, State Medicaid Expansion Status, and COVID-19 Outcomes Across US Counties", @@ -950234,65 +952274,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.03.429628", - "rel_title": "Development of a highly sensitive bioanalytical assay for the quantification of favipiravir.", - "rel_date": "2021-02-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429628", - "rel_abs": "Favipiravir (FAV; T-705) has been approved for use as an anti-influenza therapeutic and has reports against a wide range of viruses (e.g., Ebola virus, rabies and norovirus). Most recently FAV has been reported to demonstrate activity against SARS-CoV-2. Repurposing opportunities have been intensively studied with only limited success to date. If successful, repurposing will allow interventions to become more rapidly available than development of new chemical entities. Pre-clinical and clinical investigations of FAV require robust, reproducible and sensitive bioanalytical assay. Here, a liquid chromatography tandem mass spectrometry assay is presented which was linear from 0.78-200 ng/mL Accuracy and precision ranged between 89% and 110%, 101% and 106%, respectively. The presented assay here has applications in both pre-clinical and clinical research and may be used to facilitate further investigations into the application of FAV against SARS-CoV-2.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Paul Curley", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Megan Neary", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Usman Arshad", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Lee Tatham", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Henry Pertinez", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Helen Box", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Rajith K R Rajoli", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Anthony Valentijn", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Joanne Sharp", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Steve Rannard", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Andrew Owen", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.02.03.21250974", "rel_title": "Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US", @@ -951792,6 +953773,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.05.429940", + "rel_title": "Protein glycosylation is essential for SARS-CoV-2 infection", + "rel_date": "2021-02-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.05.429940", + "rel_abs": "SARS-CoV-2 extensively N-glycosylates its spike proteins, which are necessary for host cell invasion and the target of both vaccines and immunotherapies. These sugars are predicted to help mediate spike binding to the host receptor by stabilizing its open conformation and evading host immunity. Here, we investigated both the essentiality of the host N-glycosylation pathway and SARS-CoV-2 N-glycans for infection. Inhibition of host N-glycosylation using RNAi or FDA-approved drugs reduced virus infectivity, including that of several variants. Under these conditions, cells produced less virions and some completely lost their infectivity. Furthermore, partial deglycosylation of intact virions showed that surface-exposed N-glycans are critical for cell invasion. Altogether, spike N-glycosylation is a targetable pathway with clinical potential for treatment or prevention of COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Aitor Casas-Sanchez", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Alessandra Romero-Ramirez", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Eleanor Hargreaves", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Cameron C Ellis", + "author_inst": "University of Texas at El Paso, TX, USA" + }, + { + "author_name": "Brian I Grajeda", + "author_inst": "University of Texas at El Paso, TX, USA" + }, + { + "author_name": "Igor Estevao", + "author_inst": "University of Texas at El Paso, TX, USA" + }, + { + "author_name": "Edward I Patterson", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Grant L Hughes", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Igor C Almeida", + "author_inst": "University of Texas at El Paso, TX, USA" + }, + { + "author_name": "Tobias Zech", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Alvaro Acosta-Serrano", + "author_inst": "Liverpool School of Tropical Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.05.429566", "rel_title": "Serological Profile Of Specific Antibodies Against Dominant Antigens Of SARS-CoV-2 In Chilean COVID-19 Patients.", @@ -952948,57 +954988,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.01.21250537", - "rel_title": "Towards a COVID-19 symptom triad: The importance of symptom constellations in the SARS-CoV-2 pandemic", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250537", - "rel_abs": "Pandemic scenarios like SARS-Cov-2 require rapid information aggregation. In the age of eHealth and data-driven medicine, publicly available symptom tracking tools offer efficient and scalable means of collecting and analyzing large amounts of data. As a result, information gains can be communicated to front-line providers. We have developed such an application in less than a month and reached more than 500 thousand users within 48 hours. The dataset contains information on basic epidemiological parameters, symptoms, risk factors and details on previous exposure to a COVID-19 patient. Exploratory Data Analysis revealed different symptoms reported by users with confirmed contacts vs. no confirmed contacts. The symptom combination of anosmia, cough and fatigue was the most important feature to differentiate the groups, while single symptoms such as anosmia, cough or fatigue alone were not sufficient. A linear regression model from the literature using the same symptom combination as features was applied on all data. Predictions matched the regional distribution of confirmed cases closely across Germany, while also indicating that the number of cases in northern federal states might be higher than officially reported. In conclusion, we report that symptom combinations anosmia, fatigue and cough are most likely to indicate an acute SARS-CoV-2 infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Leander Edwin Melms", - "author_inst": "Institute of Artificial Intelligence, Philipps-University Marburg" - }, - { - "author_name": "Evelyn Falk", - "author_inst": "Institute of Artificial Intelligence, Philipps-University Marburg" - }, - { - "author_name": "Bernhard Schieffer", - "author_inst": "Cardiology Department, University Hospital Giessen and Marburg" - }, - { - "author_name": "Andreas Jerrentrup", - "author_inst": "Emergency Department, University Hospital Giessen and Marburg" - }, - { - "author_name": "Uwe Wagner", - "author_inst": "Department of Gynaecology, University Hospital Giessen and Marburg" - }, - { - "author_name": "Sami Matrood", - "author_inst": "Department of Gastroenterology, Endocrinology, Metabolism and Infectiology, Philipps-University, Marburg" - }, - { - "author_name": "J\u00fcrgen R Schaefer", - "author_inst": "Centre for undiagnosed and rare diseases, University Hospital Giessen and Marburg" - }, - { - "author_name": "Tobias M\u00fcller", - "author_inst": "Centre for undiagnosed and rare diseases, University Hospital Giessen and Marburg" - }, - { - "author_name": "Martin Hirsch", - "author_inst": "Institute of Artificial Intelligence, Philipps-University Marburg" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.01.21250877", "rel_title": "Optimal time to return to normality: parallel use of COVID-19 vaccines and circuit breakers", @@ -953278,6 +955267,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, + { + "rel_doi": "10.1101/2021.02.01.21250935", + "rel_title": "The effect of mobility restrictions on the SARS-CoV-2 diffusion during the first wave: what are the impacts in Sweden, USA, France and Colombia.", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250935", + "rel_abs": "ResumeCombined with sanitation and social distancing measures, control of human mobility has quickly been targeted as a major leverage to contain the spread of SARS-CoV-2 in a great majority of countries worldwide. The extent to which such measures were successful, however, is uncertain (Gibbs et al. 2020; Kraemer et al. 2020). Very few studies are quantifying the relation between mobility, lockdown strategies and the diffusion of the virus in different countries. Using the anonymised data collected by one of the major social media platforms (Facebook) combined with spatial and temporal Covid-19 data, the objective of this research is to understand how mobility patterns and SARS-CoV-2 diffusion during the first wave are connected in four different countries: the west coast of the USA, Colombia, Sweden and France. Our analyses suggest a relatively modest impact of lockdown on the spread of the virus at the national scale. Despite a varying impact of lockdown on mobility reduction in these countries (83% in France and Colombia, 55% in USA, 10% in Sweden), no country successfully implemented control measures to stem the spread of the virus. As observed in Hubei (Chinazzi et al. 2020), it is likely that the virus had already spread very widely prior to lockdown; the number of affected administrative units in all countries was already very high at the time of lockdown despite the low testing levels. The second conclusion is that the integration of mobility data considerably improved the epidemiological model (as revealed by the QAIC). If inter-individual contact is a fundamental element in the study of the spread of infectious diseases, it is also the case at the level of administrative units. However, this relational dimension is little understood beyond the individual scale mostly due to the lack of mobility data at this scale. Fortunately, these types of data are getting increasingly provided by social media or mobile operators, and they can be used to help administrations to observe changes in movement patterns and/or to better locate where to implement disease control measures such as vaccination (Pollina & Busvine 2020; Pullano et al. 2020; Romm et al. 2020).", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Olivier Telle", + "author_inst": "Centre National de la Recherche Scientifique" + }, + { + "author_name": "Samuel Benkimoun", + "author_inst": "Geographie-cites" + }, + { + "author_name": "Richard E. Paul", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.01.21250306", "rel_title": "ABC2-SPH risk score for in-hospital mortality in COVID-19 patients: development, external validation and comparison with other available scores", @@ -955166,93 +957182,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.02.21250910", - "rel_title": "Elevated mucosal antibody responses against SARS-CoV-2 are correlated with lower viral load and faster decrease in systemic COVID-19 symptoms", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250910", - "rel_abs": "Mucosal antibodies play a key role in protection against SARS-CoV-2 exposure, but their role during primary infection is not well understood. We assessed mucosal antibody responses during primary infection with SARS-CoV-2 and examined their relationship with viral load and clinical symptoms. Elevated mucosal IgM was associated with lower viral load. RBD and viral spike protein-specific mucosal antibodies were correlated with decreases in systemic symptoms, while older age was associated with an increase in respiratory symptoms. Up to 42% of household contacts developed SARS-CoV-2-specific mucosal antibodies, including children, indicating high transmission rates within households in which children might play an important role.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Janeri Fr\u00f6berg", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Joshua Gillard", - "author_inst": "Centre for molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre Nijmegen, 6525 GA Nijmegen, " - }, - { - "author_name": "Ria Philipsen", - "author_inst": "RTC CS Radboud Technology Center Clinical Studies, Radboudumc, Nijmegen" - }, - { - "author_name": "Kjerstin Lanke", - "author_inst": "Radboud Center for Infectious Diseases, Radboudumc, Nijmegen" - }, - { - "author_name": "Joyce Rust", - "author_inst": "RTC CS Radboud Technology Center Clinical Studies, Radboudumc, Nijmegen" - }, - { - "author_name": "Diana van Tuijl", - "author_inst": "RTC CS Radboud Technology Center Clinical Studies, Radboudumc, Nijmegen" - }, - { - "author_name": "Teun Bousema", - "author_inst": "Radboud Center for Infectious Diseases, Radboudumc, Nijmegen" - }, - { - "author_name": "Elles Simonetti", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Christa van der Gaast-de Jongh", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Mariska Bos", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Frank J.M. van Kuppeveld", - "author_inst": "Utrecht University, Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Utrecht, the Nether" - }, - { - "author_name": "Berend Jan Bosch", - "author_inst": "Utrecht University" - }, - { - "author_name": "Marrigje Nabuurs-Franssen", - "author_inst": "Department of medical microbiology and infectious diseases, Canisius Wilhelmina hospital, Nijmegen" - }, - { - "author_name": "Nannet van der Geest-Blankert", - "author_inst": "Department of Occupational Health, Radboud university medical centre" - }, - { - "author_name": "Charlotte van Daal", - "author_inst": "Department of Occupational Health, Radboud university medical centre" - }, - { - "author_name": "Martijn A. Huynen", - "author_inst": "Centre for molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre Nijmegen" - }, - { - "author_name": "Marien I. de Jonge", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - }, - { - "author_name": "Dimitri A Diavatopoulos", - "author_inst": "Radboud university medical center, Radboud Institute for Molecular Life Sciences, Laboratory of Medical Immunology, Section Paediatric Infectious Diseases, Nijm" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.02.21250985", "rel_title": "Rapid vaccination and early reactive partial lockdown will minimize deaths from emerging highly contagious SARS-CoV-2 variants", @@ -955500,6 +957429,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.02.02.21250630", + "rel_title": "First indication of the effect of COVID-19 vaccinations on the course of the COVID-19 outbreak in Israel", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250630", + "rel_abs": "Concomitantly with rolling out its rapid COVID-19 vaccine program, Israel is experiencing its third, and so far largest, surge in morbidity. We aimed to estimate whether the high vaccine coverage among individuals aged over 60 years old creates an observable change in disease dynamics. Using observed and simulated data, we suggest that the shape of the outbreak as measured by daily new moderate and severe cases, and in particular of patients aged over 60, has changed because of vaccination, bringing the decline in new moderate and severe cases earlier than expected, by about a week. Our analyses is consistent with the assumption that vaccination lead to higher than 50% protection in preventing clinical disease and with at least some effectiveness in blocking transmission of elderly population, and supports the importance of prioritizing vulnerable population. This is the first indication of the effectivity of COVID-19 vaccine in changing the course of an ongoing pandemic outbreak.\n\nOne Sentence SummaryWe show, by data analysis and modelling of the dynamics of COVID-19 pandemic in Israel, that the current nationwide outbreak, that had up to 0.1% of the population confirmed daily, is clearly affected by the vaccination program, that reached a coverage of more than 80% among people [≥] 60 years old.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hilla De-Leon", + "author_inst": "ECT*" + }, + { + "author_name": "Ronit Calderon-Margalit", + "author_inst": "The Hebrew University of Jerusalem" + }, + { + "author_name": "Francesco Pederiva", + "author_inst": "University of Trento" + }, + { + "author_name": "Yinon Ashkenazy", + "author_inst": "Racah Institute of Physics, The Hebrew University" + }, + { + "author_name": "Doron Gazit", + "author_inst": "Racah Institute of Physics, The Hebrew University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.02.21251022", "rel_title": "Quantifying meaningful adoption of a SARS-CoV-2 exposure notification app on the campus of the University of Arizona", @@ -957296,45 +959260,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.03.429522", - "rel_title": "Knowledge and Awareness of coronavirus disease 2019 (COVID-19) among Chinese dental students----a comparison study.", - "rel_date": "2021-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429522", - "rel_abs": "BackgroudThis study aimed to measure the knowledge and awareness of COVID-19 among Chinese dental students during the global outbreak recently.\n\nMethodA descriptive cross-sectional study was performed among dental students and nonmedical college students in China. All the participants were required to anonymously answer a reliable online questionnaire, which covered 3 different fields of COVID-19. Average scores of dental students (D group), including junior (JD group) and senior dental students (SD group), and nonmedical college students (N group) were compared respectively. Chi-square test and independent sample T test were taken for statistical analysis with SPSS.12.\n\nResultsTotally 497 questionnaires were collected, including 224 from dental students and 273 from non-medical students. The overall average score was 57{+/-}19.2. The average scores of dental students were 64.5{+/-}18. The D group had significantly higher scores on the total score, section scores, and 20 questions respectively than with the N group. No significant differences were found on 5 questions. Compared with the N group, the SD group won on all three sections while JD group failed to win on the diagnose section.\n\nConclusionAlthough the dental student showed good awareness regarding the clinical aspects of COVID-19 than non-medical students, there are still some weakness in the part of treatment and prevention, which need to be strengthened for better prepare during work. Besides, the low accuracy rate of lower grade dental students is also worth noting.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "bing Shi", - "author_inst": "Sichuan University West China College of Stomatology" - }, - { - "author_name": "Chengdan Deng", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - }, - { - "author_name": "HuangShui Ma", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - }, - { - "author_name": "Yuke Shou", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - }, - { - "author_name": "Yuke Zhao", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - }, - { - "author_name": "Yang Li", - "author_inst": "Sichuan University West China Hospital of Stomatology: Sichuan University West China College of Stomatology" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2021.02.03.429201", "rel_title": "'Phytopathological strolls' in the dual context of COVID-19 lockdown and IYPH2020: transforming constraints into an opportunity for public education about plant pathogens", @@ -957502,6 +959427,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.29.21250786", + "rel_title": "Sustainable targeted interventions to mitigate the COVID-19 pandemic: A big data-driven modeling study in Hong Kong", + "rel_date": "2021-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250786", + "rel_abs": "Nonpharmaceutical interventions (NPIs) for contact suppression have been widely used worldwide, which impose harmful burdens on the population and the local economy. The evaluation of alternative NPIs is needed to confront the pandemic with less disruption. By harnessing human mobility data, we develop an agent-based model that can evaluate the efficacies of NPIs with individualized mobility simulations. Based on the model, we propose data-driven targeted interventions to mitigate the COVID-19 pandemic in Hong Kong without city-wide NPIs. We develop a data-driven agent-based model for 7.55 million Hong Kong residents to evaluate the efficacies of various NPIs in the first 80 days of the initial outbreak. The entire territory of Hong Kong is split into 4,905 500m x 500m grids. The model can simulate detailed agent interactions based on the demographics data, public facilities and functional buildings, transportation systems, and travel patterns. The general daily human mobility patterns are adopted from Googles Community Mobility Report. The scenario without any NPIs is set as the baseline. By simulating the epidemic progression and human movement at the individual level, we proposed model-driven targeted interventions, which focus on the surgical testing and quarantine of only a small portion of regions instead of enforcing NPIs in the whole city. The efficacious of common NPIs and the proposed targeted interventions are evaluated by extensive 100 simulations. The proposed model can inform targeted interventions, which are able to effectively contain the COVID-19 outbreak with much lower disruption of the city. It represents a promising approach to sustainable NPIs to help us revive the economy of the city and the world.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hanchu ZHOU", + "author_inst": "City university of Hong Kong" + }, + { + "author_name": "Qingpeng Zhang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Zhidong Cao", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Helai Huang", + "author_inst": "Central South University" + }, + { + "author_name": "Dajun Zeng", + "author_inst": "Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.30.21250827", "rel_title": "A Logistic Formula in Biology and Its Application to Deaths by the Third Wave of COVID-19 in Japan", @@ -958970,57 +960930,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.01.429176", - "rel_title": "Host PDZ-containing proteins targeted by SARS-Cov-2", - "rel_date": "2021-02-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.01.429176", - "rel_abs": "Small linear motif targeting protein interacting domains called PDZ have been identified at the C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins E, 3a, and N. Using a high-throughput approach of affinity-profiling against the full human PDZome, we identified sixteen human PDZ binders of SARS-CoV-2 proteins E, 3A and N showing significant interactions with dissociation constants values ranging from 3 M to 82 M. Six of them (TJP1, PTPN13, HTRA1, PARD3, MLLT4, LNX2) are also recognized by SARS-CoV while three (NHERF1, MAST2, RADIL) are specific to SARS-CoV-2 E protein. Most of these SARS-CoV-2 protein partners are involved in cellular junctions/polarity and could be also linked to evasion mechanisms of the immune responses during viral infection. Seven of the PDZ-containing proteins among binders of the SARS-CoV-2 proteins E, 3a or N affect significantly viral replication under knock-down gene expression in infected cells. This PDZ profiling identifying human proteins potentially targeted by SARS-CoV-2 can help to understand the multifactorial severity of COVID19 and to conceive effective anti-coronaviral agents for therapeutic purposes.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Celia Caillet-Saguy", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Fabien Durbesson", - "author_inst": "AFMB" - }, - { - "author_name": "Veronica V. REZELJ", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Gergo Gogl", - "author_inst": "IGBMC" - }, - { - "author_name": "Quang Dinh Tran", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean-Claude Twizere", - "author_inst": "University of Liege" - }, - { - "author_name": "Marco Vignuzzi", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Renaud Vincentelli", - "author_inst": "AFMB" - }, - { - "author_name": "Nicolas Wolff", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.01.30.428979", "rel_title": "Production of SARS-CoV-2 virus-like particles in insect cells", @@ -959252,6 +961161,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.01.28.21250714", + "rel_title": "Discrimination of SARS-Cov 2 and arboviruses (DENV, ZIKV and CHIKV) clinical features using machine learning techniques: a fast and inexpensive clinical screening for countries simultaneously affected by both diseases", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250714", + "rel_abs": "SARS-Cov-2 (Covid-19) has spread rapidly throughout the world, and especially in tropical countries already affected by outbreaks of arboviruses, such as Dengue, Zika and Chikungunya, and may lead these locations to a collapse of health systems. Thus, the present work aims to develop a methodology using a machine learning algorithm (Support Vector Machine) for the prediction and discrimination of patients affected by Covid-19 and arboviruses (DENV, ZIKV and CHIKV). Clinical data from 204 patients with both Covid-19 and arboviruses obtained from 23 scientific articles and 1 dataset were used. The developed model was able to predict 93.1% of Covid-19 cases and 82.1% of arbovirus cases, with an accuracy of 89.1% and Area under Roc Curve of 95.6%, proving to be effective in prediction and possible screening of these patients, especially those affected by Covid-19, allowing early isolation.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Joao Daniel Santos Castro", + "author_inst": "Universidade do Estado da Bahia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.01.28.21250716", "rel_title": "Socioeconomic Disparities and COVID-19 Vaccination Acceptance: Experience from Israel", @@ -960700,57 +962628,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.28.21250163", - "rel_title": "Ultra-short-wave diathermy shortens the course of moderate and severe COVID-19: a randomized controlled trial", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250163", - "rel_abs": "QuestionIs ultra-short-wave diathermy (USWD) safe and effective in coronavirus disease 2019 (COVID-19) ?\n\nDesignSingle-centre, evaluator-blinded, two-arm, parallel design, randomized controlled clinical trial.\n\nParticipantsModerate and severe COVID-19 patients with acute respiratory syndrome.\n\nInterventionUSWD for 10 minutes twice daily for 12 consecutive days along with standard medical treatment (USWD group, n = 25), versus standard medical treatment alone (control group, n = 25).\n\nOutcome measuresThe primary outcomes were the duration of recovery and negative conversion rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on days 7, 14, 21, and 28. Secondary outcomes included clinical status (seven-category ordinal and systemic inflammatory response syndrome (SIRS) scores), computed tomography (CT), routine blood tests, and adverse events.\n\nResultsTime to clinical recovery (USWD 36.84{+/-}9.93 vs. control 43.56{+/-}12.15, P = 0.037) was significantly shortened with a between-group difference of 6.72 days. Clinical status was improved with significant between-group differences on day 28 (SIRS, P = 0.011; seven-category scale, P = 0.003). The rate of RNA negative conversion at days 7 (P = 0.066), 14 (P = 0.239), 21 (P = 0.269), and 28 (P = 0.490) was statistically insignificant. Moreover, insignificant differences were observed in the artificial intelligence-assisted CT analysis. No treatment-associated adverse events or worsening of pulmonary fibrosis were observed.\n\nConclusionUSWD, as adjunctive therapy, shortened the recovery course and improved clinical status of patients with COVID-19 without aggravating pulmonary fibrosis. the findings are limited due to the small sample size and early termination.\n\nRegistrationChiCTR2000029972", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "liangjiang huang", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "qian li", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "Shah Zulfiqar Ali Sayed", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "Nasb Mohammad", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "bin chen", - "author_inst": "Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China." - }, - { - "author_name": "MPhil Ali Iftikhar", - "author_inst": "Paraplegic Center, Hayatabad, Peshawar, Pakistan" - }, - { - "author_name": "Lingfeng Xie", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - }, - { - "author_name": "Jifa Hu", - "author_inst": "Office of Academic Research, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "hong chen", - "author_inst": "Department of Rehabilitation Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic o" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2021.01.29.21250757", "rel_title": "Updated SARS-CoV-2 Single Nucleotide Variants and Mortality Association", @@ -960998,6 +962875,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.30.21250844", + "rel_title": "Retinol Depletion in Severe COVID-19", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.30.21250844", + "rel_abs": "Background and PurposeVitamin A is depleted during infections. Vitamin A has been used successfully in measles, RSV and AIDS patients and is an effective vaccine adjuvant. In this study, low retinol levels were found in patients with severe COVID-19. Retinoid signaling impairment in COVID-19 disrupts Type-I interferon synthesis.\n\nMaterial and MethodTwo groups were formed in the study. The patient group consisted of 27 (Group 1) severe COVID-19 patients hospitalized in the intensive care unit with respiratory failure, and the control group consisted of 23 (Group 2) patients without COVID-19 symptoms. Serum retinol levels were analyzed by ELIZA and HPLC in both groups.\n\nFindingsRetinol levels were found to be significantly lower in the patient group (P <0.001). There was no difference in retinol between two different age groups in the patient group (P> 0.05). There was no significant difference in retinol between men and women (P> 0.05). Comorbidity did not affect serum retinol levels (P >0.05).\n\nConclusionSerum retinol levels were low in patients with severe COVID-19. Drugs preventing retinol excretion were not stopped in the patient group. Some patients took vitamin A externally. Despite this, retinol was low in COVID-19 patients. Retinol depletion impairs Type-I interferon synthesis by impairing retinoid signaling. Retinoid signaling may be the main pathogenetic disorder in COVID-19. This pathogenesis can serve as a guide for adjuvants, drug targets, and candidate drugs. Retinol, retinoic acid derivatives, and some CYP450 inhibitors may work on COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Aziz Rodan Sarohan", + "author_inst": "Private Ba\u011flar Hospital" + }, + { + "author_name": "Hakan Akelma", + "author_inst": "University of Health Sciences, Training and Research Hospital, Department of Anesthesiology and Reanimation" + }, + { + "author_name": "Esref Arac", + "author_inst": "University of Health Sciences, Training and Research Hospital, Department of Internal Medicine" + }, + { + "author_name": "Ozgur Aslan", + "author_inst": "University of Health Sciences,Training and Research Hospital, Department of Medical Biochemistry" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.29.21250790", "rel_title": "Sensitive extraction-free SARS-CoV-2 RNA virus detection using a novel RNA preparation method", @@ -962218,41 +964126,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.29.21250643", - "rel_title": "Emergence of first strains of Sars-CoV-2 lineage B.1.1.7 in Romania", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250643", - "rel_abs": "United Kingdom reported the emergence of a new and highly transmissible SARS-CoV-2 variant B.1.1.7. that rapidly spread to other contries. The impact of this new mutation that occurs in the S protein, on infectivity, virulence and current vaccine effectiveness is still under evaluation. We have identified the first cases of the B.1.1.7 variant in samples collected from Romanian patients, of which one was traced to the UK region where the new variant was originally sequenced. Mutations in the Nsp3 protein, N844S and D455N and L15F in Orf3a were also detected, indicating common ancestry with UK strains as well as remote connections with strains from Nagasaki, Japan. These results indicate, for the first time, the presence and characteristics of the new variant B.1.1.7 in Romania and underscore the need for increased genomic sequencing in confirmed COVID-19 patients.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Andrei Lobiuc", - "author_inst": "University Stefan cel Mare Suceava, Romania" - }, - { - "author_name": "Mihai Dimian", - "author_inst": "University Stefan cel Mare Suceava, Romania" - }, - { - "author_name": "Olga Sturdza", - "author_inst": "University Stefan cel Mare, Suceava, Romania" - }, - { - "author_name": "Roxana Filip", - "author_inst": "University Stefan cel Mare, Suceava, Romania" - }, - { - "author_name": "Mihai Covasa", - "author_inst": "Universitatea Stefan cel Mare Suceava, Romania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.29.21250653", "rel_title": "Robust spike antibody responses and increased reactogenicity in seropositive individuals after a single dose of SARS-CoV-2 mRNA vaccine", @@ -962532,6 +964405,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.27.21250618", + "rel_title": "Neighbourhood-level risk factors of COVID-19 incidence and mortality", + "rel_date": "2021-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250618", + "rel_abs": "BackgroundRacialized and low income communities face disproportionally high rates of coronavirus 2019 (COVID-19) infection and death. However, data on inequities in COVID-19 across granular categories of socio-demographic characteristics is more sparse.\n\nMethodsNeighbourhood-level counts of COVID-19 cases and deaths in Ontario, Canada recorded as of July 28th, 2020 were extracted from provincial and local reportable infectious disease surveillance systems. Associations between COVID-19 incidence and mortality and 18 neighbourhood-level measures of immigration, race, housing and socio-economic characteristics were estimated with Poisson generalized linear mixed models. Housing characteristic variables were subsequently added to models to explore if housing may have a confounding influence on the relationships between immigration, race, and socio-economic status and COVID-19 incidence.\n\nResultsThere were large inequities in COVID-19 incidence and mortality across the socio-demographic variables examined. Neighbourhoods having a higher proportion immigrants, racialized populations, large households and low socio-economic status were associated with COVID-19 risk. Adjusting for housing characteristics, especially unsuitably crowded housing, attenuated COVID-19 risks. However persistent risk remained for neighbourhoods having high proportions of immigrants, racialized populations, and proportion of Black, Latin American, and South Asian residents.\n\nConclusionsSocio-demographic factors account for some of the neighbourhood-level differences in COVID-19 across Ontario. Housing characteristics account for a portion, but not all, of the excess burden of COVID-19 experienced by immigrant, racialized, low income and low education populations.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Trevor van Ingen", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Kevin A Brown", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Sarah A Buchan", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Samantha Akingbola", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Nick Daneman", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Brendan T Smith", + "author_inst": "Public Health Ontario" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.27.21250642", "rel_title": "Forecasting virus outbreaks with social media data via neural ordinary differential equations", @@ -964408,37 +966320,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.01.27.21250238", - "rel_title": "Disentangling the association of hydroxychloroquine treatment with mortality in Covid-19 hospitalized patients through Hierarchical Clustering", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250238", - "rel_abs": "The efficacy of hydroxychloroquine (HCQ) in treating SARS-CoV-2 infection is harshly debated, with observational and intervention studies reporting contrasting results.\n\nTo clarify the role of HCQ in Covid-19 patients, we carried out a retrospective observational study of 4,396 unselected patients hospitalized for Covid-19 in Italy (February-May 2020). Patients characteristics were collected at entry, including age, sex, obesity, smoking status, blood parameters, history of diabetes, cancer, cardiovascular and chronic pulmonary diseases and medications in use. These were used to identify subtypes of patients with similar characteristics through hierarchical clustering based on Gower distance. Using multivariable Cox regressions, these clusters were then tested for association with mortality and modification of effect by treatment with HCQ.\n\nWe identified two clusters, one of 3,913 younger patients with lower circulating inflammation levels and better renal function, and one of 483 generally older and more comorbid subjects, more prevalently men and smokers. The latter group was at increased death risk adjusted by HCQ (HR[CI95%] = 3.80[3.08-4.67]), while HCQ showed an independent inverse association (0.51[0.43-0.61]), as well as a significant influence of cluster*HCQ interaction (p<0.001). This was driven by a differential association of HCQ with mortality between the high (0.89[0.65-1.22]) and the low risk cluster (0.46[0.39-0.54]). These effects survived adjustments for additional medications in use and were concordant with associations with disease severity and outcome.\n\nThese findings suggest a particularly beneficial effect of HCQ within low risk Covid-19 patients and may contribute clarifying the current controversy on HCQ efficacy in Covid-19 treatment.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Augusto Di Castelnuovo", - "author_inst": "Mediterranea Cardiocentro, Naples, Italy" - }, - { - "author_name": "Alessandro Gialluisi", - "author_inst": "IRCCS Neuromed" - }, - { - "author_name": "- The COVID-19 RISK and Treatments (CORIST) Collaboration", - "author_inst": "" - }, - { - "author_name": "Licia Iacoviello", - "author_inst": "Universita dell'Insubria, Varese, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.26.21250533", "rel_title": "Lumipulse G SARS-CoV-2 Ag Assay Evaluation for SARS-CoV-2 Antigen Detection Using 594 Nasopharyngeal Swab Samples from Different Testing Groups", @@ -964738,6 +966619,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250557", + "rel_title": "Covid-19 positive test cycle threshold trends predict covid-19 mortality in Rhode Island", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250557", + "rel_abs": "The cycle thresholds (Cts) at which reverse transcriptase polymerase chain reaction (rtPCR) tests for covid-19 become positive are intimately associated with both viral load, and covid-19 infectiousness (i.e., ability to culture live virus). Clinical data indicate lower Cts--and hence larger viral loads--independently predict greater covid-19 mortality when patients are hospitalized for symptomatic covid-19 pneumonia. We merged public covid-19 mortality data from the Rhode Island Department of Health with a de-identified dataset of n=5036 positive rtPCR test Cts from the Rhode Island Department of Health State Laboratory to explore the potential relationship between positive covid-19 test Ct distribution trends, and covid-19 mortality in the state of Rhode Island, from March through early to mid-June, 2020. Mean daily covid-19 positive test Ct data were compiled, and 7-day rolling average covid-19 mortality was offset by 21-days, given the lag between infection and death. We divided the Ct data into three strata, >32, 28-32, and <28, which were operationally defined as \"not infectious,\" \"maybe infectious,\" and \"infectious,\" respectively. Between late March and June, mean daily Ct values rose linearly (R-squared=0.789) so that by early June, as the covid-19 pandemic ebbed in severity, all means reached the noninfectious (Ct >32) range. Most notably, this May-June trend for Cts was accompanied by a marked, steady decline in Rhode Islands daily covid-19 mortality. Our results suggest that monitoring, and public reporting of mean population covid-19 test Cts over time is warranted to gauge the vacillations of covid-19 outbreak severity, including covid-19 mortality trends.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andrew Bostom", + "author_inst": "Brown University" + }, + { + "author_name": "Charles B. Eaton", + "author_inst": "Brown University" + }, + { + "author_name": "Todd Kenyon", + "author_inst": "Nobadeer Capital Management, LLC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.26.21250535", "rel_title": "SARS-CoV-2 seropositivity and subsequent infection risk in healthy young adults: a prospective cohort study", @@ -965910,41 +967818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.27.21250521", - "rel_title": "Induction of labour during the COVID-19 pandemic: a national survey of impact on practice in the UK", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250521", - "rel_abs": "BackgroundInduction of labour (IOL) is one of the most commonly performed interventions in maternity care, with outpatient cervical ripening increasingly offered as an option for women undergoing IOL. The COVID-19 pandemic has changed the context of practice and the option of returning home for cervical ripening may now assume greater significance. This work aimed to examine whether and how the COVID-19 pandemic has changed practice around IOL in the UK.\n\nMethodWe used an online questionnaire to survey senior obstetricians and midwives at all 156 UK NHS Trusts and Boards that currently offer maternity services. Responses were analysed to produce descriptive statistics, with free text responses analysed using a conventional content analysis approach.\n\nFindingsResponses were received from 92 of 156 UK Trusts and Boards, a 59% response rate. Many Trusts and Boards reported no change to their IOL practice, however 23% reported change in methods used for cervical ripening; 28% a change in criteria for home cervical ripening; 28% stated that more women were returning home during cervical ripening; and 24% noted changes to womens response to recommendations for IOL. Much of the change was reported as happening in response to attempts to minimise hospital attendance and restrictions on birth partners accompanying women.\n\nConclusionsThe pandemic has changed practice around induction of labour, although this varied significantly between NHS Trusts and Boards. There is a lack of formal evidence to support decision-making around outpatient cervical ripening: the basis on which changes were implemented and what evidence was used to inform decisions is not clear.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mairi Harkness", - "author_inst": "University of Stirling" - }, - { - "author_name": "Cassandra Yuill", - "author_inst": "City, University of London" - }, - { - "author_name": "Helen Cheyne", - "author_inst": "University of Stirling" - }, - { - "author_name": "Sarah Stock", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Christine McCourt", - "author_inst": "City, University of London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.01.27.21250153", "rel_title": "The prevalence of olfactory dysfunction and its associated factors in patients with COVID-19 infection", @@ -966124,6 +967997,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250561", + "rel_title": "SARS-CoV-2 antigenemia/viremia masks seroconversion in a COVID-19 patient", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250561", + "rel_abs": "Immune responses against SARS-CoV-2 have been vigorously analyzed. It has been proposed that a subset of mild or asymptomatic cases with undetectable antibodies may clear the virus in a T-cell cytotoxic-dependent manner, albeit recent data revealed the importance of B-cells in that regard. We hypothesized that underdiagnosed antigenemia/viremia may conceal humoral response possibly through immunocomplex formation. We report the first case of late-onset seroconversion detected following decline in antigenemia/viremia levels. Consequently, classification of at least a subset of COVID-19 cases as non-responders might not represent a true immunobiological phenomenon, rather reflect antibody masking due to prolonged antigenemia/viremia.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Vassilis G Gorgoulis", + "author_inst": "Medical School, National Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.28.21250096", "rel_title": "The successful use of volunteers to enhance NHS Test and Trace contact tracing of in-patients with Covid-19: a Pilot Study", @@ -967836,85 +969728,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.26.21250506", - "rel_title": "The Association Between Hypoglycemic Agents and Clinical Outcomes of COVID-19 in Patients with Diabetes: A Systematic Review and Meta-Analysis", - "rel_date": "2021-01-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250506", - "rel_abs": "BackgroundDuring the current Coronavirus Disease 2019 (COVID-19) pandemic, diabetic patients face disproportionately more. Anti-inflammatory effects of hypoglycemic agents have been reported, and their beneficial or harmful effects in patients with diabetes and COVID-19 remain controversial.\n\nPurposeThis study was performed to clarify this association.\n\nData SourcesRelevant literature was searched on China National Knowledge Infrastructure (CNKI), Wanfang Data Knowledge Service Platform, Chinese periodical service platform VIP Database, Sinomed (China Biology Medicine, CBM), MedRxiv, PubMed, ScienceDirect, Web of Science, Ovid Databases (LWW), Springer Link, Wiley Online Library, Oxford Academic, Nature Press Group, Cochrane Library and BMJ Evidence-Based Medicine up to November 14, 2020.\n\nStudy SelectionOnly observational studies of hypoglycemic agents vs. drugs or therapy without hypoglycemic agents in adult diabetic patients with COVID-19 were included.\n\nData ExtractionData of death and poor composite outcomes were extracted.\n\nData SynthesisThe pooled effects were calculated using the fixed-effects or random-effects models based on heterogeneity assessment.\n\nLimitationMost studies were retrospective cohort studies with relative weak capability to verify causality.\n\nConclusionHome use of metformin might be beneficial in decreasing mortality in diabetic patients infected with SARS-CoV-2. There is insufficient evidence to conclude that metformin and other hypoglycemic agents are associated with poor composite outcomes. More prospective studies, especially RCTs are needed.\n\nRegistration-PROSPEROCRD42020221951.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Tiantia Han", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University" - }, - { - "author_name": "Shaodi Ma", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University" - }, - { - "author_name": "Chenyu Sun", - "author_inst": "AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Huimei Zhang", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University" - }, - { - "author_name": "Guangbo Qu", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University" - }, - { - "author_name": "Yue Chen", - "author_inst": "Department of Clinical Medicine, School of the First Clinical Medicine, Anhui Medical University" - }, - { - "author_name": "Ce Cheng", - "author_inst": "The University of Arizona College of Medicine at South Campus" - }, - { - "author_name": "Eric L. Chen", - "author_inst": "Internal Medicine, AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Mubashir Ayaz Ahmed", - "author_inst": "Internal Medicine, AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Keun Young Kim", - "author_inst": "Internal Medicine, AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Reveena Manem", - "author_inst": "Internal Medicine, AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Mengshi Chen", - "author_inst": "Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University" - }, - { - "author_name": "Zhichun Guo", - "author_inst": "Massachusetts college of Pharmacy and Health sciences" - }, - { - "author_name": "Hongru Yang", - "author_inst": "Massachusetts college of Pharmacy and Health sciences" - }, - { - "author_name": "Yue Yan", - "author_inst": "Massachusetts college of Pharmacy and Health sciences" - }, - { - "author_name": "Qin Zhou", - "author_inst": "Radiation Oncology, Mayo Clinic" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2021.01.25.21250040", "rel_title": "COVID-19-related disruptions to routine vaccination services in India: perspectives from pediatricians", @@ -968174,6 +969987,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.01.26.21250420", + "rel_title": "Outcomes of Ivermectin in the treatment of COVID-19: a systematic review and meta-analysis", + "rel_date": "2021-01-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250420", + "rel_abs": "BackgroundTo assess the outcomes of ivermectin in ambulatory and hospitalized patients with COVID-19.\n\nMethodsFive databases and websites for preprints were searched until January 2021 for randomized controlled trials (RCTs) and retrospective cohorts assessing ivermectin versus control in ambulatory and hospitalized participants. The primary outcome was overall mortality. Secondary outcome was recovered patients. For meta-analysis, random-effects and inverse variance meta-analyses with logarithmic transformation were performed. ROBINS-I for cohort studies, and the Cochrane Risk of Bias 2.0 tool for trials were used. The strength of evidence was assessed using GRADE.\n\nResultsAfter the selection, twelve studies (five retrospective cohort studies, six randomized clinical trials and one case series), were included. In total, 7412 participants were reported, the mean age was 47.5 (SD 9.5) years, and 4283 (58%) were male. Ivermectin was not associated with reduced mortality (logRR: 0.89, 95% CI 0.09 to 1.70, p = 0.04, I2= 84.7%), or reduced patient recovery (logRR 5.52, 95% CI -24.36 to 35.4, p = 0.51, I2 = 92.6%). All studies had a high risk of bias, and showed a very low certainty of the evidence.\n\nConclusionsThere insufficient certainty and quality of evidence to recommend the use of ivermectin to prevent or treat ambulatory or hospitalized patients with COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alex Castaneda-Sabogal", + "author_inst": "Universidad Privada Antenor Orrego, Facultad de Medicina, Escuela de Posgrado, Trujillo, Peru" + }, + { + "author_name": "Diego Chambergo-Michilot", + "author_inst": "Universidad Cientifica del Sur, Lima, Peru" + }, + { + "author_name": "Carlos J. Toro-Huamanchumo", + "author_inst": "Universidad San Ignacio de Loyola, Unidad para la Generacion y Sintesis de Evidencias en Salud" + }, + { + "author_name": "Christian Silva-Rengifo", + "author_inst": "Universidad Privada Antenor Orrego, Facultad de Medicina, Trujillo, Peru" + }, + { + "author_name": "Jose Gonzales-Zamora", + "author_inst": "University of Miami, Miller School of Medicine, Miami, Florida, USA" + }, + { + "author_name": "Joshuan J. Barboza", + "author_inst": "Lord of Sipan University, School of Medicine, Chiclayo, Peru" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.25.21250468", "rel_title": "Association between COVID-19 mortality and population level health and socioeconomic indicators", @@ -969574,37 +971426,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.21.21249496", - "rel_title": "Management of conductive deafness from Otitis Media with Effusion (known as glue ear) in children using bone conduction headsets when grommet operations were unavailable during COVID-19.", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21249496", - "rel_abs": "BackgroundOtitis Media with Effusion (OME) causing hearing impairments affects [~]1 in 10 children starting school in UK/ Europe. 80% have at least one episode with most having conductive hearing loss. Studies showed children with OME hear better with bone conducting headsets. During COVID-19 we investigated whether children with deafness secondary OME, without access to audiology or grommet surgery, could be aided with bone conduction kits and the HearGlueEar app.\n\nMethodsStarting July 2020, during COVID-19, children aged 3-11 years with OME and on a grommet waiting list were invited to a single arm, prospective study. They received the kit, instructions and HearGlueEar app by post. By 3 weeks parents were asked to charge and pair the devices, attend a remote consultation and complete an OMQ-14 questionnaire. Remote follow-up lasted 3 months. Outcomes: ability to use the equipment, complete the questionnaire about childs hearing and behaviour before and with the equipment, declining grommet surgery or where deafness resolved, and give opinion about the intervention.\n\nFindings26 children enrolled. Families used the kit at home and school. Most found remote consultations positive and convenient. OMQ-14 responses were 90% positive. Comments were: \"Other people have said, wow his speech is clearer.\", \"It is making a real difference at home.\", \"He said over and over again, \"I can hear everybody, wow, wow, wow.\", \"It is no exaggeration to say this has made an astronomical improvement to his quality of life\". One child reported \"I can hear my best friend again\". \"She is getting on really well with the headphones - pairing them with the iPad at home is simply brilliant.\" Three families continued with the headset to avoid grommets.\n\nInterpretationPosting a bone conduction kit, HearGlueEar app and remote consultation is effective support for children with deafness secondary to OME.\n\nFundingNone", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Tamsin Mary Holland Brown", - "author_inst": "Cambridgeshire Community Services NHS Trust" - }, - { - "author_name": "Isobel Fitzgerald OConnor", - "author_inst": "Cambridge University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Jessica Bewick", - "author_inst": "Cambridge University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Colin Morley", - "author_inst": "Cambridge University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.01.20.21250204", "rel_title": "Rule of thumb in human intelligence for assessing the COVID-19 outbreak in Japan", @@ -969888,6 +971709,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.22.21250328", + "rel_title": "Seroprevalence and attainment of herd immunity against SARS CoV-2: A modelling study", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21250328", + "rel_abs": "ObjectiveThe present study is aims to predict the likelihood of and likely time required to attain herd immunity against COVID-19 in New Delhi due to natural infection.\n\nMethodAn ODE based mathematical model was constructed by extending the classical SEIR model to predict the seroprevalence rate in Delhi. We estimated the parameter values for Delhi using available data (reported cases and the seroprevalence rate) and used them for future prediction. We also attempted to capture the changes in the seroprevalence rate with different possibilities of reinfection.\n\nResultsMaximum seroprevalence rate obtained through our model is 31.65% and also a reduction in the seroprevalence rate was observed for the upcoming one month (month of January, 2021) due to the reduced transmission rate. After increasing the transmission rate to the value same as the third wave in New Delhi, we obtained a maximum value of 54.96%. This maximum value significantly decreased with the reduction in the reinfection possibilities. Also, a little impact of the duration of persistence of antibodies, 180 vs 105 days, was observed on the maximum seroprevalence.\n\nConclusionThis modelling study suggests that natural infection alone, as gauged by serial sero-surveys, will not result in attainment of herd immunity in the state of Delhi.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Abhijit Paul", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "Harshith B Kadnur", + "author_inst": "All India Institute of Medical Science" + }, + { + "author_name": "Animesh Ray", + "author_inst": "All India Institute of Medical Science" + }, + { + "author_name": "Samrat Chatterjee", + "author_inst": "Translational Health Science and Technology" + }, + { + "author_name": "Naveet Wig", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.22.21250285", "rel_title": "ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections", @@ -971468,57 +973324,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.23.21250370", - "rel_title": "Patients with Asthma and Chronic Obstructive Pulmonary Disease (COPD) have increased levels of plasma inflammatory mediators upregulated in severe COVID-19", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.23.21250370", - "rel_abs": "BackgroundChronic obstructive pulmonary disease (COPD) is associated with increased risk of severe COVID-19, but the mechanisms are unclear. Besides, patients with severe COVID-19 have been reported to have increased levels of several immune mediators.\n\nObjectiveTo perform an immunoproteomic profiling of dysregulated plasma proteins in patients with asthma and COPD and to evaluate their relationship with biomarkers of severe COVID-19.\n\nMethodsNinety-two proteins were quantified in 315 plasma samples from adult subjects (age 40-90 years) including 118 asthmatics, 99 COPD patients and 98 healthy controls, that have been recruited in two reference pneumology clinics in Colombia before the beginning of the COVID-19 pandemic. Protein levels were compared between each disease group and healthy controls.\n\nSignificant proteins were compared to the gene signatures of SARS-CoV-2 infection reported in the \"COVID-19 Drug and Gene Set Library\" and with known protein biomarkers of severe COVID-19.\n\nResultsForty-one plasma proteins showed differences between patients and controls. Asthmatic patients have increased levels in IL-6 while COPD patients have a broader systemic inflammatory dysregulation driven by HGF, OPG, and several chemokines (CXCL9, CXCL10, CXCL11, CX3CL1, CXCL1, MCP-3, MCP-4, CCL3, CCL4 and CCL11). These proteins are involved in chemokine signaling pathways related with response to viral infections and some, were found up-regulated upon SARS-CoV-2 experimental infection of Calu-3 cells as reported in the COVID-19 Related Gene Sets database. An increase of HPG, CXCL9, CXCL10, IL-6, MCP-3, TNF and EN-RAGE has also been found in patients with severe COVID-19.\n\nConclusionsCOPD patients have altered levels of plasma proteins that have been reported increased in patients with severe COVID-19. Our study suggests that COPD patients have a systemic dysregulation in chemokine networks (including HGF and CXCL9) that could make them more susceptible to severe COVID-19. Our study also suggest that IL-6 levels are increased in some asthmatics and this may influence their immune response to COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nathalie Acevedo", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - }, - { - "author_name": "Jose Miguel Escamilla-Gil", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - }, - { - "author_name": "Hector Espinoza", - "author_inst": "Universidad de Cartagena, Facultad de Ingenieria" - }, - { - "author_name": "Ronald Regino", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - }, - { - "author_name": "Jonathan Ramirez", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - }, - { - "author_name": "Lucila Florez De Arco", - "author_inst": "Clinica Respitaroria y de Alergias" - }, - { - "author_name": "Rodolfo Dennis", - "author_inst": "Fundacion Cardioinfantil" - }, - { - "author_name": "Carlos Torres-Duque", - "author_inst": "Fundacion Neumologica Colombiana" - }, - { - "author_name": "Luis Caraballo", - "author_inst": "Instituto de Investigaciones Inmunologicas, Universidad de Cartagena" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.01.25.21250233", "rel_title": "Contamination of air and surfaces in workplaces with SARS-CoV-2 virus: a systematic review", @@ -971882,6 +973687,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.24.21250387", + "rel_title": "Identification of COVID-19 Subtypes Based on Immunogenomic Profiling", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.24.21250387", + "rel_abs": "Although previous studies have shown that the host immune response is crucial in determining clinical outcomes in COVID-19 patients, the association between host immune signatures and COVID-19 patient outcomes remains unclear. Based on the enrichment levels of 11 immune signatures (eight immune-inciting and three immune-inhibiting signatures) in leukocytes of 100 COVID-19 patients, we identified three COVID-19 subtypes: Im-C1, Im-C2, and Im-C3, by clustering analysis. Im-C1 had the lowest immune-inciting signatures and high immune-inhibiting signatures. Im-C2 had medium immune-inciting signatures and high immune-inhibiting signatures. Im-C3 had the highest immune-inciting signatures while the lowest immune-inhibiting signatures. Im-C3 and Im-C1 displayed the best and worst clinical outcomes, respectively, suggesting that antiviral immune responses alleviated the severity of COVID-19 patients. We further demonstrated that the adaptive immune response had a stronger impact on COVID-19 outcomes than the innate immune response. The patients in Im-C3 were younger than those in Im-C1, indicating that younger persons have stronger antiviral immune responses than older persons. Nevertheless, we did not observe a significant association between sex and immune responses in COVID-19 patients. In addition, we found that the type II IFN response signature was an adverse prognostic factor for COVID-19. Our identification of COVID-19 immune subtypes has potential clinical implications for the management of COVID-19 patients.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Qiushi Feng", + "author_inst": "China Pharmaceutical University" + }, + { + "author_name": "Xiaosheng Wang", + "author_inst": "China Pharmaceutical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.20.21250182", "rel_title": "ESCAPE: An Open-Label Trial of Personalized Immunotherapy in Critically Ill COVID-19 Patients", @@ -973306,33 +975134,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.01.25.428191", - "rel_title": "Variant and mutation analysis of SARS-CoV-2 genomes isolated from the Kingdom of Bahrain", - "rel_date": "2021-01-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428191", - "rel_abs": "The challenges imposed by the ongoing outbreak of severe acute respiratory syndrome coronavirus-2 affects every aspect of our modern world, ranging from our health to our socio-economic needs. Our existence highly depends on the vaccines availability, which demands in-depth research of the available strains and their mutations. In this work, we have analyzed all the available SERS-CoV2 genomes isolated from the Kingdom of Bahrain in terms of their variance and origin analysis. We have predicted various known and unique mutations in the SERS-CoV2 isolated from Bahrain. The complexity of the phylogenetic tree and dot plot representation of the strains mentioned above with other isolates of Asia indicates the versatility and multiple origins of Bahrains SERS-CoV2 isolates. We have also identified two high impact spike mutations from these strains which increase the virulence of SARS-CoV2. Our research could have a high impact on vaccine development and distinguishes the source of SERS-CoV2 in the Kingdom of Bahrain.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Khalid M bindayna", - "author_inst": "Arabian gulf university" - }, - { - "author_name": "Abdel Halim Deifalla", - "author_inst": "Arabian gulf uninversity" - }, - { - "author_name": "Hicham Ezzat Mohammed Mokbel", - "author_inst": "Arabian gulf uninversity" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.25.428137", "rel_title": "Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization", @@ -973708,6 +975509,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.01.26.428302", + "rel_title": "40 minutes RT-qPCR Assay for Screening Spike N501Y and HV69-70del Mutations", + "rel_date": "2021-01-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.26.428302", + "rel_abs": "A one-step reverse transcription and real-time PCR (RT-qPCR) test was developed for rapid screening (40 minutes) of the Spike N501Y and HV69-70del mutations in SARS-CoV-2 positive samples. The test also targets a conserved region of SARS-CoV-2 Orf1ab as an internal control. The samples containing both the N501Y and HV69-70del mutations are concluded as VOC-202012/01 positive. Samples suspected to be positive for B.1.351 or P.1 are the N501Y positive and HV69-70del negative cases. Limit of detection (LOD) of the kit for Orf1ab target is 500 copies/mL, while that of the N501, Y501 and HV69-70del targets are 5000 copies/mL. The developed assay was applied to 165 clinical samples containing SARS-CoV-2 from 32 different lineages. The SARS-CoV-2 lineages were determined via the next-generation sequencing (NGS). The RT-qPCR results were in 100% agreement with the NGS results that 19 samples were N501Y and HV69-70del positive, 10 samples were N501Y positive and HV69-70del negative, 1 sample was N501Y negative and HV69-70del positive, and 135 samples were N501Y and HV69-70del negative. All the VOC-202012/01 positive samples were detected in people who have traveled from England to Turkey. The RT-qPCR test and the Sanger sequencing was further applied to 1000 SARS-CoV-2 positive clinical samples collected in Jan2021 from the 81 different provinces of Turkey. The RT-qPCR results were in 100% agreement with the Sanger sequencing results that 32 samples were N501Y positive and HV69-70del negative, 4 samples were N501Y negative and HV69-70del positive, 964 samples were N501Y and HV69-70del negative. The specificity of the 40 minutes RT-qPCR assay relative to the sequencing-based technologies is 100%. The developed assay is an advantageous tool for timely and representative estimation of the N501Y positive variants prevalence because it allows testing a much higher portion of the SARS-CoV-2 positives in much lower time compared to the sequencing-based technologies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gulay Korukluoglu", + "author_inst": "WHO National Influenza Center and Virology Reference Laboratory of Ministry of Health Turkey, Ankara, Turkey" + }, + { + "author_name": "Mustafa Kolukirik", + "author_inst": "Bioeksen R&D Technologies Limited, Istanbul Technical University Teknokent, Istanbul, Turkey" + }, + { + "author_name": "Fatma Bayrakdar", + "author_inst": "WHO National Influenza Center and Virology Reference Laboratory of Ministry of Health Turkey, Ankara, Turkey" + }, + { + "author_name": "Gozde Girgin Ozgumus", + "author_inst": "Bioeksen R&D Technologies Limited, Istanbul Technical University Teknokent, Istanbul, Turkey" + }, + { + "author_name": "Ayse Basak Altas", + "author_inst": "WHO National Influenza Center and Virology Reference Laboratory of Ministry of Health Turkey, Ankara, Turkey" + }, + { + "author_name": "Yasemin Cosgun", + "author_inst": "WHO National Influenza Center and Virology Reference Laboratory of Ministry of Health Turkey, Ankara, Turkey" + }, + { + "author_name": "Canan Zohre Ketre Kolukirik", + "author_inst": "Bioeksen R&D Technologies Limited, Istanbul Technical University Teknokent, Istanbul, Turkey" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.26.428296", "rel_title": "Variability in codon usage in Coronaviruses is mainly driven by mutational bias and selective constraints on CpG dinucleotide", @@ -975104,57 +976948,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.21.21250226", - "rel_title": "Determinants of the incidence and mortality rates of COVID-19 during the first six months of the pandemic; A cross-country study", - "rel_date": "2021-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250226", - "rel_abs": "COVID-19 pandemic raises an extraordinary challenge to the healthcare systems globally. The governments are taking key measures to constrain the corresponding health, social, and economic impacts, however, these measures vary depending on the nature of the crisis and country-specific circumstances.\n\nObjectivesConsidering different incidence and mortality rates across different countries, we aimed at explaining variance of these variables by performing accurate and precise multivariate analysis with aid of suitable predictors, accordingly, the model would proactively guide the governmental responses to the crisis.\n\nMethodsUsing linear and exponential time series analysis, this research aimed at studying the incidence and mortality rates of COVID-19 in 18 countries during the first six months of the pandemic, and further utilize multivariate techniques to explain the variance in monthly exponential growth rates of cases and deaths with aid of a set of different predictors: the recorded Google mobility trends towards six categories of places, daily average temperature, daily humidity, and key socioeconomic attributes of each country.\n\nResultsThe analysis showed that changes in mobility trends were the most significant predictors of the incidence and mortality rates, temperature and humidity were also significant but to a much lesser extent, on the other hand, the socioeconomic attributes did not contribute significantly to explaining different incidence and mortality rates across countries.\n\nConclusionChanges in mobility trends across countries dramatically affected the incidence and mortality rates across different countries, thus, it might be used as a proxy measure of contact frequency.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Noha Asem", - "author_inst": "Faculty of Medicine, Cairo University" - }, - { - "author_name": "Ahmed Mohamed Ramadan", - "author_inst": "DataClin CRO, Egypt" - }, - { - "author_name": "Mohamed Hassany", - "author_inst": "Ministry of Health and Population, Egypt" - }, - { - "author_name": "Ramy Mohamed Ghazy", - "author_inst": "High Institute of Public Health, Alexandria, Egypt" - }, - { - "author_name": "Mohamed Abdallah", - "author_inst": "Medical Research Division, National Research Center, Giza, Egypt" - }, - { - "author_name": "Eman Gamal", - "author_inst": "Ministry Of Health and Population" - }, - { - "author_name": "Shimaa Hassan", - "author_inst": "Ministry of Health and Population" - }, - { - "author_name": "Nehal Kamal", - "author_inst": "Children Cancer Hospital (CCHE) 57357" - }, - { - "author_name": "Hala Zaid", - "author_inst": "Ministry of Health and Population, Egypt" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.24.21250416", "rel_title": "Social, economic, and environmental factors influencing the basic reproduction number of COVID-19 across countries", @@ -975478,6 +977271,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.24.21250397", + "rel_title": "Using an Ecological and Biological Framing for an Anti-racist Covid-19 Approach", + "rel_date": "2021-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.24.21250397", + "rel_abs": "In the United States and the United Kingdom COVID-19 has disproportionately affected Black, Indigenous and People of Colour (BIPOC) and Black, Asian and Minority Ethnic (BAME) people respectively. Multiple studies identify environmental factors such as overcrowded housing and poor workplace conditions as contributing factors for the disproportionate COVID-19 rates amongst BAME and BIPOC communities. This paper will show that to fully understand the phenomenon, both an ecological and biological approach is needed. An ecological approach highlights how a persons habitat and the experiences within it mediate their susceptibility to disease. Moreover, to understand how this mediation works, this paper will use allostatic load as a biological pathway to link a person to their habitat and the poor health outcomes that contributed to COVID-19 susceptibility. In introducing this new approach, the paper will serve as an anti-racist framework for understanding how COVID-19 affected BAME and BIPOC communities. It is anti-racist by centring poor health outcomes on the habitats people are forced to live in due to structural racism rather than the physiology of a persons race or ethnicity. This is important in order to avoid similar crises in the future and to improve the health of marginalised communities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Araceli Camargo", + "author_inst": "The Centric Lab" + }, + { + "author_name": "Elahi Hossain", + "author_inst": "Interaction Centre, University College London" + }, + { + "author_name": "Sarah Aliko", + "author_inst": "Experimental Psychology, University College London, UK" + }, + { + "author_name": "Daniel Akinola-Odusola", + "author_inst": "The Centric Lab" + }, + { + "author_name": "Josh Artus", + "author_inst": "The Centric Lab" + }, + { + "author_name": "Ilan Kelman", + "author_inst": "Institute for Risk & Disaster Reduction, University College London" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.01.24.21250391", "rel_title": "Existence of SARS-CoV-2 RNA on ambient particulate matter samples: A nationwide study in Turkey", @@ -977010,37 +978842,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.01.23.427885", - "rel_title": "Variation analysis of SARS-CoV-2 complete sequences from Iran", - "rel_date": "2021-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.23.427885", - "rel_abs": "The SARS-CoV-2 is a new emerging coronavirus initially reported in China at the late December 2019 and rapidly spread to the whole of the world. To date, 1261903 total case and 55830 deaths are reported from Iran as 8 January. In this study, we investigated all the complete sequences of SARS-CoV-2 that publicly reported from Iran. Twenty-four sequences between March to September 2020 were analyzed to identify genome variations and phylogenetic relationships. Furthermore, we assessed the amino acid changes related to the spike glycoprotein as an important viral factor associated with the entry to the host cells and as a vaccine target. Most of the variations are occurred in the ORF1ab, S, N, intergenic and ORF7 regions. The analysis of spike protein mutations demonstrated that D614G mutation could be detected from the May and beyond. Phylogenetic analysis showed that most of the circulated viruses in Iran are belong to the B.4 lineage. Although, we found a limited number of variants associated to the B.1 lineage carrying D614G mutation. Furthermore, we detected a variant characterize as the B.1.36 lineage with sixteen mutations in the spike protein region. This study showed the frequency of the viral populations in Iran as September, therefore, there is an emergent need to genomic surveillance to track viral lineage shift in the country beyond the September. These data would help to predict future situation and apply better strategy to control of the pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jale Moradi", - "author_inst": "Assistant Professor, Microbiology Department, Faculty of Medicine, Kermanshah university of Medical Sciences, Iran" - }, - { - "author_name": "Mohsen Moghoofei", - "author_inst": "Assistant Professor, Microbiology Department, Faculty of Medicine, Kermanshah university of Medical Sciences, Iran" - }, - { - "author_name": "Amir Houshang Alvandi", - "author_inst": "Associate Professor, Microbiology Department, Faculty of Medicine, Kermanshah university of Medical Sciences, Iran" - }, - { - "author_name": "Ramin Abiri", - "author_inst": "Associate Professor, Microbiology Department, Faculty of Medicine, Kermanshah university of Medical Sciences, Iran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.01.24.427089", "rel_title": "Meta-analysis reveals consistent immune response patterns in COVID-19 infected patients at single-cell resolution", @@ -977396,6 +979197,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.01.21.21250117", + "rel_title": "Symptoms of anxiety and depression in relation to work patterns during the first wave of the COVID-19 epidemic in Philadelphia PA: a cross-sectional survey", + "rel_date": "2021-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250117", + "rel_abs": "ObjectiveWe investigated whether patterns of work during COVID-19 pandemic altered by effort to contain the outbreak affected anxiety and depression.\n\nMethodsWe conducted a cross-sectional online survey of 911 residents of Philadelphia, inquiring about their working lives during early months of the epidemic, symptoms of anxiety and depression, plus demographics, perceived sources of support, and general health.\n\nResultsOccupational contact with suspected COVID-19 cases was associated with anxiety. Concerns about return to work, childcare, lack of sick leave, and loss/reduction in work correlated with anxiety and depression, even when there was no evidence of occupational contact with infected persons; patterns differed by gender.\n\nConclusionsHeightened anxiety and depression during COVID-19 pandemic can be due to widespread disruption of working lives, especially in \"non-essential\" low-income industries, on par with experience in healthcare.\n\nThe significance to clinical practice of the information being presented: Anxiety and depression symptoms that emerged during COVID-19 pandemic may be related to disruption of working lives even among people who are not the \"essential\" workers with one-one-one contact with infected persons. Clinicians may find this evidence of occupational correlates and articulated specific worries useful in treating such patients.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Igor Burstyn", + "author_inst": "Drexel University" + }, + { + "author_name": "Tran Huynh", + "author_inst": "Drexel University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.01.20.21249888", "rel_title": "Exploring support needs of people living with diabetes during the coronavirus COVID-19 pandemic: insights from a UK survey.", @@ -978504,45 +980328,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.01.21.427315", - "rel_title": "DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins", - "rel_date": "2021-01-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.21.427315", - "rel_abs": "MotivationRecent efforts to computationally identify inhibitors for SARS-CoV-2 proteins have largely ignored the issue of receptor flexibility. We have implemented a computational tool for ensemble docking with the SARS-CoV-2 proteins, including the main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp).\n\nResultsEnsembles of other SARS-CoV-2 proteins are being prepared and made available through a user-friendly docking interface. Plausible binding modes between conformations of a selected ensemble and an uploaded ligand are generated by DINC, our parallelized meta-docking tool. Binding modes are scored with three scoring functions, and account for the flexibility of both the ligand and receptor. Additional details on our methods are provided in the supplementary material.\n\nAvailabilitydinc-covid.kavrakilab.org\n\nSupplementary informationDetails on methods for ensemble generation and docking are provided as supplementary data online.\n\nContactgeancarlo.zanatta@ufc.br, kavraki@rice.edu", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sarah Hall-Swan", - "author_inst": "Rice University" - }, - { - "author_name": "Dinler A Antunes", - "author_inst": "Rice University" - }, - { - "author_name": "Didier Devaurs", - "author_inst": "University of Grenoble Alpes" - }, - { - "author_name": "Mauricio M Rigo", - "author_inst": "Rice University" - }, - { - "author_name": "Lydia E Kavraki", - "author_inst": "Rice University" - }, - { - "author_name": "Geancarlo Zanatta", - "author_inst": "Federal University of Cear\u00e1" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.01.22.427737", "rel_title": "Human embryonic stem cell-derived cardiomyocytes express SARS-CoV-2 host entry proteins: screen to identify inhibitors of infection", @@ -978958,6 +980743,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.01.22.427830", + "rel_title": "Exploring the natural origins of SARS-CoV-2", + "rel_date": "2021-01-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.22.427830", + "rel_abs": "The lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2, and the large geographical distance between Wuhan and where the closest evolutionary related coronaviruses circulating in horseshoe bats (Sarbecoviruses) have been identified, is fuelling speculation on the natural origins of SARS-CoV-2. We have comprehensively analysed phylogenetic relations between SARS-CoV-2, and the related bat and pangolin Sarbecoviruses sampled so far. Determining the likely recombination events reveals a highly reticulate evolutionary history within this group of coronaviruses. Clustering of the inferred recombination events is non-random with evidence that Spike, the main target for humoral immunity, is beside a recombination hotspot likely driving antigenic shift in the ancestry of bat Sarbecoviruses. Coupled with the geographic ranges of their hosts and the sampling locations, across southern China, and into Southeast Asia, we confirm horseshoe bats, Rhinolophus, are the likely SARS-CoV-2 progenitor reservoir species. By tracing the recombinant sequence patterns, we conclude that there has been relatively recent geographic movement and co-circulation of these viruses ancestors, extending across their bat host ranges in China and Southeast Asia over the last 100 years or so. We confirm that a direct proximal ancestor to SARS-CoV-2 is yet to be sampled, since the closest relative shared a common ancestor with SARS-CoV-2 approximately 40 years ago. Our analysis highlights the need for more wildlife sampling to (i) pinpoint the exact origins of SARS-CoV-2s animal progenitor, and (ii) survey the extent of the diversity in the related Sarbecoviruses phylogeny that present high risk for future spillover.\n\nHighlightsO_LIThe origin of SARS-CoV-2 can be traced to horseshoe bats, genus Rhinolophus, with ranges in both China and Southeast Asia.\nC_LIO_LIThe closest known relatives of SARS-CoV-2 exhibit frequent transmission among their Rhinolophus host species.\nC_LIO_LISarbecoviruses have undergone extensive recombination throughout their evolutionary history.\nC_LIO_LIAccounting for the mosaic patterns of these recombinants is important when inferring relatedness to SARS-CoV-2.\nC_LIO_LIBreakpoint patterns are consistent with recombination hotspots in the coronavirus genome, particularly upstream of the pike open reading frame with a coldspot in S1.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Spyros Lytras", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Joseph Hughes", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Darren Martin", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Arne de Klerk", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rentia Lourens", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Sergei L Kosakovsky Pond", + "author_inst": "Temple University Institute for Genomics and Evolutionary Medicine" + }, + { + "author_name": "Wei Xia", + "author_inst": "South China Agricultural University" + }, + { + "author_name": "David L Robertson", + "author_inst": "University of Glasgow" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.01.19.21250126", "rel_title": "Changes in healthcare workers' knowledge, attitudes, practices, and stress during the COVID-19 pandemic", @@ -980066,37 +981898,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2021.01.16.21249935", - "rel_title": "The Socioeconomic Impact of COVID-19 in Urban Informal Settlements", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.16.21249935", - "rel_abs": "The COVID-19 pandemic has reached almost every corner of the world. Without a pharmaceutical solution, governments have been forced to implement regulations and public policies to control social behavior and prevent the spread of the virus. There is dramatic evidence of the social and economic effects of these measures and their disparate impact on vulnerable communities. Individuals living in urban informal settlements are in a structurally disadvantaged position to cope with a health crisis such as the COVID-19 pandemic. This paper examines the socioeconomic impact of the crisis brought by the pandemic in informal settlements in Chile. We use a three-wave panel study to compare the situation in informal settlements before and during the health crisis. We show that households living in informal settlements are paying a high toll. Their employment loss is dramatic, substantially larger than the loss reported in the general population, and has particularly affected the inmigrant population. We also find that the pandemic has triggered neighborhood cooperation within the settlements. Targeted government assistance programs have reached these communities; however, this groups coverage is not enough to counteract the magnitude of the crisis. Our results suggest that governments, the non-profit sector, and the community need to urgently provide economic support and protections to individuals living in informal settlements and consider this opportunity for long-term improvements in these marginalized communities.\n\nHighlightsO_LIGovernments have implemented large-scale non-pharmaceutical interventions to control the spread of the COVID-19 pandemic\nC_LIO_LIThese measures have had dramatic social and economic effects on the population, particularly affecting vulnerable communities\nC_LIO_LIIndividuals living in urban informal settlements are in a structurally disadvantaged position to cope with this crisis\nC_LIO_LIUsing panel data, we document a dramatic employment loss among informal settlements dwellers, substantially larger than the general population\nC_LIO_LIThe pandemic has also triggered neighborhood cooperation within the settlements as well as targeted government assistance, but not enough to counteract the magnitude of the economic loss\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Diego Gil", - "author_inst": "Escuela de Gobierno, Pontificia Universidad Catolica de Chile, Santiago, Chile" - }, - { - "author_name": "Patricio Dominguez", - "author_inst": "Department of Research, Inter-American Development Bank, Washington DC" - }, - { - "author_name": "Eduardo A Undurraga", - "author_inst": "Escuela de Gobierno, Pontificia Universidad Catolica de Chile, Santiago, Chile" - }, - { - "author_name": "Eduardo Valenzuela", - "author_inst": "Department of Sociology, Pontificia Universidad Catolica de Chile, Santiago, Chile" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.18.21250025", "rel_title": "COVID-19 in 823 Transplant patients: A Systematic Scoping Review", @@ -980296,6 +982097,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.01.17.21249970", + "rel_title": "Optimizing SARS-CoV-2 vaccination strategies in France: Results from a stochastic agent-based model", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.17.21249970", + "rel_abs": "The COVID-19 pandemic is a major global societal, economic and health threat. The availability of COVID-19 vaccines has raised hopes for a decline in the pandemic. We built upon a stochastic agent-based microsimulation model of the COVID-19 epidemic in France. We examined the potential impact of different vaccination strategies, defined according to the age, medical conditions, and expected vaccination acceptance of the target non-immunized adult population, on disease cumulative incidence, mortality, and number of hospital admissions. Specifically, we examined whether these vaccination strategies would allow to lift all non-pharmacological interventions (NPIs), based on a sufficiently low cumulative mortality and number of hospital admissions. While vaccinating the full adult non-immunized population, if performed immediately, would be highly effective in reducing incidence, mortality and hospital-bed occupancy, and would allow discontinuing all NPIs, this strategy would require a large number of vaccine doses. Vaccinating only adults at higher risk for severe SARS-CoV-2 infection, i.e. those aged over 65 years or with medical conditions, would be insufficient to lift NPIs. Immediately vaccinating only adults aged over 45 years, or only adults aged over 55 years with mandatory vaccination of those aged over 65 years, would enable lifting all NPIs with a substantially lower number of vaccine doses, particularly with the latter vaccination strategy. Benefits of these strategies would be markedly reduced if the vaccination was delayed, was less effective than expected on virus transmission or in preventing COVID-19 among older adults, or was not widely accepted.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Nicolas Hoertel", + "author_inst": "Universite de Paris" + }, + { + "author_name": "Martin Blachier", + "author_inst": "Public health expertise" + }, + { + "author_name": "Frederic Limosin", + "author_inst": "Universite de Paris" + }, + { + "author_name": "Marina Sanchez-Rico", + "author_inst": "Universidad Complutense de Madrid" + }, + { + "author_name": "Carlos Blanco", + "author_inst": "National Institute on Drug Abuse" + }, + { + "author_name": "Mark Olfson", + "author_inst": "Columbia University/New York State Psychiatric Institute" + }, + { + "author_name": "Stephane Luchini", + "author_inst": "Aix-Marseille University" + }, + { + "author_name": "Michael Schwarzinger", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Henri Leleu", + "author_inst": "Public health expertise" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.01.11.21249636", "rel_title": "Issues of Random Sampling with Rapid Antigen Tests for COVID-19 Diagnosis: A Special Reference to Kalmunai RDHS Division", @@ -981484,69 +983336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.01.18.21249414", - "rel_title": "Temporal Trends in COVID-19 associated AKI from March to December 2020 in New York City", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21249414", - "rel_abs": "Acute Kidney Injury (AKI) is among the most common complications of Coronavirus Disease 2019 (COVID-19). Throughout 2020 pandemic, the clinical approach to COVID-19 has progressively improved, but it is unknown how these changes have affected AKI incidence and severity. In this retrospective analysis, we report the trend over time of COVID-19 associated AKI and need of renal replacement therapy in a large health system in New York City, the first COVID-19 epicenter in United States.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sergio Dellepiane", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Akhil Vaid", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Suraj K Jaladanki", - "author_inst": "Icahn School of Medicine at Mount Sinai (ISMMS)" - }, - { - "author_name": "Ishan Paranjpe", - "author_inst": "Ican School of Medicine at Mount Sinai" - }, - { - "author_name": "Stevn Coca", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Zahi Fayad", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alexander Charney", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Erwin P Bottinger", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "John Cijiang He", - "author_inst": "Icahn School of Medicineat Mount Sinai" - }, - { - "author_name": "Benjamin S Glicksberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lili Chan", - "author_inst": "ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI" - }, - { - "author_name": "Girish Nadkarni", - "author_inst": "Mount Sinai Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.01.18.21249976", "rel_title": "Covid-19 respiratory protection: the filtration efficiency assessment of decontaminated FFP2 masks responding to associated shortages", @@ -982178,6 +983967,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.19.21250094", + "rel_title": "Diagnosis of SARS-Cov-2 infection using specimens other than naso- and oropharyngeal swabs: a systematic review and meta-analysis", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250094", + "rel_abs": "BackgroundThe rapid and accurate testing of SARS-CoV-2 infection is still crucial to mitigate, and eventually halt, the spread of this disease. Currently, nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the recommended standard sampling, yet, with some limitations. Several specimens that are easier to collect are being tested as alternatives to nasal/throat swabs in nucleic acid assays for SARS-CoV-2 detection. This study aims to critically appraise and compare the clinical performance of RT-PCR tests using oral saliva, deep-throat saliva/ posterior oropharyngeal saliva (DTS/POS), sputum, urine, feces, and tears/conjunctival swab [CS]) against standard specimens (NPS, OPS, or a combination of both).\n\nMethodsIn this systematic review and meta-analysis, five databases (PubMed, Scopus, Web of Science, ClinicalTrial.gov and NIPH Clinical Trial) were searched up to the 30th of December 2020. Case-control and cohort studies on the detection of SARS-CoV-2 were included. Methodological quality was assessed through the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2).\n\nFindingsWe identified 3022 entries, 33 of which (1.1%) met all required criteria and were included for the quantitative data analysis. Saliva presented the higher accuracy, 92.1% (95% CI: 70.0-98.3), with an estimated sensitivity of 83.9% (95% CI: 77.4-88.8) and specificity of 96.4% (95% CI: 89.5-98.8). DTS/POS samples had an overall accuracy of 79.7% (95% CI: 43.3-95.3), with an estimated sensitivity of 90.1% (95% CI: 83.3-96.9) and specificity of 63.1% (95% CI: 36.8-89.3). Remaining index specimens presented uncertainty given the lack of studies available.\n\nInterpretationOur meta-analysis shows that saliva samples from oral region provide a high sensitivity and specificity, being the best candidate as an alternative specimen to NPS/OPS for COVID-19 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial since DTS/POS samples may induce a higher rate of false positives. Urine, feces, tears/CS and sputum seem unreliable for diagnosis. Saliva testing may increase testing capacity, ultimately promoting the implementation of truly deployable COVID-19 tests, which could either work at the point-of-care (e.g. hospitals, clinics) or outbreak control spots (e.g. schools, airports, and nursing homes).\n\nFundingNothing to declare.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe lack of systematized data on the accuracy performance of alternative specimens for the detection of SARS-CoV-2 (against the standard NPS/OPS). The ever-growing number of studies available, made this updated systematic review timely and of the utmost importance\n\nAdded value of this studyOur meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity, being the best candidate as an alternative specimen to NPS/OPS for COVID-19 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial since DTS/POS samples may induce a higher rate of false positives.\n\nImplications of all the available evidenceSaliva samples simply taken from the oral cavity are promising alternatives to the currently used nasal/throat swabs. Saliva specimens can be self-collected, mitigate the discomfort caused by sampling, reduce the transmission risk and increase testing capacity. Therefore, the validation of this alternative specimen will promote the implementation of truly deployable rapid tests for SARS-CoV-2 detection at the point-of-care or outbreak spots.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Vania M. Moreira", + "author_inst": "ISEL" + }, + { + "author_name": "Paulo Mascarenhas", + "author_inst": "Egas Moniz - Cooperativa de Ensino Superior, CRL" + }, + { + "author_name": "Vanessa Machado", + "author_inst": "Egas Moniz - Cooperativa de Ensino Superior, CRL" + }, + { + "author_name": "Joao Botelho", + "author_inst": "Egas Moniz - Cooperativa de Ensino Superior, CRL" + }, + { + "author_name": "Jose Joao Mendes", + "author_inst": "Egas Moniz - Cooperativa de Ensino Superior, CRL" + }, + { + "author_name": "Nuno Taveira", + "author_inst": "University of Lisbon" + }, + { + "author_name": "Maria Gabriela Almeida", + "author_inst": "Egas Moniz - Cooperativa de Ensino Superior, CRL" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.16.21249946", "rel_title": "Immunisation, asymptomatic infection, herd immunity and the new variants of COVID-19", @@ -983510,37 +985342,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.19.21250139", - "rel_title": "Overcrowding and Exposure to Secondhand Smoke Increase Risk for COVID-19 Infection Among Latinx Families in Greater San Francisco Bay Area", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250139", - "rel_abs": "BackgroundThe novel coronavirus (COVID-19) has disproportionately impacted the Latinx community in the United States. Environmental risk factors, including community level pollution burden and exposure to smoking and secondhand smoke, have not been evaluated in relation to risk for infection with COVID-19.\n\nMethodsWe evaluated self-reported infection rates of COVID-19 in three, preexisting, longitudinal, Latinx family cohorts in the San Francisco Bay Area from May through September 2020 (N=383 households, 1,875 people). All households were previously recruited during pregnancy and postpartum at Zuckerberg San Francisco General Hospital (ZSFG) and UCSF Benioff before the pandemic. For the COVID-19 sub-study, participants responded to a 15-minute telephonic interview where we assessed food consumption patterns, housing and employment status, and history of COVID-19 infection based on community and hospital-based testing. We also evaluated secondhand smoke exposure based on previously collected self-reported data. Environmental pollution exposure was determined from census tract residence using Californias EnviroScreen 2.0 data. Non-parametric tests and multiple logistic regression were used to assess possible associations and independent predictors of COVID-19 infection.\n\nResultsIn the combined Latinx, Eating and Diabetes Cohort (LEAD) and Hispanic, Eating and Nutrition (HEN) cohorts there was a 7.6% household infection rate (14/183) with a lower rate of 3.5% (7/200) in the Telomeres at Birth (TAB) cohort. Larger household size increased risk for infection (OR, 1.43 (95%CI 1.10-1.87)) in the combined LEAD/HEN cohorts and increasing number of children trended towards significance in the TAB cohort (OR 1.82, 95% CI 0.98-3.37). Any exposure to secondhand smoke in the household also trended towards increasing risk after adjusting for household size and other exposures (OR 3.20, 95%CI 0.80-12.73) and (OR 4.37, 95% CI 0.80-23.70). We did not find any associations between neighborhood pollution level based on census track location and risk of infection. Furthermore, we found weak evidence between dietary exposure and risk of COVID-19 infection after adjusting for possible confounders.\n\nConclusionCrowding as indicated by household size increases risk for COVID-19 infection in Latinx families. Exposure to secondhand smoke may also increase risk for COVID-19 through increased coughing, respiratory impairment and increased travel of virus on smoke particles. Public policy and health interventions need to ensure that multiunit residential complexes prevent any exposure to secondhand smoke.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Andrea DeCastro Mendez", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Milagro Escobar", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Maria Romero Encinas", - "author_inst": "University of California,San Francisco" - }, - { - "author_name": "Janet Wojcicki", - "author_inst": "UCSF" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.19.21250137", "rel_title": "A Label-Free SARS-CoV-2 Surrogate Virus Neutralization Test and a Longitudinal Study of Antibody Characteristics in COVID-19 Patients", @@ -983700,6 +985501,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.19.21250116", + "rel_title": "The Association of COVID-19 Incidence with Sport and Face Mask Use in United States High School Athletes", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250116", + "rel_abs": "PurposeTo evaluate the influence of sport characteristics and face mask use on COVID-19 incidence among high school athletes.\n\nMethodsSurveys were distributed to high school athletic directors throughout the United States regarding sport re-initiation, COVID-19 cases, and risk reduction procedures in fall 2020.\n\nSeparate mixed effects Poisson regression models were developed to evaluate the associations between reported COVID-19 incidence and 1) sport characteristics (contact/non-contact, individual/team, indoor/outdoor) and 2) face mask use while playing (yes/no).\n\nResults991 schools had restarted fall sports, representing 152,484 athletes on 5,854 teams. 2,565 cases of COVID-19 were reported, representing a case rate of 1,682 cases per 100,000 athletes and an incidence rate of 24.6 cases per 100,000 player-days. COVID-19 incidence was lower among outdoor versus indoor sports (incidence rate ratio [IRR]=0.54, 95% CI=0.49-0.60, p<0.001) and non-contact versus contact sports (IRR=0.78 [0.70-0.87], p<0.001), but not team versus individual sports (IRR=0.96 [0.84-1.1], p=0.49). Face mask use was associated with a decreased incidence in girls volleyball (IRR=0.53 [0.37-0.73], p<0.001), boys basketball (IRR=0.53 [0.33-0.83], p=0.008) and girls basketball (IRR=0.36 [0.19-0.63], p<0.001), and approached statistical significance in football (IRR=0.79 [0.59-1.04], p=0.10) and cheer/dance (IRR=0.75 [0.53-1.03], p=0.081).\n\nConclusionsIn this nationwide survey of US high school athletic directors representing 152,484 athletes, lower COVID-19 incidence was independently associated with participation in outdoor versus indoor and non-contact versus contact sports, but not team versus individual sports. Face mask use was associated with decreased COVID-19 incidence among indoor sports, and may be protective among outdoor sports with prolonged close contact between participants.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andrew Watson", + "author_inst": "University of Wisconsin School of Medicine and Public Health, Department of Orthopedics and Rehabilitation" + }, + { + "author_name": "Kristin Haraldsdottir", + "author_inst": "University of Wisconsin School of Medicine and Public Health, Department of Orthopedics and Rehabilitation" + }, + { + "author_name": "Kevin Biese", + "author_inst": "University of Wisconsin - Madison, Department of Kinesiology" + }, + { + "author_name": "Leslie Goodavish", + "author_inst": "University of Wisconsin School of Medicine and Public Health, Department of Orthopedics and Rehabilitation" + }, + { + "author_name": "Bethany Stevens", + "author_inst": "University of Wisconsin - Madison, Department of Kinesiology" + }, + { + "author_name": "Timothy McGuine", + "author_inst": "University of Wisconsin School of Medicine and Public Health, Department of Orthopedics and Rehabilitation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2021.01.13.21249761", "rel_title": "Invasive Mould Disease in Fatal COVID-1 19: A Systematic Review of Autopsies", @@ -985472,97 +987312,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.01.17.425424", - "rel_title": "Large scale genomic and evolutionary study reveals SARS-CoV-2 virus isolates from Bangladesh strongly correlate with European origin and not with China.", - "rel_date": "2021-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.17.425424", - "rel_abs": "RationaleThe global public health is in serious crisis due to emergence of SARS-CoV-2 virus. Studies are ongoing to reveal the genomic variants of the virus circulating in various parts of the world. However, data generated from low- and middle-income countries are scarce due to resource limitation. This study was focused to perform whole genome sequencing of 151 SARS-CoV-2 isolates from COVID-19 positive Bangladeshi patients. The goal of this study was to identify the genomic variants among the SARS-CoV-2 virus isolates in Bangladesh, to determine the molecular epidemiology and to develop a relationship between host clinical trait with the virus genomic variants.\n\nMethodSuspected patients were tested for COVID-19 using one step commercial qPCR kit for SARS-CoV-2 Virus. Viral RNA was extracted from positive patients, converted to cDNA which was amplified using Ion AmpliSeq SARS-CoV-2 Research Panel. Massive parallel sequencing was carried out using Ion AmpliSeq Library Kit Plus. Assembly of raw data is done by aligning the reads to a pre-defined reference genome (NC_045512.2) while retaining the unique variations of the input raw data by creating a consensus genome. A random forest-based association analysis was carried out to correlate the viral genomic variants with the clinical traits present in the host.\n\nResultAmong the 151 viral isolates, we observed the 413 unique variants. Among these 8 variants occurred in more than 80 % of cases which include 241C to T, 1163A to T, 3037C to T,14408C to T, 23403A to G, 28881G to A, 28882 G to A, and finally the 28883G to C. Phylogenetic analysis revealed a predominance of variants belonging to GR clade, which have a strong geographical presence in Europe, indicating possible introduction of the SARS-CoV-2 virus into Bangladesh through a European channel. However, other possibilities like a route of entry from China cannot be ruled out as viral isolate belonging to L clade with a close relationship to Wuhan reference genome was also detected. We observed a total of 37 genomic variants to be strongly associated with clinical symptoms such as fever, sore throat, overall symptomatic status, etc. (Fishers Exact Test p-value<0.05). The most mention-worthy among those were the 3916CtoT (associated with causing sore throat, p-value 0.0005), the 14408C to T (associated with protection from developing cough, p-value= 0.027), and the 28881G to A, 28882G to A, and 28883G to C variant (associated with causing chest pain, p-value 0.025).\n\nConclusionTo our knowledge, this study is the first large scale phylogenomic studies of SARS-CoV-2 virus circulating in Bangladesh. The observed epidemiological and genomic features may inform future research platform for disease management, vaccine development and epidemiological study.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Mohammad Fazle Alam Rabbi", - "author_inst": "University of Dhaka" - }, - { - "author_name": "Md. Imran Khan", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Saam Hasan", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Mauricio Chalita", - "author_inst": "Chun Lab Inc." - }, - { - "author_name": "Kazi Nadim Hasan", - "author_inst": "North South University" - }, - { - "author_name": "Abu Sufian", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Md. Bayejid Hosen", - "author_inst": "Dhaka Medical College" - }, - { - "author_name": "Mohammed Nafiz Imtiaz Polol", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Jannatun Naima", - "author_inst": "DNA Solution Ltd." - }, - { - "author_name": "Kihyun Lee", - "author_inst": "Chun Lab Inc." - }, - { - "author_name": "Yeong Ouk Kim", - "author_inst": "Chun Lab Inc." - }, - { - "author_name": "Mamudul Hasan Razu", - "author_inst": "Designated Reference Institute for Chemical Measurements" - }, - { - "author_name": "Mala Khan", - "author_inst": "Designated Reference Institute for Chemical Measurements" - }, - { - "author_name": "Md. Mizanur Rahman", - "author_inst": "NIPRO JMI Pharma" - }, - { - "author_name": "Jongsik Chun", - "author_inst": "Chun Lab Inc." - }, - { - "author_name": "Md. Abdul Khaleque", - "author_inst": "North South University" - }, - { - "author_name": "Nur A Hasan", - "author_inst": "Ezbiome Inc." - }, - { - "author_name": "Rita R Colwell", - "author_inst": "University of Maryland" - }, - { - "author_name": "Sharif Akhteruzzaman", - "author_inst": "University of Dhaka" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2021.01.18.427092", "rel_title": "A national analysis of trends in COVID-19 infection and clinical management in Veterans Health Administration medical facilities", @@ -986518,6 +988267,189 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.01.15.21249810", + "rel_title": "SARS-CoV-2 seropositivity and seroconversion in patients undergoing active cancer-directed therapy", + "rel_date": "2021-01-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.21249810", + "rel_abs": "Multiple studies have demonstrated the negative impact of cancer care delays during the COVID-19 pandemic, and transmission mitigation techniques are imperative for continued cancer care delivery. To gauge the effectiveness of these measures at the University of Pennsylvania, we conducted a longitudinal study of SARS-CoV-2 antibody seropositivity and seroconversion in patients presenting to infusion centers for cancer-directed therapy between 5/21/2020 and 10/8/2020. Participants completed questionnaires and had up to five serial blood collections. Of 124 enrolled patients, only two (1.6%) had detectable SARS-CoV-2 antibodies on initial blood draw, and no initially seronegative patients developed newly detectable antibodies on subsequent blood draw(s), corresponding to a seroconversion rate of 0% (95%CI 0.0-4.1%) over 14.8 person-years of follow up, with a median of 13 healthcare visits per patient. These results suggest that cancer patients receiving in-person care at a facility with aggressive mitigation efforts have an extremely low likelihood of COVID-19 infection.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Lova Sun", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Sanjna Surya", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Noah G.", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Anh N. Le", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Gregory Kelly", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Olutosin Owoyemi", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Heena Desai", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Cathy Zheng", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Shannon DeLuca", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Madeline L. Good", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Jasmin Hussain", + "author_inst": "Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Seth D. Jeffries", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Yolanda R. Kry", + "author_inst": "Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Emily M. Kugler", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Maikel Mansour", + "author_inst": "Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "John Ndicu", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "AnnaClaire Osei-Akoto", + "author_inst": "Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Timothy Prior", + "author_inst": "Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Stacy L. Pundock", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Lisa A. Varughese", + "author_inst": "Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "JoEllen Weaver", + "author_inst": "Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Abigail Doucette", + "author_inst": "Department of Radiation Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Scott Dudek", + "author_inst": "Department of Neurosurgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Shefali Setia Verma", + "author_inst": "Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Sigrid Gouma", + "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Madison E. Weirick", + "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Christopher M. McAllister", + "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Erin Bange", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Peter Gabriel", + "author_inst": "Department of Radiation Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Marylyn Ritchie", + "author_inst": "Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Daniel J. Rader", + "author_inst": "Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Robert H. Vonderheide", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Lynn M Schuchter", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Anurag Verma", + "author_inst": "Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Ivan Maillard", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Ronac Mamtani", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Scott E. Hensley", + "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Robert Gross", + "author_inst": "Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "E. Paul Wileyto", + "author_inst": "Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Alexander C. Huang", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Kara N. Maxwell", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + }, + { + "author_name": "Angela DeMichele", + "author_inst": "Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.01.16.21249221", "rel_title": "Reduction in transfer of micro-organisms between patients and staff using short-sleeved gowns and hand/arm hygiene in Intensive Care during the Covid pandemic: a simulation-based randomised trial.", @@ -987893,33 +989825,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.13.20249064", - "rel_title": "Optimising SARS-CoV-2 pooled testing strategies on social networks for low-resource settings", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.20249064", - "rel_abs": "Controlling the COVID-19 pandemic is an urgent global challenge. The rapid geographic spread of SARS-CoV-2 directly reflects the social structure. Before effective vaccines and treatments are widely available, we have to rely on alternative, non-pharmaceutical interventions, including frequency testing, contact tracing, social distancing, mask wearing, and hand-washing, as public health practises to slow down the spread of the disease. However frequent testing is the key in the absence of any alternative. We propose a network approach to determine the optimal low resources setting oriented pool testing strategies that identifies infected individuals in a small number of tests and few rounds of testing, at low prevalence of the virus. We simulate stochastic infection curves on societies under quarantine. Allowing some social interaction is possible to keep the COVID-19 curve flat. However, similar results can be strategically obtained searching and isolating infected persons to preserve a healthier social structure. Here, we analyze which are the best strategies to contain the virus applying an algorithm that combine samples and testing them in groups [1]. A relevant parameter to keep infection curves flat using this algorithm is the dairy frequency of testing at zones where a high infection rate is reported. On the other hand, the algorithm efficiency is low for random search of infected people.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Karina I Mazzitello", - "author_inst": "University of Mar del Plata, ICYTE-CONICET" - }, - { - "author_name": "Yi Jiang", - "author_inst": "Department of Mathematics and Statistics, Georgia State University, Atlanta, GA 30303, USA" - }, - { - "author_name": "Constancio Miguel Arizmendi", - "author_inst": "Universidad Nacional de Mar del Plata, ICYTE, Argentina" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.14.21249853", "rel_title": "The Use of Procalcitonin as an Antimicrobial Stewardship Tool and a Predictor of Disease Severity in COVID-19", @@ -988127,6 +990032,85 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.01.14.426521", + "rel_title": "Structural characterization of cocktail-like targeting polysaccharides from Ecklonia kurome Okam and their anti-SARS-CoV-2 activities in vitro", + "rel_date": "2021-01-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.14.426521", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent responsible for the worldwide coronavirus disease 2019 (COVID-19) outbreak. Investigation has confirmed that polysaccharide heparan sulfate can bind to the spike protein and block SARS-CoV-2 infection. Theoretically, similar structure of nature polysaccharides may also have the impact on the virus. Indeed, some marine polysaccharide has been reported to inhibit SARS-Cov-2 infection in vitro, however the convinced targets and mechanism are still vague. By high throughput screening to target 3CLpro enzyme, a key enzyme that plays a pivotal role in the viral replication and transcription using nature polysaccharides library, we discover the mixture polysaccharide 375 from seaweed Ecklonia kurome Okam completely block 3Clpro enzymatic activity (IC50, 0.48 {micro}M). Further, the homogeneous polysaccharide 37502 from the 375 may bind to 3CLpro molecule well (kD value : 4.23 x 10-6). Very interestingly, 37502 also can potently disturb spike protein binding to ACE2 receptor (EC50, 2.01 {micro}M). Importantly, polysaccharide 375 shows good anti-SARS-CoV-2 infection activity in cell culture with EC50 values of 27 nM (99.9% inhibiting rate at the concentration of 20 {micro}g/mL), low toxicity (LD50: 136 mg/Kg on mice). By DEAE ion-exchange chromatography, 37501, 37502 and 37503 polysaccharides are purified from native 375. Bioactivity test show that 37501 and 37503 may impede SARS-Cov-2 infection and virus replication, however their individual impact on the virus is significantly less that of 375. Surprisingly, polysaccharide 37502 has no inhibition effect on SARS-Cov-2. The structure study based on monosaccharide composition, methylation, NMR spectrum analysis suggest that 375 contains guluronic acid, mannuronic acid, mannose, rhamnose, glucouronic acid, galacturonic acid, glucose, galactose, xylose and fucose with ratio of 1.86 : 9.56 : 6.81 : 1.69 : 1.00 : 1.75 : 1.19 : 11.06 : 4.31 : 23.06. However, polysaccharide 37502 is an aginate which composed of mannuronic acid (89.3 %) and guluronic acid (10.7 %), with the molecular weight (Mw) of 27.9 kDa. These results imply that mixture polysaccharides 375 works better than the individual polysaccharide on SARS-Cov-2 may be the cocktail-like polysaccharide synergistic function through targeting multiple key molecules implicated in the virus infection and replication. The results also suggest that 375 may be a potential drug candidate against SARS-CoV-2.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kan Ding", + "author_inst": "Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Bo Zhang", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China" + }, + { + "author_name": "Xinwen Chen", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China" + }, + { + "author_name": "Yechun Xu", + "author_inst": "Shanghai Institute of Materia Medica Chinese Academy of Sciences" + }, + { + "author_name": "Chunfan Huang", + "author_inst": "Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. Chi" + }, + { + "author_name": "Can Jin", + "author_inst": "Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. Chi" + }, + { + "author_name": "Zhenyun Du", + "author_inst": "Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. Chi" + }, + { + "author_name": "Xia Chen", + "author_inst": "Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. Chi" + }, + { + "author_name": "Yaqi Ding", + "author_inst": "Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. Chi" + }, + { + "author_name": "Hao Sun", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China" + }, + { + "author_name": "Meixia Li", + "author_inst": "Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. Chi" + }, + { + "author_name": "Rongjuan Pei", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China" + }, + { + "author_name": "Shihai Zhang", + "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" + }, + { + "author_name": "Minbo Su", + "author_inst": "National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Science, No.19" + }, + { + "author_name": "Yi Zhang", + "author_inst": "National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, University of Chin" + }, + { + "author_name": "Jia Li", + "author_inst": "National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, University of Chin" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.01.14.426613", "rel_title": "Enhanced Cholesterol-dependent Hemifusion by Internal Fusion Peptide 1 of SARS Coronavirus-2 Compared to its N-terminal Counterpart", @@ -989835,49 +991819,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2021.01.13.21249460", - "rel_title": "Physicians' Reactions to COVID-19: The Results of an International Internet Survey", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.21249460", - "rel_abs": "ObjectivesPhysicians across the world have been disproportionately affected by the COVID-19 pandemic. This study was designed and conducted to assess the emotional, cognitive, and behavioural reactions of physicians to the initial phase of the COVID-19 pandemic.\n\nMaterials and methodsAn online survey questionnaire using the google forms platform was constructed by the authors. The items in the questionnaire were based on clinical experience, relevant literature review and discussion with peers. A list of issues that were deemed as essential components of the experience of the pandemic relevant to physicians was arrived at. Thereafter these issues were operationalized into question form and hosted on the google forms platform. The link to this questionnaire was circulated by the authors among their peer groups in the month of April 2020.\n\nResultsWe received 295 responses and 3 were unusable. Most of the responses were from India, the United States of America, Australia, Canada and the United Kingdom. About 60% of the respondents identified themselves as frontline and had a decade of clinical experience. Most respondents reported being anxious due to the pandemic and also observed the same in their peers and families. A majority also observed changes in behaviour in self and others and advanced a variety of reasons and concerns. A sense of duty was the most commonly employed coping mechanism.\n\nConclusionPhysicians are not immune from information and misinformation, or cues in the environment. Behavioural choices are not always predicted by knowledge but by a combination of knowledge, emotional state, personality and environment. Healthcare settings need to be ready for emergencies and should focus on reducing uncertainty in physicians. These factors may also be gainfully used in the mental health promotion of physicians in COVID-19 care roles.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Parul Aneja", - "author_inst": "UPMC Pinnacle" - }, - { - "author_name": "Inderjit Singh", - "author_inst": "Roche Diabetes Care Inc." - }, - { - "author_name": "Bhupinder Singh", - "author_inst": "University of Illinois college of Medicine" - }, - { - "author_name": "Pardeep Singh Kundi", - "author_inst": "Vancouver General Hospital" - }, - { - "author_name": "Inderbir Singh", - "author_inst": "Essex Partnership University MHS Foundation Trust, UK" - }, - { - "author_name": "Sanjana Kathiravan", - "author_inst": "PGIMER, Chandigarh" - }, - { - "author_name": "Shubh Mohan Singh", - "author_inst": "PGIMER, Chandigarh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.01.11.21249324", "rel_title": "A national survey of potential acceptance of COVID-19 vaccines in healthcare workers in Egypt", @@ -990125,6 +992066,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.01.12.21249581", + "rel_title": "Dynamical Pool-Size Optimization for the SARS-CoV-2 PCR Test", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249581", + "rel_abs": "In this work, we put forward a novel test strategy, that allows to significantly increase the test capacity for SARS-CoV-2. The test strategy is based on an a priory risk assessment scheme, that allows to dynamically find and adapt an optimal clustering size of test pools. We, furthermore, suggest a method to overcome the efficiency loss of test clustering by avoiding concentration losses in the test samples. We validated our method with several thousand probe pools performing RT-PCR tests, and found it highly effective.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Juri Smirnov", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Thomas Fenner", + "author_inst": "Institute for Clinical Pathology Dr. Fenner and Colleagues" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.01.14.21249782", "rel_title": "COVID-19 dynamics in an Ohio prison", @@ -991621,57 +993585,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.14.426652", - "rel_title": "Natural SARS-CoV-2 infection in kept ferrets, Spain", - "rel_date": "2021-01-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.14.426652", - "rel_abs": "We found SARS-CoV-2 RNA in 6 of 71 ferrets (8.4%) and isolated the virus from one rectal swab. Natural SARS-CoV-2 infection does occur in kept ferrets, at least under circumstances of high viral circulation in the human population. However, small ferret collections are probably unable to maintain prolonged virus circulation.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Christian Gortazar", - "author_inst": "Universidad de Castilla La Mancha" - }, - { - "author_name": "Sandra Barroso-Arevalo", - "author_inst": "Universidad Complutense" - }, - { - "author_name": "Elisa Ferreras", - "author_inst": "Universidad de Castilla La Mancha" - }, - { - "author_name": "Julio Isla", - "author_inst": "Sabiotec" - }, - { - "author_name": "Gabriela de la Fuente", - "author_inst": "Sabiotec" - }, - { - "author_name": "Belen Rivera", - "author_inst": "Universidad Complutense" - }, - { - "author_name": "Lucas Dominguez", - "author_inst": "Universidad Complutense de Madrid" - }, - { - "author_name": "Jose de la Fuente", - "author_inst": "IREC" - }, - { - "author_name": "Jose M Vizcaino", - "author_inst": "Universidad Complutense" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.08.21249273", "rel_title": "Modeling the COVID-19 transmission in Italy: The roles of asymptomatic cases, social distancing, and lockdowns", @@ -992135,6 +994048,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.13.426628", + "rel_title": "Susceptibility of white-tailed deer (Odocoileus virginianus) to SARS-CoV-2", + "rel_date": "2021-01-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.13.426628", + "rel_abs": "The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing the global coronavirus disease 19 (COVID-19) pandemic, remains a mystery. Current evidence suggests a likely spillover into humans from an animal reservoir. Understanding the host range and identifying animal species that are susceptible to SARS-CoV-2 infection may help to elucidate the origin of the virus and the mechanisms underlying cross-species transmission to humans. Here we demonstrated that white-tailed deer (Odocoileus virginianus), an animal species in which the angiotensin converting enzyme 2 (ACE2) - the SARS-CoV-2 receptor - shares a high degree of similarity to humans, are highly susceptible to infection. Intranasal inoculation of deer fawns with SARS-CoV-2 resulted in established subclinical viral infection and shedding of infectious virus in nasal secretions. Notably, infected animals transmitted the virus to non-inoculated contact deer. Viral RNA was detected in multiple tissues 21 days post-inoculation (pi). All inoculated and indirect contact animals seroconverted and developed neutralizing antibodies as early as day 7 pi. The work provides important insights into the animal host range of SARS-CoV-2 and identifies white-tailed deer as a susceptible wild animal species to the virus.\n\nIMPORTANCEGiven the presumed zoonotic origin of SARS-CoV-2, the human-animal-environment interface of COVID-19 pandemic is an area of great scientific and public- and animal-health interest. Identification of animal species that are susceptible to infection by SARS-CoV-2 may help to elucidate the potential origin of the virus, identify potential reservoirs or intermediate hosts, and define the mechanisms underlying cross-species transmission to humans. Additionally, it may also provide information and help to prevent potential reverse zoonosis that could lead to the establishment of a new wildlife hosts. Our data show that upon intranasal inoculation, white-tailed deer became subclinically infected and shed infectious SARS-CoV-2 in nasal secretions and feces. Importantly, indirect contact animals were infected and shed infectious virus, indicating efficient SARS-CoV-2 transmission from inoculated animals. These findings support the inclusion of wild cervid species in investigations conducted to assess potential reservoirs or sources of SARS-CoV-2 of infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Mitchell V Palmer", + "author_inst": "USDA-ARS National Animal Disease Center" + }, + { + "author_name": "Mathias Martins", + "author_inst": "Cornell University" + }, + { + "author_name": "Shollie Falkenberg", + "author_inst": "National Animal Disease Center" + }, + { + "author_name": "Alexandra C Buckley", + "author_inst": "National Animal Disease Center" + }, + { + "author_name": "Leonardo C Caserta", + "author_inst": "Cornell University" + }, + { + "author_name": "Patrick K. Mitchell", + "author_inst": "Cornell University" + }, + { + "author_name": "Eric Cassmann", + "author_inst": "USDA ARS" + }, + { + "author_name": "Alicia Rollins", + "author_inst": "Cornell University" + }, + { + "author_name": "Nancy C Zylich", + "author_inst": "Cornell University" + }, + { + "author_name": "Randall Wayne Renshaw", + "author_inst": "Cornell University" + }, + { + "author_name": "Cassandra Guarino", + "author_inst": "Cornell University" + }, + { + "author_name": "Bettina Wagner", + "author_inst": "Cornell University" + }, + { + "author_name": "Kelly Lager", + "author_inst": "USDA, Agricultural Research Service" + }, + { + "author_name": "Diego G Diel", + "author_inst": "Cornell University College of Veterinary Medicine" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.12.426365", "rel_title": "The lethal triad: SARS-CoV-2 Spike, ACE2 and TMPRSS2. Mutations in host and pathogen may affect the course of pandemic.", @@ -993583,101 +995567,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.11.21249547", - "rel_title": "Impact of the Coronavirus Disease (COVID-19) on the Mental Health and Physical Activity of Pharmacy Students at the University of Zambia: A Cross-Sectional Study", - "rel_date": "2021-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249547", - "rel_abs": "BackgroundThe novel coronavirus disease (COVID-19) is a serious global health problem that has negatively impacted the mental health of students.\n\nMethodsWe conducted an online descriptive cross-sectional study among 273 undergraduate pharmacy students at the University of Zambia. A partial proportional odds regression model was used to determine the predictors of anxiety. All statistical tests were set at 95% confidence level (p<0.05).\n\nResultsA response rate of 70% was obtained with the majority of the students being female 51.6%. Of the 273 respondents, 23.8% did not experience anxiety, 34.4% experienced mild anxiety, 24.9% experienced moderate anxiety while 16.9% experienced severe anxiety about COVID-19. It was also found that 61.2% of students reported that their attention to mental health increased during the COVID-19 pandemic whereas 44.3% reported an increased resting time with a significant reduction in relaxation 51.3% and physical activity 45.4% time. Factors that affected mental health included; reduced family care (OR: 2.27; 95% CI: 1.09-4.74), not changing attention to mental health (OR: 0.33; 95% CI: 0.18-0.62), being in the final year of study (OR: 0.33; 95% CI: 0.13-0.84), reduced time of resting (OR: 2.10; 95% CI: 1.26-3.50) and feeling helpless (OR: 0.42; 95% CI:0.23-0.75).\n\nConclusionCOVID-19 negatively impacted the mental health and physical activity of pharmacy students at the University of Zambia. This can have negative health and academic outcomes for students going forward. Higher learning institutions and key stakeholders should implement measures to aid students to recover from the impact of COVID-19 on their mental health and physical activity.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Steward Mudenda", - "author_inst": "University of Zambia" - }, - { - "author_name": "Moses Mukosha", - "author_inst": "University of Zambia" - }, - { - "author_name": "Chiluba Mwila", - "author_inst": "University of Zambia" - }, - { - "author_name": "Zikria Saleem", - "author_inst": "University of Lahore" - }, - { - "author_name": "Aubrey Chichoni Kalungia", - "author_inst": "University of Zambia" - }, - { - "author_name": "Derick Munkombwe", - "author_inst": "University of Zambia" - }, - { - "author_name": "Victor Daka", - "author_inst": "Copperbelt University" - }, - { - "author_name": "Bwalya Angel Witika", - "author_inst": "DDT College of Medicine" - }, - { - "author_name": "Martin Kampamba", - "author_inst": "University of Zambia" - }, - { - "author_name": "Misheck Chileshe", - "author_inst": "Mary Begg Health Services" - }, - { - "author_name": "Christabel Hikaambo", - "author_inst": "University of Zambia" - }, - { - "author_name": "Maisa Kasanga", - "author_inst": "Zhengzhou University, College of Public Health" - }, - { - "author_name": "Webrod Mufwambi", - "author_inst": "University of Zambia" - }, - { - "author_name": "Ruth Lindizyani Mfune", - "author_inst": "Copperbelt University" - }, - { - "author_name": "Scott Kaba Matafwali", - "author_inst": "Copperbelt University" - }, - { - "author_name": "Angela Gono Bwalya", - "author_inst": "University of Zambia" - }, - { - "author_name": "David Chimbizgani Banda", - "author_inst": "Chreso University" - }, - { - "author_name": "Akashi Gupta", - "author_inst": "Ramniranjan Jhunjhunwala College" - }, - { - "author_name": "Maureen Nkandu Phiri", - "author_inst": "University of Zambia" - }, - { - "author_name": "Eustarckio Kazonga", - "author_inst": "University of Lusaka" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.11.21249626", "rel_title": "Aerosol tracer testing in the cabin of wide-bodied Boeing 767 and 777 aircraft to simulate exposure potential of infectious particulate such as SARS-CoV-2", @@ -993973,6 +995862,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2021.01.11.21249526", + "rel_title": "Hospital load and increased COVID-19 related mortality - a nationwide study in Israel", + "rel_date": "2021-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249526", + "rel_abs": "The spread of Coronavirus disease 19 (COVID-19) has led to many healthcare systems being overwhelmed by the rapid emergence of new cases within a short period of time. We explore the ramifications of hospital load due to COVID-19 morbidity on COVID-19 in-hospital patient mortality. We address this question with a nationwide study based on the records of all 22,636 COVID-19 patients hospitalized in Israel from mid-July 2020 to mid-January 2021. We show that even under moderately heavy patient load (>500 countrywide hospitalized severely-ill patients; the Israeli Ministry of Health defined 800 severely-ill patients as the maximum capacity allowing adequate treatment), in-hospital mortality rate of patients with COVID-19 significantly increased compared to periods of lower patient load (250-500 severely-ill patients): 14-day mortality rates were 22.1% (Standard Error 3.1%) higher (mid-September to mid-October) and 27.2% (Standard Error 3.3%) higher (mid-December to mid-January). We further show this higher mortality rate cannot be attributed to changes in the patient population during periods of heavier load.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Hagai Rossman", + "author_inst": "Weizmann institute of science" + }, + { + "author_name": "Tomer Meir", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Jonathan Somer", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Smadar Shilo", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Rom Gutman", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Asaf Ben Arie", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Eran Segal", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Uri Shalit", + "author_inst": "Technion - Israeli Institute of Technology" + }, + { + "author_name": "Malka Gorfine", + "author_inst": "Tel Aviv University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.01.12.21249707", "rel_title": "Modelling the impact of household size distribution on the transmission dynamics of COVID-19", @@ -995161,73 +997101,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.09.21249515", - "rel_title": "Impact of Residential Neighborhood and Race/Ethnicity on Outcomes of Hospitalized Patients with COVID-19 in the Bronx", - "rel_date": "2021-01-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.09.21249515", - "rel_abs": "The socially vulnerable have been most affected due to the COVID-19 pandemic, similar to the aftermath of any major disaster. Racial and social minorities are experiencing a disproportionate burden of morbidity and mortality.\n\nThe aim of this study was to evaluate the impact of residential location/community and race/ethnicity on outcomes of COVID-19 infection among hospitalized patients within the Bronx. This was a single center retrospective observational cohort study that included SARS-CoV2 positive adult residents of the Bronx (stratified as residents of South Bronx vs Rest of Bronx) hospitalized between March-May 2020. Data extracted from hospital electronic medical records included residential addresses, race, comorbidities, and insurance details. Comorbidity burden other clinical and laboratory details were also assessed to determine their correlation to COVID-19 severity of illness and outcomes of mortality and length of stay.\n\nAs expected, the COVID-19 pandemic differentially affected outcomes in those in the more socially disadvantaged area of the South Bronx versus the rest of the Bronx borough. Residents of the South Bronx had a significantly higher comorbidity burden and had public insurance to access medical care in comparison to the remainder of the Bronx. Interestingly, for the patient population studied there was no observed difference in 30-day mortality by race/ethnicity among those infected with COVID- 19 in spite of the increased disease burden observed.\n\nThis adds an interesting perspective to the current literature, and highlights the need to address the social/economic factors contributing to health access disparity to reduce the adverse impact of COVID-19 in these communities.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Dwayvania Miller", - "author_inst": "Lincoln Mental and Medical Health Center" - }, - { - "author_name": "Amara Sarwal", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Bo Yu", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Edgar Gomez", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Victor Perez-Gutierrez", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Marcia Gossai", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Elisenda Valdez", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Astrid Mendez", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Sarah Chaudry", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Usha Venugopal", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Vihren Dimitrov", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Moiz Kasubhai", - "author_inst": "Lincoln Medical and Mental Health Center" - }, - { - "author_name": "Vidya Menon", - "author_inst": "Lincoln Medical and Mental Health Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.09.21249505", "rel_title": "Wastewater Virus Detection Complements Clinical COVID-19 Testing to Limit Spread of Infection at Kenyon College", @@ -995555,6 +997428,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.09.21249384", + "rel_title": "International risk of the new variant COVID-19 importations originating in the United Kingdom", + "rel_date": "2021-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.09.21249384", + "rel_abs": "A fast-spreading SARS-CoV-2 variant identified in the United Kingdom in December 2020 has raised international alarm. We estimate that, in all 15 countries analyzed, there is at least a 50% chance the variant was imported by travelers from the United Kingdom by December 7th.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Zhanwei Du", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Lin Wang", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Bingyi Yang", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Sheikh Taslim Ali", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Tim K. Tsang", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Songwei Shan", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Peng Wu", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Eric Lau", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Benjamin J Cowling", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Lauren Ancel Meyers", + "author_inst": "The University of Texas at Austin" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.10.21249524", "rel_title": "Using excess deaths and testing statistics to improve estimates of COVID-19 mortalities", @@ -997031,81 +998959,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.11.426218", - "rel_title": "Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class", - "rel_date": "2021-01-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.11.426218", - "rel_abs": "Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent SARS-CoV-2-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes of recognition, we determined structures of the SARS-CoV-2 spike in complex with three VH1-2-derived antibodies: 2-15, 2-43, and H4. All three utilized VH1-2-encoded motifs to recognize the receptor-binding domain (RBD), with heavy chain N53I enhancing binding and light chain tyrosines recognizing F486RBD. Despite these similarities, class members bound both RBD-up and -down conformations of the spike, with a subset of antibodies utilizing elongated CDRH3s to recognize glycan N343 on a neighboring RBD - a quaternary interaction accommodated by an increase in RBD separation of up to 12 [A]. The VH1-2-antibody class thus utilizes modular recognition encoded by modular genetic elements to effect potent neutralization, with VH-gene component specifying recognition of RBD and CDRH3 component specifying quaternary interactions.\n\nHighlightsO_LIDetermine structures of VH1-2-derived antibodies 2-43, 2-15, and H4 in complex with SARS-CoV-2 spike\nC_LIO_LIDefine a multi-donor VH1-2-antibody class with modular components for RBD and quaternary recognition\nC_LIO_LIReveal structural basis of RBD-up and RBD-down recognition within the class\nC_LIO_LIShow somatic hypermutations and avidity to be critical for potency\nC_LIO_LIDelineate changes in spike conformation induced by CDRH3-mediated quaternary recognition\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Micah Rapp", - "author_inst": "Columbia University" - }, - { - "author_name": "Yicheng Guo", - "author_inst": "Columbia University" - }, - { - "author_name": "Eswar Reddy Reddem", - "author_inst": "Columbia University" - }, - { - "author_name": "Lihong Liu", - "author_inst": "Columbia University" - }, - { - "author_name": "Pengfei Wang", - "author_inst": "Columbia University" - }, - { - "author_name": "Jian Yu", - "author_inst": "Columbia University" - }, - { - "author_name": "Gabriele Cerutti", - "author_inst": "Columbia University" - }, - { - "author_name": "Jude Bimela", - "author_inst": "Columbia University" - }, - { - "author_name": "Fabiana Bahna", - "author_inst": "Columbia University" - }, - { - "author_name": "Seetha Mannepalli", - "author_inst": "Columbia University" - }, - { - "author_name": "Baoshan Zhang", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Peter D. Kwong", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "David D. Ho", - "author_inst": "Columbia University" - }, - { - "author_name": "Lawrence Shapiro", - "author_inst": "Columbia University" - }, - { - "author_name": "Zizhang Sheng", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.09.426032", "rel_title": "Immunogenicity and efficacy of the COVID-19 candidate vector vaccine MVA SARS 2 S in preclinical vaccination", @@ -997453,6 +999306,85 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.10.426114", + "rel_title": "The hyperlipidaemic drug fenofibrate significantly reduces infection by SARS-CoV-2 in cell culture models", + "rel_date": "2021-01-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.10.426114", + "rel_abs": "The SARS-CoV-2 pandemic has caused a significant number of fatalities and worldwide disruption. To identify drugs to repurpose to treat SARS-CoV-2 infections, we established a screen to measure dimerization of ACE2, the primary receptor for the virus. This screen identified fenofibric acid, the active metabolite of fenofibrate. Fenofibric acid also destabilized the receptor binding domain (RBD) of the viral spike protein and inhibited RBD binding to ACE2 in ELISA and whole cell binding assays. Fenofibrate and fenofibric acid were tested by two independent laboratories measuring infection of cultured Vero cells using two different SARS-CoV-2 isolates. In both settings at drug concentrations which are clinically achievable, fenofibrate and fenofibric acid reduced viral infection by up to 70%. Together with its extensive history of clinical use and its relatively good safety profile, these studies identify fenofibrate as a potential therapeutic agent requiring urgent clinical evaluation to treat SARS-CoV-2 infection.\n\nTeaserThe approved drug fenofibrate inhibits infection by SARS-COV-2", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Scott P Davies", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Courtney J Mycroft-West", + "author_inst": "Keele University" + }, + { + "author_name": "Isabel Pagani", + "author_inst": "San Raffaele Scientific Institute" + }, + { + "author_name": "Harriet J Hill", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Yen-Hsi Chen", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Richard T Karlsson", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Ieva Bagdonaite", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Scott E Guimond", + "author_inst": "Keele University" + }, + { + "author_name": "Zania Stamataki", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Marcelo A Lima", + "author_inst": "Keele University" + }, + { + "author_name": "Jeremy E Turnbull", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Zhang Yang", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Elisa E Vicenzi", + "author_inst": "Ospedale San Raffaele" + }, + { + "author_name": "Mark A Skidmore", + "author_inst": "Keele University" + }, + { + "author_name": "Farhat Khanim", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Alan Richardson", + "author_inst": "Keele University" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.01.06.21249243", "rel_title": "Combining science and social engagement againstCovid-19 in a Brazilian Slum", @@ -999285,41 +1001217,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.06.21249272", - "rel_title": "Integrated Vaccination and Non-Pharmaceutical Interventions based Strategies in Ontario, Canada, as a Case Study: a Mathematical Modeling Study", - "rel_date": "2021-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249272", - "rel_abs": "BackgroundRecently, two \"Coronavirus disease 2019\" (COVID-19) vaccine products have been authorized in Canada. It is of crucial importance to model an integrated/combined package of non-pharmaceutical (physical/social distancing) and pharmaceutical (immunization) public health control measures.\n\nMethodsA modified epidemiological, compartmental SIR model was utilized and fit to the cumulative COVID-19 case data for the province of Ontario, Canada, from September 8, 2020 to December 8, 2020. Different vaccine roll-out strategies were simulated until 75 percent of the population is vaccinated, including a no-vaccination scenario. We compete these vaccination strategies with relaxation of non-pharmaceutical interventions. Non-pharmaceutical interventions were supposed to remain enforced and began to be relaxed on either January 31, March 31, or May 1, 2021.\n\nResultsBased on projections from the data and long-term extrapolation of scenarios, relaxing the public health measures implemented by re-opening too early would cause any benefits of vaccination to be lost by increasing case numbers, increasing the effective reproduction number above 1 and thus increasing the risk of localized outbreaks. If relaxation is, instead, delayed and 75 percent of the Ontarian population gets vaccinated by the end of the year, re-opening can occur with very little risk.\n\nInterpretationRelaxing non-pharmaceutical interventions by re-opening and vaccine deployment is a careful balancing act. Our combination of model projections from data and simulation of different strategies and scenarios, can equip local public health decision- and policy-makers with projections concerning the COVID-19 epidemiological trend, helping them in the decision-making process.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Matthew Betti", - "author_inst": "Mount Allison University" - }, - { - "author_name": "Nicola Bragazzi", - "author_inst": "York University" - }, - { - "author_name": "Jane Heffernan", - "author_inst": "York University" - }, - { - "author_name": "Jude Dvezela Kong", - "author_inst": "York University" - }, - { - "author_name": "Angie Raad", - "author_inst": "York University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.06.21249349", "rel_title": "Identifying silent COVID-19 infections among children is critical for controlling the pandemic", @@ -999723,6 +1001620,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.06.21249365", + "rel_title": "Modeling the effect of vaccination strategies in an Excel spreadsheet: The rate of vaccination, and not only the vaccination coverage, is a determinant for containing COVID-19 in urban areas", + "rel_date": "2021-01-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249365", + "rel_abs": "We have investigated the importance of the rate of vaccination to contain COVID-19 in urban areas. We used an extremely simple epidemiological model that is amenable to implementation in an Excel spreadsheet and includes the demographics of social distancing, efficacy of massive testing and quarantine, and coverage and rate of vaccination as the main parameters to model the progression of COVID-19 pandemics in densely populated urban areas. Our model predicts that effective containment of pandemic progression in densely populated cities would be more effectively achieved by vaccination campaigns that consider the fast distribution and application of vaccines (i.e., 50% coverage in 6 months) while social distancing measures are still in place. Our results suggest that the rate of vaccination is more important than the overall vaccination coverage for containing COVID-19. In addition, our modeling indicates that widespread testing and quarantining of infected subjects would greatly benefit the success of vaccination campaigns. We envision this simple model as a friendly, readily accessible, and cost-effective tool for assisting health officials and local governments in the rational design/planning of vaccination strategies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mario Moises Alvarez", + "author_inst": "Tecnologico de Monterrey" + }, + { + "author_name": "Sergio Bravo-Gonzalez", + "author_inst": "Tecnologico de Monterrey" + }, + { + "author_name": "Grissel Trujillo-de Santiago", + "author_inst": "Tecnologico de Monterrey" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.06.21249368", "rel_title": "Optimal design for phase 2 studies of SARS-CoV-2 antiviral drugs", @@ -1000954,49 +1002878,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.08.425825", - "rel_title": "Artemisia annua L. extracts prevent in vitro replication of SARS-CoV-2", - "rel_date": "2021-01-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.08.425825", - "rel_abs": "Ethnopharmacological relevanceArtemisia annua L. has been used for millennia in Southeast Asia to treat \"fever\". Many infectious microbial and viral diseases have been shown to respond to A. annua and communities around the world use the plant as a medicinal tea, especially for treating malaria.\n\nAim of the StudySARS-CoV-2 (the cause of Covid-19) globally has infected and killed millions of people. Because of the broad-spectrum antiviral activity of artemisinin that includes blockade of SARS-CoV-1, we queried whether A. annua suppressed SARS-CoV-2.\n\nMaterials and MethodsUsing Vero E6 and Calu-3 cells, we measured anti viral activity SARS-CoV-2 activity against fully infectious virusof dried leaf extracts of seven cultivars of A. annua sourced from four continents. IC50s were calculated and defined as (the concentrations that inhibited viral replication by 50%.) and CC50s (the concentrations that kill 50% of cells) were calculated.\n\nResultsHot-water leaf extracts based on artemisinin, total flavonoids, or dry leaf mass showed antiviral activity with IC50 values of 0.1-8.7 M, 0.01-0.14 g, and 23.4-57.4 g, respectively. Antiviral efficacy did not correlate with artemisinin or total flavonoid contents of the extracts. One dried leaf sample was >12 years old, yet the hot-water extract was still found to be active. The UK and South African variants, B1.1.7 and B1.351, were similarly inhibited. While all hot water extracts were effective, concentrations of artemisinin and total flavonoids varied by nearly 100-fold in the extracts. Artemisinin alone showed an estimated IC50 of about 70 M, and the clinically used artemisinin derivatives artesunate, artemether, and dihydroartemisinin were ineffective or cytotoxic at elevated micromolar concentrations. In contrast, the antimalarial drug amodiaquine had an IC50 = 5.8 M. Extracts had minimal effects on infection of Vero E6 or Calu-3 cells by a reporter virus pseudotyped by the SARS-CoV-2 spike protein. There was no cytotoxicity within an order of magnitude above the antiviral IC90 values.\n\nConclusionsA. annua extracts inhibit SARS-CoV-2 infection, and the active component(s) in the extracts is likely something besides artemisinin or a combination of components that block virus infection at a step downstream of virus entry. Further studies will determine in vivo efficacy to assess whether A. annua might provide a cost-effective therapeutic to treat SARS-CoV-2 infections.\n\nList of compounds studiedAmodiaquine\nArtemisinin\nArtesunate\nArtemether\nDeoxyartemisinin\nDihydroartemisinin\n\n\nHighlightsO_LIArtemisia annua is effective in stopping replication of SARS-CoV-2 including 2 new variants.\nC_LIO_LIThe anti-viral effect does not correlate to artemisinin, nor to the total flavonoid content.\nC_LIO_LIThe anti-viral mechanism does not appear to involve blockade virus entry into cell.\nC_LIO_LIThe plant offers two additional benefits: a decreased inflammatory response and blunting of fibrosis.\nC_LIO_LIA. annua may provide a safe, low-cost alternative for treating patients infected with SARS-CoV-2.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Manoj S Nair", - "author_inst": "Columbia University" - }, - { - "author_name": "Yaoxing Huang", - "author_inst": "Columbia University" - }, - { - "author_name": "David A Fidock", - "author_inst": "Columbia University" - }, - { - "author_name": "Stephen J Polyak", - "author_inst": "University of Washington" - }, - { - "author_name": "Jessica Wagoner", - "author_inst": "University of Washington" - }, - { - "author_name": "Melissa Towler", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Pamela Weathers", - "author_inst": "Worcester Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.08.425915", "rel_title": "Ad26.COV2.S-elicited immunity protects against G614 spike variant SARS-CoV-2 infection in Syrian hamsters and does not enhance respiratory disease in challenged animals with breakthrough infection after sub-optimal vaccine dosing", @@ -1001332,6 +1003213,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.07.425674", + "rel_title": "CpG-adjuvanted stable prefusion SARS-CoV-2 spike protein protected hamsters from SARS-CoV-2 challenge", + "rel_date": "2021-01-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.07.425674", + "rel_abs": "The COVID-19 pandemic presents an unprecedented challenge to global public health. Rapid development and deployment of safe and effective vaccines are imperative to control the pandemic. In the current study, we applied our adjuvanted stable prefusion SARS-CoV-2 spike (S-2P)-based vaccine, MVC-COV1901, to hamster models to demonstrate immunogenicity and protection from virus challenge. Golden Syrian hamsters immunized intramuscularly with two injections of 1 {micro}g or 5 {micro}g of S-2P adjuvanted with CpG 1018 and aluminum hydroxide (alum) were challenged intranasally with SARS-CoV-2. Prior to virus challenge, the vaccine induced high levels of neutralizing antibodies with 10,000-fold higher IgG level and an average of 50-fold higher pseudovirus neutralizing titers in either dose groups than vehicle or adjuvant control groups. Six days after infection, vaccinated hamsters did not display any weight loss associated with infection and had significantly reduced lung pathology and most importantly, lung viral load levels were reduced to lower than detection limit compared to unvaccinated animals. Vaccination with either 1 g or 5 g of adjuvanted S-2P produced comparable immunogenicity and protection from infection. This study builds upon our previous results to support the clinical development of MVC-COV1901 as a safe, highly immunogenic, and protective COVID-19 vaccine.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Chia-En Lien", + "author_inst": "Medigen Vaccine Biologics Corporation, Taipei City, Taiwan" + }, + { + "author_name": "Yi-Jiun Lin", + "author_inst": "Medigen Vaccine Biologics Corporation, Taipei City, Taiwan" + }, + { + "author_name": "Charles Chen", + "author_inst": "Medigen Vaccine Biologics Corporation, Taipei City, Taiwan" + }, + { + "author_name": "Wei-Cheng Lian", + "author_inst": "Medigen Vaccine Biologics Corporation, Taipei City, Taiwan" + }, + { + "author_name": "Tsun-Yung Kuo", + "author_inst": "Department of Biotechnology and Animal Science, National Ilan University, Yilan County, Taiwan" + }, + { + "author_name": "John D Campbell", + "author_inst": "Dynavax Technologies, Emeryville, CA 94608, USA" + }, + { + "author_name": "Paula Traquina", + "author_inst": "Dynavax Technologies, Emeryville, CA 94608, USA" + }, + { + "author_name": "Meei-Yun Lin", + "author_inst": "Medigen Vaccine Biologics Corporation, Taipei City, Taiwan" + }, + { + "author_name": "Luke Tzu Chi Liu", + "author_inst": "Medigen Vaccine Biologics Corporation, Taipei City, Taiwan" + }, + { + "author_name": "Ya-Shan Chuang", + "author_inst": "Medigen Vaccine Biologics Corporation, Taipei City, Taiwan" + }, + { + "author_name": "Hui-Ying Ku", + "author_inst": "Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Chun-Che Liao", + "author_inst": "Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Yen-Hui Chen", + "author_inst": "Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Jia-Tsrong Jan", + "author_inst": "Genomic Research Center, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Cheng-Pu Sun", + "author_inst": "Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Yin-Shiou Lin", + "author_inst": "Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Ping-Yi Wu", + "author_inst": "Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Yu-Chiuan Wang", + "author_inst": "Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Mi-Hua Tao", + "author_inst": "Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Yi-Ling Lin", + "author_inst": "Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.06.425497", "rel_title": "Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation", @@ -1002672,61 +1004648,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.06.21249314", - "rel_title": "Impaired performance of SARS-CoV-2 antigen-detecting rapid tests at elevated temperatures", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249314", - "rel_abs": "Rapid antigen-detecting tests (Ag-RDTs) can complement molecular diagnostics for COVID-19. The recommended temperature for storage of SARS-CoV-2 Ag-RDTs ranges between 5-30{degrees}C. In many countries that would benefit from SARS-CoV-2 Ag-RDTs, mean temperatures exceed 30{degrees}C. We assessed analytical sensitivity and specificity of eleven commercially available SARS-CoV-2 Ag-RDTs using different storage and operational temperatures, including (i) long-term storage and testing at recommended conditions, (ii) recommended storage conditions followed by 10 minutes exposure to 37{degrees}C and testing at 37{degrees}C and (iii) 3 weeks storage followed by testing at 37{degrees}C. The limits of detection of SARS-CoV-2 Ag-RDTs under recommended conditions ranged from 8.2x105-7.9x107 genome copies/ml of infectious SARS-CoV-2 cell culture supernatant. Despite long-term storage at recommended conditions, 10 minutes pre-incubation of Ag-RDTs and testing at 37{degrees}C resulted in about ten-fold reduced sensitivity for 46% of SARS-CoV-2 Ag-RDTs, including both Ag-RDTs currently listed for emergency use by the World Health Organization. After 3 weeks of storage at 37{degrees}C, 73% of SARS-CoV-2 Ag-RDTs exhibited about ten-fold reduced sensitivity. Specificity of SARS-CoV-2 Ag-RDTs using cell culture-derived human coronaviruses HCoV-229E and HCoV-OC43 was not affected by storage and testing at 37{degrees}C. In summary, short- and long-term exposure to elevated temperatures likely impairs sensitivity of several SARS-CoV-2 Ag-RDTs that may translate to false-negative test results at clinically relevant virus concentrations compatible with inter-individual transmission. Ensuring appropriate transport and storage conditions, and development of tests that are more robust across temperature fluctuations will be important for accurate use of SARS-CoV-2 Ag-RDTs in tropical settings.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Verena Claudia Haage", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Edmilson Ferreira de Oliveira-Filho", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Andres Moreira-Soto", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Arne K\u00fchne", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Carlo Fischer", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Jilian Sacks", - "author_inst": "Foundation for Innovative New Diagnostics" - }, - { - "author_name": "Victor Max Corman", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Marcel A. M\u00fcller", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Jan Felix Drexler", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.05.21249131", "rel_title": "Ivermectin shows clinical benefits in mild to moderate Covid19 disease: A randomised controlled double blind dose response study in Lagos.", @@ -1002942,6 +1004863,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.01.05.425516", + "rel_title": "RNA-protein interaction analysis of SARS-CoV-2 5'- and 3'-untranslated regions identifies an antiviral role of lysosome-associated membrane protein-2", + "rel_date": "2021-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.05.425516", + "rel_abs": "Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is a positive-strand RNA virus. Viral genome is capped at the 5-end, followed by an untranslated region (UTR). There is poly-A tail at 3-end, preceded by an UTR. Self-interaction between the RNA regulatory elements present within 5- and 3-UTRs as well as their interaction with host/virus-encoded proteins mediate the function of 5- and 3-UTRs. Using RNA-protein interaction detection (RaPID) assay coupled to liquid chromatography with tandem mass-spectrometry, we identified host interaction partners of SARS-CoV-2 5- and 3-UTRs and generated an RNA-protein interaction network. By combining these data with the previously known protein-protein interaction data proposed to be involved in virus replication, we generated the RNA-protein-protein interaction (RPPI) network, likely to be essential for controlling SARS-CoV-2 replication. Notably, bioinformatics analysis of the RPPI network revealed the enrichment of factors involved in translation initiation and RNA metabolism. Lysosome-associated membrane protein-2a (Lamp2a) was one of the host proteins that interact with the 5-UTR. Further studies showed that Lamp2 level is upregulated in SARS-CoV-2 infected cells and overexpression of Lamp2a and Lamp2b variants reduced viral RNA level in infected cells and vice versa. In summary, our study provides an useful resource of SARS-CoV-2 5- and 3-UTR binding proteins and reveal the antiviral function of host Lamp2 protein.\n\nImportanceReplication of a positive-strand RNA virus involves an RNA-protein complex consisting of viral genomic RNA, host RNA(s), virus-encoded proteins and host proteins. Dissecting out individual components of the replication complex will help decode the mechanism of viral replication. 5- and 3-UTRs in positive-strand RNA viruses play essential regulatory roles in virus replication. Here, we identified the host proteins that associate with the UTRs of SARS-CoV-2, combined those data with the previously known protein-protein interaction data (expected to be involved in virus replication) and generated the RNA-protein-protein interaction (RPPI) network. Analysis of the RPPI network revealed the enrichment of factors involved in translation initiation and RNA metabolism, which are important for virus replication. Analysis of one of the interaction partners of the 5-UTR (Lamp2a) demonstrated its antiviral role in SARS-CoV-2 infected cells. Collectively, our study provides a resource of SARS-CoV-2 UTR-binding proteins and identifies an antiviral role of host Lamp2a protein.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rohit Verma", + "author_inst": "Translational Health Science and Technology Institutealth" + }, + { + "author_name": "Sandhini Saha", + "author_inst": "Regional Centre for Biotechnology" + }, + { + "author_name": "Shiv Kumar", + "author_inst": "Translational Health Science and Technology Institute" + }, + { + "author_name": "Shailendra Mani", + "author_inst": "Translational Health Science and Technology Instituteealth" + }, + { + "author_name": "Tushar Kanti Maiti", + "author_inst": "Regional Centre for Biotechnology" + }, + { + "author_name": "Milan Surjit", + "author_inst": "Translational Health Science and Technology Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.04.425128", "rel_title": "Protein scaffold-based multimerization of soluble ACE2 efficiently blocks SARS-CoV-2 infection in vitro", @@ -1004118,65 +1006078,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.30.20249062", - "rel_title": "Outbreak or pseudo-outbreak? Integrating SARS-CoV-2 sequencing to validate infection control practices in an end stage renal disease facility", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20249062", - "rel_abs": "BackgroundThe COVID-19 pandemic of 2020 poses a particularly high risk for End Stage Renal Disease (ESRD) patients and led to a need for facility-wide control plans to prevent introduction and spread of infection within ESRD facilities. Rapid identification of clusters of contemporaneous cases is essential, as these may be indicative of within-facility spread. Nevertheless, in a setting of high community COVID-19 prevalence, a series of ESRD patients may test positive at around the same time without their shared ESRD facility being the nexus for disease spread. Here we describe a series of five cases occurring within an eleven-day period in November 2020 in a hospital-based 32-station ESRD facility in southwest Wisconsin, the subsequent facility-wide testing, and the use of genetic sequence analysis of positive specimens to evaluate whether these cases were linked.\n\nMethodsFour patient cases and one staff case were identified in symptomatic individuals by RT-PCR. Facility-wide screening was initiated at the request of local public health and conducted using Abbot BinaxNOW antigen tests. SARS-CoV-2 genome sequences were obtained from residual diagnostic test specimens using an amplicon-based approach on an Ion Torrent S5 sequencer.\n\nResultsResidual specimens from 4 of 5 cases were available for sequence analysis. Each sequence was very clearly genetically distinct from the others, indicating that these contemporaneous cases were not linked. Facility-wide screening of 47 staff and 107 patients did not identify any additional cases.\n\nConclusionsThese data indicate that despite the outward appearance of a case cluster, the facility did not experience within-facility spread nor serve as the epicenter of a new outbreak, suggesting that the enacted rigorous infection control procedures (screening, masking, distancing) practiced stringently by patients and staff were sufficient to permit dialysis to proceed safely in a very high-risk population under pressure from increasing community spread. These data also demonstrate the utility of rapid turnaround SARS-CoV-2 sequencing in outbreak investigations in settings like ESRD facilities.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Bridget L Pfaff", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Craig S Richmond", - "author_inst": "Gundersen Medical Foundation" - }, - { - "author_name": "Arick P Sabin", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Deena M Athas", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Jessica C Adams", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Megan E Meller", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Kumari Usha", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Sarah A Schmitz", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Brian J Simmons", - "author_inst": "Gundersen Health System" - }, - { - "author_name": "Andrew J Borgert", - "author_inst": "Gundersen Medical Foundation" - }, - { - "author_name": "Paraic A Kenny", - "author_inst": "Gundersen Medical Foundation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.03.21249175", "rel_title": "Modelling COVID -19 Transmission in a Hemodialysis Centre Using Simulation Generated Contacts Matrices", @@ -1004444,6 +1006345,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.31.20249106", + "rel_title": "Optimizing testing for COVID-19 in India", + "rel_date": "2021-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.31.20249106", + "rel_abs": "COVID-19 testing across India uses a mix of two types of tests. Rapid Antigen Tests (RATs) are relatively inexpensive point-of-care lateral-flow-assay tests, but they are also less sensitive. The reverse-transcriptase polymerase-chain-reaction (RT-PCR) test has close to 100% sensitivity and specificity in a laboratory setting, but delays in returning results, as well as increased costs relative to RATs, may vitiate this advantage.\n\nIndia-wide, about 49% of COVID-19 tests are RATs, but some Indian states, including the large states of Uttar Pradesh (pop. 227.9 million) and Bihar (pop. 121.3 million) use a much higher proportion of such tests. Here we show, using simulations based on epidemiological network models, that the judicious use of RATs can yield epidemiological outcomes comparable to those obtained through RT-PCR-based testing and isolation of positives, provided a few conditions are met. These are (a) that RAT test sensitivity is not too low, (b) that a reasonably large fraction of the population, of order 0.5% per day, can be tested, (c) that those testing positive are isolated for a sufficient duration, and that (d) testing is accompanied by other non-pharmaceutical interventions for increased effectiveness. We assess optimal testing regimes, taking into account test sensitivity and specificity, background seroprevalence and current test pricing. We find, surprisingly, that even 100% RAT test regimes should be acceptable, from both an epidemiological as well as a economic standpoint, provided the conditions outlined above are met.\n\nAuthor summaryUsing network models, we study optimal ways of combining low sensitivity, relatively inexpensive point-of-care rapid antigen tests for COVID-19 with higher sensitivity but more expensive laboratory RT-PCR tests. We take into account background seroprevalence and current test pricing for such tests in India, finding that even purely rapid antigen test-based regimes can produce the same reduction in overall infections that pure RT-PCR tests are capable of. This is provided one can test at scale and isolate those testing positive effectively, that the sensitivity of the rapid test is not too low and that non-pharmaceutical interventions proceed in parallel for increased effectiveness.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Philip Cherian", + "author_inst": "Ashoka University" + }, + { + "author_name": "Sandeep Krishna", + "author_inst": "National Centre for Biological Sciences" + }, + { + "author_name": "Gautam I Menon", + "author_inst": "Ashoka University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.03.21249173", "rel_title": "Empty Streets, Speeding and Motor Vehicle Collisions during Covid-19 Lockdowns: Evidence from Northern Ireland", @@ -1005576,49 +1007504,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.12.29.20248869", - "rel_title": "High levels of plasminogen activator inhibitor-1, tissue plasminogen activator and fibrinogen in patients with severe COVID-19", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20248869", - "rel_abs": "We measured plasma levels of fibrinogen, plasminogen, tissue plasminogen activator (t-PA) and plasminogen activation inhibitor 1 (PAI-1) in blood from 37 patients with severe coronavirus disease-19 (COVID-19) and 23 controls. PAI-1, t-PA and fibrinogen levels were significantly higher in the COVID-19 group. Increased levels of PAI-1 likely result in lower plasmin activity and hence decreased fibrinolysis. These observations provide a partial explanation for the fibrin- mediated increase in blood viscosity and hypercoagulability that has previously been observed in COVID-19. Our data suggest that t-PA administration may be problematic, but that other interventions designed to enhance fibrinolysis might prove useful in the treatment of the coagulopathy that is often associated with severe COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "David Cabrera-Garcia", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Andrea Miltiades", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Samantha M Parsons", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Katerina Elisman", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Mohammad Taghi Mansouri", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Gebhard Wagener", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Neil L Harrison", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.12.29.20248975", "rel_title": "COVID-19: Can early home treatment with Azithromycin alone or with Zinc help prevent hospitalisation, death, and long-COVID-19? A review", @@ -1005858,6 +1007743,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.28.20248552", + "rel_title": "COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and may be modified by dexamethasone", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248552", + "rel_abs": "We performed comparative lower respiratory tract transcriptional profiling of 52 critically ill patients with ARDS from COVID-19 or other etiologies, or without ARDS. We found no evidence of cytokine storm but instead observed complex host response dysregulation driven by genes with non-canonical roles in inflammation and immunity that were predicted to be modulated by dexamethasone. Compared to other viral ARDS, COVID-19 was characterized by impaired interferon-stimulated gene expression.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Aartik Sarma", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Stephanie A. Christenson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Eran Mick", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Catherine DeVoe", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Thomas Deiss", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Angela Oliveira Pisco", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Rajani Ghale", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alejandra Jauregui", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ashley Byrne", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Farzad Moazed", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Natasha Spottiswoode", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Pratik Sinha", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Beth Shoshana Zha", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Paula Hayakawa Serpa", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "K. Mark Ansel", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jennifer G. Wilson", + "author_inst": "Stanford University" + }, + { + "author_name": "Aleksandra Leligdowicz", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Emily R. Siegel", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Marina Sirota", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Joseph L. DeRisi", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Michael A. Matthay", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "- COMET Consortium", + "author_inst": "" + }, + { + "author_name": "Carolyn M. Hendrickson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kirsten N. Kangelaris", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew Krummel", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Prescott G. Woodruff", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "David J. Erle", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Carolyn S. Calfee", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Charles R. Langelier", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.12.28.20248906", "rel_title": "SARS-CoV-2 Variant Under Investigation 202012/01 has more than twofold replicative advantage", @@ -1007006,29 +1009022,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.28.20248936", - "rel_title": "Lockdown Effects on Sars-CoV-2 Transmission - The evidence from Northern Jutland", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248936", - "rel_abs": "The exact impact of lockdowns and other NPIs on Sars-CoV-2 transmission remain a matter of debate as early models assumed 100% susceptible homogenously transmitting populations, an assumption known to overestimate counterfactual transmission, and since most real epidemiological data are subject to massive confounding variables. Here, we analyse the unique case-controlled epidemiological dataset arising from the selective lockdown of parts of Northern Denmark, but not others, as a consequence of the spread of mink-related mutations in November 2020. Our analysis shows that while infection levels decreased, they did so before lockdown was effective, and infection numbers also decreased in neighbour municipalities without mandates. Direct spill-over to neighbour municipalities or the simultaneous mass testing do not explain this. Instead, control of infection pockets possibly together with voluntary social behaviour was apparently effective before the mandate, explaining why the infection decline occurred before and in both the mandated and non-mandated areas. The data suggest that efficient infection surveillance and voluntary compliance make full lockdowns unnecessary at least in some circumstances.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Kasper Planeta Kepp", - "author_inst": "Technical University of Denmark" - }, - { - "author_name": "Christian Bjornskov", - "author_inst": "Aarhus University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.30.20248908", "rel_title": "Unsupervised Discovery of Risk Profiles on Negative and Positive COVID-19 Hospitalized Patients", @@ -1007188,6 +1009181,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.12.29.20248994", + "rel_title": "Respiratory and non-respiratory manifestations in children admitted with COVID 19 in Rio de Janeiro city, Brazil", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20248994", + "rel_abs": "IntroductionCOVID 19 is still a challenge in pediatrics due to variety of symptoms and different presentations\n\nAimTo describe clinical, laboratorial and treatment of confirmed COVID-19 pediatric admitted in hospitals.\n\nMethodsA retrospective study was conducted in children (0-18 years), admitted between March and November 15, 2020, with confirmed COVID-19 by reverse transcription polymerase chain reaction or serological tests. Clinical data about symptoms, laboratorial exams and treatments were analysed. Patients were evaluated according predominant (PRS) or non-predominant respiratory symptoms (non-PRS)\n\nResultsSixty-four patients were evaluated, being the median age 5.6 years. Forty-seven (73.4%) children were admitted with PRS and 17 (26.4%) with non-PRS. The main symptoms in the PRS group were fever in 74.5% of children and cough in 66%; and fever in 76.5% and edema/cavitary effusion in 29.4% in the non-PRS group. The median of C-reactive protein (in mg/dl) was 2.5 in the PRS group and 6.1 in the non-PRS group. Antibiotics were used in 85.1% of the PRS group and 94.1% of non-group. Comorbidity was present in 30/47 (63.8%) of PRS group and 8/17 (47.1%) of non-PRS group (p=0.22). Length of stay until 7 days in patients with comorbidity was present in 27/64 (42.1%) and more than 7 days in 11/64 (17.1%) (p= 0.2)\n\nConclusionNon-PRS represented more than one quarter of admitted patients. Fever was the main symptom detected, elevated CRP was frequent and antibiotics were commonly prescribed. Comorbidity was found in both groups and his presence was not associated with a longer length of stay.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "ANDRE RICARDO ARAUJO ARAUJO DA SILVA", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "CARLOS GABRIEL BRANDAO FOINSECA", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "JACKSON LINO PAULA SANTANA DE MIRANDA", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "BEATRIZ VALLADARES TRAVASSOS", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "CAROLINA RODRIGUES BAIAO", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "KALINA DOMINIK SILVA", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "LINO BRENO AZEVEDO ESTEVAM DOS SANTOS", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "MARIANNA MELO RODRIGUES DE BRITTO", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "PABLO AUGUSTO LUCAS DE SOUZA CERQUEIRA", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "SILVIA NAZARE BRAGA PEREIRA", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "REBECA BITTENCOURT JAQUEIRA RIOS", + "author_inst": "FEDERAL FLUMINENSE UNIVERSITY" + }, + { + "author_name": "CRISTINA SOUZA VIEIRA", + "author_inst": "PRONTOBABY GROUP" + }, + { + "author_name": "IZABEL ALVES LEAL", + "author_inst": "PRONTOBABY GROUP" + }, + { + "author_name": "NATALIA COCHRANE MARTINS", + "author_inst": "PRONTOBABY GROUP" + }, + { + "author_name": "LIEGE MARIA ABREU DE CARVALHO", + "author_inst": "PRONTOBABY GROUP" + }, + { + "author_name": "ANDREA BARCHIK PEREIRA", + "author_inst": "PRONTOBABY GOUP" + }, + { + "author_name": "CRISTIANE HENRIQUES TEIXEIRA", + "author_inst": "PRONTOBABY GROUP" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.12.31.20249101", "rel_title": "Strategies to minimize SARS-CoV-2 transmission in classroom settings: Combined impacts of ventilation and mask effective filtration efficiency", @@ -1008288,33 +1010364,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.02.20248940", - "rel_title": "Brazilian model estimation for SARS-CoV-2 peak contagion (BMESPC): first and second wave", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.02.20248940", - "rel_abs": "With newer data for SARS-CoV-2 and entering the second wave of contagion required the improvement of the forecasting model, structuring its model to forecast the peak of the first and second contagion wave in Brazil. The Brazilian model estimation for SARS-CoV-2 peak contagion (BMESPC) was structured, capable of estimating the peak of contagion for SARS-CoV-2 in the first and second waves, as the main objective of this work. Using the BMESPC model, it was possible to estimate, with a certain reliability degree, the peak of contagion for the first and second waves in Brazil, with one day difference from the real to the forecast. While at the state level, the calculated confidence interval proved to be more accurate. In this way, it is possible to use BMESPC to forecast the peak of contagion for several regions, provided that the necessary structure and calibration are respected.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Guilherme Asai", - "author_inst": "University of Illinois at Urbana Champaing" - }, - { - "author_name": "Andre Kuroiva", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Manuella Lucca Terra", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.03.20248715", "rel_title": "Humoral and cell-mediated response in colostrum after exposure to severe acute respiratory syndrome coronavirus 2", @@ -1008818,6 +1010867,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.03.21249169", + "rel_title": "The Impact of the November 2020 English National Lockdown on COVID-19 case counts", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.03.21249169", + "rel_abs": "In the UK the epidemic of COVID-19 continues to pose a significant threat to public health. On the 14th October the English government introduced a tier system for control of the epidemic but just 3 weeks later a National lockdown across all areas of England was implemented. When English areas emerged from Lockdown many were placed in different tiers (most typically moved up at least one tier). However, the effectiveness of the tier system has been challenged by the emergence of a new variant of SARS-CoV-2 which appears to be much more infectious. In addition, from early November a trial mass testing service was being run in Liverpool. We used publicly available data of daily cases by local authority (local government areas) and estimated the reproductive rate (R value) of the epidemic based on 7-day case numbers compared with the previous 7-day period. There was a clear surge in infections from a few days before to several days after the lockdown was implemented. But this surge was almost exclusively associated with Tier 1 and Tier 2 authorities. In Tier 3 authorities where hospitality venues were only allowed to operate as restaurants there was no such surge. After this initial surge, cases declined in all three tiers with the R value dropping to a mean of about 0.7 independent of tier. London, The South East and East of England Regions saw rising infection rates in the last week or so of lockdown primarily in children of secondary school age. We could find no obvious benefit of the trial mass screening programme in Liverpool city. We conclude that in Tiers 1 and 2 much of the beneficial impact of the national lockdown was lost probably because of the leak of its likely implementation five days early leading to increased socialising in these areas before the start of lockdown. We further conclude that given that the new variant is estimated to have an R value of between 0.39 and 0.93 greater than previous variants, any lockdown as strict as the November one would be insufficient to reverse the increase in infections by itself. The value of city-wide mass testing to control the epidemic remains uncertain.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Paul R Hunter", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Julii Suzanne Brainard", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Alastair R Grant", + "author_inst": "University of East Anglia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.03.20248972", "rel_title": "How vaccination and contact isolation might interact to suppress transmission of Covid-19: a DCM study", @@ -1010210,49 +1012286,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.12.28.20248920", - "rel_title": "Determinants of in-hospital mortality in COVID-19; a prospective cohort study from Pakistan", - "rel_date": "2021-01-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248920", - "rel_abs": "A prospective cohort study was conducted at the Indus Hospital Karachi, Pakistan between March and June 2020 to describe the determinants of mortality among hospitalized COVID-19 patients. 186 adult patients were enrolled and all-cause mortality was found to be 36% (67/186). Those who died were older and more likely to be males (p<0.05). Temperature and respiratory rate were higher among non-survivors while Oxygen saturation was lower (p<0.05). Serum CRP, D-dimer and IL-6 were higher while SpO2 was lower on admission among non-survivors (p<0.05). Non-survivors had higher SOFA and CURB-65 scores while thrombocytopenia, lymphopenia and severe ARDS was more prevalent among them (p<0.05). Use of non-invasive ventilation in emergency room, ICU admission and invasive ventilation were associated with mortality in our cohort (p<0.05). Length of hospital stay and days of intubation were longer in non-survivors (p<0.05). Use of azithromycin, hydroxychloroquine, steroids, tocilizumab, antibiotics, IVIG or anticoagulation showed no mortality benefit (p>0.05). Multivariable logistic regression showed that age > 60 years, oxygen saturation <93% on admission, pro-calcitonin > 2 ng/ml, unit rise in temperature and SOFA score, ICU admission and sepsis during hospital stay were associated with higher odds of mortality. Larger prospective studies are needed to further strengthen these findings.\n\nKey FindingsO_LIAge greater than 60 years is associated with in-hospital mortality among COVID-19 patients\nC_LIO_LIOxygen saturation less than 93% and ICU admission are associated with higher odds of mortality\nC_LIO_LIInflammatory markers including CRP, Ferritin and IL-6 were significantly higher among non-survivors\nC_LIO_LISerum pro-calcitonin greater than 2 ng/ml and sepsis during hospital stay are associated with higher odds of mortality among COVID-19 patients\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Samreen Sarfaraz", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Quratulain Shaikh", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Syed Ghazanfar Saleem", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Anum Rahim", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Fivzia Farooq Herekar", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Samina Junejo", - "author_inst": "The Indus Hospital" - }, - { - "author_name": "Aneela Hussain", - "author_inst": "The Indus Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.27.20248896", "rel_title": "Vaccination and Non-Pharmaceutical Interventions: when can the UK relax about COVID-19?", @@ -1010512,6 +1012545,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.27.20232934", + "rel_title": "A renewal equation model to assess roles andlimitations of contact tracing for diseaseoutbreak control", + "rel_date": "2021-01-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.27.20232934", + "rel_abs": "We propose a deterministic model capturing essential features of contact tracing as part of public health non-pharmaceutical interventions to mitigate an outbreak of an infectious disease. By incorporating a mechanistic formulation of the processes at the individual level, we obtain an integral equation (delayed in calendar time and advanced in time since infection) for the probability that an infected individual is detected and isolated at any point in time. This is then coupled with a renewal equation for the total incidence to form a closed system describing the transmission dynamics involving contact tracing. We define and calculate basic and effective reproduction numbers in terms of pathogen characteristics and contact tracing implementation constraints. When applied to the case of SARS-CoV-2, our results show that only combinations of diagnosis of symptomatic infections and contact tracing that are almost perfect in terms of speed and coverage can attain control, unless additional measures to reduce overall community transmission are in place. Under constraints on the testing or tracing capacity, a temporary interruption of contact tracing may, depending on the overall growth rate and prevalence of the infection, lead to an irreversible loss of control even when the epidemic was previously contained.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Francesca Scarabel", + "author_inst": "York University" + }, + { + "author_name": "Lorenzo Pellis", + "author_inst": "The University of Manchester" + }, + { + "author_name": "Nicholas H Ogden", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Jianhong Wu", + "author_inst": "York University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.26.20248891", "rel_title": "Perception and awareness of COVID-19 among health science students and staff of Kuwait University: An online cross-sectional study", @@ -1011612,25 +1013676,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.12.24.20248842", - "rel_title": "Simulating Retarded SEIRS model for COVID-19: will the second epidemic happen?", - "rel_date": "2020-12-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.24.20248842", - "rel_abs": "In this paper, we want to simulate the COVID-19 epidemic according to the Retarded SEIRS model. One of the main questions in the human mind is whether the COVID-19 epidemic will happen again. Therefore, a criterion must be set for the occurrence or non-occurrence of the disease. With the Retarded SEIRS model and this criterion, we can predict whether the Covid-19 will re-emerge. So far, a large number of researches that have been presented in scientific groups or communities have been based on the SIR or SEIR model. But we assume that each recovered individual is immune to the disease for a limited time, and then will be susceptible again. As we know, this assumption was also true for SARS.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Hamid Pour Mohammad", - "author_inst": "Sharif University of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.24.20248814", "rel_title": "S gene dropout patterns in SARS-CoV-2 tests suggest spread of the H69del/V70del mutation in the US.", @@ -1011966,6 +1014011,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.25.20248860", + "rel_title": "Will Proton Pump Inhibitors Lead to a Higher Risk of COVID-19 Infection and Progression to Severe Disease? A Meta-analysis", + "rel_date": "2020-12-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.25.20248860", + "rel_abs": "BackgroundPrevious researches on the association between proton pump inhibitors (PPIs) use and the treatment and prevention of COVID-19 have generated inconsistent findings. Therefore, this Meta-analysis was conducted to clarify the outcome in patients who take PPIs.\n\nMethodsWe carried out a systematic search to identify potential studies until November 2020. Heterogeneity was assessed using the I-squared statistic. Odds ratios (ORs) with its 95% confidence intervals (CIs) were calculated by fixed-effects or random-effects models according to the heterogeneity. Sensitivity analyses and tests for publication bias were also performed.\n\nResultsEight articles with more than 268,683 subjects were included. PPI use was not associated with increased or decreased risk of COVID-19 infection (OR:3.16, 95%CI = 0.74-13.43, P=0.12) or mortality risk of COVID-19 patients (OR=1.91, 95% CI=0.86-4.24, P=0.11). While it can add risk of severe disease (OR=1.54, 95% CI=1.20-1.99, P<0.001;) and secondary infection (OR=4.33, 95% CI=2.57-7.29). No publication bias was detected.\n\nConclusionsPPI use is not associated with increased risk infection and may not change the mortality risk of COVID-19, but appeared to be associated with increased risk of progression to severe disease and secondary infection. However, more original studies to further clarify the relationship between PPI and COVID-19 are still urgently needed.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Cunye Yan", + "author_inst": "Department of Breast and Thyroid Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences" + }, + { + "author_name": "Yue Chen", + "author_inst": "Department of Clinical Medicine, School of the First Clinical Medicine, Anhui Medical University" + }, + { + "author_name": "Chenyu Sun", + "author_inst": "AMITA Health Saint Joseph Hospital Chicago" + }, + { + "author_name": "Mubashir Ayaz Ahmed", + "author_inst": "AMITA Health Saint Joseph Hospital Chicago" + }, + { + "author_name": "Chandur Bhan", + "author_inst": "AMITA Health Saint Joseph Hospital Chicago" + }, + { + "author_name": "Ce Cheng", + "author_inst": "The University of Arizona College of Medicine at South Campus" + }, + { + "author_name": "Lei Hu", + "author_inst": "Department of Clinical Medicine, School of the First Clinical Medicine, Anhui Medical University" + }, + { + "author_name": "Zhichun Guo", + "author_inst": "School of Pharmacy, Massachusetts college of Pharmacy and Health sciences" + }, + { + "author_name": "Hongru Yang", + "author_inst": "School of Pharmacy, Massachusetts college of Pharmacy and Health sciences" + }, + { + "author_name": "Chenyu Cao", + "author_inst": "School of Pharmacy, Massachusetts college of Pharmacy and Health sciences" + }, + { + "author_name": "Ziwei Ji", + "author_inst": "School of Nursing, Massachusetts college of Pharmacy and Health sciences" + }, + { + "author_name": "Yue Yan", + "author_inst": "School of Arts and Sciences, Massachusetts college of Pharmacy and Health sciences" + }, + { + "author_name": "Yijing Zuo", + "author_inst": "School of Nursing, Massachusetts college of Pharmacy and Health sciences" + }, + { + "author_name": "Yiceng Sun", + "author_inst": "Department of Breast and Thyroid Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences" + }, + { + "author_name": "Yao Li", + "author_inst": "Department of Breast and Thyroid Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences" + }, + { + "author_name": "Qin Zhou", + "author_inst": "Radiation Oncology, Mayo Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.25.20248824", "rel_title": "Staff to staff transmission as a driver of healthcare worker infections with COVID-19", @@ -1013280,49 +1015404,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.12.27.424507", - "rel_title": "Losartan promotes cell survival following SARS-CoV-2 infection in vitro", - "rel_date": "2020-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.27.424507", - "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) can be associated with mortality and high morbidity worldwide. There is an extensive effort to control infection and disease caused by SARS-CoV-2. This study addressed the hypothesis that angiotensin II type I receptor blocker, Losartan, may restrict pathogenesis caused by SARS-CoV-2 by decreasing viral-induced cytopathological changes by blocking angiotensin II type 1 receptor (AT1R), thus reducing the affinity of the virus for ACE2, and inhibiting papain-like protease of the virus.\n\nMethodLosartan inhibitory effect on deubiquitination and deISGylation properties of papain-like protease was investigated using a fluorescence method and gel shift analysis determining its inhibitory effects.\n\nThe inhibitory effect of Losartan on SARS-CoV-2 cell replication was investigated both when losartan was added to the cell culture 1 hour before (pre-infection group) and 1 hour after (post-infection group) SARS-CoV-2 infection of Vero E6 cells.\n\nResultsLosartan treatment of Vero E6 cells prior to and after SARS-CoV-2 infection reduced SARS-CoV-2 replication by 80% and 70% respectively. Losartan was not a strong deubiquitinase and deISGylase inhibitor of PLpro.\n\nConclusionLosartan added pre- and post-infection to the Vero E6 cell culture significantly prevents cell destruction and replication by SARS-CoV2. Losartan has low side-effects, is readily available, and can be produced at high levels globally, all features of a promising drug in treatment of COVID-19 if validated by clinical trials.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Reza Nejat", - "author_inst": "Bazarganan Hospital" - }, - { - "author_name": "Ahmad Shahir Sadr", - "author_inst": "Cheragh Medical Institute and Hospital" - }, - { - "author_name": "Brendan T. Freitas", - "author_inst": "University of Georgia, Athens, Georgia 30602, USA" - }, - { - "author_name": "Jackelyn Crabtree", - "author_inst": "University of Georgia, Athens, Georgia 30602, USA" - }, - { - "author_name": "Scott D. Pegan", - "author_inst": "University of Georgia, Athens, Georgia 30602, USA" - }, - { - "author_name": "Ralph A. Tripp", - "author_inst": "University of Georgia, Athens, Georgia 30602, USA" - }, - { - "author_name": "David J. Najafi", - "author_inst": "alliance retina consultants" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.12.28.424554", "rel_title": "Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions and monocytes for optimal therapeutic protection", @@ -1013642,6 +1015723,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.28.424533", + "rel_title": "Rapid inactivation in vitro of SARS-CoV-2 in saliva by black tea and green tea", + "rel_date": "2020-12-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.28.424533", + "rel_abs": "Saliva plays major roles in human-to-human transmission of the SARS-CoV-2. Recently we reported that black, green and oolong tea significantly inactivated SARS-CoV-2 within 1 min. Theaflavin-3,3-di-gallate (TFDG), theasinensin A (TSA) and (-) epigallocatechin gallate (EGCG) were involved in the anti-viral activities. Here we examined how long period is required for the compounds to inactivate the virus. We also assessed whether tea inactivates SARS-CoV-2 diluted in human saliva. Treatment of SARS-CoV-2 with 500 M TFDG or TSA for 10 sec reduced the virus titer to undetectable levels (less than 1/1,000). Black and green tea decreased virus titer to less than 1/100 within 10 sec even in saliva. These findings suggest a possibility that intake of, or gargling with, tea may inactivate SARS-CoV-2 in saliva in infected individuals, which may eventually attenuate spread of COVID-19 within a population, although clinical studies are required to test this hypothesis by determining the intensity and duration of the anti-viral effect of tea in saliva in humans.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Eriko Ohgitani", + "author_inst": "Department of Immunology, Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Masaharu Shin-Ya", + "author_inst": "Department of Immunology, Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Masaki Ichitani", + "author_inst": "Central Research Institute, ITO EN, Ltd." + }, + { + "author_name": "Makoto Kobayashi", + "author_inst": "Central Research Institute, ITO EN, Ltd." + }, + { + "author_name": "Takanobu Takihara", + "author_inst": "Central Research Institute, ITO EN, Ltd." + }, + { + "author_name": "Masaya Kawamoto", + "author_inst": "Department of Immunology, Kyoto Prefectural University of Medicine" + }, + { + "author_name": "Hitoshi Kinugasa", + "author_inst": "Central Research Institute, ITO EN, Ltd." + }, + { + "author_name": "Osam Mazda", + "author_inst": "Department of Immunology, Kyoto Prefectural University of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.24.20248813", "rel_title": "Quantifying the online news media coverage of the COVID-19 pandemic.", @@ -1015098,53 +1017226,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.23.424231", - "rel_title": "Genomic diversity of SARS-CoV-2 can be accelerated by a mutation in the nsp14 gene", - "rel_date": "2020-12-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424231", - "rel_abs": "Coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), encode a proofreading exonuclease, nonstructural protein 14 (nsp14), that helps ensure replication competence at a low evolutionary rate compared with other RNA viruses. In the current pandemic, SARS-CoV-2 has accumulated diverse genomic mutations including in nsp14. Here, to clarify whether amino acid substitutions in nsp14 affect the genomic diversity and evolution of SARS-CoV-2, we searched for amino acid substitutions in nature that may interfere with nsp14 function. We found that viruses carrying a proline-to-leucine change at position 203 (P203L) have a high evolutionary rate and that a recombinant SARS-CoV-2 virus with the P203L mutation acquired more diverse genomic mutations than wild-type virus during its replication in hamsters. Our findings suggest that substitutions, such as P203L, in nsp14 may accelerate the genomic diversity of SARS-CoV-2, contributing to virus evolution during the pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kosuke Takada", - "author_inst": "Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Mahoko Takahashi Ueda", - "author_inst": "Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University" - }, - { - "author_name": "Shintaro Shichinohe", - "author_inst": "Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Yurie Kida", - "author_inst": "Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Chikako Ono", - "author_inst": "Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Yoshiharu Matsuura", - "author_inst": "Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Tokiko Watanabe", - "author_inst": "Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "So Nakagawa", - "author_inst": "Department of Molecular Life Science, Tokai University School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.23.424283", "rel_title": "The SARS-CoV-2 S1 spike protein mutation N501Y alters the protein interactions with both hACE2 and human derived antibody: A Free energy of perturbation study", @@ -1015368,6 +1017449,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.26.424422", + "rel_title": "Extensive High-Order Complexes within SARS-CoV-2 Proteome Revealed by Compartmentalization-Aided Interaction Screening", + "rel_date": "2020-12-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.26.424422", + "rel_abs": "Bearing the largest single-stranded RNA genome in nature, SARS-CoV-2 utilizes sophisticated replication/transcription complexes (RTCs), mainly composed of a network of nonstructural proteins and nucleocapsid protein, to establish efficient infection. Here, we developed an innovative interaction screening strategy based on phase separation in cellulo, namely compartmentalization of protein-protein interactions in cells (CoPIC). Utilizing CoPIC screening, we mapped the interaction network among RTC-related viral proteins. We identified a total of 47 binary interactions among 14 proteins governing replication, discontinuous transcription, and translation of coronaviruses. Further exploration via CoPIC led to the discovery of extensive ternary complexes composed of these components, which infer potential higher-order complexes. Taken together, our results present an efficient, and robust interaction screening strategy, and indicate the existence of a complex interaction network among RTC-related factors, thus opening up new opportunities to understand SARS-CoV-2 biology and develop therapeutic interventions for COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Weifan Xu", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Gaofeng Pei", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Hongrui Liu", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Jing Wang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Pilong Li", + "author_inst": "Tsinghua University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.24.20248830", "rel_title": "A New State-Space Epidemiological Model for Cost-Effectiveness Analysis of Non-Medical Interventions- A Study on COVID-19 in California and Florida", @@ -1016928,105 +1019044,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.12.23.20248612", - "rel_title": "Coronavirus GenBrowser for monitoring adaptive evolution and transmission of SARS-CoV-2", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248612", - "rel_abs": "Genomic epidemiology is important to study the COVID-19 pandemic and more than two million SARS-CoV-2 genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challenges. Here, we present the Coronavirus GenBrowser (CGB) based on a highly efficient analysis framework and a movie maker strategy. In total, 1,002,739 high quality genomic sequences with the transmission-related metadata were analyzed and visualized. The size of the core data file is only 12.20 MB, efficient for clean data sharing. Quick visualization modules and rich interactive operations are provided to explore the annotated SARS-CoV-2 evolutionary tree. CGB binary nomenclature is proposed to name each internal lineage. The pre-analyzed data can be filtered out according to the user-defined criteria to explore the transmission of SARS-CoV-2. Different evolutionary analyses can also be easily performed, such as the detection of accelerated evolution and on-going positive selection. Moreover, the 75 genomic spots conserved in SARS-CoV-2 but non-conserved in other coronaviruses were identified, which may indicate the functional elements specifically important for SARS-CoV-2. The CGB not only enables users who have no programming skills to analyze millions of genomic sequences, but also offers a panoramic vision of the transmission and evolution of SARS-CoV-2.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Dalang Yu", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Xiao Yang", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Bixia Tang", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Yi-Hsuan Pan", - "author_inst": "East China Normal University" - }, - { - "author_name": "Jianing Yang", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Guangya Duan", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Junwei Zhu", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Zi-Qian Hao", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Hailong Mu", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Long Dai", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Wangjie Hu", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Mochen Zhang", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Ying Cui", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Tong Jin", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Cuiping Li", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Lina Ma", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "- Language translation team", - "author_inst": "" - }, - { - "author_name": "Xiao Su", - "author_inst": "Institut Pasteur of Shanghai" - }, - { - "author_name": "Guo-Qing Zhang", - "author_inst": "Shanghai Institute of Nutrition and Health" - }, - { - "author_name": "Wenming Zhao", - "author_inst": "Beijing Institute of Genomics (China National Center for Bioinformation)" - }, - { - "author_name": "Haipeng Li", - "author_inst": "Shanghai Institute of Nutrition and Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.12.17.20248360", "rel_title": "Identifying communities at risk for COVID-19-related burden across 500 U.S. Cities and within New York City", @@ -1017330,6 +1019347,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.22.20248741", + "rel_title": "Analysis of genome characteristics and transmission of SARS-CoV-2 strains in North-East of Romania during the first COVID-19 outbreak", + "rel_date": "2020-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248741", + "rel_abs": "Romania officially declared its first SARS-CoV-2 case on February 26, 2020. The first and largest COVID-19 outbreak in Romania was recorded in Suceava, N/E region of the country, and originated at the Suceava regional county hospital. Following sheltering-in-place measures, infection rates decreased, only to rise again after relaxation of measures. This study describes the incursion of SARS-CoV-2 in Suceava and other parts of Romania and analyzes the mutations and their association with clinical manifestation of the disease during the period of COVID-19 outbreak. Phylogenetic analysis indicated multiple sites of origin for SARS-CoV-2 strains in Suceava, specifically from Spain, Italy and Russia, but also other strains related to those from Czech Republic, Belgium and France. Most Suceava samples contained mutations common to European lineages, such as A20268G, however aproximately 10% of samples were missing such mutations, indicating a possible different origin. While overall genome regions ORF1ab, S and ORF7 were subject to most mutations, several recurring mutations such as C27707T were identified, and these were mainly present in severe forms of the disease. Non-synonymous mutations, such as C3225A (Thr987Asn in NSP3a domain), associated with changes in a protein responsible for decreasing viral tethering in human host were also present. Patients with diabetes and hypertension exhibited eight and three time,s respectively, higher odds ratios of acquiring severe forms of the disease and these were mainly related to C27707T mutation. These results will aid in tracing virus movement throughout Romania and identification of infectivity, virulence and pathogenicity.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andrei Lobiuc", + "author_inst": "University of Suceava, Romania" + }, + { + "author_name": "Mihai Dimian", + "author_inst": "University of Suceava, Romania" + }, + { + "author_name": "Roxana Puscaselu", + "author_inst": "University of Suceava, Romania" + }, + { + "author_name": "Olga Sturdza", + "author_inst": "University of Suceava, Romania" + }, + { + "author_name": "Mihai Covasa", + "author_inst": "University of Suceava, Romania" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.22.20248327", "rel_title": "COVID-19 deaths detected in a systematic post-mortem surveillance study in Africa", @@ -1018674,20 +1020726,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.12.24.424322", - "rel_title": "Inferring Toll-Like Receptor induced epitope subunit vaccine candidate against SARS-CoV-2: A Reverse Vaccinology approach", - "rel_date": "2020-12-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.24.424322", - "rel_abs": "Toll-Like Receptors (TLRs) are a group of Pattern Recognition Receptors (PRRs) which bind to the exogenous pathogen associated molecular patterns (PAMPs) like other PRRs; hence the main function is to sense the harmness and mediate the innate immune response to pathogens. TLRs play an important role in innate immune responses to infection. The host has evolved to use other TLR and PAMP agonists as agents to stimulate a protective inflammatory immune response against infection. Because only a small number of doses are given, TLR agonists appear to have greater potential and fewer safety concerns than other uses as vaccine adjuvants. In the present days, development of peptides targeting immune response can be approved for survival in biological monitoring systems before vaccine exposures. Peptide vaccines are easy to synthesize, more stable and relatively safe. In addition, production of peptides becomes simple, easily reproducible, fast and cost effective. Getting vaccinated against Covid-19, which has become a pandemic in the human population, is the most practical way to control the outbreak. The new coronavirus does not contain a drug or vaccine to prevent it from spreading to humans. To getting a proper vaccine candidate against the novel coronavirus, the present study used the reverse vaccinology approach by using a complete set of SARS-CoV-2 proteins; such as: Spike, Envelope, Nucleocapsid, Membrane, NSPs, and ORFs to extract the antigenic elements that produce B-cell, T-cell and IFN positive epitopes. These epitopes with precise binding to the Toll-Like receptors (1-10) have developed epitope based vaccine candidates. We have prioritized a set of epitopes based on their antigenicity, allergenicity, sequence conservation and projected population coverage world-wide. The selected epitopes were employed for in-silico docking interactions with Toll-Like receptors and molecular dynamic simulation confirmed the stability of the vaccine candidates resulting epitope of spike proteins with both the TLR 7 and 8 shows the best binding affinity. We believe that this ideal epitope vaccine candidate could enhance the immune response of the host and reduce the reinfection risk.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.12.23.424232", "rel_title": "Remdesivir-Ivermectin combination displays synergistic interaction with improved in vitro antiviral activity against SARS-CoV-2", @@ -1018955,6 +1020993,41 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2020.12.22.423940", + "rel_title": "No evidence for human monocyte-derived macrophage infection and antibody-mediated enhancement of SARS-CoV-2 infection", + "rel_date": "2020-12-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.423940", + "rel_abs": "Vaccines are essential to control the spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and to protect the vulnerable population. However, one safety concern of vaccination is the possible development of antibody-dependent enhancement (ADE) of SARS-CoV-2 infection. The potential infection of Fc receptor bearing cells such as macrophages, would support continued virus replication and inflammatory responses, and thereby potentially worsen the clinical outcome of COVID-19. Here we demonstrate that SARS-CoV-2 and SARS-CoV-1 neither infect human monocyte-derived macrophages nor induce inflammatory cytokines in these cells, in sharp contrast to Middle East respiratory syndrome (MERS) coronavirus and the common cold human coronavirus 229E. Furthermore, serum from convalescent COVID-19 patients neither induced enhancement of SARS-CoV-2 infection nor innate immune response in human macrophages. These results support the view that ADE may not be involved in the immunopathological processes associated with COVID-19, however, more studies are necessary to understand the potential contribution of antibodies-virus complexes with other cells expressing FcR receptors.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Obdulio Garcia-Nicolas", + "author_inst": "Institute of Virology and Immunology IVI" + }, + { + "author_name": "Ferdinand Zettl", + "author_inst": "Institute of Virology and Immunology IVI" + }, + { + "author_name": "Gert Zimmer", + "author_inst": "Institute of Virology and Immunology IVI" + }, + { + "author_name": "Volker Thiel", + "author_inst": "Institute for Virology and Immunology IVI" + }, + { + "author_name": "Artur Summerfield", + "author_inst": "institute of Virology and Immunology IVI" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.22.423906", "rel_title": "Host Cell Proteases Drive Early or Late SARS-CoV-2 Penetration", @@ -1020523,45 +1022596,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.18.20248499", - "rel_title": "Mental Disorder Prevalence Among Populations Impacted by Coronavirus Pandemics: A Multilevel Meta-Analytic Study of COVID-19, MERS & SARS", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248499", - "rel_abs": "ObjectiveThrough a systematic review and meta-analysis of research on COVID-19, severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS) pandemics, we investigated whether mental disorder prevalence: (a) was elevated among populations impacted by coronavirus pandemics (relative to unselected populations reported in the literature), and (b) varied by disorder (undifferentiated psychiatric morbidity, anxiety, depressive, posttraumatic stress disorders [PTSD]) and impacted population (community, infected/recovered, healthcare provider, quarantined).\n\nMethodFrom 68 publications (N=87,586 participants), 808 estimates were included in a series of multilevel meta-analyses/regressions including random effects to account for estimates nested within studies.\n\nResultsMedian summary point prevalence estimates varied by disorder and population. Psychiatric morbidity (20%-56%), PTSD (10-26%) and depression (9-27%) were most prevalent in most populations. The highest prevalence of each disorder was found among infected/recovered adults (18-56%), followed by healthcare providers (11-28%) and community adults (11-20%). Prevalence estimates were often notably higher than reported for unselected samples. Sensitivity analyses demonstrated that overall prevalence estimates moderately varied by pandemic, study location, and mental disorder measure type.\n\nConclusionCoronavirus pandemics are associated with multiple mental disorders in several impacted populations. Needed are investigations of causal links between specific pandemic-related stressors, threats, and traumas and mental disorders.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matthew Boden", - "author_inst": "VA Palo Alto Health Care System Menlo Park Division" - }, - { - "author_name": "Nicole Cohen", - "author_inst": "University of Kansas" - }, - { - "author_name": "Jessilyn Froelich", - "author_inst": "VA Palo Alto Healthcare System" - }, - { - "author_name": "Katherine Hoggatt", - "author_inst": "San Francisco VA Medical Center" - }, - { - "author_name": "Hoda Abdel Magid", - "author_inst": "Stanford University" - }, - { - "author_name": "Swapandeep Mushiana", - "author_inst": "University of San Francisco" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.12.16.423122", "rel_title": "Immune-Based Prediction of COVID-19 Severity and Chronicity Decoded Using Machine Learning", @@ -1020793,6 +1022827,85 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.20.20248572", + "rel_title": "An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.20.20248572", + "rel_abs": "While genome-wide associations studies (GWAS) have successfully elucidated the genetic architecture of complex human traits and diseases, understanding mechanisms that lead from genetic variation to pathophysiology remains an important challenge. Methods are needed to systematically bridge this crucial gap to facilitate experimental testing of hypotheses and translation to clinical utility. Here, we leveraged cross-phenotype associations to identify traits with shared genetic architecture, using linkage disequilibrium (LD) information to accurately capture shared SNPs by proxy, and calculate significance of enrichment. This shared genetic architecture was examined across differing biological scales through incorporating data from catalogs of clinical, cellular, and molecular GWAS. We have created an interactive web database (interactive Cross-Phenotype Analysis of GWAS database (iCPAGdb); http://cpag.oit.duke.edu) to facilitate exploration and allow rapid analysis of user-uploaded GWAS summary statistics. This database revealed well-known relationships among phenotypes, as well as the generation of novel hypotheses to explain the pathophysiology of common diseases. Application of iCPAGdb to a recent GWAS of severe COVID-19 demonstrated unexpected overlap of GWAS signals between COVID-19 and human diseases, including with idiopathic pulmonary fibrosis driven by the DPP9 locus. Transcriptomics from peripheral blood of COVID-19 patients demonstrated that DPP9 was induced in SARS-CoV-2 compared to healthy controls or those with bacterial infection. Further investigation of cross-phenotype SNPs with severe COVID-19 demonstrated colocalization of the GWAS signal of the ABO locus with plasma protein levels of a reported receptor of SARS-CoV-2, CD209 (DC-SIGN), pointing to a possible mechanism whereby glycosylation of CD209 by ABO may regulate COVID-19 disease severity. Thus, connecting genetically related traits across phenotypic scales links human diseases to molecular and cellular measurements that can reveal mechanisms and lead to novel biomarkers and therapeutic approaches.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Liuyang Wang", + "author_inst": "Duke University" + }, + { + "author_name": "Thomas J Balmat", + "author_inst": "Duke University" + }, + { + "author_name": "Alejandro L Antonia", + "author_inst": "Duke University" + }, + { + "author_name": "Florica J Constantine", + "author_inst": "Duke University" + }, + { + "author_name": "Ricardo Henao", + "author_inst": "Duke University" + }, + { + "author_name": "Thomas W Burke", + "author_inst": "Duke University" + }, + { + "author_name": "Andy Ingham", + "author_inst": "Duke University" + }, + { + "author_name": "Micah T McClain", + "author_inst": "Duke University Medical Center" + }, + { + "author_name": "Ephraim L Tsalik", + "author_inst": "Duke University" + }, + { + "author_name": "Emily R Ko", + "author_inst": "Durham Regional Hospital" + }, + { + "author_name": "Geoffrey Ginsburg", + "author_inst": "Duke University" + }, + { + "author_name": "Mark DeLong", + "author_inst": "Duke University" + }, + { + "author_name": "Xiling Shen", + "author_inst": "Duke University" + }, + { + "author_name": "Christopher W Woods", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Elizabeth R Hauser", + "author_inst": "Duke University" + }, + { + "author_name": "Dennis C Ko", + "author_inst": "Duke University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.12.18.20248331", "rel_title": "Kinetics of antibody responses dictate COVID-19 outcome", @@ -1022041,25 +1024154,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.21.20248605", - "rel_title": "Modeling the flow of the COVID-19 in Germany: The cohort SEIR model based on the system dynamics approach", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248605", - "rel_abs": "This study develops a computer simulation in understanding the flow of the COVID-19 in Germany between January 2020 and July 2020. This aims to analyze not only the flow of the COVID-19 but also the efficacy of taken measures during the given period. The computer model is based on the SEIR concept and it is based on the system dynamics approach in which some uncertain parameters are estimated through the calibration process. Moreover, the SEIR computer model is developed by considering different flows of COVID-19 cases in older and young people in Germany. This study successfully reproduces similar patterns of infected, recovered, and death cases. Moreover, as the SEIR model can successfully reproduce similar patterns, the SEIR model can be a basis to estimate other resources such as health workers, and bed capacities.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Muhamad Khairulbahri", - "author_inst": "Bandung Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.20.20248581", "rel_title": "Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020", @@ -1022311,6 +1024405,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.21.20248467", + "rel_title": "Experiences of the COVID-19 pandemic: cross-sectional analysis of risk perceptions and mental health in a student cohort", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248467", + "rel_abs": "ObjectiveThis study examined the COVID-19 risk perceptions and mental health of university students on returning to campus in the midst of the COVID-19 pandemic.\n\nMethodsAn online survey was completed during the first four weeks of the academic year (October 2020) by 897 university students. The survey included demographics and measures of experiences of COVID-19 testing, self-isolation, shielding, perceived risk, mental health and indices capturing related psychological responses to the pandemic.\n\nResultsWe observed higher levels of depression and anxiety, but not stress, in students compared with pre- pandemic normative data, but lower than levels reported earlier in the pandemic in other similar cohorts. Depression, anxiety and stress were independently associated with greater loneliness and reduced positive mood. Greater worry about COVID-19 was also independently associated with anxiety and stress. Female students and those with pre-existing mental health disorders were at greatest risk of poor mental health outcomes.\n\nConclusionAlthough students perceived themselves at only moderate risk of COVID-19, the prevalence of depression and anxiety among university students should remain a concern. Universities should provide adequate support for students mental health during term-time. Interventions to reduced loneliness and worry, and improve mood, may benefit students overall mental well-being.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Ru Jia", + "author_inst": "Division of Primary Care, University of Nottingham, University Park, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Holly Knight", + "author_inst": "Division of Epidemiology and Public Health, University of Nottingham, City Hospital, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Holly Blake", + "author_inst": "School of Health Sciences, University of Nottingham, QMC, Nottingham, NG7 2HA, UK & NIHR Nottingham Biomedical Research Centre, Nottingham, UK" + }, + { + "author_name": "Jessica Corner", + "author_inst": "University Executive Board, University of Nottingham, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Chris Denning", + "author_inst": "Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Jonathan Ball", + "author_inst": "School of Life Sciences, The University of Nottingham, Nottingham, UK" + }, + { + "author_name": "Kirsty Bolton", + "author_inst": "School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Joanne R Morling", + "author_inst": "Division of Epidemiology and Public Health, University of Nottingham, City Hospital, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Carol Coupland", + "author_inst": "Division of Primary Care, University of Nottingham, University Park, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Grazziela Figueredo", + "author_inst": "School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, UK" + }, + { + "author_name": "David Ed Morris", + "author_inst": "Bioengineering Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Patrick Tighe", + "author_inst": "School of Life Sciences, The University of Nottingham, Nottingham, UK" + }, + { + "author_name": "Armando Villalon", + "author_inst": "Bioengineering Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Kieran Aylling", + "author_inst": "Division of Primary Care, University of Nottingham, University Park, Nottingham, NG7 2RD, UK" + }, + { + "author_name": "Kavita Vedhara", + "author_inst": "Division of Primary Care, University of Nottingham, University Park, Nottingham, NG7 2RD, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.20.20248600", "rel_title": "Covid-19 Prediction in USA using modified SIR derived model", @@ -1024111,37 +1026280,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.21.20248621", - "rel_title": "A Systematic Review and Network Meta-Analysis for COVID-19 Treatments", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248621", - "rel_abs": "BackgroundNumerous interventions for coronavirus disease 2019 (COVID-19) have been investigated by randomized controlled trials (RCTs). This systematic review and Bayesian network meta-analysis (NMA) aim to provide a comprehensive evaluation of efficacy of available treatments for COVID-19.\n\nMethodsWe searched for candidate COVID-19 studies in WHO COVID-19 Global Research Database, PubMed, PubMed Central, LitCovid, Proquest Central and Ovid up to December 19, 2020. RCTs for suspected or confirmed COVID-19 patients were included, regardless of publication status or demographic characteristics. Bayesian NMA with fixed effects was conducted to estimate the effect sizes using posterior means and 95% equal-tailed credible intervals (CrIs), while that with random effects was carried out as well for sensitivity analysis. Bayesian hierarchical models were used to estimate effect sizes of treatments grouped by their drug classifications.\n\nResultsWe identified 96 eligible RCTs with a total of 51187 patients. Compared with the standard of care (SOC), this NMA showed that dexamethasone led to lower risk of mortality with an odds ratio (OR) of 0.85 (95% CrI [0.76, 0.95]; moderate certainty) and lower risk of mechanical ventilation (MV) with an OR of 0.68 (95% CrI [0.56, 0.83]; low certainty). For hospital discharge, remdesivir (OR 1.37, 95% CrI [1.15, 1.64]; moderate certainty), dexamethasone (OR 1.20, 95% CrI [1.08, 1.34]; low certainty), interferon beta (OR 2.15, 95% CrI [1.26, 3.74]; moderate certainty), tocilizumab (OR 1.40, 95% CrI [1.05, 1.89]; moderate certainty) and baricitinib plus remdesivir (OR 1.75, 95% CrI [1.28, 2.39]; moderate certainty) could all increase the discharge rate respectively. Recombinant human granulocyte colony-stimulating factor indicated lower risk of MV (OR 0.20, 95% CrI [0.10, 0.40]; moderate certainty); and patients receiving convalescent plasma resulted in better viral clearance (OR 2.28, 95% CrI [1.57, 3.34]; low certainty). About two-thirds of the studies included in this NMA were rated as high risk of bias, and the certainty of evidence was either low or very low for most of the comparisons.\n\nConclusionThe Bayesian NMA identified superiority of several COVID-19 treatments over SOC in terms of mortality, requirement of MV, hospital discharge and viral clearance. These results provide a comprehensive comparison of current COVID-19 treatments and shed new light on further research and discovery of potential COVID-19 treatments.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Chenyang Zhang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Huaqing Jin", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yifeng Wen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Guosheng Yin", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.21.20248288", "rel_title": "Comparative analysis of loop-mediated isothermal amplification (LAMP)-based assays for rapid detection of SARS-CoV-2 genes", @@ -1024401,6 +1026539,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.22.20248604", + "rel_title": "A longitudinal seroprevalence study in a large cohort of working adults reveals that neutralising SARS-CoV-2 RBD-specific antibodies persist for at least six months independent of the severity of symptoms", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248604", + "rel_abs": "BackgroundIn spring 2020, at the beginning of the first pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) wave in Europe, we set up an assay system for large-scale testing of virus-specific and protective antibodies including their longevity.\n\nMethodsWe analysed the sera of 1655 adult employees for SARS-CoV-2-specific antibodies using the S1 subunit of the spike protein of SARS-CoV-2. Sera containing S1-reactive antibodies were further evaluated for receptor-binding domain (RBD)- and nucleocapsid protein (NCP)-specific antibodies in relation to the neutralisation test (NT) results at 0, three and six months.\n\nFindingsWe found immunoglobulin G (IgG) and/or IgA antibodies reactive to the S1 protein in 10.15% (n=168) of the participants. In total, 0.97% (n=16) were positive for S1-IgG, 0.91% (n=15) were S1-IgG-borderline and 8.28% (n=137) exhibited only S1-IgA antibodies. Next, we evaluated the 168 S1-reactive sera for RBD- and NCP specificity: 8.33% (n=14) had detectable RBD-specific and 6.55% (n=11) NCP-specific antibodies. The latter correlated with NTs (kappa coefficient = 0.8660) but started to decline already after 3 months. RBD-specific antibodies correlated best with the NT (kappa = 0.9448) and only these antibodies were stable for up to six months. All participants with virus-neutralising antibodies reported symptoms, of which, anosmia and/or dysgeusia correlated best with the detection of virus-neutralising antibodies.\n\nInterpretationRBD-specific antibodies were most reliably detected post infection, independent of the number/severity of symptoms, and correlated best with protective neutralising antibodies at least for six months. They thus qualify best for large-scale seroepidemiological evaluation of both seroprevalence and seroprotection.\n\nFundingThis study received funding from the Austrian Ministry of Education, Science and Research within the research framework in relation to the coronavirus disease 2019 pandemic (GZ 2020 0225 104).\n\nKey pointsPersistence of SARS-CoV-2 antibodies depends on their specificity. Total RBD-specific antibodies are those that are stable for up to at least six months and correlate best with neutralisation independent of the presence and severity of COVID-19 symptoms.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSAt the beginning of the study (early pandemic in April 2020), the SARS-Cov-2 specific seroprevalence was totally unknown. Additionally, S1-specific antibody assays being the first on the market were tested with limited sample size showing a lower sensitivity and specificity at that time. Furthermore, at that time, there were no unambiguous interpretations of antibody test results with regard to immunity/protection against reinfection. It was also not clear whether the detection of different antibody specificities could yield an essential input into the interpretation of the antibodys qualities. Another open question was how long antibodies of the various specificities as well as antibodies with protective capacities would persist.\n\nAdded value of this studyWe provide data to confirm the most reliable correlation of RBD-specific antibodies with neutralising antibodies that are stable for at least six months. S1- and NCP-specific antibodies wane more quickly than RBD-specific antibodies, rendering them not as ideal candidates for longitudinal seroprevalence studies. Concerning symptoms, anosmia/dysgeusia was strongly associated with NT-seropositivity and seroprotection in the overall study population.\n\nImplications of all the available evidenceOur data suggest that RBD-specific total antibody measurements with assays of high specificity can be used for cross-sectional as well as longitudinal seroepidemiological studies, even in low-prevalence settings. Detection of these antibodies also indicates robust seroprotection for at least six months. Due to the substantial loss of S1- and NCP-specific antibodies within the first months, assays targeting these antigen specificities - in contrast to RBD-specific antibody measurements - are not optimal to assess the duration of seroprotection. Overall, respiratory symptoms alone were not useful in predicting a past infection with SARS-CoV-2. However, anosmia/dysgeusia appeared to be a significant diagnostic marker, in particular for mild COVID-19.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Angelika Wagner", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Angela Guzek", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Johanna Ruff", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Joanna Jasinska", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Ute Scheikl", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Ines Zwazl", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Michael Kundi", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Hannes Stockinger", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Maria R. Farcet", + "author_inst": "Baxter AG, now part of Takeda" + }, + { + "author_name": "Thomas Kreil", + "author_inst": "Baxter AG, now part of Takeda" + }, + { + "author_name": "Eva Hoeltl", + "author_inst": "Erste Bank" + }, + { + "author_name": "Ursula Wiedermann", + "author_inst": "Medical University of Vienna" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.19.20248508", "rel_title": "Several forms of SARS-CoV-2 RNA can be detected in wastewaters : implication for wastewater-based epidemiology and risk assessment.", @@ -1026033,69 +1028234,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.12.20.422693", - "rel_title": "A recombinant protein SARS-CoV-2 candidate vaccine elicits high-titer neutralizing antibodies in macaques.", - "rel_date": "2020-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.20.422693", - "rel_abs": "Vaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection are urgently required. We assessed the potential of vaccine candidates based on the SARS-CoV-2 spike in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit, either the N-terminal domain (NTD) or an extended C-terminal domain containing the receptor-binding domain (RBD) and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. A robust IgG response to the spike protein was detected as early as 2 weeks after immunization with either protein and maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins to the ACE2 receptor, shown by in vitro binding assays, while sera from animals immunized with the NTD alone lacked this activity. Crucially, sera from animals immunized with the RBD but not the NTD had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. These data support the utility of spike subunit-based antigens as a vaccine for use in humans.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Gary Baisa", - "author_inst": "Intuitive Biosciences, Inc." - }, - { - "author_name": "David Rancour", - "author_inst": "Lytic Solutions" - }, - { - "author_name": "Keith Mansfield", - "author_inst": "Novartis Institutes for Biomedical Research" - }, - { - "author_name": "Monika Burns", - "author_inst": "Novartis Institutes for Biomedical Research" - }, - { - "author_name": "Lori Martin", - "author_inst": "Novartis Institutes for Biomedical Research" - }, - { - "author_name": "Daise Cunha", - "author_inst": "Covance Greenfield Laboratories" - }, - { - "author_name": "Jessica Fischer", - "author_inst": "Covance Greenfield Laboratories" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University" - }, - { - "author_name": "Paul Bieniasz", - "author_inst": "Howard Hughes Medical Institute, The Rockefeller University" - }, - { - "author_name": "Frtiz Schomburg", - "author_inst": "Lytic Solutions" - }, - { - "author_name": "Kimberly Luke", - "author_inst": "Intuitive Biosciences, Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.20.423603", "rel_title": "Fatty Acid Synthase inhibition prevents palmitoylation of SARS-CoV2 SpikeProtein and improves survival of mice infected with murine hepatitis virus.", @@ -1026439,6 +1028577,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.21.423787", + "rel_title": "Binding strength and hydrogen bond numbers between Covid-19 RBD and HVR of antibody", + "rel_date": "2020-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.21.423787", + "rel_abs": "The global battle against the Covid-19 pandemic relies strongly on the human defence of antibody, which is assumed to bind the antigens Receptor Binding Domain with its Hypervariable Region. Due to the similarity to other viruses such as SARS, however, our understanding of the antibody-virus interaction has been largely limited to the genomic sequencing, which poses serious challenges to the containment, vaccine exploration and rapid serum testing. Based on the physical/chemical nature of the interaction, infrared spectroscopy was employed to reveal the binding disparity, when unusual temperature dependence was discovered from the 1550cm-1 absorption band, attributed to the hydrogen bonds by carboxyl/amino groups, binding the SARS-CoV-2 spike protein and closely resembled SARS-CoV-2 or SARS-CoV-1 antibodies. The infrared absorption intensity, associated with the number of hydrogen bonds, was found to increase sharply between 27{degrees}C and 31{degrees}C, with the relative absorbance matches at 37{degrees}C the hydrogen bonding numbers of the two antibody types (19 vs 12). Meanwhile the ratio of bonds at 27{degrees}C, calculated by thermodynamic exponentials rather than by the laymans guess, produces at least 5% inaccuracy. As a result, the specificity of the SARS-CoV-2 antibody will be more conclusive beyond 31{degrees}C, instead of at the usual room temperature of 20{degrees}C - 25{degrees}C, when the vaccine research and antibody diagnosis would likely be undermined. Beyond genomic sequencing, the temperature dependence, as well as the bond number match at 37{degrees}C between relative absorbance and the hydrogen bonding numbers of the two antibody types, are not only of clinical significance in particular, but also of a sample for the physical/chemical understanding of the vaccine-antibody interactions in general.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ryan Taoran Wang", + "author_inst": "McMaster University" + }, + { + "author_name": "Alex Fan Xu", + "author_inst": "McMaster University" + }, + { + "author_name": "Qi Zhou", + "author_inst": "McMaster University" + }, + { + "author_name": "Tinglu Song", + "author_inst": "Beijing Institute of Technology" + }, + { + "author_name": "Kelvin J. Xu", + "author_inst": "Columbia University" + }, + { + "author_name": "Gu Xu", + "author_inst": "McMaster University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.21.423721", "rel_title": "The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes - endothelial cells through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease", @@ -1027882,85 +1030059,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.12.18.20248447", - "rel_title": "Epidemiological feature, viral shedding, and antibody seroconversion among asymptomatic carriers and symptomatic/ presymptomatic COVID-19 patients", - "rel_date": "2020-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248447", - "rel_abs": "Novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pandemic. However, data concerning the epidemiological features, viral shedding, and antibody dynamics between asymptomatic SARS-CoV-2 carriers and COVID-19 patients remain controversial. We enrolled 193 subjects infected with SARS-CoV-2 in Ningbo and Zhoushan, Zhejiang, China from January 21 to March 6, 2020. All subjects were followed up to monitor the dynamics of immunoglobulin M (IgM) and IgG against SARS-CoV-2. Of those, 31 were asymptomatic carriers, 149 were symptomatic patients, and 14 were presymptomatic patients. Compared to symptomatic patients, asymptomatic carriers were younger and had higher levels of white blood cell and lymphocyte, lower levels of C-reactive protein and viral load, and shorter viral shedding duration. Conversion of IgM from positive to negative was shorter in asymptomatic carriers than in COVID-19 patients (P=0.030). The proportion of those persistently seropositive for IgG was higher in COVID-19 patients than in asymptomatic carriers (P=0.037). Viral load was higher in symptomatic than presymptomatic patients. Viral shedding was longer in presymptomatic patients than in asymptomatic carriers. Conclusively, asymptomatic carriers have a higher antiviral immunity to clear SARS-CoV-2 than do symptomatic patients and this antiviral immunity is not contributable to humoral immunity.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Yi Chen", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Ping Li", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Yibo Ding", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Miao Liu", - "author_inst": "Center of Disease Control and Prevention of Putuo district, Zhoushan" - }, - { - "author_name": "Leijie Liu", - "author_inst": "Center of Disease Control and Prevention of Putuo district, Zhoushan" - }, - { - "author_name": "Bo Yi", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Ting Wu", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Hongjun Dong", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Xuying Lao", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Keqing Ding", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Haibo Wang", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Dongliang Zhang", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Xiaojie Tan", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Zhongfa Wang", - "author_inst": "Center of Disease Control and Prevention of Putuo district, Zhoushan" - }, - { - "author_name": "Guozhang Xu", - "author_inst": "Ningbo Municipal center for disease control and prevention" - }, - { - "author_name": "Guangwen Cao", - "author_inst": "Second Military Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.18.423106", "rel_title": "Furin cleaves SARS-CoV-2 spike-glycoprotein at S1/S2 and S2'for viral fusion/entry: indirect role for TMPRSS2", @@ -1028348,6 +1030446,121 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.12.18.423524", + "rel_title": "Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2", + "rel_date": "2020-12-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.18.423524", + "rel_abs": "In COVID-19, the immune response largely determines disease severity and is key to therapeutic strategies. Cellular mechanisms contributing to inflammatory lung injury and tissue repair in SARS-CoV-2 infection, particularly endothelial cell involvement, remain ill-defined. We performed detailed spatiotemporal analyses of cellular and molecular processes in SARS-CoV-2 infected Syrian hamsters. Comparison of hamster single-cell sequencing and proteomics with data sets from COVID-19 patients demonstrated inter-species concordance of cellular and molecular host-pathogen interactions. In depth vascular and pulmonary compartment analyses (i) supported the hypothesis that monocyte-derived macrophages dominate inflammation, (ii) revealed endothelial inflammation status and T-cell attraction, and (iii) showed that CD4+ and CD8+ cytotoxic T-cell responses precede viral elimination. Using the Syrian hamster model of self-limited moderate COVID-19, we defined the specific roles of endothelial and epithelial cells, among other myeloid and non-myeloid lung cell subtypes, for determining the disease course.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Geraldine Nouailles", + "author_inst": "Division of Pulmonary Inflammation, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Emanuel Wyler", + "author_inst": "Berlin Institute for Medical Systems Biology (BIMSB), Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin" + }, + { + "author_name": "Peter Pennitz", + "author_inst": "Division of Pulmonary Inflammation, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Dylan Postmus", + "author_inst": "Institute of Virology, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Daria Vladimirova", + "author_inst": "Institute of Virology, Free University Berlin" + }, + { + "author_name": "Julia Kazmierski", + "author_inst": "Institute of Virology, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Fabian Pott", + "author_inst": "Institute of Virology, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Kristina Dietert", + "author_inst": "Institute of Veterinary Pathology, Free University Berlin" + }, + { + "author_name": "Michael M\u00fclleder", + "author_inst": "Core Facility - High-Throughput Mass Spectrometry, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Vadim Farztdinov", + "author_inst": "Core Facility - High-Throughput Mass Spectrometry, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Benedikt Obermayer", + "author_inst": "Core Unit Bioinformatics, Berlin Institute of Health (BIH)" + }, + { + "author_name": "Sandra-Maria Wienhold", + "author_inst": "Division of Pulmonary Inflammation, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Sandro Andreotti", + "author_inst": "Bioinformatics Solution Center, Free University Berlin" + }, + { + "author_name": "Thomas H\u00f6fler", + "author_inst": "Institute of Virology, Free University Berlin" + }, + { + "author_name": "Birgit Sawitzki", + "author_inst": "Institute of Medical Immunology, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Institute of Virology, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Leif Erik Sander", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Norbert Suttorp", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Markus Ralser", + "author_inst": "The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London; Department of Biochemistry, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Dieter Beule", + "author_inst": "Core Unit Bioinformatics, Berlin Institute of Health (BIH)" + }, + { + "author_name": "Achim Dieter Gruber", + "author_inst": "Institute of Veterinary Pathology, Free University Berlin" + }, + { + "author_name": "Christine Goffinet", + "author_inst": "Institute of Virology, Charit\u00e9 - University Hospital Berlin" + }, + { + "author_name": "Markus Landthaler", + "author_inst": "Berlin Institute for Medical Systems Biology (BIMSB), Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin" + }, + { + "author_name": "Jakob Trimpert", + "author_inst": "Institute of Virology, Free University Berlin" + }, + { + "author_name": "Martin Witzenrath", + "author_inst": "Division of Pulmonary Inflammation, Charite\u00e9 - University Hospital Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.19.423586", "rel_title": "A comprehensive library of fluorescent constructs of SARS-CoV-2 proteins and their initial characterization in different cell types", @@ -1029556,25 +1031769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.16.20248139", - "rel_title": "The Persistence of Vaccine Hesitancy: COVID-19 Vaccination Intention", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248139", - "rel_abs": "Building public trust and willingness to vaccinate against COVID-19 is as important as developing an effective vaccine. However, a significant minority of the public are unwilling or hesitant to take a COVID-19 vaccine, when available. A nationally representative sample survey (N=1040) was conducted in July 2020 in New Zealand to identify factors associated with COVID-19 vaccine intention. Trust in experts and general vaccine hesitancy were significantly associated with COVID-19 vaccine intention. A communication campaign from trusted scientific experts, with information that addresses prevailing concerns about vaccines, is likely to help increase COVID-19 vaccine uptake.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jagadish Thaker", - "author_inst": "Massey University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.16.20248180", "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibodies, risk factors for infection and associated symptoms in Geneva, Switzerland: a population-based study", @@ -1030174,6 +1032368,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.18.423418", + "rel_title": "Human Surfactant Protein D Binds S1 and Receptor Binding Domain of Spike protein and acts as an entry inhibitor of SARS-CoV-2 Pseudotyped viral particles in vitro", + "rel_date": "2020-12-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.18.423418", + "rel_abs": "Human SP-D is a potent innate immune molecule whose presence at pulmonary mucosal surfaces allows immune surveillance role against pulmonary pathogens. Higher levels of serum SP-D have been reported in patients with severe acute respiratory syndrome coronavirus-1 (SARS-CoV). Studies have suggested the ability of human SP-D to recognise spike glycoprotein of SARS-CoV; its interaction with HCoV-229E strain leads to viral inhibition in human bronchial epithelial (16HBE) cells. Previous studies have reported that a recombinant fragment of human SP-D (rfhSP-D) composed of 8 Gly-X-Y repeats, neck and CRD region, can act against a range of viral pathogens including influenza A Virus and Respiratory Syncytial Virus in vitro, in vivo and ex vivo models. In this context, this study was aimed at examining the likely protective role of rfhSP-D against SARS-CoV-2 infection. rfhSP-D showed a dose-responsive binding to S1 spike protein of SARS-CoV-2 and its receptor binding domain. Importantly, rfhSP-D inhibited interaction of S1 protein with the HEK293T cells overexpressing Angiotensin Converting Enzyme 2. The protective role of rfhSP-D against SARS-CoV-2 infection as an entry inhibitor was further validated by the use of pseudotyped lentiviral particles expressing SARS-CoV-2 S1 protein; ~0.5 RLU fold reduction in viral entry was seen following rfhSP-D treatment (10 g/ml). The results highlight the therapeutic potential of rfhSP-D in SARS-CoV-2 infection and merits pre-clinical studies in murine models.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Miao-Hsi Hsieh", + "author_inst": "Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan" + }, + { + "author_name": "Nazar Beirag", + "author_inst": "Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, United Kingdom" + }, + { + "author_name": "Valarmathy Murugaiah", + "author_inst": "Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, United Kingdom" + }, + { + "author_name": "Yu-Chi Chou", + "author_inst": "Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 115, Taiwan" + }, + { + "author_name": "Wen-Shuo Kuo", + "author_inst": "Center for Allergy & Clinical Immunology Research (ACIR), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, " + }, + { + "author_name": "Hui-Fan Kao", + "author_inst": "Center for Allergy & Clinical Immunology Research (ACIR), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, " + }, + { + "author_name": "Taruna Madan", + "author_inst": "Department of Innate Immunity, ICMR-National Institute for Research in Reproductive Health, Mumbai, India" + }, + { + "author_name": "Uday Kishore", + "author_inst": "Brunel University London" + }, + { + "author_name": "Jiu-Yao Wang", + "author_inst": "Department of Pediatrics, College of Medicine, National Cheng Kung University Hospital and Department of Biochemistry and Molecular Biology, National Cheng Kung" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.18.423358", "rel_title": "An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies", @@ -1031502,53 +1033747,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.16.20248166", - "rel_title": "Using Administrative Data to Incorporate Age and Sex-Dependent Resource Use for COVID-19 Acute Care Resource Use Simulations in Ontario, Canada", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248166", - "rel_abs": "As the COVID-19 pandemic has progressed, more local data has become available, enabling a more granular modeling approach. In March 2020, we developed a COVID-19 Resource Estimator (CORE) model to estimate the acute care resource use in Ontario, Canada. In this paper, we describe the evolution of CORE2.0 to incorporate age, sex, and time-dependent acute care resource use, length of stay, and mortality to simulate hospital occupancy. Demographics (e.g., age and sex) of infected cases are informed by 4-month averages between March-June, and July-October using 10-year age groups. The probability of hospitalization, ICU admission, and requiring mechanical ventilation are all age and sex-dependent. LOS for each acute care level ranges from 5.7 to 16.15 days in the ward, 6.5 to 10.7 days in the ICU without ventilation, and 14.8 to 21.6 days on the ventilator, depending on month of infection. We calibrated some LOS components to reported ward and ICU occupancy between June 15 and October 31, 2020. Furthermore, we demonstrate the use of CORE2.0 for a regional analysis of Region of Waterloo, Ontario, Canada to simulate the ward bed, ICU bed, and ventilator occupancies for 30 days starting December 2020 for three case trajectory scenarios. Moving forward, this model has become highly flexible and customizable to data updates, and can better inform acute care planning and public measures as the pandemic progresses.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Stephen Mac", - "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada" - }, - { - "author_name": "Raphael Ximenes", - "author_inst": "Toronto Health Economics and Technology Assessment (THETA) Collaborative, University Health Network, Toronto, Canada" - }, - { - "author_name": "Kali Barrett", - "author_inst": "University Health Network, Toronto, Canada" - }, - { - "author_name": "Yasin A Khan", - "author_inst": "University Health Network, Toronto, Canada" - }, - { - "author_name": "Petros Pechlivanoglou", - "author_inst": "Hospital for Sick Children, Toronto, Canada" - }, - { - "author_name": "Juan David Rios", - "author_inst": "Hospital for Sick Children, Toronto, Canada" - }, - { - "author_name": "David MJ Naimark", - "author_inst": "University of Toronto" - }, - { - "author_name": "Beate Sander", - "author_inst": "University Health Network" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.16.20248357", "rel_title": "Understanding the net benefit of antigen-based rapid diagnostic tests for COVID-19: An enhanced decision-curve analysis", @@ -1031848,6 +1034046,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.16.20248310", + "rel_title": "COVID19 is a seasonal climate-driven disease across both hemispheres", + "rel_date": "2020-12-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248310", + "rel_abs": "The role of climate in the population dynamics of COVID-19 remains poorly understood, and a true seasonal signature has remained elusive. Data from both hemispheres and the second wave provide opportunities to further examine climatic drivers. With a statistical method designed to detect transitory associations, we show consistent negative effects of temperature and absolute humidity at large spatial scales. At finer spatial resolutions we substantiate these connections during the seasonal rise and fall of COVID-19. Strong disease responses are identified between 12-18{degrees}C for Temperature and 4-12 g/m3 for Absolute Humidity. These results classify COVID-19 as a seasonal low-temperature infection, and point to the airborne pathway as an important contribution to transmission for SARS-CoV-2, with implications for control measures we discuss.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alejandro Fontal", + "author_inst": "ISGlobal" + }, + { + "author_name": "Menno J. Bouma", + "author_inst": "London School of Hygiene and Tropical Medicine, University of London, London WC1 E7HT, UK" + }, + { + "author_name": "Adria San Jose", + "author_inst": "ISGlobal" + }, + { + "author_name": "Mercedes Pascual", + "author_inst": "Department of Ecology and Evolution. University of Chicago, Chicago, Illinois, USA" + }, + { + "author_name": "Xavier Rodo", + "author_inst": "ISGlobal" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.16.20248272", "rel_title": "Large-Scale Measurement of Aggregate Human Colocation Patterns for Epidemiological Modeling", @@ -1033036,149 +1035269,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.14.20247874", - "rel_title": "Rapid detection of SARS-CoV-2 with Cas13", - "rel_date": "2020-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20247874", - "rel_abs": "Rapid nucleic acid testing is a critical component of a robust infrastructure for increased disease surveillance. Here, we report a microfluidic platform for point-of-care, CRISPR-based molecular diagnostics. We first developed a nucleic acid test which pairs distinct mechanisms of DNA and RNA amplification optimized for high sensitivity and rapid kinetics, linked to Cas13 detection for specificity. We combined this workflow with an extraction-free sample lysis protocol using shelf-stable reagents that are widely available at low cost, and a multiplexed human gene control for calling negative test results. As a proof-of-concept, we demonstrate sensitivity down to 40 copies/L of SARS-CoV-2 in unextracted saliva within 35 minutes, and validated the test on total RNA extracted from patient nasal swabs with a range of qPCR Ct values from 13-35. To enable sample-to-answer testing, we integrated this diagnostic reaction with a single-use, gravity-driven microfluidic cartridge followed by real-time fluorescent detection in a compact companion instrument. We envision this approach for Diagnostics with Coronavirus Enzymatic Reporting (DISCoVER) will incentivize frequent, fast, and easy testing.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Shreeya Agrawal", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Alison Fanton", - "author_inst": "Department of Bioengineering, University of California, Berkeley, CA" - }, - { - "author_name": "Sita S. Chandrasekaran", - "author_inst": "Department of Bioengineering, University of California, Berkeley, CA" - }, - { - "author_name": "B\u00e9r\u00e9nice Charrez", - "author_inst": "University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA" - }, - { - "author_name": "Arturo M. Escajeda", - "author_inst": "Wainamics Inc., Pleasanton, CA, USA." - }, - { - "author_name": "Sungmin Son", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Roger Mcintosh", - "author_inst": "Wainamics Inc., Pleasanton, CA, USA." - }, - { - "author_name": "Abdul Bhuiya", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Mar\u00eda D\u00edaz de Le\u00f3n Derby", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Neil A. Switz", - "author_inst": "Department of Physics and Astronomy, San Jos\u00e9 State University, San Jos\u00e9, CA, USA" - }, - { - "author_name": "Maxim Armstrong", - "author_inst": "Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA" - }, - { - "author_name": "Andrew R. Harris", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Noam Prywes", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley , California 94704 , United States." - }, - { - "author_name": "Maria Lukarska", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Scott B. Biering", - "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Dylan C. J. Smock", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Amanda Mok", - "author_inst": "Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Gavin J. Knott", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA" - }, - { - "author_name": "Qi Dang", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Erik Van Dis", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA" - }, - { - "author_name": "Eli Dugan", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Shin Kim", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Tina Y. Liu", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley, California, USA" - }, - { - "author_name": "- IGI Testing Consortium", - "author_inst": "" - }, - { - "author_name": "Eva Harris", - "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370 USA" - }, - { - "author_name": "Sarah A. Stanley", - "author_inst": "School of Public Health, University of California, Berkeley, CA 94720, USA" - }, - { - "author_name": "Liana F. Lareau", - "author_inst": "Department of Bioengineering, University of California, Berkeley, CA" - }, - { - "author_name": "Ming X. Tan", - "author_inst": "Wainamics Inc., Pleasanton, CA, USA." - }, - { - "author_name": "Daniel A. Fletcher", - "author_inst": "Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "Jennifer A. Doudna", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA." - }, - { - "author_name": "David F. Savage", - "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley, California, USA" - }, - { - "author_name": "Patrick D. Hsu", - "author_inst": "Department of Bioengineering, University of California, Berkeley, CA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.14.20248209", "rel_title": "The Presence of Ambulatory Hypoxia as an Early Predictor of Moderate to Severe COVID-19 Disease", @@ -1033358,6 +1035448,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.15.20248247", + "rel_title": "Large differences in community COVID-19 testing across geographic areas in a Swedish region with 385,000 inhabitants", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248247", + "rel_abs": "BackgroundDiagnostic testing is essential for disease surveillance and test-trace-isolate efforts. Here, we aimed to investigate if residential area sociodemographic characteristics and test accessibility were associated with COVID-19 testing rates.\n\nMethodsWe included information on 421 542 patient-initiated COVID-19 PCR tests from Uppsala County in Sweden from 24 June, 2020 to 9 February, 2022. Using Poisson regression analyses, we investigated whether the Care Need Index (CNI; median 1.0, IQR 0.8, 1.4), a composite measure of sociodemographic factors used in Sweden to allocate primary healthcare resources, was associated with aggregated COVID-19 daily testing rates after adjustments for community transmission. We further assessed if distance to the nearest testing station influenced testing. Lastly, we performed a difference-in-difference analysis of the opening of a testing station targeting a disadvantaged neighbourhood.\n\nResultsWe observed that CNI, i.e. primary healthcare need, was negatively associated with COVID-19 testing rates in inhabitants aged 5-69 years. More pronounced differences were noted across younger age groups and in Uppsala City, with test rate ratios in children (5-14 years) ranging from 0.56 (95% CI 0.47-0.66) to 0.88 (95% CI 0.81-0.95) across the three pandemic waves. Longer distance to testing station was linked to lower testing rates, foremost in less densely populated areas. Furthermore, the opening of the targeted testing station was associated with increased testing, including twice as high testing rates in individuals aged 70-105, supporting an intervention effect.\n\nConclusionsEnsuring accessible testing across all residential areas constitutes a promising tool to decrease differences and inequalities in testing.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Beatrice Kennedy", + "author_inst": "Department of Medical Sciences, Molecular Epidemiology, and Science for Life Laboratory, Uppsala University, Sweden" + }, + { + "author_name": "Georgios Varotsis", + "author_inst": "Department of Medical Sciences, Molecular Epidemiology, and Science for Life Laboratory, Uppsala University, Sweden" + }, + { + "author_name": "Ulf Hammar", + "author_inst": "Department of Medical Sciences, Molecular Epidemiology, and Science for Life Laboratory, Uppsala University, Sweden" + }, + { + "author_name": "Diem Nguyen", + "author_inst": "Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Germ\u00e1n D. Carrasquilla", + "author_inst": "Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark" + }, + { + "author_name": "Vera van Zoest", + "author_inst": "Department of Information Technology, Uppsala University, Sweden" + }, + { + "author_name": "Robert S Kristiansson", + "author_inst": "Department of Public Health and Caring Sciences, Health Services Research, Uppsala University, Sweden; Primary Care and Health, Uppsala County Council, Sweden" + }, + { + "author_name": "Hugo Fitipaldi", + "author_inst": "Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences Malmo, Lund University Diabetes Centre, Skane University Hospital, Malmo, Sweden" + }, + { + "author_name": "Koen Dekkers", + "author_inst": "Department of Medical Sciences, Molecular Epidemiology, and Science for Life Laboratory, Uppsala University, Sweden" + }, + { + "author_name": "Meena Daivadanam", + "author_inst": "Department of Women's and Children's Health (Global Health and Migration), Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Mats Martinell", + "author_inst": "Department of Public Health and Caring Sciences, Health Services Research, Uppsala University, Sweden; Primary Care and Health, Uppsala County Council, Sweden" + }, + { + "author_name": "Jonas Bjork", + "author_inst": "Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden; Clinical Studies Sweden, Forum South, Skane University Hospital, Lund, Swede" + }, + { + "author_name": "Tove Fall", + "author_inst": "Department of Medical Sciences, Molecular Epidemiology, and Science for Life Laboratory, Uppsala University, Sweden" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.14.20248144", "rel_title": "Association Between Sampling Method and Covid-19 Test Positivity Among Undergraduate Students: Testing Friendship Paradox in Covid-19 Network of Transmission", @@ -1034958,49 +1037115,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.12.16.423002", - "rel_title": "EXPERIMENTAL INVESTIGATION OF PULSE STERILIZATION OF VIRAL INFECTION", - "rel_date": "2020-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.16.423002", - "rel_abs": "The results of experimental investigations of the effect of high-intensity pulsed UV radiation on the influenza virus type A (H1N1) are presented. The research methodology is developed and the structure of the experiments is described. An end-face plasma accelerator was used as a radiation source, which provides a power pulsed discharge in an open atmosphere. The high efficiency of inactivation of the infectiousness of the virus was shown within a short period of time. The possibility of providing urgent 100% sterilization of a viral infection has been shown for the first time. A model for calculating the efficiency of pulse sterilization has been developed. The prospects for the application of pulse sterilization technology to combat coronavirus infection are considered.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Volodymyr I Chumakov", - "author_inst": "Kharkiv National University of Radioelectronics" - }, - { - "author_name": "Mykhailo Ostryzhny", - "author_inst": "Kharkiv National University of Radioelectronics" - }, - { - "author_name": "Oksana Kharchenko", - "author_inst": "Kharkiv National University of Radioelectronics" - }, - { - "author_name": "Krystina Naumenko", - "author_inst": "Danylo Zabolotny Institute of Microbiology and Virology of the National Academy of Science of Ukraine" - }, - { - "author_name": "Svitlana Zagorodnya", - "author_inst": "Danylo Zabolotny Institute of Microbiology and Virology of the National Academy of Science of Ukraine," - }, - { - "author_name": "Vasiliy Muraveinyk", - "author_inst": "Independed scholar" - }, - { - "author_name": "Aleksandr Tarasevich", - "author_inst": "Independent scholar" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.12.16.423071", "rel_title": "One Year of SARS-CoV-2: How Much Has the Virus Changed?", @@ -1035184,6 +1037298,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.16.20248325", + "rel_title": "The impact of working during the Covid-19 pandemic on health care workers and first responders: mental health, function, and professional retention", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248325", + "rel_abs": "BackgroundThe COVID-19 pandemic has greatly affected front line health care workers (HCW) and first responders (FR). The infection risk from SARS CoV-2, the high mortality of hospitalized COVID-19 patients and the duration of the pandemic have created sustained and often traumatic stressors affecting HCW and FR.\n\nObjectivesTo assess the relationship of COVID-19 stressor frequency scores to psychiatric rating scale scores amongst HCW and FR. To determine if psychiatric rating scale scores mediate stressor effects on perceived work function and likelihood of remaining in current occupation.\n\nDesignObservational, self-report in a convenience sample.\n\nParticipants118 HCW and FR caring for COVID-19 patients in the United States.\n\nMain MeasureCOVID-19 related stressor frequencies were assessed using a 17-item questionnaire. Psychiatric symptoms were assessed with the PTSD Checklist 5 (PCL5), the Patient Health Questionnaire 9 (for depression) (PHQ9), the Insomnia Severity Index (ISI), and the General Anxiety Disorder 7 (GAD7).\n\nKey ResultsStressor frequency scores correlated significantly with PCL5 scores (R=.57, p<1e-8), PHQ scores (R=.35, P<.001), ISI scores (R=.38, p<1e-4), and GAD7 scores (R=.39, p<.001), likelihood of staying in current occupation (R=-.39,p<1e-4), and trouble doing usual work (R=.33,p<.001). 51% of HCW and 44% of FR indicated decreased likelihood of staying in their current occupation. PCL5 scores substantially mediated the association between stress frequency scores and work function impairment.\n\nConclusionsThese results direct attention to recognizing potentially treatable psychiatric symptoms, particularly those of PTSD, in HCW and FR experiencing COVID-19 related stressors. They also suggest that mitigating COVID-19 related stressors when possible, such as by providing adequate personal protective equipment, can improve HCW and FR mental health, work function and retention in the health care work force.\n\nStrengths and Limitations of this StudyO_LIDetailed assessments of participants exposure to covid-19 related occupational stressors, current psychiatric symptoms, and self-reported occupational functioning and likelihood of remaining in their current field (functional outcomes).\nC_LIO_LIAssessment of the dose-response relationship between exposure to covid-19 related occupational stressors and current psychiatric symptoms and functional outcomes.\nC_LIO_LIMediation analysis quantifying the potential for current psychiatric symptoms to mediate the relationship between exposure to covid-19 related occupational stressors and functional outcomes.\nC_LIO_LILimitations: convenience sample, limited numbers of first responder participants\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rebecca C Hendrickson", + "author_inst": "VA Puget Sound Health Care System" + }, + { + "author_name": "Rois\u00edn A. Slevin", + "author_inst": "VA Puget Sound Health Care System" + }, + { + "author_name": "Bernard P. Chang", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Ellen Sano", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Catherine A. McCall", + "author_inst": "VA Puget Sound Health Care System" + }, + { + "author_name": "Murray A. Raskind", + "author_inst": "VA Puget Sound Health Care System" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.12.16.20248302", "rel_title": "Assessing the Safety of Home Oximetry for Covid-19: A multi-site retrospective observational study.", @@ -1036556,53 +1038709,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.14.20248152", - "rel_title": "SARS-CoV-2 among migrants and forcibly displaced populations: a rapid systematic review", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248152", - "rel_abs": "The economic and health consequences of the COVID-19 pandemic pose a particular threat to vulnerable groups, such as migrants, particularly forcibly displaced populations. The aim of this review is (i) to synthesise the evidence on risk of infection and transmission among migrants, refugees, asylum seekers and internally displaced populations, and (ii) the effect of lockdown measures on these populations. We searched MEDLINE and WOS, preprint servers, and pertinent websites between 1st December 2019 and 26th June 2020. The included studies showed a high heterogeneity in study design, population, outcome and quality. The incidence risk of SARS-CoV-2 varied from 0{middle dot}12% to 2{middle dot}08% in non-outbreak settings and from 5{middle dot}64% to 21{middle dot}15% in outbreak settings. Migrants showed a lower hospitalisation rate compared to non-migrants. Negative impacts on mental health due to lockdown measures were found across respective studies. However, findings show a tenuous and heterogeneous data situation, showing the need for more robust and comparative study designs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Maren Hintermeier", - "author_inst": "Section for Health Equity Studies and Migration, Department of General Practice and Health Services Research, University Hospital Heidelberg, Germany" - }, - { - "author_name": "Hande Gencer", - "author_inst": "Leibniz-Institute for Prevention Research and Epidemiology (BIPS), Department Prevention and Evaluation, Unit Social Epidemiology, Bremen, Germany" - }, - { - "author_name": "Katja Kajikhina", - "author_inst": "Robert Koch Institute, Unit 28 Social Determinants of Health, Department of Health monitoring and Epidemiology, Berlin, Germany" - }, - { - "author_name": "Sven Rohleder", - "author_inst": "Department of Population Medicine and Health Services Research, School of Public Health, Bielefeld University & Section for Health Equity Studies and Migration," - }, - { - "author_name": "Claudia Santos-Hoevener", - "author_inst": "Robert Koch Institute, Unit 28 Social Determinants of Health, Department of Health monitoring and Epidemiology, Berlin, Germany" - }, - { - "author_name": "Marie Tallarek", - "author_inst": "Department of Public Health, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany" - }, - { - "author_name": "Jacob Spallek", - "author_inst": "Department of Public Health, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany" - }, - { - "author_name": "Kayvan Bozorgmehr", - "author_inst": "Department of Population Medicine and Health Services Research, School of Public Health, Bielefeld University & Section for Health Equity Studies and Migration," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.13.20248142", "rel_title": "COVID-19 vaccines that reduce symptoms but do not block infection need higher coverage and faster rollout to achieve population impact", @@ -1036874,6 +1038980,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.13.20248143", + "rel_title": "Decay of Fc-dependent antibody functions after mild to moderate COVID-19", + "rel_date": "2020-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.13.20248143", + "rel_abs": "The capacity of antibodies to engage with innate and adaptive immune cells via the Fc region is important in preventing and controlling many infectious diseases, and is likely critical in SARS-CoV-2 infection. The evolution of such antibodies during convalescence from COVID-19 is largely unknown. We developed novel assays to measure Fc-dependent antibody functions against SARS-CoV-2 spike (S)-expressing cells in serial samples from a cohort of 53 subjects primarily with mild-moderate COVID-19, out to a maximum of 149 days post-infection. We found that S-specific antibodies capable of engaging dimeric Fc{gamma}RIIa and Fc{gamma}RIIIa decayed linearly over time. S-specific antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent phagocytosis (ADP) activity within plasma declined linearly as well, in line with the decay of S-specific IgG. Although there was significant decay in S-specific plasma ADCC and ADP activity, they remained readily detectable by all assays in 94% of our cohort at the last timepoint studied, in contrast with neutralisation activity which was only detectable in 70% of our cohort by the last timepoint. Our results suggest that Fc effector functions such as ADCC and ADP could contribute to the durability of SARS-CoV-2 immunity, particularly late in convalescence when neutralising antibodies have waned. Understanding the protective potential of antibody Fc effector functions is critical for defining the durability of immunity generated by infection or vaccination.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Wen Shi Lee", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Kevin John Selva", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Samantha K Davis", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Bruce D Wines", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Arnold Reynaldi", + "author_inst": "Kirby Institute, The University of New South Wales" + }, + { + "author_name": "Robyn Esterbauer", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Hannah G Kelly", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Ebene R Haycroft", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Hyon-Xhi Tan", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Jennifer A Juno", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Adam K Wheatley", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "P Mark Hogarth", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Deborah Cromer", + "author_inst": "Kirby Institute, The University of New South Wales" + }, + { + "author_name": "Miles P Davenport", + "author_inst": "Kirby Institute, The University of New South Wales" + }, + { + "author_name": "Amy W Chung", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Stephen J Kent", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.11.20238410", "rel_title": "A rapid, high-sensitivity SARS-CoV-2 nucleocapsid immunoassay to aid diagnosis of acute COVID-19 at the point of care", @@ -1038358,65 +1040543,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.13.422589", - "rel_title": "Profiling of oral microbiota and cytokines in COVID-19 patients", - "rel_date": "2020-12-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.13.422589", - "rel_abs": "SARS-CoV-2 presence has been recently demonstrated in the sputum or saliva, suggesting how the shedding of viral RNA outlasts the end of symptoms. Recent data from transcriptome analysis show that oral cavity mucosa harbors high levels of ACE2 and TMPRSS2, highlighting its role as a double-edged sword for SARS-CoV-2 body entrance or interpersonal transmission. In the present study, for the first time, we demonstrate the oral microbiota structure and inflammatory profile of COVID-19 patients. Hospitalized COVID-19 patients and matched healthy controls underwent naso/oral-pharyngeal and oral swabs. Microbiota structure was analyzed by 16S rRNA V2 automated targeted sequencing, while oral and sera concentrations of 27 cytokines were assessed using magnetic bead-based multiplex immunoassays. A significant diminution in species richness was observed in COVID-19 patients, along with a marked difference in beta-diversity. Species such as Prevotella salivae and Veillonella infantium were distinctive for COVID-19 patients, while Neisseria perflava and Granulicatella elegans were predominant in controls. Interestingly, these two groups of oral species oppositely clustered within the bacterial network, defining two distinct Species Interacting Group (SIGs). Pro-inflammatory cytokines were distinctive for COVID-19 in both oral and serum samples, and we found a specific bacterial consortium able to counteract them, following a novel index called C4 firstly proposed here. We even introduced a new parameter, named CytoCOV, able to predict COVID-19 susceptibility for an unknown subject at 71% of power with an AUC equal to 0.995. This pilot study evidenced a distinctive oral microbiota composition in COVID-19 subjects, with a definite structural network in relation to secreted cytokines. Our results would pave the way for a theranostic approach in fighting COVID-19, trying to enlighten the intimate relationship among microbiota and SARS-CoV-2 infection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Valerio Iebba", - "author_inst": "University of Trieste" - }, - { - "author_name": "Nunzia Zanotta", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - }, - { - "author_name": "Giuseppina Campisciano", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - }, - { - "author_name": "Verena Zerbato", - "author_inst": "Infectious Diseases Department, Udine University, 33100 Udine, Italy." - }, - { - "author_name": "Stefano Di Bella", - "author_inst": "Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa, 1, 34127 Trieste, Italy." - }, - { - "author_name": "Carolina Cason", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - }, - { - "author_name": "Sara Morassut", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - }, - { - "author_name": "Roberto Luzzati", - "author_inst": "Department of Medical, Surgical and Health Sciences, University of Trieste, Piazzale Europa, 1, 34127 Trieste, Italy." - }, - { - "author_name": "Marco Confalonieri", - "author_inst": "Pulmonology Department, University Hospital of Cattinara, 34149 Trieste, Italy." - }, - { - "author_name": "Anna Teresa Palamara", - "author_inst": "IRCCS San Raffaele Pisana, 00166 Rome, Italy; Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory Affiliated to Institu" - }, - { - "author_name": "Manola Comar", - "author_inst": "Laboratory of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS Burlo-Garofolo, Trieste, Italy." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.13.420406", "rel_title": "Identification of bis-benzylisoquinoline alkaloids as SARS-CoV-2 entry inhibitors from a library of natural products in vitro", @@ -1038656,6 +1040782,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.14.420133", + "rel_title": "Targeting Scavenger Receptor Type B-1 (SR-B1) and Cholesterol Inhibits Entry of SARS-CoV-2 Pseudovirus in Cell Culture", + "rel_date": "2020-12-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.14.420133", + "rel_abs": "The novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan, China in late 2019 and has now caused a global pandemic. The disease caused by SARS-CoV-2 is known as COVID-19. To date, few treatments for COVID-19 have proven effective, and the current standard of care is primarily supportive. As a result, novel therapeutic strategies are in high demand. Viral entry into target cells is frequently sensitive to cell membrane lipid composition and membrane organization. Evidence suggests that cell entry of SARS-CoV-2 is most efficient when the target cell plasma membrane is replete with cholesterol; and recent data implicate cholesterol flux through the high-affinity receptor for cholesterol-rich high-density lipoprotein (HDL), called scavenger receptor type B-1 (SR-B1), as critical for SARS-CoV-2 entry. Here, we demonstrate that a cholesterol-poor synthetic biologic high-density lipoprotein (HDL NP) targets SR-B1 and inhibits cell entry of a SARS-CoV-2 spike protein pseudovirus. Human cells expressing SR-B1 are susceptible to SARS-CoV-2 infection, and viral entry can be inhibited by 50-80% using HDL NPs in an SR-B1-dependent manner. These results indicate that HDL NP targeting of SR-B1 is a powerful potential therapy to combat COVID-19 and other viral diseases.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Stephen E Henrich", + "author_inst": "Northwestern University" + }, + { + "author_name": "Kaylin M McMahon", + "author_inst": "Northwestern University" + }, + { + "author_name": "Nicole Palacio", + "author_inst": "Northwestern University" + }, + { + "author_name": "Pankaj Bhalla", + "author_inst": "Northwestern University" + }, + { + "author_name": "Pablo Penaloza-MacMaster", + "author_inst": "Northwestern University" + }, + { + "author_name": "Colby Shad Thaxton", + "author_inst": "Northwestern University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.14.422737", "rel_title": "SARS-CoV-2 Requires Cholesterol for Viral Entry and Pathological Syncytia Formation", @@ -1040043,121 +1042208,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.04.20243949", - "rel_title": "The burden of active infection and anti-SARS-CoV-2 IgG antibodies in the general population: Results from a statewide survey in Karnataka, India", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20243949", - "rel_abs": "BackgroundGlobally, the routinely used case-based reporting and IgG serosurveys underestimate the actual prevalence of COVID-19. Simultaneous estimation of IgG antibodies and active SARS-CoV-2 markers can provide a more accurate estimation.\n\nMethodsA cross-sectional survey of 16416 people covering all risk groups was done between 3-16 September 2020 using the state of Karnatakas infrastructure of 290 hospitals across all 30 districts. All participants were subjected to simultaneous detection of SARS-CoV-2 IgG using a commercial ELISA kit, SARS-CoV-2 antigen using a rapid antigen detection test (RAT), and reverse transcription-polymerase chain reaction (RT-PCR) for RNA detection. Maximum-likelihood estimation was used for joint estimation of the adjusted IgG, active, and total prevalence, while multinomial regression identified predictors.\n\nFindingsThe overall adjusted prevalence of COVID-19 in Karnataka was 27 {middle dot}3% (95% CI: 25 {middle dot}7-28 {middle dot}9), including IgG 16 {middle dot}4% (95% CI: 15 {middle dot}1 - 17 {middle dot}7) and active infection 12 {middle dot}7% (95% CI: 11 {middle dot}5-13 {middle dot}9). The case-to-infection ratio was 1:40, and the infection fatality rate was 0 {middle dot}05%. Influenza-like symptoms or contact with a COVID-19 positive patient are good predictors of active infection. The RAT kits had higher sensitivity (68%) in symptomatic participants compared to 47% in asymptomatic.\n\nInterpretationThis is the first comprehensive survey providing accurate estimates of the COVID-19 burden anywhere in the world. Further, our findings provide a reasonable approximation of population immunity threshold levels. Using the RAT kits and following the syndromic approach can be useful in screening and monitoring COVID-19. Leveraging existing surveillance platforms, coupled with appropriate methods and sampling framework, renders our model replicable in other settings.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Giridhara R Babu", - "author_inst": "Indian Institute of Public Health, Public Health Foundation of India, Bangalore" - }, - { - "author_name": "Rajesh Sundaresan", - "author_inst": "Indian Institute of Science, Bengaluru" - }, - { - "author_name": "Siva Athreya", - "author_inst": "Indian Statistical Institute Bangalore Centre" - }, - { - "author_name": "Jawaid Akhtar", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Pankaj Kumar Pandey", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Parimala S Maroor", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Padma MR", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Lalitha R", - "author_inst": "UNICEF, India" - }, - { - "author_name": "Mohammed Shariff", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Lalitha Krishnappa", - "author_inst": "MS Ramaiah Medical College" - }, - { - "author_name": "CN Manjunath", - "author_inst": "Sri Jayadeva Institute of Cardiovascular Sciences and Research" - }, - { - "author_name": "MK Sudarshan", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Gururaj G", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Ranganath TS", - "author_inst": "Bangalore Medical College and Research Institute" - }, - { - "author_name": "Vasanth Kumar DE", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Pradeep Banandur", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Deepa R", - "author_inst": "Indian Institute of Public Health Bengaluru, Public Health Foundation of India" - }, - { - "author_name": "Shilpa Shiju", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Eunice Lobo", - "author_inst": "Indian Institute of Public Health Bengaluru, Public Health Foundation of India" - }, - { - "author_name": "Asish Satapathy", - "author_inst": "WHO NPSP, India" - }, - { - "author_name": "Lokesh Alahari", - "author_inst": "WHO NPSP, India" - }, - { - "author_name": "Prameela", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Vinitha T", - "author_inst": "Department of Health and Family Welfare Services Government of Karnataka" - }, - { - "author_name": "Anita Desai", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "V Ravi", - "author_inst": "National Institute of Mental Health and Neurosciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.08.20246314", "rel_title": "Antibody landscape against SARS-CoV-2 proteome revealed significant differences between non-structural/ accessory proteins and structural proteins", @@ -1040405,6 +1042455,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.08.20246173", + "rel_title": "Impact of Convalescent Plasma Transfusion (CCP) In Patients With Previous Circulating Neutralizing Antibodies (nAb) to COVID-19", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246173", + "rel_abs": "INTRODUCTIONCOVID-19 convalescent plasma (CCP) transfusion has emerged in the past months as an alternative approach to treat pneumonia cases of SARS-CoV-2. Current evidence regarding characteristics of the plasma product, the titer of neutralizing antibodies (nAbs) in the transfused units, time to onset of intervention, and impact of nAbs produced by the patient are limited and heterogeneous.\n\nMATERIAL AND METHODSWe describe the preliminary results of 104 patients with severe pneumonia due to SARS-CoV-2 transfused with CCP at three medical centers in Brazil. All enrolled patients were transfused with doses between 200 mL through 600mL of ABO compatible CCP on days 0-2 after enrolment. Clinical parameters were monitored and nAbs titration was performed using the cytopathic effect-based virus neutralization test with SARS-CoV-2 (GenBank MT126808.1).\n\nRESULTSForty-one patients achieved clinical improvement on day 14, and multivariable logistic regression showed that nAbs T (from CCP units transfused) (p= 0.001), nAbs P0 (on day of enrolment) (p=0.009) and use of other supportive therapies (p<0.001) were associated with higher odds for this clinical improvement. Considering ICU length of stay (LOS) and length of mechanical ventilation, in our analysis, nAbs P0 were associated with a significant reduction in ICU LOS (p=0.018) and duration of mechanical ventilation (p<0.001). Administration of CCP after 10 days of symptom onset was associated with increases in ICU length of stay (p<0.001).\n\nDISCUSSION/CONCLUSIONDespite the study limitations, our data have shown an association between patients previously acquired nAbs and clinical outcomes. The potential value of timely administration of CCP transfusion before day 10 of disease onset was demonstrated and nAbsP0, but not nAbsT, were associated with ICU LOS, and duration of mechanical ventilation on the improvement of clinical outcomes was also demonstrated. In conclusion, we consider these data are useful parameters to guide future CPP transfusion strategies to COVID-19.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Ana Paula Hitomi Yokoyama", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Silvano Wendel", + "author_inst": "Hospital Sirio-Libanes Blood Bank" + }, + { + "author_name": "Carolina Bonet-Bub", + "author_inst": "Hospital Israelita Albert Einstein" + }, + { + "author_name": "Roberta M Fachini", + "author_inst": "Hospital Sirio-Libanes Blood Bank, Sao Paulo, Brazil" + }, + { + "author_name": "Ana Paula F Dametto", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Fernando Blumm", + "author_inst": "Hospital Sirio-Libanes, Brasilia, Brazil" + }, + { + "author_name": "Valeria F Dutra", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Gabriela Candelaria", + "author_inst": "Hospital Sirio-Libanes Blood Bank, Sao Paulo, Brazil" + }, + { + "author_name": "Araci M Sakashita", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Rafael Rahal Guaragna Machado", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Rita Fontao-Wendel", + "author_inst": "Hospital Sirio-Libanes Blood Bank, Sao Paulo, Brazil" + }, + { + "author_name": "Nelson Hamerschlak", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Ruth Achkar", + "author_inst": "Hospital Sirio-Libanes Blood Bank, Sao Paulo, Brazil" + }, + { + "author_name": "Murillo Assuncao", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Patricia Scuracchio", + "author_inst": "Hospital Sirio-Libanes Blood Bank, Sao Paulo, Brazil" + }, + { + "author_name": "Victor Nudelman", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Laerte Pastore", + "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil" + }, + { + "author_name": "Joao Renato R Pinho", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Mirian Dal Ben", + "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil" + }, + { + "author_name": "Roberto Kalil Filho", + "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil / University of Sao Paulo Heart Institute (Incor), Sao Paulo, Brazil" + }, + { + "author_name": "Alexandre R Marra", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil / Office of Clinical Quality, Safety, and Performance Improvement, University of Iowa Hospitals and Clinic" + }, + { + "author_name": "Mariane T Amano", + "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil" + }, + { + "author_name": "Esper Kallas", + "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil / Department of Infectious and Parasitic Diseases, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Alfredo Salim Helito", + "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil" + }, + { + "author_name": "Carlos Roberto R Carvalho", + "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil / Cardio-Pulmonary Department, Pulmonary Division, Heart Institute (Incor), University of Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Danielle Bastos Araujo", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil / Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Edison Luiz Durigon", + "author_inst": "Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil / Scientific Platform Pasteur USP, Sao Paulo, Brazil" + }, + { + "author_name": "Anamaria A Camargo", + "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil" + }, + { + "author_name": "Luiz V Rizzo", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Luiz Fernando L Reis", + "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil" + }, + { + "author_name": "Jose Mauro Kutner", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.09.20245175", "rel_title": "BNT162b2 induces SARS-CoV-2-neutralising antibodies and T cells in humans", @@ -1041853,45 +1044042,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.09.20246629", - "rel_title": "Optimal test allocation strategy for COVID-19", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.09.20246629", - "rel_abs": "Testing for active SARS-CoV-2 infections is key to controlling the spread of the virus and preventing severe disease. A central public health challenge is defining test allocation strategies in the presence of limited resources. Inthis paper, we provide a mathematical framework for defining anoptimal strategy for allocating viral tests. The framework accounts for imperfect test results, selective testing in certain high-risk patient populations, practical constraints in terms of budget and/or total number of available tests, and the purpose of testing. Our method is not only useful for detecting infected cases, but can also be used for long-time surveillance to monitor for new outbreaks, which will be especially important during ongoing vaccine distribution across the world. In our proposed approach, tests can be allocated across population strata defined by symptom severity and other patient characteristics, allowing the test allocation plan to prioritize higher risk patient populations. We illustrate our framework using historical data from the initial wave of the COVID-19 outbreak in New York City. We extend our proposed method to address the challenge of allocating two different types of tests with different costs and accuracy (for example, the expensive but more accurate RT-PCR test versus the cheap but less accurate rapid antigen test), administered under budget constraints. We show how this latter framework can be useful to reopening of college campuses where university administrators are challenged with finite resources for community surveillance. We provide a R Shiny web application allowing users to explore test allocation strategies across a variety of pandemic scenarios. This work can serve as a useful tool for guiding public health decision-making at a community level and adapting to different stages of an epidemic, and it has broader relevance beyond the COVID-19 outbreak.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jiacong Du", - "author_inst": "University of Michigan" - }, - { - "author_name": "Lauren J Beesley", - "author_inst": "University of Michigan" - }, - { - "author_name": "Seunggeun Lee", - "author_inst": "Graduate School of Data Science, Seoul National University, Republic of Korea" - }, - { - "author_name": "Xiang Zhou", - "author_inst": "University of Michigan" - }, - { - "author_name": "Walter Dempsey", - "author_inst": "University of Michigan" - }, - { - "author_name": "Bhramar Mukherjee", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.09.20246538", "rel_title": "The trade-off between mobility and vaccination for COVID-19 control: a metapopulation modeling approach", @@ -1042123,6 +1044273,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.09.20239467", + "rel_title": "SARS-CoV-2 Viral Load in Saliva Rises Gradually and to Moderate Levels in Some Humans", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.09.20239467", + "rel_abs": "Transmission of SARS-CoV-2 in community settings often occurs before symptom onset, therefore testing strategies that can reliably detect people in the early phase of infection are urgently needed. Early detection of SARS-CoV-2 infection is especially critical to protect vulnerable populations who require frequent interactions with caretakers. Rapid COVID-19 tests have been proposed as an attractive strategy for surveillance, however a limitation of most rapid tests is their low sensitivity. Low-sensitivity tests are comparable to high sensitivity tests in detecting early infections when two assumptions are met: (1) viral load rises quickly (within hours) after infection and (2) viral load reaches and sustains high levels (>105- 106 RNA copies/mL). However, there are no human data testing these assumptions. In this study, we document a case of presymptomatic household transmission from a healthy young adult to a sibling and a parent. Participants prospectively provided twice-daily saliva samples. Samples were analyzed by RT-qPCR and RT-ddPCR and we measured the complete viral load profiles throughout the course of infection of the sibling and parent. This study provides evidence that in at least some human cases of SARS-CoV-2, viral load rises slowly (over days, not hours) and not to such high levels to be detectable reliably by any low-sensitivity test. Additional viral load profiles from different samples types across a broad demographic must be obtained to describe the early phase of infection and determine which testing strategies will be most effective for identifying SARS-CoV-2 infection before transmission can occur.\n\nOne sentence summaryIn some human infections, SARS-CoV-2 viral load rises slowly (over days) and remains near the limit of detection of rapid, low-sensitivity tests.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Alexander Winnett", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Matthew M. Cooper", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Natasha Shelby", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Anna E. Romano", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Jessica A. Reyes", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Jenny Ji", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Michael K. Porter", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Emily S. Savela", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Jacob T. Barlow", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Reid Akana", + "author_inst": "California Institute of Technology" + }, + { + "author_name": "Colten Tognazzini", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Matthew Feaster", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Ying-Ying Goh", + "author_inst": "Pasadena Public Health Department" + }, + { + "author_name": "Rustem F. Ismagilov", + "author_inst": "California Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.10.20246975", "rel_title": "QT Interval Prolongation in Patients Treated for COVID-19", @@ -1043687,69 +1045908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.10.417758", - "rel_title": "EVs analysis in the COVID-19 era: insights on serum inactivation protocols towards downstream isolation and analysis", - "rel_date": "2020-12-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.10.417758", - "rel_abs": "Since the outbreak of COVID-19 crisis, the handling of biological samples from confirmed or suspected SARS-CoV-2 positive individuals demanded the use of inactivation protocols to ensure laboratory operators safety. While not standardized, these practices can be roughly divided in two categories, namely heat inactivation and solvent-detergent treatments. As such, these routine procedures should also apply to samples intended for Extracellular Vesicles (EVs) analysis. Assessing the impact of virus inactivating pre-treatments is therefore of pivotal importance, given the well-known variability introduced by different pre-analytical steps on downstream EVs isolation and analysis. Arguably, shared guidelines on inactivation protocols tailored to best address EVs-specific requirements will be needed among the EVs community, yet deep investigations in this direction havent been reported so far.\n\nIn the attempt of sparking interest on this highly relevant topic, we here provide preliminary insights on SARS-CoV-2 inactivation practices to be adopted prior serum EVs analysis by comparing solvent/detergent treatment vs. heat inactivation. Our analysis entailed the evaluation of EVs recovery and purity along with biochemical, biophysical and biomolecular profiling by means of Nanoparticle Tracking Analysis, Western Blotting, Atomic Force Microscopy, miRNA content (digital droplet PCR) and tetraspanin assessment by microarrays. Our data suggest an increase in ultracentrifugation (UC) recovery following heat-treatment, however accompanied by a marked enrichment in EVs-associated contaminants. On the contrary, solvent/detergent treatment is promising for small EVs (< 150 nm range), yet a depletion of larger vesicular entities was detected. This work represents a first step towards the identification of optimal serum inactivation protocols targeted to EVs analysis.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Roberto Frigerio", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Angelo Music\u00f2", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Marco Brucale", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Andrea Ridolfi", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Silvia Galbiati", - "author_inst": "IRCSS Ospedale San Raffaele" - }, - { - "author_name": "Riccardo Vago", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Greta Bergamaschi", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Anna Ferretti", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Marcella Chiari", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Francesco Valle", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Alessandro Gori", - "author_inst": "National Research Council of Italy" - }, - { - "author_name": "Marina Cretich", - "author_inst": "Consiglio Nazionale delle Ricerche" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.12.11.416818", "rel_title": "Duplex formation between the template and the nascent strand in the transcription-regulating sequences determines the site of template switching in SARS - CoV-2", @@ -1044261,6 +1046419,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.10.420489", + "rel_title": "A traditional Chinese medicine, Respiratory Detox Shot (RDS), inhibits the infection of SARS-CoV, SARS-CoV-2, and the Influenza A virus in vitro", + "rel_date": "2020-12-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.10.420489", + "rel_abs": "The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has resulted in the infection of over 60 million people and has caused over 1.4 million deaths as of December 2020 in more than 220 countries and territories. Currently, there is no effective treatment for COVID-19 to reduce mortality. We investigated the potential anti-coronavirus activities from an oral liquid of traditional medicine, Respiratory Detox Shot (RDS), which contains mostly herbal ingredients traditionally used to manage lung diseases. Here we report that RDS inhibited the infection of target cells by SARS-CoV and SARS-CoV-2 pseudoviruses, and by infectious wild-type SARS-CoV-2. We further demonstrated that RDS inhibits viral early infection steps. In addition, we found that RDS can also block the infection of target cells by Influenza A virus. These results suggest that RDS may broadly inhibit the infection of respiratory viruses.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Brian Hetrick", + "author_inst": "George Mason University" + }, + { + "author_name": "Dongyang Yu", + "author_inst": "Virongy LLC" + }, + { + "author_name": "Adeyemi Olanrewaju", + "author_inst": "George Mason University" + }, + { + "author_name": "Linda Chilin", + "author_inst": "George Mason University" + }, + { + "author_name": "Sijia He", + "author_inst": "George Mason University" + }, + { + "author_name": "Deemah Debbagh", + "author_inst": "George Mason University" + }, + { + "author_name": "Yuan-Chun Ma", + "author_inst": "Dr Ma Laboratories" + }, + { + "author_name": "Lewis Hofmann", + "author_inst": "World Health Science Organization" + }, + { + "author_name": "Ramin Hakami", + "author_inst": "George Mason University" + }, + { + "author_name": "Yuntao Wu", + "author_inst": "George Mason University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.09.20246389", "rel_title": "Untargeted metabolomics of COVID-19 patient serum reveals potential prognostic markers of both severity and outcome.", @@ -1045633,85 +1047846,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.08.20245811", - "rel_title": "Six-month antibody response to SARS-CoV-2 in healthcare workers assessed by virus neutralisation and commercial assays", - "rel_date": "2020-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20245811", - "rel_abs": "We conducted a prospective study in healthcare workers (n=296) of the University Hospital of Lyon, France. Serum samples (n=296) collected six months after disease onset were tested using three commercial assays: the Wantai Ab assay detecting total antibodies against the receptor binding domain (RBD) of the S protein, the bioMerieux Vidas assay detecting IgG to the RBD and the Abbott Architect assay detecting IgG to the N protein. The neutralising antibody (NAb) titre was also determined for all samples with a virus neutralisation assay (VNA) using live virus. The positivity rate was 100% with the Wantai assay, 84.8% with the bioMerieux assay and 55.4% with the Abbott assay. Only 51% of HCWs were positive for the presence of NAb. Less than 10 % of HCWs had a NAb titre greater than 80. At a neutralising titre of 80, the area under the curves [IC 95%] was 0.71 [0.62-0.81], 0.75 [0.65-0.85] and 0.95 [0.92-0.97] for Wantai, Abbott and Vidas respectively. The data presented herein suggest that commercial assays detecting antibodies against the N protein must not be used in long-term seroprevalence surveys while the Wantai assay could be useful for this purpose. VNA should remain the gold standard to assess the protective antibody response, but some commercial assays could be used as first-line screening of long-term presence of NAb.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Antonin Bal", - "author_inst": "Hospices civils de Lyon" - }, - { - "author_name": "Mary-Anne Trabaud", - "author_inst": "HCL" - }, - { - "author_name": "Jean-Baptiste Fassier", - "author_inst": "HCL" - }, - { - "author_name": "Muriel Rabilloud", - "author_inst": "HCL" - }, - { - "author_name": "Kahina Saker", - "author_inst": "HCL" - }, - { - "author_name": "Carole Langlois", - "author_inst": "HCL" - }, - { - "author_name": "Nicolas Guibert", - "author_inst": "HCL" - }, - { - "author_name": "Constance d'Aubarede", - "author_inst": "HCL" - }, - { - "author_name": "Adele Paul", - "author_inst": "HCL" - }, - { - "author_name": "Dulce Alfaiate", - "author_inst": "HCL" - }, - { - "author_name": "Amelie Massardier", - "author_inst": "HCL" - }, - { - "author_name": "Virginie Pitiot", - "author_inst": "HCL" - }, - { - "author_name": "Florence Morfin", - "author_inst": "HCL" - }, - { - "author_name": "Bruno Lina", - "author_inst": "HCL" - }, - { - "author_name": "Bruno Pozzetto", - "author_inst": "CHU de Saint-Etienne" - }, - { - "author_name": "Sophie Trouillet-Assant", - "author_inst": "Hospices Civils de Lyon" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.08.20245910", "rel_title": "SARS-CoV-2 infections in kindergartens and associated households at the start of the second wave in Berlin, Germany - a cross sectional study", @@ -1045903,6 +1048037,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.08.20245829", + "rel_title": "Prevalence of anxiety and depressive symptoms among physicians during the COVID-19 pandemic in Bangladesh: a cross-sectional study", + "rel_date": "2020-12-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20245829", + "rel_abs": "ObjectivesIn addition to risking their physical well-being, frontline physicians are enduring significant emotional burden both at work and home during the COVID-19 pandemic. This study aims to investigate the levels of anxiety and depressive symptoms and to identify associated factors among Bangladeshi physicians during the COVID-19 outbreak.\n\nMethods and designA cross-sectional study using an online survey was conducted between April 21 and May 10, 2020. Outcomes assessed included demographic questions, COVID-19 related questions, and the Hospital Anxiety and Depression Scale (HADS).\n\nResultsThe survey was completed by 412 Bangladeshi physicians. The findings revealed that, in terms of standardized HADS cut-off points, the prevalence of anxiety and depressive symptoms among physicians was 67.72% and 48.5% respectively. Risk factors for higher rates of anxiety or depressive symptoms were: being female, physicians who had experienced COVID-19 like symptoms during the pandemic, those who had not received incentives, those who used self-funded PPE, not received adequate training, lacking perceived self-efficacy to manage COVID -19 positive patients, greater perceived stress of being infected, fear of getting assaulted/humiliated, being more connected with social media, having lower income levels to support the family, feeling more agitated, less than 2 hours of leisure activity per day and short sleep duration. All these factors were found to be positively associated with anxiety and depression in unadjusted and adjusted statistical models.\n\nConclusionsThis study identifies a real concern about the prevalence of anxiety and depressive symptoms among Bangladeshi physicians and identifies several associated factors during the COVID-19 pandemic. Given the vulnerability of the physicians in this extraordinary period whilst they are putting their own lives at risk to help people infected by COVID-19, health authorities should address the psychological needs of medical staff and formulate effective strategies to support vital frontline health workers.\n\nSTHRENGHTS & LIMITATIONS OF THE STUDYO_LIThis study reports a novel and concerning findings on the prevalence of anxiety and depression symptoms with identification of several important associated factors among Bangladeshi physicians during the COVID-19 pandemic.\nC_LIO_LIThe cross-sectional nature of the study design could not establish causal relationship between the dependent and independent variables.\nC_LIO_LIThis study was carried out by conducting a web-based survey, which might generate sampling bias by excluding the physicians who do not have access to internet or inactive in social medias, and thus limit the generalizability of the findings.\nC_LI", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "M Tasdik Hasan", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Sahadat Hossain", + "author_inst": "Jahangirnagar University, Savar, Dhaka, Bangladesh" + }, + { + "author_name": "Farhana Safa", + "author_inst": "University of Toronto" + }, + { + "author_name": "Afifa Anjum", + "author_inst": "Jahangirnagar University, Savar, Dhaka, Bangladesh" + }, + { + "author_name": "Abid Hasan Khan", + "author_inst": "Jahangirnagar University, Savar, Dhaka, Bangladesh" + }, + { + "author_name": "Kamrun Nahar Koly", + "author_inst": "ICDDR,B" + }, + { + "author_name": "Syeda Fatema Alam", + "author_inst": "Shaheed Suhrawardy Medical College Dhaka, Bangladesh" + }, + { + "author_name": "Md. Abdur Rafi", + "author_inst": "Rajshahi Medical College" + }, + { + "author_name": "Vivek Podder", + "author_inst": "TMMC" + }, + { + "author_name": "Tonima Islam Trisa", + "author_inst": "ICDDR,B" + }, + { + "author_name": "Rhedeya Nury Nodi", + "author_inst": "PHF,BD" + }, + { + "author_name": "Dewan Tasnia Azad", + "author_inst": "Jashore Medical College" + }, + { + "author_name": "Fatema Ashraf", + "author_inst": "Shaheed Suhrawardy Medical College, Dhaka, Bangladesh" + }, + { + "author_name": "S.M Quamrul Akther", + "author_inst": "Shaheed Suhrawardy Medical College, Dhaka, Bangladesh" + }, + { + "author_name": "Helal Uddin Ahmed", + "author_inst": "NIMH, Dhaka, Bangladesh" + }, + { + "author_name": "Simon Rosenbaum", + "author_inst": "School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, Australia" + }, + { + "author_name": "Graham Thornicroft", + "author_inst": "Centre for Global Mental Health and Centre for Implementation Science, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.12.08.20245936", "rel_title": "Efficacy of pulmonary rehabilitation in severe and critical-ill COVID-19 patients: a controlled study", @@ -1047346,89 +1049563,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.08.416339", - "rel_title": "Natural SARS-CoV-2 infections, including virus isolation, among serially tested cats and dogs in households with confirmed human COVID-19 cases in Texas, USA", - "rel_date": "2020-12-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.08.416339", - "rel_abs": "The natural infections and epidemiological roles of household pets in SARS-CoV-2 transmission are not understood. We conducted a longitudinal study of dogs and cats living with at least one SARS-CoV-2 infected human in Texas and found 47.1% of 17 cats and 15.3% of 59 dogs from 25.6% of 39 households were positive for SARS-CoV-2 via RT-PCR and genome sequencing or neutralizing antibodies. Virus was isolated from one cat. The majority (82.4%) of infected pets were asymptomatic. Re-sampling of one infected cat showed persistence of viral RNA at least 32 d-post human diagnosis (25 d-post initial test). Across 15 antibody-positive animals, titers increased (33.3%), decreased (33.3%) or were stable (33.3%) over time. A One Health approach is informative for prevention and control of SARS-CoV-2 transmission.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Sarah A Hamer", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Alex Pauvolid-Correa", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Italo B Zecca", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Edward Davila", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Lisa D Auckland", - "author_inst": "Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, USA" - }, - { - "author_name": "Christopher M Roundy", - "author_inst": "Department of Entomology, Texas A&M University and AgriLife Research, Texas, USA" - }, - { - "author_name": "Wendy Tang", - "author_inst": "Department of Entomology, Texas A&M University and AgriLife Research, Texas, USA" - }, - { - "author_name": "Mia K Torchetti", - "author_inst": "National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA" - }, - { - "author_name": "Mary Lea Killian", - "author_inst": "National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA" - }, - { - "author_name": "Melinda Jenkins-Moore", - "author_inst": "National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA" - }, - { - "author_name": "Katie Mozingo", - "author_inst": "National Veterinary Services Laboratories, USDA APHIS VS, Ames, IA, USA" - }, - { - "author_name": "Yao Akpalu", - "author_inst": "Brazos County Health Department, Bryan, Texas, USA" - }, - { - "author_name": "Ria R Ghai", - "author_inst": "U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Jessica R Spengler", - "author_inst": "U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Casey Barton Behravesh", - "author_inst": "U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Rebecca Fischer", - "author_inst": "School of Public Health, Texas A&M University, Texas, USA" - }, - { - "author_name": "Gabriel L Hamer", - "author_inst": "Department of Entomology, Texas A&M University and AgriLife Research, Texas, USA." - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "zoology" - }, { "rel_doi": "10.1101/2020.12.08.415836", "rel_title": "Anti-SARS-CoV-2 activity of Andrographis paniculata extract and its major component Andrographolide in human lung epithelial cells and cytotoxicity evaluation in major organ cell representatives", @@ -1047676,6 +1049810,105 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.08.415505", + "rel_title": "Binding of SARS-CoV-2 spike protein to ACE2 is disabled by thiol-based drugs; evidence from in vitro SARS-CoV-2 infection studies.", + "rel_date": "2020-12-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.08.415505", + "rel_abs": "Neutrophil-induced oxidative stress is a mechanism of lung injury in COVID-19, and drugs with a functional thiol group (\"thiol drugs\"), especially cysteamine, have anti-oxidant and anti-inflammatory properties that could limit this injury. Thiol drugs may also alter the redox status of the cysteine-rich SARS-CoV-2 spike glycoprotein (SARS-2-S) and thereby disrupt ACE2 binding. Using ACE2 binding assay, reporter virus pseudotyped with SARS-CoV-2 spikes (ancestral and variants) and authentic SARS-CoV-2 (Wuhan-1), we find that multiple thiol drugs inhibit SARS-2-S binding to ACE2 and virus entry into cells. Pseudoviruses carrying variant spikes were less efficiently inhibited as compared to pseudotypes bearing an ancestral spike, but the most potent drugs still inhibited the Delta variant in the low millimolar range. IC50 values followed the order of their cystine cleavage rates and lower thiol pKa values. In hamsters infected with SARS-CoV-2, intraperitoneal (IP) cysteamine decreased neutrophilic inflammation and alveolar hemorrhage in the lungs but did not decrease viral infection, most likely because IP delivery could not achieve millimolar concentrations in the airways. These data show that thiol drugs inhibit SARS-CoV-2 infection in vitro and reduce SARS-CoV-2-related lung injury in vivo and provide strong rationale for trials of systemically delivered thiol drugs as COVID-19 treatments. We propose that antiviral effects of thiol drugs in vivo will require delivery directly to the airways to ensure millimolar drug concentrations and that thiol drugs with lower thiol pKa values are most likely to be effective.\n\nOne Sentence SummaryThe effect of cysteamine to decrease SARS-CoV-2 pneumonia in vivo and of multiple thiol drugs to inhibit SARS-CoV-2 infection in vitro provides rationale for clinical trials of thiol drugs in COVID-19.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Kritika Khanna", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Wilfred Raymond", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jing Jin", + "author_inst": "Vitalant Research Institute, San Francisco, California." + }, + { + "author_name": "Annabelle R Charbit", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Irina Gitlin", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Monica Tang", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Adam D. Werts", + "author_inst": "Lovelace Biomedical Research Institute, Albuquerque, New Mexico" + }, + { + "author_name": "Edward G. Barrett", + "author_inst": "Lovelace Biomedical Research Institute, Albuquerque, New Mexico" + }, + { + "author_name": "Jason M. Cox", + "author_inst": "Lovelace Biomedical Research Institute, Albuquerque, New Mexico" + }, + { + "author_name": "Sharla M. Birch", + "author_inst": "Lovelace Biomedical Research Institute, Albuquerque, New Mexico" + }, + { + "author_name": "Rachel Martinelli", + "author_inst": "Vitalant Research Institute, San Francisco, California" + }, + { + "author_name": "Hannah S Sperber", + "author_inst": "Vitalant Research Institute, San Francisco, California." + }, + { + "author_name": "Sergej Franz", + "author_inst": "Vitalant Research Institute, San Francisco, California." + }, + { + "author_name": "Satish Pillai", + "author_inst": "Vitalant Research Institute, San Francisco, California." + }, + { + "author_name": "Anne Marie Healy", + "author_inst": "School of Pharmacy and Pharmaceutical Sciences, Panoz Institute, Trinity College Dublin, Ireland. SSPC, The Science Foundation Ireland Research Centre for Phar" + }, + { + "author_name": "Thomas Duff", + "author_inst": "Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Dublin, Ireland" + }, + { + "author_name": "Stefan Oscarson", + "author_inst": "Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Dublin, Ireland" + }, + { + "author_name": "Markus Hoffmann", + "author_inst": "Infection Biology Unit, German Primate Center, Gottingen, Germany. Faculty of Biology and Psychology, Georg-August-University Gottingen, Gottingen, Germany" + }, + { + "author_name": "Stefan Pohlmann", + "author_inst": "Infection Biology Unit, German Primate Center, Gottingen, Germany. Faculty of Biology and Psychology, Georg-August-University Gottingen, Gottingen, Germany" + }, + { + "author_name": "Graham Simmons", + "author_inst": "Vitalant Research Institute, San Francisco, California." + }, + { + "author_name": "John V Fahy", + "author_inst": "University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.03.20242941", "rel_title": "Contrasting factors associated with COVID-19-related ICU and death outcomes: interpretable multivariable analyses of the UK CHESS dataset.", @@ -1048667,57 +1050900,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.04.20243741", - "rel_title": "SARS-CoV-2 infection and COVID-19 severity in individuals with prior seasonal coronavirus infection.", - "rel_date": "2020-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20243741", - "rel_abs": "A sizable fraction of healthy blood donors have cross-reactive T cells to SARS-CoV-2 peptides due to prior infection with seasonal coronavirus. Understanding the role of cross-reactive T cells in immunity to SARS-CoV-2 has implications for managing the COVID-19 pandemic. We show that individuals with documented history of seasonal coronavirus have a similar SARS-CoV-2 infection rate and COVID-19 severity as those with no prior history of seasonal coronavirus. Our findings suggest prior infection with seasonal coronavirus does not provide immunity to subsequent infection with SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Saurabh Gombar", - "author_inst": "Stanford University" - }, - { - "author_name": "Timothy Bergquist", - "author_inst": "University of Washington" - }, - { - "author_name": "Vikas Pejaver", - "author_inst": "University of Washington" - }, - { - "author_name": "Noah Hammarlund", - "author_inst": "University of Washington" - }, - { - "author_name": "Kanagavel Murugesan", - "author_inst": "Stanford University" - }, - { - "author_name": "Sean Mooney", - "author_inst": "University of Washington" - }, - { - "author_name": "Nigam Shah", - "author_inst": "Stanford University" - }, - { - "author_name": "Benjamin Pinsky", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Niaz Banaei", - "author_inst": "Stanford Univ" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.05.20244673", "rel_title": "Handling and accuracy of four rapid antigen tests for the diagnosis of SARS-CoV-2 compared to RT-qPCR.", @@ -1049017,6 +1051199,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.04.20241059", + "rel_title": "Sensitive detection and quantification of SARS-CoV-2 in saliva", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20241059", + "rel_abs": "Saliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Mustafa Fatih Abasiyanik", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Blake Flood", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Jing Lin", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Sefika Ozcan", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Sherin Rouhani", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Athalia Pyzer", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Jonathan Trujillo", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Chaojie Zhen", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Ping Wu", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Stephen Jumic", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Andrew Wang", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Thomas Gajewski", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Peng Wang", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Madeline Hartley", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Bekim Ameti", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Rachel Niemiec", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Marian Fernando", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Bulent Aydogan", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Cindy Bethel", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Scott Matushek", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Kathleen Beavis", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Nishant Agrawal", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Jeremy Segal", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Savas Tay", + "author_inst": "UNIVERSITY OF CHICAGO" + }, + { + "author_name": "Evgeny Izumchenko", + "author_inst": "UNIVERSITY OF CHICAGO" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.05.20244442", "rel_title": "Seroconversion stages COVID19 into distinct pathophysiological states", @@ -1050285,65 +1052582,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.04.411736", - "rel_title": "Genetic variability in COVID-19-related genes in the Brazilian population", - "rel_date": "2020-12-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.04.411736", - "rel_abs": "SARS-CoV-2 employs the angiotensin-converting enzyme 2 (ACE2) receptor and the transmembrane serine protease (TMPRSS2) to infect human lung cells. Previous studies have suggested that different host genetic backgrounds in ACE2 and TMPRSS2 could contribute to differences in the rate of infection or severity of COVID-19. Recent studies also showed that variants in 15 genes related to type I interferon immunity to influenza virus could predispose to life-threatening COVID-19 pneumonia. Additional genes (SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, XCR1, IL6, CTSL, ABO, and FURIN) and HLA alleles have also been implicated in response to infection with SARS-CoV-2. Currently, Brazil has recorded the third-highest number of COVID-19 patients worldwide. We aim to investigate the genetic variation present in COVID-19-related genes in the Brazilian population. We analysed 27 candidate genes and HLA alleles in 954 admixed Brazilian exomes. We used the information available in two public databases (http://www.bipmed.org and http://abraom.ib.usp.br/), and additional exomes from individuals born in southeast Brazil, the region with the highest number of COVID-19 patients in the country. Variant allele frequencies were compared with the 1000 Genomes Project phase 3 (1KGP) and the gnomAD databases. We found 395 non-synonymous variants; of these, 325 were also found in the 1000 Genome Project phase 3 (1KGP) and/or gnomAD. Six of these variants were previously reported as putatively influencing the rate of infection or clinical prognosis for COVID-19. The remaining 70 variants were identified exclusively in the Brazilian sample, with a mean allele frequency of 0.0025. In silico prediction of the impact in protein function revealed that three of these rare variants were pathogenic. Furthermore, we identified HLA alleles that were previously associated with COVID-19 response at loci DQB1 and DRB1. Our results showed genetic variability common to other populations, but also rare and ultra-rare variants exclusively found in the Brazilian population. These findings could potentially lead to differences in the rate of infection or response to infection by SARS-CoV-2 and should be further investigated in patients with the disease.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rodrigo Secolin", - "author_inst": "University of Campinas (UNICAMP). School of Medical Sciences. Department of Medical Genetics and Genomic Medicine" - }, - { - "author_name": "Tania K de Araujo", - "author_inst": "University of Campinas (UNICAMP). School of Medical Sciences. Department of Medical Genetics and Genomic Medicine" - }, - { - "author_name": "Marina C. Gonsales", - "author_inst": "University of Campinas (UNICAMP). School of Medical Sciences. Department of Medical Genetics and Genomic Medicine" - }, - { - "author_name": "Cristiane S. Rocha", - "author_inst": "University of Campinas (UNICAMP). School of Medical Sciences. Department of Medical Genetics and Genomic Medicine" - }, - { - "author_name": "Michel Satya Naslavsky", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Luiz De Marco", - "author_inst": "Federal University of Minas Gerais (UFMG)" - }, - { - "author_name": "Maria Bicalho", - "author_inst": "Federal University of Minas Gerais (UFMG)" - }, - { - "author_name": "Vinicius L Vazquez", - "author_inst": "Barretos Cancer Hospital" - }, - { - "author_name": "Mayana Zatz", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Wilson A Silva Jr.", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Iscia Lopes-Cendes", - "author_inst": "University of Campinas - UNICAMP" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.12.04.410092", "rel_title": "Ribavirin shows antiviral activity against SARS-CoV-2 and downregulates the activity of TMPRSS2 and the expression of ACE2 in vitro", @@ -1050771,6 +1053009,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.11.30.20236570", + "rel_title": "THE THERAPEUTIC POTENTIAL OF IVERMECTIN FOR COVID-19: A REVIEW OF MECHANISMS AND EVIDENCE", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20236570", + "rel_abs": "IntroductionIvermectin is a commonly used antihelminthic agent with over 35 years of established safety data in humans. Recent data demonstrates antiviral activity in vitro against SARS-CoV-2, in addition to a range of viruses. In vitro and animal models also provide evidence of immunomodulatory action. These additional modes of action are supported by in silico modelling, which propose a number of viral and host targets that would mediate these effects.\n\nObjectivesThe aim of this study is to systematically review the published and preprint clinical literature and study results that assessed the potential role of ivermectin as a COVID-19 therapeutic and prophylactic agent.\n\nMethodsWe conducted a comprehensive review of PubMed, medRxiv, ClinicalTrials.gov, Global Coronavirus COVID-19 Clinical Trial Tracker, World Health Organization International Clinical Trials Registry Platform, EU Clinical Trials Register, ANZ clinical trials registry, and references from relevant articles.\n\nResultsSearch keywords- \"COVID-19 (and synonyms) AND ivermectin\"- generated 86 articles on PubMed, 48 on medRvix and 37 on clinicaltrials.gov at the time of writing. Twelve of these were listed as completed clinical trials and of these, 8 were included as investigators had released results. Positive mortality benefit, reduced time to clinical recovery, reduced incidence of disease progression and decreased duration of hospital admission were reported in patients across all stages of clinical severity.\n\nLimitationsDue to the time-critical nature of the COVID-19 pandemic our review included preprint data, which must be interpreted with caution while it awaits peer review.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Stefanie Kalfas", + "author_inst": "Florey Institute of Neuroscience and Mental Health, University of Melbourne" + }, + { + "author_name": "Kumar Visvanathan", + "author_inst": "Department of Medicine, Dentistry and Health Sciences, University of Melbourne" + }, + { + "author_name": "Kim Chan", + "author_inst": "Sydney Pharmacy School, Faculty of Medicine and Health, University of Sydney" + }, + { + "author_name": "John Drago", + "author_inst": "Florey Institute of Neuroscience and Mental Health, University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.02.20242644", "rel_title": "Model for evaluating cost-effectiveness of surveillance testing for SARS-CoV2", @@ -1052315,37 +1054584,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.03.20243352", - "rel_title": "Association between Participation in Government Subsidy Program for Domestic Travel and Symptoms Indicative of COVID-19 Infection", - "rel_date": "2020-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243352", - "rel_abs": "ImportanceAs countermeasures against the economic downturn caused by the coronavirus 2019 (COVID-19) pandemic, many countries have introduced or considering financial incentives for people to engage in economic activities such as travel and use restaurants. Japan has implemented a large-scale, nationwide government-funded program that subsidizes up to 50% of all travel expenses since July 2020 with the aim of reviving the travel industry. However, it remains unknown as to how such provision of government subsidies for travel impacted the COVID-19 pandemic.\n\nObjectiveTo investigate the association between participation in government subsidies for domestic travel in Japan and the incidence of COVID-19 infections.\n\nDesign, Setting, and ParticipantsUsing the data from a large internet survey conducted between August 25 and September 30, 2020, in Japan, we examined whether individuals who used subsidies experienced a higher likelihood of symptoms indicative of the COVID-19 infection.\n\nExposureParticipation in the government subsidy program for domestic travel.\n\nMain Outcomes and MeasuresFive symptoms indicative of the COVID-19 infection (high fever, sore throat, cough, headache, and smell and taste disorder) within the past one month of the survey.\n\nResultsOf the 25,482 respondents (50.3% [12,809] women; mean [SD] age, 48.4 [17.4] years), 3,289 (12.9%) participated in the subsidy program at the time of survey. After adjusting for potential confounders, we found that participants in the subsidy program exhibited higher incidence of high fever (adjusted rate, 4.8% for participants vs. 3.7% for non-participants; adjusted odds ratio [aOR], 1.90; 95%CI, 1.42-2.54; p<0.001), sore throat (19.8% vs. 11.3%; aOR, 2.09; 95%CI, 1.37-3.20; p=0.002), cough (19.1% vs. 11.2%; aOR 1.96; 95%CI, 1.27-3.02; p=0.007), headache (29.1% vs. 25.5%; aOR, 1.24; 95%CI, 1.07-1.43; p=0.007), and smell and taste disorder (2.6% vs. 1.8%; aOR 1.98; 95%CI; 1.15-3.40; p=0.01) compared with non-participants.\n\nConclusion and RelevanceThe participants of government subsidies for domestic travel experienced a higher incidence of symptoms indicative of the COVID-19 infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Atsushi Miyawaki", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Takahiro Tabuchi", - "author_inst": "Cancer Control Center, Osaka International Cancer Institute" - }, - { - "author_name": "Yasutake Tomata", - "author_inst": "Faculty of Health and Social Services, Kanagawa University of Human Services" - }, - { - "author_name": "Yusuke Tsugawa", - "author_inst": "UCLA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.03.20243345", "rel_title": "Long Covid and the role of physical activity: a qualitative study", @@ -1052609,6 +1054847,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.03.20238840", + "rel_title": "Galectin antagonist use in mild cases of SARS-CoV-2 cases; pilot feasibility randomised, open label, controlled trial", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20238840", + "rel_abs": "ImportanceNovel SARS-CoV-2 virus has infected nearly half a billion people across the world and is highly contagious. There is a need for a novel mechanism to block viral entry and stop its replication.\n\nBackgroundSpike protein N terminal domain (NTD) of the novel SARS-CoV-2 is essential for viral entry and replication in human cell. Thus the S1 NTD of human coronavirus family, which is similar to a galectin binding site - human galactose binding lectins, is a potential novel target for early treatment in COVID-19.\n\nObjectivesTo study the feasibility of performing a definitive trial of using galectin antagonist - Prolectin-M as treatment for mild, symptomatic, rRT-PCR positive, COVID-19.\n\nMain outcomes and measuresCycle threshold (Ct) value is number of cycles needed to express fluorescence, on real time reverse transcriptase polymerase chain reaction. Ct values expressed for RNA polymerase (Rd/RP) gene +Nucleocapsid gene and the small envelope (E) genes determine infectivity of the individual. A digital droplet PCR based estimation of the Nucleocapid genes (N1+N2) in absolute copies/L determines active viral replication.\n\nDesign and interventionPilot Feasibility Randomised Controlled Open-Label, parallel arm, study. Oral tablets of Prolectin-M were administered along with the best practice, Standard of Care (SoC) and compared against SoC. Voluntarily, consenting individuals, age >18 years, and able to provide frequent nasopharyngeal and oropharyngeal swabs were randomly allocated by REDCap software.\n\nThe intervention, Prolectin-M was administered as a multi dose regime of 4 gram tablets. Each tablet contained 2 grams of (1-6)-Alpha-D-mannopyranosil mixed with 2 grams of dietary fibre. Each participant took a single chewable tablet every hour, to a maximum of 10 hours in a day. Tablets were administered only during the daytime, for total of 5 days.\n\nResultsThis pilot trial demonstrated the feasibility to recruit and randomize participants. By day 7, following treatment with Prolectin-M, Ct value of Rd/Rp + N gene increased by16.41 points, 95% (CI - 0.3527 to 32.48, p=0.047). Similarly, small envelope (E) gene also increased by 17.75 points (95% CI;-0.1321 to 35.63, p = 0.05). The expression of N1, N2 genes went below detectable thresholds by day 3 (Mann Whitney U = 0.000, p<0.029).\n\nrRT-PCR testing done in the clinic on day 1, 7, and 14 had 3 participants (60%) turn negative by day 7 and all turned negative by day 14 and stayed negative until day 28. In the SoC group 2 participants had zero detectable viral loads at baseline, 2 participants tested negative on day 14, and the last participant tested remained positive on day 28. There were no serious adverse events, and all participants were clinically asymptomatic before day 28 with reactive immunoglobulin G (IgG).\n\nTrial relevanceThis pilot study proves that it is feasible and safe to perform a trial using a Galectin antagonist in COVID-19. This is a novel mechanism for blocking viral entry and its subsequent replication.\n\nTrial RegistrationClinical Trials.gov identifier NCT04512027; CTRI ref. CTRI/2020/09/027833", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "ALBEN SIGAMANI", + "author_inst": "NARAYANA HRUDAYALAYA LIMITED" + }, + { + "author_name": "ALBEN SIGAMANI", + "author_inst": "NARAYANA HRUDAYALAYA LIMITED" + }, + { + "author_name": "MADHAVI KADAMBI", + "author_inst": "NARAYANA HRUDAYALAYA LIMITED" + }, + { + "author_name": "MATHU RUTHRA", + "author_inst": "NARAYANA HRUDAYALAYA LIMITED" + }, + { + "author_name": "SUDHISHMA SHIVAPRASAD", + "author_inst": "NARAYANA HRUDAYALAYA LIMITED" + }, + { + "author_name": "ANUP CHUGANI", + "author_inst": "MEDGENOME PRIVATE LIMITED" + }, + { + "author_name": "HANA CHEN-WALDEN", + "author_inst": "PHARMALECTIN INC" + }, + { + "author_name": "THOMASKUTTY ALUMPARAMBILL", + "author_inst": "Baylor Scott& White Health" + }, + { + "author_name": "DAVID PLATT", + "author_inst": "PHARMALECTIN INC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.03.20243659", "rel_title": "Risk factors for severe illness and death in COVID-19: a systematic review and meta-analysis", @@ -1053873,25 +1056162,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.11.30.20241224", - "rel_title": "COVID-19 Trends in Florida K-12 Schools, August 10 - November 14, 2020", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241224", - "rel_abs": "Data collected from 38 states from August 3 - November 15, 2020 showed more than 250,000 confirmed student and staff cases of SARS-CoV-2 in K-12 schools1. Yet, analysis of COVID-19 case data in USA schools has been extremely limited2,3. To date, no large-scale or state-wide analyses by school level and grade has been published, opening a wide gap in understanding COVID-19 in American schools. A large-scale assessment of available data and trends could provide a baseline for understanding the virus in the K-12 learning environment and dispel misconceptions about the prevalence of COVID-19 in schools.\n\nTable of Contents SummaryUsing the most comprehensive database of K-12 COVID-19 case data in the country, Florida provides clues for understanding student and staff cases in schools.\n\nWhats known on this subjectFlorida schools began reopening to in-person instruction in August have reported more than 18,000 student and staff cases of COVID-19 as of November 14, 2020. Incidence of COVID-19 cases in K-12 students and staff is of urgent public health concern.\n\nWhat this study addsCOVID-19 cases reported in Florida schools were most influenced by community case rates, district mask policies, and percent of students attending face-to-face. Student case rates were highest in high schools (12.5 per 1,000).", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Rebekah D Jones", - "author_inst": "The Covid Monitor" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.30.20239095", "rel_title": "Establishment of CORONET; COVID-19 Risk in Oncology Evaluation Tool to identify cancer patients at low versus high risk of severe complications of COVID-19 infection upon presentation to hospital", @@ -1054207,6 +1056477,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.01.20241695", + "rel_title": "Which COVID policies are most effective? A Bayesian analysis of COVID-19 by jurisdiction", + "rel_date": "2020-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241695", + "rel_abs": "This paper reports the results of a Bayesian analysis on large-scale empirical data to assess the effectiveness of eleven types of COVID-control policies that have been implemented at various levels of intensity in 40 countries and U.S. states since the onset of the pandemic. The analysis estimates the marginal impact of each type and level of policy as implemented in concert with other policies. The purpose is to provide policymakers and the general public with an estimate of the relative effectiveness of various COVID-control strategies. We find that a set of widely implemented core policies reduces the spread of virus but not by enough to contain the pandemic except in a few highly compliant jurisdictions. The core policies include the cancellation of public events, restriction of gatherings to fewer than 100 people, recommendation to stay at home, recommended restrictions on internal movement, implementation of a partial international travel ban, and coordination of information campaigns. For the median jurisdiction, these policies reduce growth rate in new infections from an estimated 270% per week to approximately 49% per week, but this impact is insufficient to prevent eventual transmission throughout the population because containment occurs only when a jurisdiction reduces growth in COVID infection to below zero. Most jurisdictions must also implement additional policies, each of which has the potential to reduce weekly COVID growth rate by 10 percentage points or more. The slate of these additional high-impact policies includes targeted or full workplace closings for all but essential workers, stay-at-home requirements, and targeted school closures.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Phebo D Wibbens", + "author_inst": "INSEAD" + }, + { + "author_name": "Wesley Wu-Yi Koo", + "author_inst": "INSEAD" + }, + { + "author_name": "Anita M McGahan", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.01.20241646", "rel_title": "An evidence-based online COVID-19 risk calculator", @@ -1055227,85 +1057524,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.02.408823", - "rel_title": "A single intranasal or intramuscular immunization with chimpanzee adenovirus vectored SARS-CoV-2 vaccine protects against pneumonia in hamsters.", - "rel_date": "2020-12-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.02.408823", - "rel_abs": "The development of an effective vaccine against SARS-CoV-2, the etiologic agent of COVID-19, is a global priority. Here, we compared the protective capacity of intranasal and intramuscular delivery of a chimpanzee adenovirus-vectored vaccine encoding a pre-fusion stabilized spike protein (ChAd-SARS-CoV-2-S) in Golden Syrian hamsters. While immunization with ChAd-SARS-CoV-2-S induced robust spike protein specific antibodies capable or neutralizing the virus, antibody levels in serum were higher in hamsters immunized by an intranasal compared to intramuscular route. Accordingly, ChAd-SARS-CoV-2-S immunized hamsters were protected against a challenge with a high dose of SARS-CoV-2. After challenge, ChAd-SARS-CoV-2-S-immunized hamsters had less weight loss and showed reductions in viral RNA and infectious virus titer in both nasal swabs and lungs, and reduced pathology and inflammatory gene expression in the lungs, compared to ChAd-Control immunized hamsters. Intranasal immunization with ChAd-SARS-CoV-2-S provided superior protection against SARS-CoV-2 infection and inflammation in the upper respiratory tract. These findings support intranasal administration of the ChAd-SARS-CoV-2-S candidate vaccine to prevent SARS-CoV-2 infection, disease, and possibly transmission.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Traci Bricker", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Tamarand Darling", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Ahmed Hassan", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Houda Harastani", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Allison Soung", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Xiaoping Jiang", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Ya-Nan Dai", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Haiyan Zhao", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Lucas Adams", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Michael Holtzman", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Adam Bailey", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "James Brett Case", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Daved Fremont", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Robyn S Klein", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael Diamond", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Adrianus Boon", - "author_inst": "Washington University in St Louis" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.02.408575", "rel_title": "In Vitro Analysis of the Anti-viral Potential of nasal spray constituents against SARS-CoV-2", @@ -1055625,6 +1057843,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.03.409763", + "rel_title": "SARS-CoV-2 D614 and G614 spike variants impair neuronal synapses and exhibit differential fusion ability", + "rel_date": "2020-12-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.03.409763", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Coronavirus disease 2019 (COVID-19) exhibits two major variants based on mutations of its spike protein, i.e., the D614 prototype and G614 variant. Although neurological symptoms have been frequently reported in patients, it is still unclear whether SARS-CoV-2 impairs neuronal activity or function. Here, we show that expression of both D614 and G614 spike proteins is sufficient to induce phenotypes of impaired neuronal morphology, including defective dendritic spines and shortened dendritic length. Using spike protein-specific monoclonal antibodies, we found that D614 and G614 spike proteins show differential S1/S2 cleavage and cell fusion efficiency. Our findings provide an explanation for higher transmission of the G614 variant and the neurological manifestations observed in COVID-19 patients.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Chiung-Ya Chen", + "author_inst": "Institute of Molecular Biology, Academia Sinica" + }, + { + "author_name": "Yu-Chi Chou", + "author_inst": "Biomedical Translation Research Center (BioTReC), Academia Sinica" + }, + { + "author_name": "Yi-Ping Hsueh", + "author_inst": "Institute of Molecular Biology, Academia Sinica" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2020.12.03.409441", "rel_title": "Identification of low micromolar SARS-CoV-2 Mpro inhibitors from hits identified by in silico screens", @@ -1056713,49 +1058958,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.30.20241232", - "rel_title": "Bridging the gaps in test interpretation of SARS-CoV-2 through Bayesian network modelling", - "rel_date": "2020-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241232", - "rel_abs": "BackgroundIn the absence of an established gold standard, an understanding of the testing cycle from individual exposure to test outcome report is required to guide the correct interpretation of SARS-CoV-2 reverse transcriptase real-time polymerase chain reaction (RT-PCR) results and optimise the testing processes. Bayesian network (BN) models have been used within healthcare to bring clarity to complex problems. We use this modelling approach to construct a comprehensive framework for understanding the real world predictive value of individual RT-PCR results.\n\nMethodsWe elicited knowledge from domain experts to describe the test process from viral exposure to interpretation of the laboratory test, through a facilitated group workshop. A preliminary model was derived based on the elicited knowledge, then subsequently refined, parameterised and validated with a second workshop and one-on-one discussions.\n\nResultsCausal relationships elicited describe the interactions of multiple variables and their impact on a RT-PCR result. Some interactions are infrequently observable and accounted for across the testing cycle such as pre-testing factors, sample collector experience and RT-PCR platform. By setting the input variables as evidence for a given subject and preliminary parameterisation, three scenarios were simulated to demonstrate potential uses of the model.\n\nConclusionsThe core value of this model is a deep understanding of the total testing cycle, bridging the gap between a persons true infection status and their test outcome. This model can be adapted to different settings, testing modalities and pathogens, adding much needed nuance to the interpretations of results.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yue Wu", - "author_inst": "The University of Sydney" - }, - { - "author_name": "David Foley", - "author_inst": "Perth Childrens Hospital" - }, - { - "author_name": "Jessica Ramsay", - "author_inst": "Telethon Kids Institute" - }, - { - "author_name": "Owen Woodberry", - "author_inst": "Monash University" - }, - { - "author_name": "Steven Mascaro", - "author_inst": "Monash University" - }, - { - "author_name": "Ann E Nicholson", - "author_inst": "Monash University" - }, - { - "author_name": "Tom Snelling", - "author_inst": "The university of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.30.20241208", "rel_title": "Rapid and accurate point-of-care testing for SARS-CoV2 antibodies", @@ -1057107,6 +1059309,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.30.20239566", + "rel_title": "Smart Investment of Virus RNA Testing Resources to Enhance Covid-19 Mitigation", + "rel_date": "2020-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20239566", + "rel_abs": "Covid-19 mitigation commonly involves contact tracing (CT) and social distancing. Due to its high economic toll and its impact on personal freedom, we need to ease social distancing and deploy alternative measures, while preventing further waves of infections. While reliable mass testing (for virus RNA) would require too many resources to be effective, CT, which focuses on isolating symptomatic cases and their contacts, has been implemented in many countries. However, the latter approach has reduced efficiency when high numbers of positive patients are burdening the tracing centers. Moreover, CT misses transmissions by asymptomatic cases. Therefore, its effect in reducing the reproduction number has a theoretical limit.\n\nTo improve effectiveness of contact tracing, we propose to complement it with a strategy relying on identifying and testing symptom free subgroups with a significantly higher than average virus prevalence. We call this smart testing (ST). By testing everybody in these subgroups, in addition to symptomatic cases, also large fractions of pre- and asymptomatic persons can be identified, which enhances the effectiveness of contact tracing. High prevalence subgroups can be found in different ways, which are discussed in this paper. A particularly efficient way is via preselection using cheap and fast virus antigen tests, as proposed recently. Mathematical modeling quantifies the potential reduction of the reproduction number by such a two-stage ST strategy. In addition to global scenarios, also more realistic local applications of two-stage ST have been investigated, that is, within counties, institutions, schools, companies, etc., where members have internal as well as external contacts. All involved model parameters have been varied within realistic ranges and results are presented with probabilities. Even with the most pessimistic parameter set, these results suggest that the effect of two-stage ST on the reproduction number would clearly outweigh its economic cost. Two-stage ST is technically and logistically feasible. Further, it is locally effective also when only applied within small local subpopulations. Thereby, two-stage ST efficiently complements the portfolio of mitigation strategies, which allow easing social distancing without compromising public health.\n\nSingle Sentence SummaryIdentification of high prevalence groups within subpopulations to enhance detection rate of Covid-19 infections by virus RNA tests combined with subsequent isolation.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hossein Gorji", + "author_inst": "EPFL" + }, + { + "author_name": "Markus Arnoldini", + "author_inst": "ETH Zurich" + }, + { + "author_name": "David F Jenny", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Wolf-Dietrich Hardt", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Patrick Jenny", + "author_inst": "ETH Zurich" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.01.20241539", "rel_title": "COVID-19 prevalence in 161 countries and over time", @@ -1058927,101 +1061164,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.12.01.407148", - "rel_title": "Mucosal Associated Invariant T (MAIT) Cell Responses Differ by Sex in COVID-19", - "rel_date": "2020-12-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.407148", - "rel_abs": "Sexual dimorphisms in immune responses contribute to coronavirus disease 2019 (COVID-19) outcomes, yet the mechanisms governing this disparity remain incompletely understood. We carried out sex-balanced sampling of peripheral blood mononuclear cells from confirmed COVID-19 inpatients and outpatients, uninfected close contacts, and healthy controls for 36-color flow cytometry and single cell RNA-sequencing. Our results revealed a pronounced reduction of circulating mucosal associated invariant T (MAIT) cells in infected females. Integration of published COVID-19 airway tissue datasets implicate that this reduction represented a major wave of MAIT cell extravasation during early infection in females. Moreover, female MAIT cells possessed an immunologically active gene signature, whereas male counterparts were pro-apoptotic. Collectively, our findings uncover a female-specific protective MAIT profile, potentially shedding light on reduced COVID-19 susceptibility in females.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Chen Yu", - "author_inst": "Duke University" - }, - { - "author_name": "Sejiro Littleton", - "author_inst": "Duke University" - }, - { - "author_name": "Nicholas Giroux", - "author_inst": "Duke University" - }, - { - "author_name": "Rose Mathew", - "author_inst": "Duke University" - }, - { - "author_name": "Shengli Ding", - "author_inst": "Duke University" - }, - { - "author_name": "Joan Kalnitsky", - "author_inst": "Duke University" - }, - { - "author_name": "Elizabeth Petzold", - "author_inst": "Duke University" - }, - { - "author_name": "Hong Chung", - "author_inst": "Duke University" - }, - { - "author_name": "Grecia rivera Palomino", - "author_inst": "Duke University" - }, - { - "author_name": "Tomer Rotstein", - "author_inst": "Duke University" - }, - { - "author_name": "Rui Xi", - "author_inst": "Duke University" - }, - { - "author_name": "Emily R Ko", - "author_inst": "Duke University" - }, - { - "author_name": "Ephraim L Tsalik", - "author_inst": "Duke University" - }, - { - "author_name": "gregory sempowski", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Thomas N Denny", - "author_inst": "Duke University" - }, - { - "author_name": "Thomas W Burke", - "author_inst": "Duke University" - }, - { - "author_name": "Micah T McClain", - "author_inst": "Duke University" - }, - { - "author_name": "Christopher W. Woods", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Xiling Shen", - "author_inst": "Duke University" - }, - { - "author_name": "Daniel R Saban", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.01.407007", "rel_title": "Multimodal Single-Cell Omics Analysis of COVID-19 Sex Differences in Human Immune Systems", @@ -1059337,6 +1061479,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.28.20240325", + "rel_title": "Seroprevalence of anti-SARS-COV-2 antibodies in blood donors from Nuevo Leon state, Mexico, during the beginning of the COVID-19 pandemic", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.28.20240325", + "rel_abs": "BackgroundThe progression and distribution of SARS-CoV-2 is unknown because typically only symptomatic individuals are diagnosed.\n\nAimWe evaluated the seroprevalence of anti-SARS-CoV-2 in blood donors in Nuevo Leon, Mexico as a strategy for asymptomatic case detection of COVID-19 and epidemic progression.\n\nMethods/MaterialsWe tested 1968 blood donors that attended two regional donation centers in Northeast Mexico from January 1st to August 30, 2020, to identify anti-SARS-CoV-2 IgG by chemiluminescent immunoassay. Additionally, routine tests for donors including Brucella, Chagas, HCV, VDRL, HIV-1, and HBsAg identification were performed.\n\nResultsWe found 77 donors reactive for anti-SARS-CoV-2 IgG (seroprevalence 3.99%) and none of them had reported recent COVID-19 symptoms. Donors aged 18 to 49 years (89.5%) were more likely to be seropositive compared to those aged 50 years or older (10.5%) (P<0.001). Prevalence of antibodies increased each epidemiological (EPI) week, parallel to the report of confirmed cases by RT-PCR, identifying the highest prevalence between EPI week 33 and 35 (10.2% to 19%). The metropolitan area of Monterrey recorded the highest number of cases. Routine tests showed that the prevalence of anti-Brucella was 0.13%, anti-HCV 0.5%, anti-HIV-1-2 0.14%, HBsAg 0.16%, Chagas 0.48% and syphilis 1.06%.\n\nConclusionsThere is a growing trend of seroprevalence over time, parallel to the constantly increasing epidemic curve in our region and it was higher under 49 years of age associated with asymptomatic infection in donors from the Nuevo Leon area. Detection of anti-SARS-CoV-2 in blood donors is a potential tool for tracking the progression and identifying population exposure during the SARS-CoV-2 outbreak.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Natalia Martinez-Acuna", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Diana Avalos-Nolazco", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Diana Rodriguez-Rodriguez", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Cynthia Martinez-Liu", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Rogelio Cazares-Tamez", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Amador Flores-Arechiga", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Fernando Perez-Chavez", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Sergio Ayala-de-la-Cruz", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Eduardo Cienfuegos-Pecina", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Erik Diaz-Cuc", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Daniel Arellanos-Soto", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Gerardo Padilla-Rivas", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Javier Ramos-Jimenez", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Kame Galan-Huerta", + "author_inst": "Autonomous university of Nuevo Leon" + }, + { + "author_name": "Sonia Lozano-Sepulveda", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Elvira Garza-Gonzalez", + "author_inst": "Autonomous University of Nuevo Leon" + }, + { + "author_name": "Consuelo Trevino-Garza", + "author_inst": "Autonomous University of Nuevo Leon, Secretaria de Salud NL" + }, + { + "author_name": "Roberto Montes-de-Oca-Luna", + "author_inst": "Autonomous University of Nuevo Leon, Secretaria de Salud NL" + }, + { + "author_name": "Aurora Lee", + "author_inst": "Secretaria de Salud NL" + }, + { + "author_name": "Manuel De-la-O-Cavazos", + "author_inst": "Autonomous University of Nuevo Leon, Secretaria de Salud NL" + }, + { + "author_name": "Ana M Rivas-Estilla", + "author_inst": "Universidad Autonoma de Nuevo Leon" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.26.20238733", "rel_title": "Automated Western immunoblotting detection of anti-SARS-CoV-2 serum antibodies.", @@ -1060457,29 +1062698,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.26.20239434", - "rel_title": "The evolving worldwide dynamic state of the COVID-19 outbreak", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239434", - "rel_abs": "The dynamic characterization of the COVID-19 outbreak is critical to implement effective actions for its control and eradication but the information available at a global scale is not sufficiently reliable to be used directly. Here, we integrate multiple data sources through dynamical constraints to quantify its temporal evolution and controllability around the world and within the United States. Overall, the numbers of actively infectious individuals have remained high beyond targeted controllability, with worldwide estimates of 10.24 million on November 24, 2020, totaling in 266.1 million cumulative infections growing at a rate of 11.12 million new infections per week. The actively infectious population reached a local maximum of 7.33 million on July 16, 2020 and remained virtually stagnant at a global scale, with growth rates for most countries around zero that compensated each other, until reverting to net growth on September 22, 2020. We validated the approach, contrasting with prevalence data and the effects of nonpharmaceutical interventions, and we identified general patterns of recession, stabilization, and resurgence. The diversity of dynamic behaviors of the outbreak across countries is paralleled by those of states and territories in the United States, converging to remarkably similar global states in both cases. Our results offer precise insights into the dynamics of the outbreak and an efficient avenue for the estimation of the prevalence rates over time.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Jose M. G. Vilar", - "author_inst": "Biofisika Intitute (CSIC-UPV/EHU) and Ikerbasque" - }, - { - "author_name": "Leonor Saiz", - "author_inst": "University of California, Davis" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.26.20239418", "rel_title": "Predictors of QT Interval Prolongation in Critically-ill Patients with SARS-CoV-2 Infection Treated with Hydroxychloroquine", @@ -1060695,6 +1062913,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.27.20239087", + "rel_title": "Dietary supplements during the COVID-19 pandemic: insights from 1.4M users of the COVID Symptom Study app - a longitudinal app-based community survey", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20239087", + "rel_abs": "ObjectivesDietary supplements may provide nutrients of relevance to ameliorate SARS-CoV-2 infection, although scientific evidence to support a role is lacking. We investigate whether the regular use of dietary supplements can reduce the risk of testing positive for SARS-CoV-2 infection in around 1.4M users of the COVID Symptom Study App who completed a supplement use questionnaire.\n\nDesignLongitudinal app-based community survey and nested case control study.\n\nSettingSubscribers to an app that was launched to enable self-reported information related to SARS-CoV-2 infection for use in the general population in three countries.\n\nMain ExposureSelf-reported regular dietary supplement usage since the beginning of the pandemic.\n\nMain Outcome MeasuresSARS-CoV-2 infection confirmed by viral RNA polymerase chain reaction test (RT-PCR) or serology test. A secondary outcome was new-onset anosmia.\n\nResultsIn an analysis including 327,720 UK participants, the use of probiotics, omega-3 fatty acids, multivitamins or vitamin D was associated with a lower risk of SARS-CoV-2 infection by 14%(95%CI: [8%,19%]), 12%(95%CI: [8%,16%]), 13%(95%CI: [10%,16%]) and 9%(95%CI: [6%,12%]), respectively, after adjusting for potential confounders. No effect was observed for vitamin C, zinc or garlic supplements. When analyses were stratified by sex, age and body mass index (BMI), the protective associations for probiotics, omega-3 fatty acids, multivitamins and vitamin D were observed in females across all ages and BMI groups, but were not seen in men. The same overall pattern of association was observed in both the US and Swedish cohorts. Results were further confirmed in a sub-analysis of 993,365 regular app users who were not tested for SARS-CoV-2 with cases (n= 126,556) defined as those with new onset anosmia (the strongest COVID-19 predictor).\n\nConclusionWe observed a modest but significant association between use of probiotics, omega-3 fatty acid, multivitamin or vitamin D supplements and lower risk of testing positive for SARS-CoV-2 in women. No clear benefits for men were observed nor any effect of vitamin C, garlic or zinc for men or women. Randomised controlled trials of selected supplements would be required to confirm these observational findings before any therapeutic recommendations can be made.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Panayiotis Louca", + "author_inst": "King's College London" + }, + { + "author_name": "Benjamin Murray", + "author_inst": "King's College London" + }, + { + "author_name": "Kerstin Klaser", + "author_inst": "King's College London" + }, + { + "author_name": "Mark S Graham", + "author_inst": "King's College London" + }, + { + "author_name": "Mohsen Mazidi", + "author_inst": "King's College London" + }, + { + "author_name": "Emily R Leeming", + "author_inst": "King's College London" + }, + { + "author_name": "Ellen J Thompson", + "author_inst": "King's College London" + }, + { + "author_name": "Ruth Bowyer", + "author_inst": "King's College London" + }, + { + "author_name": "David Alden Drew", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Long Alden Nguyen", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Jordi Merino", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Maria F Gomez", + "author_inst": "Lund University" + }, + { + "author_name": "Olatz Mompeo", + "author_inst": "King's College London" + }, + { + "author_name": "Ricardo Costeira", + "author_inst": "King's College London" + }, + { + "author_name": "Carole H Sudre", + "author_inst": "University College London" + }, + { + "author_name": "Rachel Gibson", + "author_inst": "King's College London" + }, + { + "author_name": "Claire Steves", + "author_inst": "King's College London" + }, + { + "author_name": "Jonathan Wolf", + "author_inst": "Zoe Global Limited" + }, + { + "author_name": "Paul W Franks", + "author_inst": "Lund University" + }, + { + "author_name": "Sebastien Ourselin", + "author_inst": "King's College London" + }, + { + "author_name": "Andrew T Chan", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Sarah E Berry", + "author_inst": "King's College London" + }, + { + "author_name": "Ana Valdes", + "author_inst": "King's College London" + }, + { + "author_name": "Philip Calder", + "author_inst": "University of Southampton" + }, + { + "author_name": "Tim D Spector", + "author_inst": "King's College London" + }, + { + "author_name": "Cristina Menni", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.27.20239616", "rel_title": "Obesity as a predictor for adverse outcomes among COVID-19 patients: A meta-analysis", @@ -1061911,29 +1064248,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.27.20239970", - "rel_title": "Willingness to vaccinate against COVID-19 in the US: Longitudinal evidence from a nationally representative sample of adults from April-October 2020", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20239970", - "rel_abs": "IntroductionVaccines against COVID-19 have been developed in unprecedented time. However, the effectiveness of any vaccine is dictated by the proportion of the population willing to be vaccinated. In this observational population-based study we examined intentions to be vaccinated against COVID-19 over the course of the pandemic.\n\nMethodsWe analyzed longitudinal data from a nationally representative sample of 7,547 US adults enrolled in the Understanding America Study (UAS). Participants reporting being willing, undecided and unwilling to get vaccinated against coronavirus across 13 assessments conducted from April-October, 2020. Public attitudes to vaccination against the coronavirus were also assessed.\n\nResultsWillingness to vaccinate declined from 71% in April to 53.6% in October. This was explained by an increase in the percentage of participants undecided about vaccinating (from 10.5% to 14.4%) and the portion of the sample unwilling to vaccinate (from 18.5% to 32%). The population subgroups most likely to be undecided/unwilling to vaccinate were those without a degree (undecided: RRR=2.47, 95% CI: 2.04-3.00; unwilling: RRR=1.92, 95% CI: 1.67-2.20), Black participants (undecided: RRR=2.18, 95% CI: 1.73-2.74; unwilling: RRR=1.98, 95% CI: 1.63-2.42), and females (undecided: RRR=1.41, 95% CI: 1.20-1.65; unwilling: RRR=1.29, 95% CI: 1.14-1.46). Those aged 65+, those on high incomes, and other race/ethnicity participants were least likely to be undecided or unwilling to vaccinate. Concerns about potential side effects of a vaccine were common.\n\nConclusionsIntentions to be vaccinated against coronavirus have declined rapidly during the pandemic and close to half of Americans are undecided or unwilling to be vaccinated.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Michael Daly", - "author_inst": "Maynooth University" - }, - { - "author_name": "Eric Robinson", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.29.20240614", "rel_title": "AI4CoV: Matching COVID-19 Patients to Treatment Options Using Artificial Intelligence", @@ -1062177,6 +1064491,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.29.20240549", + "rel_title": "Nationwide SARS-CoV-2 Surveillance Study for Sewage and Sludges of Wastewater Treatment Plants in Turkey", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.29.20240549", + "rel_abs": "1.Since the announcement of the pandemic of Covid-19 by WHO on March 11, 2020, the countries have started to monitor surveillance of SARS-CoV-2 through medical tests. However, people with no and very light symptoms are usually not medically tested or never hospitalized and they are missed. In the study of Wu et al. [1], it was realized that the urine and faeces of all infected people contain SARS-CoV-2. After that, sewage, and sludge-based SARS-CoV-2 surveillance studies have gained significant importance around the world (Fig.1). SARS-CoV-2 was detected in wastewaters in The Netherlands [2,3,4], USA [1,5,6,7, 8, 9, 10], Australia [11], France [12, 13, 14], China [15], Spain [16,17,18,19,20], Italy [21, 22,23], Israel [24], Turkey[25], Germany[26], Japan [27,28], India [29,30], Pakistan [31], Brazil [32,33], Chile [34], Denmark, France, Belgium[35], Equator [36] and Sweden [37] using different virus concentration techniques. Published data show that high concentrations of the SARS-CoV-2 RNA reaches to wastewater treatment plants (WWTPs). On 7th of May 2020, Turkey took its place among a few country which have been started wastewater based surveillance studies at the early stages of pandemic by reporting SARS-CoV-2 RT-qPCR levels of major WWTPs of Istanbul [25]. Turkey [38] first detected SARS-CoV-2 in both primary and waste activated sludges of Istanbul WWTPs. Later, USA [39] and Spain [40] were also studied on sludge samples. There are also studies evaluating the SARS-CoV-2 in WWTPs effluents [10,13,14, 28, 29,30, 34, 36].\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC=\"FIGDIR/small/20240549v1_fig1.gif\" ALT=\"Figure 1\">\nView larger version (59K):\norg.highwire.dtl.DTLVardef@ba8798org.highwire.dtl.DTLVardef@1c3cbeorg.highwire.dtl.DTLVardef@1d7f284org.highwire.dtl.DTLVardef@72e423_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 1.C_FLOATNO Worldwide SARS-CoV-2 surveillance studies in wastewater (https://www.google.com/maps/)\n\nC_FIG This study aimed to scan distribution of Covid-19 through Turkey by SARS-CoV-2 measurements in influent, effluent and sludge samples of WWTPs. The influent, effluent and sludge samples were collected from main WWTPs located in 81 cities of Turkey through May 2020-July 2020. Among those 81 cities, Istanbul metropole with 15.5 million inhabitants was chosen as the pilot city since 65% of all cases in Turkey were present here. Hence, all treatment plants in Istanbul were scanned through the study. The viral activity tests were also conducted for the influent, effluent and sludge samples resulting high qPCR.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Bilge Alpaslan Kocamemi", + "author_inst": "Marmara University" + }, + { + "author_name": "Halil Kurt", + "author_inst": "Saglik Bilimleri University, Hamidiye International Scholl of Medicine, Department of Medical Biology" + }, + { + "author_name": "Ahmet Sait", + "author_inst": "Ministry of Agriculture and Forestry, Republic of Turkey, Veterinary Control Central Research Institute, Pendik, Istanbul, Turkey." + }, + { + "author_name": "Hamza Kadi", + "author_inst": "Ministry of Agriculture and Forestry, Republic of Turkey, Veterinary Control Central Research Institute, Samsun, Turkey" + }, + { + "author_name": "Fahriye Sarac", + "author_inst": "Ministry of Agriculture and Forestry, Republic of Turkey, Veterinary Control Central Research Institute, Pendik, Istanbul, Turkey" + }, + { + "author_name": "Ismail Aydin", + "author_inst": "Ministry of Agriculture and Forestry, Republic of Turkey, Veterinary Control Central Research Institute, Samsun, Turkey" + }, + { + "author_name": "Ahmet Mete Saatci", + "author_inst": "Turkish Water Institute, Istanbul, Turkey" + }, + { + "author_name": "Bekir Pakdemirli", + "author_inst": "Ministry of Agriculture and Forestry, Republic of Turkey, Ankara, Turkey" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.30.20240739", "rel_title": "Comparative analysis of variation in the quality and completeness of local outbreak control plans for SARS-CoV-2 in English local authorities", @@ -1063549,37 +1065910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.11.25.20238766", - "rel_title": "The psychosocial impact on frontline health and social care professionals in the UK during the COVID-19 pandemic: a qualitative interview study.", - "rel_date": "2020-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20238766", - "rel_abs": "ObjectivesTo explore the psychosocial well-being of health and social care professionals working during the COVID-19 pandemic.\n\nDesignThis was a qualitative study deploying in-depth, individual interviews, which were audio-recorded and transcribed verbatim. Thematic analysis was used for coding.\n\nParticipantsThis study involved 25 participants from a range of frontline professions in health and social care.\n\nSettingInterviews were conducted over the phone or video call, depending on participant preference.\n\nResultsFrom the analysis, we identified 5 overarching themes: communication challenges, work-related stressors, support structures, personal growth, and individual resilience. The participants expressed difficulties such as communication challenges and changing work conditions, but also positive factors such as increased team unity at work, and a greater reflection on what matters in life.\n\nConclusionsThis study provides evidence on the support needs of health and social care professionals amid continued and future disruptions caused by the pandemic. It also elucidates some of the successful strategies (such as mindfulness, hobbies, restricting news intake, virtual socialising activities) deployed by health and social care professionals that can support their resilience and well-being and be used to guide future interventions.\n\nStrengths and limitations of this studyO_LIThis is the first study in the UK to interview both health and social care professionals working in a range of settings on their experiences working through COVID-19.\nC_LIO_LIThis study used a strong theoretical approach to inform the topic guide, and one-to-one interviews allowed in-depth analysis of the psychosocial experiences of health and social care professionals, complementing the wider availability of quantitative evidence.\nC_LIO_LIWe interviewed a wide range of professions, which provided breadth of experience but might limit the specificity of findings.\nC_LIO_LIGiven the fluctuating nature of the pandemic, attitudes of health and social care professionals may change over time. This can be challenging to capture during a single interview, however we did ask questions on how their experience had progressed longitudinally.\nC_LIO_LIOur sample may have been biased towards people who had more free time to participate and so were coping better than others. However, our sample still described a number of stressful experiences during the pandemic, and it is also possible that workers who were frustrated or stressed wished to express their views.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Henry Aughterson", - "author_inst": "University College London" - }, - { - "author_name": "Alison Mckinlay", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Alexandra Burton", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.25.20238675", "rel_title": "Autosomal Dominant Polycystic Kidney Disease does not significantly alter major COVID-19 outcomes among veterans", @@ -1063827,6 +1066157,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.25.20236224", + "rel_title": "The Impact of COVID-19 on Care Seeking Behavior of Patients at Tertiary Care Follow-up Clinics: A Cross-Sectional Telephone Survey. Addis Ababa, Ethiopia.", + "rel_date": "2020-11-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20236224", + "rel_abs": "BackgroundCOVID-19, the disease caused by the new coronavirus SARS-CoV-2 is among the most obscure global pandemics resulting in diverse health and economic disruptions. It adversely affects the routine health care delivery and health service uptake by patients. However, its impact on care-seeking behaviour is largely unknown in Ethiopia.\n\nObjectiveThis study was to determine the impact of the pandemic on care-seeking behaviour of patients with chronic health condition at Tikur Anbessa Specialized hospital in Addis Ababa.\n\nMethodsA cross-sectional hospital-based survey conducted between May and July 2020 on patients whose appointment was between March to June 2020. Sample of 750 patients were approached using phone call and data collection was done using a pretested questionnaire. After cleaning, the data entered in to IBM SPSS software package for analysis.\n\nResultsA total of 644 patients with a median age of 25 years, and M: F ratio of 1:1.01 was described with a response rate of 86%. A loss to follow up, missed medication and death occurred in 70%, 12%, and 1.3% of the patients respectively. In the multivariable logistic regression analysis, patients above 60 years old were more likely to miss follow-up (OR-23.28 (9.32-58.15), P<001). Patients who reported fear of COVID-19 at the hospital were 19 times more likely to miss follow-up (adjusted OR=19.32, 95% CI:10.73-34.79, P<0.001), while patients who reported transportation problems were 6.5 times more likely to miss follow-up (adjusted OR=6.11, 95% CI:3.06-12.17, P<0.001).\n\nConclusionsCOVID-19 pandemic affected the care-seeking behaviour of patients with chronic medical condition adversely and the impact was more pronounced among patients with severe disease, fear of COVID19 and with transportation problems. Education on preventive measures of COVID-19, use of phone clinic and improving chronic illness services at the local health institutions may reduce loss to follow-up among these patients.\n\nWhat is already known?O_LIAs a result of COVID-19, an essential maternal, newborn and child health (MNCH) services in Addis Ababa city showed that first antenatal attendance and under-five pneumonia treatment decreased by 12 and 35%.\nC_LIO_LIA drop in client flow was ascribed to fear of acquiring COVID-19 at health facilities, limited access due to movement restrictions, and dedication of health facilities as COVID-19 treatment centers.\nC_LI\n\nWhat are the new findings?O_LIA cross-sectional hospital-based telephone survey indicated that a loss to follow up, missed medication and death occurred in 70%, 12%, and 1.3% of patients with chronic medical conditions respectively.\nC_LI\n\nWhat do the new findings imply?O_LIFear of COVID-19 and transportation problems are the most commonly stated reasons thus, the finding implies that since health care services to patients with chronic medical conditions is concentrated in specialized referral hospitals mostly aggregated in big cities, patients who travel long distance to get the service are at high risk of Loss to follow up.\nC_LIO_LIStrengthening the chronic care service at a local health institutions, and promoting COVD-19 preventive measures, may help decrease the LTFU and associated complications.\nC_LI", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Tamirat Moges", + "author_inst": "Addis Abeba university" + }, + { + "author_name": "Workeabeba Abebe", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Alemayehu Worku", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Henok Tadele", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Tewodros Haile", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Damte Shimelis", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Desalew Mekonin", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Wondowossen Amogne", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Ayalew Moges", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Abebe Tamire", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Rahel Argaw", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Sewagegn Yeshiwas", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Hyleyesus Adam", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Asrat Dimtse", + "author_inst": "Addis Ababa university" + }, + { + "author_name": "Wakgari Deressaw", + "author_inst": "Addis Ababa university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.11.25.20238600", "rel_title": "Spatially resolved simulations of the spread of COVID-19 in European countries", @@ -1064663,37 +1067068,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.11.24.20237040", - "rel_title": "Rapid environmental monitoring, capture, and destruction activities of SARS-CoV-2 during the Covid-19 health emergency", - "rel_date": "2020-11-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237040", - "rel_abs": "ObjectivesSARS-CoV-2 pandemic is a health emergency for occupational healthcare workers at COVID19 hospital wards in Italy. The objective of the study was to investigate if U-Earth AIRcel bioreactors were effective in monitoring and improving air quality via detection, capture, and destruction of the SARS-CoV-2 virus, reducing the risk of transmission among healthcare workers.\n\nMethodsU-Earth AIRcel bioreactors are a demonstrated effective biomonitoring system. We implemented a methodological approach wherein they were placed at various hospitals treating COVID-19 patients in Italy. The detection of the SARS-CoV-2 virus was achieved through rapid biomonitoring testing of the solutes from the AIRcel bioreactors via SARS-CoV-2 rapid test antigen and consecutive reverse transcription-polymerase chain reaction (RT-PCR) analysis with the multiplex platform (XABT) and the Real-Time PCR Rotor-Gene.\n\nResultsThe marked presence of the SARS-CoV-2 virus was found in multiple water samples via the detection of ORF1ab + N and/or E gene involved in gene expression and cellular signaling of the SARS-CoV virus. The AIRcel bioreactors were able to neutralize the virus effectively as traces of the viruses were no longer found in multiple solute samples after an overnight period.\n\nConclusionsTransmission of COVID-19 via bio-aerosols, transmitted by infected patients, remains a viable threat for health workers. AIRcel bioreactors allow for rapid biomonitoring testing for early virus detection within the environment, reducing the risk of exponential contagion exposure and maintaining good air quality without endangering health workers. This same protocol can also be extended to public spaces as a bio-monitoring tool for hotpots early detection.\n\nKey messagesO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LITransmission of SARS-CoV-2 virus via bio-aerosols is a threat to health care workers. Only few studies have conducted investigations on how to limit the spread of the virus via air purifiers.\nC_LIO_LIExisting studies show a higher risk to health care workers serving at COVID-19 wards with a higher risk of viral transmission.\nC_LI\n\nWhat are the new findings?O_LIIn this study, SARS-CoV-2 virus traces were captured by U-Earth air purifier bioreactor units placed at several hospitals in Italy.\nC_LIO_LIAIRcel bioreactors achieved early detection of the SARS-CoV-2 virus within the environment via rapid biomonitoring testing.\nC_LIO_LIAIRcel bioreactors have proved effective in biomonitoring via the detection, capture, and destruction of SARS-CoV-2 virus through reverse transcription-polymerase chain reaction (RT-PCR) analysis with the multiplex platform (XABT) Multiple Real-Time PCR Rotor-Gene.\nC_LI\n\nHow might this impact on policy or clinical practice in the foreseeable future?O_LIThis study shows the need for effective surveillance and biomonitoring to contain the spread of the SARS-CoV-2 virus. AIRcel bioreactors, an effective occupational surveillance system, can reduce the transmission of the virus to health care workers serving COVID-19 infected patients at hospital wards.\nC_LIO_LIAIRcel bioreactors can also be used in public spaces and other settings, such as schools, to increase the speed of detection of the SARS-CoV-2 virus and improve control of the environment, thereby decreasing the exponential growth of the pandemic.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Roberto Marchetti", - "author_inst": "Laboratori Clodia Diagnostics & Services" - }, - { - "author_name": "Martina Stella", - "author_inst": "Laboratori Clodia Diagnostics & Services" - }, - { - "author_name": "Debjyoti Talukdar", - "author_inst": "Teerthanker Mahaveer University, Moradabad Campus" - }, - { - "author_name": "Rosaria Erika Pileci", - "author_inst": "U-Earth Biotech Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.11.19.20234237", "rel_title": "Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males", @@ -1065205,6 +1067579,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.25.20234195", + "rel_title": "Are we ready for COVID-19's Golden Passport? Insights from a Global Physician Survey", + "rel_date": "2020-11-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20234195", + "rel_abs": "IntroductionCOVID-19 immunity passports could protect the right to free movement, but critics worry about insufficient evidence, privacy, fraud, and discrimination. We aimed to characterize the global physician communitys opinion regarding immunity passports.\n\nMethodsCross sectional, random stratified sample of physicians registered with Sermo, a global networking platform open to verified and licensed physicians. The survey aimed to sample 1,000 physicians divided among the USA, EU and rest of the world. The survey question on immunology asked physicians to offer their insights into whether we know enough about COVID-19 immunity and its duration to offer immunity passports at the present time.\n\nResultsThe survey was completed by 1004 physicians (67 specialties, 40 countries, 49% frontline specialties) with a mean (SD) age of 49.14 (12) years. Overall, 52% answered NO, 17% were UNCERTAIN, and 31% answered YES (P <0.05). EU physicians were more likely to sayYES but even among them it did not exceed 35% approval. US physicians (60%) were more likely to say NO.\n\nConclusionOur findings suggest a current lack of support among physicians for immunity passports. It is hoped that ongoing research and vaccine trials will provide further clarity.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "P. Murali Doraiswamy", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Mohan Chilukuri", + "author_inst": "University of North Carolina School of Medicine" + }, + { + "author_name": "Alexandra Rose Linares", + "author_inst": "Duke University School of Medicine" + }, + { + "author_name": "Katrina A. Bramstedt", + "author_inst": "Bond University Medical Program" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.24.20236661", "rel_title": "A COVID-19 Model for Local Authorities of the United Kingdom", @@ -1066861,101 +1069266,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.25.398008", - "rel_title": "Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection", - "rel_date": "2020-11-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.25.398008", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control SARS-CoV-2 infection remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively which cellular and viral RBPs are involved in SARS-CoV-2 infection. We reveal that the cellular RNA-bound proteome is remodelled upon SARS-CoV-2 infection, having widespread effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Wael Kamel", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland (UK); Department of Biochemistry, University of Oxford, South " - }, - { - "author_name": "Marko Noerenberg", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland (UK); Department of Biochemistry, University of Oxford, South " - }, - { - "author_name": "Berati Cerikan", - "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partne" - }, - { - "author_name": "Honglin Chen", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Aino I. J\u00e4rvelin", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Mohamed Kammoun", - "author_inst": "German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany" - }, - { - "author_name": "Jeff Lee", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Ni Shuai", - "author_inst": "German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany" - }, - { - "author_name": "Manuel Garcia-Moreno", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Anna Andrejeva", - "author_inst": "Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA" - }, - { - "author_name": "Michael J. Deery", - "author_inst": "Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA" - }, - { - "author_name": "Christopher J. Neufeldt", - "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partne" - }, - { - "author_name": "Mirko Cortese", - "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partne" - }, - { - "author_name": "Michael L. Knight", - "author_inst": "Sir William Dunn School of Pathology, University of Oxford, South Parks road, OX1 3RE, Oxford, UK" - }, - { - "author_name": "Kathryn S. Lilley", - "author_inst": "Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA" - }, - { - "author_name": "Javier Martinez", - "author_inst": "Center of Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9/2, 1030, Vienna, Austria" - }, - { - "author_name": "Ilan Davis", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK" - }, - { - "author_name": "Ralf Bartenschlager", - "author_inst": "Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partne" - }, - { - "author_name": "Shabaz Mohammed", - "author_inst": "Department of Biochemistry, University of Oxford, South Parks road, OX1 3QU, Oxford, UK; Department of Chemistry, Chemistry Research Laboratory, Mansfield Road," - }, - { - "author_name": "Alfredo Castello", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland (UK); Department of Biochemistry, University of Oxford, South " - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.21.20236216", "rel_title": "Use of alternative RNA storage and extraction reagents and development of a hybrid PCR-based method for SARS-CoV-2 detection", @@ -1067159,6 +1069469,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.11.23.20236828", + "rel_title": "HIV infection alters SARS-CoV-2 responsive immune parameters but not clinical outcomes in COVID-19 disease", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20236828", + "rel_abs": "There are conflicting reports on the effects of HIV on COVID-19. Here we analyzed disease severity and immune cell changes during and after SARS-CoV-2 infection in 236 participants from South Africa, of which 39% were people living with HIV (PLWH), during the first and second ({beta} dominated) infection waves. The second wave had more PLWH requiring supplemental oxygen relative to HIV negative participants. Higher disease severity was associated with low CD4 T cell counts and higher neutrophil to lymphocyte ratios (NLR). Yet, CD4 counts recovered and NLR stabilized after SARS-CoV-2 clearance in wave 2 infected PLWH, arguing for an interaction between SARS-CoV-2 and HIV infection leading to low CD4 and high NLR. The first infection wave, where severity in HIV negative and PLWH was similar, still showed some HIV modulation of SARS-CoV-2 immune responses. Therefore, HIV infection can synergize with the SARS-CoV-2 variant to change COVID-19 outcomes.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Farina Karim", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Inbal Gazy", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform" + }, + { + "author_name": "Sandile Cele", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Yenzekile Zungu", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Robert Krause", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Mallory Bernstein", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Yashica Ganga", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Hylton Rodel", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Ntombifuthi Mthabela", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Matilda Mazibuko", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Khadija Khan", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Daniel Muema", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Dirhona Ramjit", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Gila Lustig", + "author_inst": "Centre for the AIDS Programme of Research in South Africa" + }, + { + "author_name": "Thumbi Ndung'u", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Willem Hanekom", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Bernadett I Gosnell", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "COMMIT-KZN Team", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Emily Wong", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Mahomed-Yunus S Moosa", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Alasdair Leslie", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Henrik Kloverpris", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2020.11.23.20233155", "rel_title": "Disaggregating Asian Race Reveals COVID-19 Disparities among Asian Americans at New York City's Public Hospital System", @@ -1068439,33 +1070860,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.24.20237644", - "rel_title": "Excess mortality across regions of Europe during the first wave of the COVID-19 pandemic - impact of the winter holiday travelling and government responses", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237644", - "rel_abs": "BackgroundThis aggregated population study of 219 regions in 11 European countries investigated the effect of the seemingly quasi-randomly assigned school winter holiday week on excess mortality associated with the COVID-19 pandemic during spring 2020. A secondary aim was to evaluate the impact of stringency and timing of the government responses to the early inflow of infected cases.\n\nMethodsRegional data on mortality week 14-23 in 2020 compared with the same period 2015-2019 were retrieved from Eurostat and national statistical agencies. Data on initial government responses were obtained from the Oxford COVID-19 Government Response Tracker. Variance-weighted least square regression was used with further adjustment for population density and age distribution.\n\nResultsBeing a region with winter holiday exclusively in week 9 was in the adjusted analysis associated with 16 weekly excess deaths (95% confidence interval 13 to 20) per million inhabitants, which corresponds to 38% of the excess mortality during the study period in these regions. A more stringent response implemented in week 11, corresponding to 10 additional units on the 0-100 ordinal scale, was associated with 20 fewer weekly deaths (95% confidence interval 18 to 22) per million inhabitants.\n\nConclusionsTravelling during winter holiday in week 9 was an amplifying event that contributed importantly to the excess mortality observed in the study area during the spring 2020. Timely government responses to the resulting early inflow of cases was associated with lower excess mortality.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jonas Bjork", - "author_inst": "Lund University" - }, - { - "author_name": "Kristoffer Mattisson", - "author_inst": "Lund University" - }, - { - "author_name": "Anders Ahlbom", - "author_inst": "Karolinska Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.23.20237487", "rel_title": "How closely is COVID-19 related to HCoV, SARS, and MERS? : Clinical comparison of coronavirus infections and identification of risk factors influencing the COVID-19 severity using common data model (CDM)", @@ -1068801,6 +1071195,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.11.23.20235465", + "rel_title": "Mobile outreach testing for COVID-19 in twenty homeless shelters in Toronto, Canada", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20235465", + "rel_abs": "BackgroundIt is unclear what the best strategy is for detecting COVID-19 among homeless shelter residents and what individual factors are associated with positivity.\n\nMethodsWe conducted a retrospective chart audit obtaining repeated cross-sectional data from outreach testing done at homeless shelters between April 1st and July 31st, 2020 in Toronto, Canada. We compared the positivity rate for shelters tested because of an outbreak (at least one known case) versus surveillance (no known cases). A patient-level analysis examined differences in demographic, health, and behavioural characteristics of residents who did and did not test positive for COVID-19.\n\nFindingsOne thousand nasopharyngeal swabs were done on 872 unique residents at 20 shelter locations. Among the 504 tests done in outbreak settings, 69 (14%) were positive and 1 (0.2%) was indeterminate. Among the 496 tests done for surveillance, 11 (2%) were positive and none were indeterminate. Shelter residents who tested positive were significantly less likely to have a health insurance card (54% vs 72%, p=0.03) or have visited another shelter in the last 14 days (0% vs 18%, p<0.01) compared to those who tested negative; There was no association between COVID-19 positivity and medical history (p=0.40) or symptoms (p=0.43).\n\nInterpretationOur findings support testing of asymptomatic shelter residents for COVID-19 when a positive case is identified at the same shelter but suggest limited utility of testing all shelter residents in the absence of a known case. Visiting another shelter in the last 14 days is associated with a decreased risk of COVID-19 positivity.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Tara Kiran", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Amy Craig-Neil", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Paul Das", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Joel Lockwood", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Ri Wang", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Nikki Nathanielsz", + "author_inst": "University of Toronto" + }, + { + "author_name": "Esther Rosenthal", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Carolyn Snider", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Stephen Hwang", + "author_inst": "St. Michael's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.23.20237412", "rel_title": "Reducing travel-related SARS-CoV-2 transmission with layered mitigation measures: Symptom monitoring, quarantine, and testing", @@ -1070073,41 +1072518,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.21.20236117", - "rel_title": "Antibody persistency and dynamic trend after SARS-CoV-2 infection over 8 months", - "rel_date": "2020-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.21.20236117", - "rel_abs": "An improved understanding of the immunity offered by the antibodies developed against SARS-CoV-2 is critical for the development of diagnostic tests and vaccines. Our study aimed at the longitudinal analysis of antibody presence, persistence and its trend over a period of eight months in a group of COVID-19 recovered patients who tested positive by real-time quantitative PCR for SARS-CoV-2 in the period between the 18th and 30th of March, 2020. The subjects were divided into two groups based on disease severity: mild and moderately-severe. The MAGLUMI 2019-nCoV lgM/lgG chemiluminescent analytical system (CLIA) assay was used to analyse the antibody titres. Robust IgG antibody persistency was demonstrated in 76.7 % of the subjects (23 out of 30) at eight months post-infection. The results of this study highlight an important point in terms of the association between humoral immune response and disease severity. Patients who might have experienced a relatively moderate-severe infection may develop a robust immunity that could persist for a longer duration.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Puya Dehgani-Mobaraki", - "author_inst": "Associazione Naso Sano, Italy" - }, - { - "author_name": "Asiya Kamber Zaidi", - "author_inst": "Mahatma Gandhi Memorial Medical College , Indore, India and Member of Associazione Naso Sano,Italy" - }, - { - "author_name": "Annamaria Porreca", - "author_inst": "Department of Economics, University \"G.d'Annunzio\", chieti-Pescara, Italy." - }, - { - "author_name": "Alessandro Floridi", - "author_inst": "Laboratory of Nuclear Lipid BioPathology, Centro Ricerche Analisi Biochimico Specialistiche, Perugia, Italy" - }, - { - "author_name": "Emanuela Floridi", - "author_inst": "Laboratory of Nuclear Lipid BioPathology, Centro Ricerche Analisi Biochimico Specialistiche, Perugia, Italy." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.20.20231696", "rel_title": "Antibody response patterns in COVID-19 patients with different levels of disease severity-Japan", @@ -1070367,6 +1072777,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.18.20234161", + "rel_title": "Peginterferon Lambda-1a for treatment of outpatients with uncomplicated COVID-19: a randomized placebo-controlled trial", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234161", + "rel_abs": "Type III interferons have been touted as promising therapeutics in outpatients with coronavirus disease 2019 (COVID-19). We conducted a randomized placebo-controlled trial in 120 patients with mild to moderate COVID-19 to determine whether a single, 180 mcg subcutaneous dose of Peginterferon Lambda-1a (Lambda) could shorten the duration of viral shedding (primary endpoint) or symptoms (secondary endpoint, NCT04331899). In both the 60 patients receiving Lambda and the 60 receiving placebo, the median time to cessation of viral shedding was 7 days (hazard ratio [HR] = 0.81; 95% confidence interval [CI] 0.56 to 1.19). Symptoms resolved in 8 and 9 days in Lambda and placebo, respectively (HR 0.94; 95% CI 0.64 to 1.39). At enrollment; 41% of subjects were SARS-CoV-2 IgG seropositive; compared to placebo, lambda tended to delay shedding cessation in seronegatives (aHR 0.66, 95% CI 0.39-1.10) and to hasten shedding cessation in seropositives (aHR 1.58, 95% CI 0.88-2.86; p for interaction = 0.03). Liver transaminase elevations were more common in the Lambda vs. placebo arm (15/60 vs 5/60; p = 0.027). In this study, a single dose of subcutaneous Peginterferon Lambda-1a neither shortened the duration of SARS-CoV-2 viral shedding nor improved symptoms in outpatients with uncomplicated COVID-19.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Prasanna Jagannathan", + "author_inst": "Stanford University" + }, + { + "author_name": "Jason Andrews", + "author_inst": "Stanford University" + }, + { + "author_name": "Hector Bonilla", + "author_inst": "Stanford University" + }, + { + "author_name": "Haley Hedlin", + "author_inst": "Stanford University" + }, + { + "author_name": "Karen Jacobson", + "author_inst": "Stanford University" + }, + { + "author_name": "Vidhya Balasubramanian", + "author_inst": "Stanford University" + }, + { + "author_name": "Natasha Purington", + "author_inst": "Stanford University" + }, + { + "author_name": "Savita Kamble", + "author_inst": "Stanford University" + }, + { + "author_name": "Christiaan de Vries", + "author_inst": "Stanford University" + }, + { + "author_name": "Orlando Quintero", + "author_inst": "Stanford University" + }, + { + "author_name": "Kent Feng", + "author_inst": "Stanford University" + }, + { + "author_name": "Catherine Ley", + "author_inst": "Stanford University" + }, + { + "author_name": "Dean Winslow", + "author_inst": "Stanford University" + }, + { + "author_name": "Jennifer Newberry", + "author_inst": "Stanford University" + }, + { + "author_name": "Karlie Edwards", + "author_inst": "Stanford University" + }, + { + "author_name": "Colin Hislop", + "author_inst": "Eiger BioPharmaceuticals" + }, + { + "author_name": "Ingrid Choong", + "author_inst": "Eiger BioPharmaceuticals" + }, + { + "author_name": "Yvonne Maldonado", + "author_inst": "Stanford University" + }, + { + "author_name": "Jeffrey Glenn", + "author_inst": "Stanford University" + }, + { + "author_name": "Ami Bhatt", + "author_inst": "Stanford University" + }, + { + "author_name": "Catherine Blish", + "author_inst": "Stanford University" + }, + { + "author_name": "Taia Wang", + "author_inst": "Stanford University" + }, + { + "author_name": "Chaitan Khosla", + "author_inst": "Stanford University" + }, + { + "author_name": "Benjamin Pinsky", + "author_inst": "Stanford University" + }, + { + "author_name": "Manisha Desai", + "author_inst": "Stanford University" + }, + { + "author_name": "Julie Parsonnet", + "author_inst": "Stanford University" + }, + { + "author_name": "Upinder Singh", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.20.20232140", "rel_title": "Persisting antibody response to SARS-CoV-2 in a local Austrian population", @@ -1071495,81 +1074028,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.11.23.393967", - "rel_title": "Building a virtual summer research experience in cancer for high school and early undergraduate students: lessons from the COVID-19 pandemic", - "rel_date": "2020-11-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.23.393967", - "rel_abs": "BackgroundThe COVID-19 pandemic posed a unique challenge for summer research programs in 2020, particularly for programs aimed at hands-on experience for younger trainees. The Indiana University Melvin and Bren Simon Comprehensive Cancer Center supports two pipeline programs, which traditionally immerse high school juniors, seniors, and early undergraduate students from underrepresented populations in science in hands-on projects in cancer biology labs. However, due to social distancing policies during the pandemic and reduction of research operations, these students were not physically allowed on campus. Thus, the authors set out to strategically pivot to a wholly virtual curriculum and evaluate the Virtual Summer Research Experience in Cancer outcomes.\n\nMethodsThe virtual program included four components: 1. a core science and professional development curriculum led by high school teachers and senior undergraduates; 2. faculty-delivered didactic sessions on cancer science; 3. mentored, virtual research projects with research faculty; and 4. online networking events to encourage vertical mentoring. Outcomes data were measured using an 11-item Research Preparation scale, daily electronic feedback, and structured evaluation and feedback via Zoom weekly.\n\nResultsOutcome data suggested high self-reported satisfaction with the virtual program. Outcome data also revealed the importance of coordination between multiple entities for seamless program implementation. This includes the active recruitment and participation of high school teachers and further investment in information technology capabilities of institutions.\n\nConclusionsFindings reveal a path to educate and train high school and early undergraduate students in cancer research when hands-on, in-person training is not feasible. Virtual research experiences are not only useful to engage students during public health crises but can provide an avenue for cancer centers to expand their cancer education footprints to remotely located schools and universities with limited resources to provide such experiences to their students.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Timothy W Corson", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Shannon M Hawkins", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Elmer Sanders", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Jessica Byram", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Leigh-Ann Cruz", - "author_inst": "Riverside High School" - }, - { - "author_name": "Jacob Olson", - "author_inst": "Decatur Central High School" - }, - { - "author_name": "Emily Speidell", - "author_inst": "Decatur Central High School" - }, - { - "author_name": "Rose Schnabel", - "author_inst": "Indiana University" - }, - { - "author_name": "Adhitya Balaji", - "author_inst": "Indiana University" - }, - { - "author_name": "Osas Ogbeide", - "author_inst": "Indiana University" - }, - { - "author_name": "Julie Dinh", - "author_inst": "Indiana University" - }, - { - "author_name": "Amy Hinshaw", - "author_inst": "Lawrence Township Schools" - }, - { - "author_name": "Laura Cummings", - "author_inst": "Herron High School" - }, - { - "author_name": "Vicki Bonds", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Harikrishna Nakshatri", - "author_inst": "Indiana University School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2020.11.20.20235440", "rel_title": "Coagulation factors and COVID-19 severity: Mendelian randomization analyses and supporting evidence", @@ -1071801,6 +1074259,233 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, + { + "rel_doi": "10.1101/2020.11.19.20234120", + "rel_title": "Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234120", + "rel_abs": "Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "Liam Gaziano", + "author_inst": "VA Boston Healthcare System, University of Cambridge" + }, + { + "author_name": "Claudia Giambartolomei", + "author_inst": "Instituto Italiano di Tecnologia, University of California Los Angeles" + }, + { + "author_name": "Alexandre C Pereira", + "author_inst": "University of Sao Paulo, Harvard University" + }, + { + "author_name": "Anna Gaulton", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute" + }, + { + "author_name": "Daniel C Posner", + "author_inst": "VA Boston Healthcare System" + }, + { + "author_name": "Sonja A Swanson", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Yuk Lam Ho", + "author_inst": "VA Boston Healthcare System" + }, + { + "author_name": "Sudha K Iyengar", + "author_inst": "Case Western Reserve University and Louis Stoke Cleveland VAMC" + }, + { + "author_name": "Nicole M Kosik", + "author_inst": "VA Boston Healthcare System" + }, + { + "author_name": "Marijana Vujkovic", + "author_inst": "The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "David R Gagnon", + "author_inst": "Boston University, VA Boston Healthcare System" + }, + { + "author_name": "A Patricia Bento", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute" + }, + { + "author_name": "Pedro Beltrao", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute" + }, + { + "author_name": "Inigo Barrio Hernandez", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute" + }, + { + "author_name": "Lars Ronnblom", + "author_inst": "Uppsala University" + }, + { + "author_name": "Niklas Hagberg", + "author_inst": "Uppsala University" + }, + { + "author_name": "Christian Lundtoft", + "author_inst": "Uppsala University" + }, + { + "author_name": "Claudia Langenberg", + "author_inst": "Charite University Medicine Berlin, Universityof Cambridge" + }, + { + "author_name": "Maik Pietzner", + "author_inst": "Universityof Cambridge" + }, + { + "author_name": "Dennis Valentine", + "author_inst": "University College London" + }, + { + "author_name": "Elias Allara", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Praveen Surendran", + "author_inst": "Wellcome Genome Campus and University of Cambridge" + }, + { + "author_name": "Stephen Burgess", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Jing Hua Zhao", + "author_inst": "University of Cambridge" + }, + { + "author_name": "James E Peters", + "author_inst": "Imperial College London" + }, + { + "author_name": "Bram P Prins", + "author_inst": "Wellcome Genome Campus and University of Cambridge" + }, + { + "author_name": "John Danesh", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Poornima Devineni", + "author_inst": "VA Boston Healthcare System" + }, + { + "author_name": "Yunling Shi", + "author_inst": "VA Boston Healthcare System" + }, + { + "author_name": "Kristine E Lynch", + "author_inst": "VA Salt Lake City Health Care System, University of Utah" + }, + { + "author_name": "Scott L DuVall", + "author_inst": "VA Salt Lake City Health Care System, University of Utah" + }, + { + "author_name": "Helene Garcon", + "author_inst": "VA Boston Healthcare System" + }, + { + "author_name": "Lauren Thomann", + "author_inst": "VA Boston Healthcare System" + }, + { + "author_name": "Jin J Zhou", + "author_inst": "University of Arizona, Phoenix VA Health Care System" + }, + { + "author_name": "Bryan R Gorman", + "author_inst": "VA Boston Healthcare System" + }, + { + "author_name": "Jennifer E Huffman", + "author_inst": "VA Boston Healthcare System" + }, + { + "author_name": "Christopher J O'Donnell", + "author_inst": "VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Philip S Tsao", + "author_inst": "VA Palo Alto Health Care System, Stanford University School of Medicine" + }, + { + "author_name": "Jean C Beckham", + "author_inst": "Durham VA Medical Center, Duke University School of Medicine" + }, + { + "author_name": "Saiju Pyarajan", + "author_inst": "VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Sumitra Muralidhar", + "author_inst": "Department of Veterans Affairs" + }, + { + "author_name": "Grant D Huang", + "author_inst": "Department of Veterans Affairs" + }, + { + "author_name": "Rachel Ramoni", + "author_inst": "Department of Veterans Affairs" + }, + { + "author_name": "Adriana M Hung", + "author_inst": "Department of Veterans Affairs, Vanderbilt University" + }, + { + "author_name": "Kyong-Mi Chang", + "author_inst": "The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania" + }, + { + "author_name": "Yan V Sun", + "author_inst": "Atlanta VA Health Care System, Emory University Rollins School of Public Health" + }, + { + "author_name": "Jacob Joseph", + "author_inst": "VA Boston Healthcare System and Brigham & Women's Hospital" + }, + { + "author_name": "Andrew R Leach", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute" + }, + { + "author_name": "Todd L Edwards", + "author_inst": "Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center" + }, + { + "author_name": "Kelly Cho", + "author_inst": "VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "J Michael Gaziano", + "author_inst": "VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Adam S Butterworth", + "author_inst": "University of Cambridge, Wellcome Genome Campus and University of Cambridge" + }, + { + "author_name": "Juan P Casas", + "author_inst": "VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.20.20235903", "rel_title": "Modeling the spread of Covid-19 under active management", @@ -1073665,81 +1076350,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.18.20233932", - "rel_title": "REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020", - "rel_date": "2020-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20233932", - "rel_abs": "BackgroundEngland is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020.\n\nMethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020.\n\nResultsOverall weighted prevalence of infection in the community in England was 1.3% or 130 people per 10,000 infected, up from 60 people per 10,000 in the round 5 report (18th September to 5th October 2020), doubling every 24 days on average since the prior round. The corresponding R number was estimated to be 1.2. Prevalence of infection was highest in North West (2.4%, up from 1.2%), followed by Yorkshire and The Humber (2.3% up from 0.84%), West Midlands (1.6% up from 0.60%), North East (1.5% up from 1.1%), East Midlands (1.3% up from 0.56%), London (0.97%, up from 0.54%), South West (0.80% up from 0.33%), South East (0.69% up from 0.29%), and East of England (0.69% up from 0.30%). Rapid growth in the South observed in the first half of round 6 was no longer apparent in the second half of round 6. We also observed a decline in prevalence in Yorkshire and The Humber during this period. Comparing the first and second halves of round 6, there was a suggestion of decline in weighted prevalence in participants aged 5 to 12 years and in those aged 25 to 44 years. While prevalence remained high, in the second half of round 6 there was suggestion of a slight fall then rise that was seen nationally and also separately in both the North and the South.\n\nConclusionThe impact of the second national lockdown in England is not yet known. We provide here a detailed description of swab-positivity patterns at national, regional and local scales for the period immediately preceding lockdown, against which future trends in prevalence can be evaluated.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Steven Riley", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Kylie E. C. Ainslie", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Oliver Eales", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Caroline E. Walters", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Haowei Wang", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Christina Atchinson", - "author_inst": "School of Public Health, Imperial College London, UK" - }, - { - "author_name": "Claudio Fronterre", - "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" - }, - { - "author_name": "Peter J. Diggle", - "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" - }, - { - "author_name": "Deborah Ashby", - "author_inst": "School of Public Health, Imperial College London, UK" - }, - { - "author_name": "Christl A Donnelly", - "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" - }, - { - "author_name": "Graham Cooke", - "author_inst": "Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic" - }, - { - "author_name": "Wendy Barclay", - "author_inst": "Department of Infectious Disease, Imperial College London, UK" - }, - { - "author_name": "Helen Ward", - "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" - }, - { - "author_name": "Ara Darzi", - "author_inst": "Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a" - }, - { - "author_name": "Paul Elliott", - "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.17.20231290", "rel_title": "Secondary Attack Rate (SAR) in household contacts of expired primary cases of COVID-19: A study from Western India", @@ -1074047,6 +1076657,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.18.20233288", + "rel_title": "CLINICAL APPLICATIONS OF MACHINE LEARNING ON COVID-19: THE USE OF A DECISION TREE ALGORITHM FOR THE ASSESSMENT OF PERCEIVED STRESS IN MEXICAN HEALTHCARE PROFESSIONALS.", + "rel_date": "2020-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20233288", + "rel_abs": "Stress and anxiety have shown to be indirect effects of the COVID-19 pandemic, therefore managing stress becomes essential. One of the most affected populations by the pandemic are healthcare professionals. Thus, it is paramount to understand and categorize their perceived levels of stress, as it can be a detonating factor leading to mental illness. In our study, we used a machine learning prediction model to help measure perceived stress; a C5.0 decision tree algorithm was used to analyze and classify datasets obtained from healthcare professionals of the northeast region of Mexico. Our analysis showed that 6 out of 102 instances were incorrectly classified. Missing two cases for mild, three for moderate and 1 for severe (accuracy of 94.1%), statistical correlation analysis was performed to ensure integrity of the method, in addition we concluded that severe stress cases can be related mostly to high levels of Xenophobia and Compulsive stress.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Juan Luis Delgado-Gallegos", + "author_inst": "Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Gener Aviles-Rodriguez", + "author_inst": "Universidad Autonoma de Baja California" + }, + { + "author_name": "Gerardo Raymundo Padilla-Rivas", + "author_inst": "Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Maria de los Angeles Cosio-Leon", + "author_inst": "Univerisdad Politecnica de Pachuca" + }, + { + "author_name": "Hector Franco-Villareal", + "author_inst": "Althian" + }, + { + "author_name": "Erika Zuniga-Violante", + "author_inst": "Universidad de Montemorelos" + }, + { + "author_name": "Gerardo Salvador Romo-Cardenas", + "author_inst": "Universidad Autonoma de Baja California" + }, + { + "author_name": "Jose Francisco Islas-Cisneros", + "author_inst": "Universidad Autonoma de Nuevo Leon" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.17.20233726", "rel_title": "Risk of evolutionary escape from neutralizing antibodies targeting SARS-CoV-2 spike protein", @@ -1075619,41 +1078276,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.18.20234088", - "rel_title": "Knowledge and perceptions on COVID-19 among Senior High School students in Ghana: a cross-sectional study", - "rel_date": "2020-11-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234088", - "rel_abs": "BackgroundThe COVID-19 pandemic is associated with high morbidity and mortality. In Ghana, policy interventions have been implemented by the Government to combat the pandemic. However, the knowledge and perceptions of Senior High School students are not investigated on the COVID-19 symptoms, transmission and the government policy measures.\n\nObjectivesThe present study surveyed senior high school students to assess their knowledge and perceptions of COVID-19 and the government policy measures to address the outbreak.\n\nMethodsThe study employed a descriptive cross-sectional study design to assess the knowledge and perceptions of senior high school students on the COVID-19 pandemic and the measures put in place to address it. 624 senior high school students aged 18 years old and above were surveyed. Descriptive analysis was performed to assess knowledge and perceptions of COVID-19 symptoms, mode of transmissions and prevention.\n\nFindingsMost students were knowledgeable about COVID-19 symptoms, transmission and preventive measures. Majority of the students obtained information about COVID-19 from television, radio, social media, and from family and friends. Overall, the students also demonstrated a positive perception towards COVID-19 mode of transmission and preventive measures.\n\nConclusionsOverall, senior high school students in the Bawku Municipality in Ghana demonstrated an appreciable level of knowledge and positive perception of COVID-19. Students cited television, radio, peer education and social media as their information sources for COVID-19. These media outlets should be prioritized in disseminating COVID 19 information to the public, especially students.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Isaac Bador kamal Lettor", - "author_inst": "Bawku Technical Institute" - }, - { - "author_name": "Paschal Awingura Apanga", - "author_inst": "University of Nevada, Reno, School of Community of Health Sciences, Reno, USA" - }, - { - "author_name": "Maxwell Tii Kumbeni", - "author_inst": "Ghana Health Service, Nabdam District Health Directorate, Nangodi, Ghana" - }, - { - "author_name": "Ramatu Akunvane", - "author_inst": "Nursing and Midwifery Training College, Zuarungu, Upper East Region, Ghana" - }, - { - "author_name": "Robert Akparibo", - "author_inst": "School of Health and Related Research (ScHARR), University of Sheffield, Sheffield, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.19.20234716", "rel_title": "A precise measure of the impact of the first wave of Covid-19 on life expectancy. Regional differentials in Switzerland", @@ -1075949,6 +1078571,61 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.11.18.388868", + "rel_title": "Improved production of SARS-CoV-2 spike receptor-binding domain (RBD) for serology assays", + "rel_date": "2020-11-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.18.388868", + "rel_abs": "The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a commonly used antigen for serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Different versions of the RBD protein have been developed and utilized in assays, with higher sensitivity attributed to particular forms of the protein. To improve the yield of these high-sensitivity forms of RBD and support the increased demand for this antigen in serology assays, we investigated several protein expression variables including DNA elements such as promoters and signal peptides, cell culture expression parameters, and purification processes. Through this investigation, we developed a simplified and robust purification strategy that consistently resulted in high levels of the high-sensitivity form of RBD and demonstrated that a carboxyterminal tag is responsible for the increased sensitivity in the ELISA. These improved reagents and processes produce high-quality proteins which are functional in serology assays and can be used to investigate seropositivity to SARS-CoV-2 infection.\n\nHighlights: O_LIImproved yields of SARS-CoV-2 spike RBD through modification of DNA constructs and purification parameters\nC_LIO_LITwo versions of RBD show different sensitivity in serology assays\nC_LIO_LIYields of greater than 50 mg/l obtained under optimal conditions\nC_LIO_LIMagnetic bead purification technology improves throughput of protein production\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jennifer Mehalko", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Matthew Drew", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Kelly Snead", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "John-Paul Denson", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Vanessa Wall", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Troy Taylor", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Kaitlyn Sadtler", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Simon Messing", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "William Gillette", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Dominic Esposito", + "author_inst": "Frederick National Laboratory for Cancer Research" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.11.15.20229971", "rel_title": "Genetic Liability to Cannabis Use Disorder and COVID-19 Hospitalization", @@ -1077229,93 +1079906,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.16.20232835", - "rel_title": "Convalescent COVID-19 patients are susceptible to endothelial dysfunction due to persistent immune activation", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232835", - "rel_abs": "The rapid rise of coronavirus disease 2019 patients who suffer from vascular events after their initial recovery is expected to lead to a worldwide shift in disease burden. We aim to investigate the impact of COVID-19 on the pathophysiological state of blood vessels in convalescent patients. Here, convalescent COVID-19 patients with or without preexisting conditions (i.e. hypertension, diabetes, hyperlipidemia) were compared to non-COVID-19 patients with matched cardiovascular risk factors or healthy participants. Convalescent patients had elevated circulating endothelial cells (CECs), and those with underlying cardiovascular risk had more pronounced endothelial activation hallmarks (ICAM1, P-selectin or CX3CL1) expressed by CECs. Multiplex microbead-based immunoassays revealed some levels of cytokine production sustained from acute infection to recovery phase. Several proinflammatory and activated T lymphocyte-associated cytokines correlated positively with CEC measures, implicating cytokine-driven endothelial dysfunction. Finally, the activation markers detected on CECs mapped to the counter receptors (i.e. ITGAL, SELPLG, and CX3CR1) found primarily on CD8+ T cells and natural killer cells, suggesting that activated endothelial cells could be targeted by cytotoxic effector cells. Clinical trials in preventive therapy for post-COVID-19 vascular complications may be needed.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC=\"FIGDIR/small/20232835v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (19K):\norg.highwire.dtl.DTLVardef@d34a61org.highwire.dtl.DTLVardef@1b82feeorg.highwire.dtl.DTLVardef@152ea88org.highwire.dtl.DTLVardef@a3b382_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Florence WJ Chioh", - "author_inst": "Nanyang Technological University Singapore, Lee Kong Chian School of Medicine" - }, - { - "author_name": "Siew-Wai Fong", - "author_inst": "Singapore Immunology Network, A*STAR" - }, - { - "author_name": "Barnaby Young", - "author_inst": "National Centre for Infectious Diseases, Singapore" - }, - { - "author_name": "Kan-Xing Wu", - "author_inst": "Nanyang Technological University Singapore, Lee Kong Chian School of Medicine" - }, - { - "author_name": "Anthony Siau", - "author_inst": "Nanyang Technological University Singapore" - }, - { - "author_name": "Shuba Krishnan", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Yi-Hao Chan", - "author_inst": "Singapore Immunology Network" - }, - { - "author_name": "Louis LY Teo", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Fei Gao", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Ru San Tan", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Liang Zhong", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Angela SM Koh", - "author_inst": "National Heart Centre Singapore" - }, - { - "author_name": "Seow Yen Tan", - "author_inst": "Changi General Hospital" - }, - { - "author_name": "Paul A Tambyah", - "author_inst": "National University Hospital, Singapore" - }, - { - "author_name": "Laurent Renia", - "author_inst": "A-Star" - }, - { - "author_name": "Lisa F. P. Ng", - "author_inst": "Singapore Immunology Network" - }, - { - "author_name": "David Chien Boon Lye", - "author_inst": "National Centre of Infectious Diseases" - }, - { - "author_name": "Christine Cheung", - "author_inst": "Nanyang Technological University Singapore" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.11.17.20220681", "rel_title": "An efficient distributed algorithm with application to COVID-19 data from heterogeneous clinical sites", @@ -1077559,6 +1080149,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.18.20233833", + "rel_title": "COVID-19 patients and cancer in northern Italy", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20233833", + "rel_abs": "The aim of this population-based study was to evaluate the impact of having had cancer on COVID-19 risk and prognosis during the first wave of the pandemic (27 February - 13 May 2020) in Reggio Emilia Province. Prevalent cancer cases diagnosed between 1996 and December 2019 were linked with the provincial COVID-19 surveillance system. We compared cancer survivors (CS) cumulative incidence of being tested, testing positive for SARS-CoV-2, being hospitalized, and dying of COVID-19 with that of the general population; we compared COVID-19 prognosis in CS and in patients without cancer.\n\n15,391 people (1527 CS) underwent RT-PCR for SARS-CoV-2, of whom 4541 (447 CS) tested positive; 541 (113 CS) died of COVID-19. The cumulative incidences of being tested, testing positive, COVID-19 hospitalization, and death were lower in CS: age- and sex-adjusted incidence rate ratios were 1.28 [95%CI = 1.21, 1.35], 1.06 [95%CI = 0.96, 1.18], 1.27 [95%CI = 1.09, 1.48], and 1.39 [95%CI = 1.12, 1.71], respectively. CS had worse prognosis when diagnosed with COVID-19, particularly those below the age of 70 (age- and sex-adjusted odds ratio (OR) of death 5.03; [95%CI = 2.59, 9.75]), while the OR decreased after age 70. The OR of death was higher for patients with a recent diagnosis, i.e. <2 years (OR=2.92; 95%CI = 1.64, 5.21), or metastases (OR=2.09; 95%CI = 0. 88, 4.93).\n\nCancer patients showed the same probability of being infected, despite a slightly higher probability of being tested, than the general population, nevertheless they were at higher risk of death once infected.\n\nNovelty and impactCancer survivors during the first wave of the pandemic showed higher COVID-19 cumulative incidence and mortality. When infected, they had worse prognosis, particularly in people younger than age 70 or those with a recent diagnosis.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Lucia Mangone", + "author_inst": "AUSL-IRCCS Reggio Emilia" + }, + { + "author_name": "Francesco Gioia", + "author_inst": "AUSL-IRCCS Reggio Emilia" + }, + { + "author_name": "Pamela Mancuso", + "author_inst": "AUSL-IRCCS Reggio Emilia" + }, + { + "author_name": "Isabella Bisceglia", + "author_inst": "AUSL-IRCCS Reggio Emilia" + }, + { + "author_name": "Marta Ottone", + "author_inst": "AUSL-IRCCS Reggio Emilia" + }, + { + "author_name": "Massimo Vicentini", + "author_inst": "AUSL-IRCCS Reggio Emilia" + }, + { + "author_name": "Carmine Pinto", + "author_inst": "AUSL-IRCCS Reggio Emilia" + }, + { + "author_name": "Paolo Giorgi Rossi", + "author_inst": "AUSL-IRCCS Reggio Emilia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.17.20226407", "rel_title": "Using A Socio-Ecological System (SES) Framework to Explain Factors Influencing Countries Success Level in Curbing COVID-19", @@ -1078523,41 +1081160,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.17.20210211", - "rel_title": "The impacts of COVID-19 mitigation on dengue virus transmission: a modelling study", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20210211", - "rel_abs": "BackgroundThe COVID-19 pandemic has induced unprecedented reductions in human mobility and social contacts throughout the world. Because dengue virus (DENV) transmission is strongly driven by human mobility, behavioral changes associated with the pandemic have been hypothesized to impact dengue incidence. By discouraging human contact, COVID-19 control measures have also disrupted dengue vector control interventions, the most effective of which require entry into homes.\n\nMethodWe used an agent-based model with a realistic treatment of human mobility and vector control to investigate how and why dengue incidence could differ under a lockdown scenario with a proportion of the population sheltered at home.\n\nResultWe found that a lockdown in which 70% of the population sheltered at home led to a small average increase in cumulative DENV infections of up to 10%, depending on the time of year lockdown occurred. Lockdown had a more pronounced effect on the spatial distribution of DENV infections, with higher incidence under lockdown in regions with high mosquito abundance. Transmission was also more focused in homes following lockdown. The proportion of people infected in their own home rose from 54% under normal conditions to 66% under lockdown, and the household secondary attack rate rose from 0.109 to 0.128, a 17% increase. When we considered that lockdown measures could disrupt regular, city-wide vector control campaigns, the increase in incidence was more pronounced than with lockdown alone, especially if lockdown occurred at the optimal time for vector control.\n\nDiscussionOur results indicate that an unintended outcome of COVID-19 control measures may be to adversely alter the epidemiology of dengue. This observation has important implications for an improved understanding of dengue epidemiology and effective application of dengue vector control. When coordinating public health responses during a syndemic, it is important to monitor multiple infections and understand that an intervention against one disease may exacerbate another.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sean M. Cavany", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Guido Espa\u00f1a", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Gonzalo M Vazquez-Prokopec", - "author_inst": "Emory University" - }, - { - "author_name": "Thomas W Scott", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Alex Perkins", - "author_inst": "University of Notre Dame" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.16.20232900", "rel_title": "High throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county", @@ -1078841,6 +1081443,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2020.11.17.20233023", + "rel_title": "Resuming professional football during the Covid-19 pandemic in a country with high infection ratesA prospective cohort study", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20233023", + "rel_abs": "ObjectivesThe risk of viral transmission associated with contact sports such as football (soccer) during the COVID-19 pandemic is unknown. The aim of this study was to describe the infective and immune status of professional football players, team staff and league officials over a truncated football season resumed at the height of the COVID-19 pandemic in a country with high infection rates and to investigate the clinical symptoms related to COVID-19 infection in professional football players.\n\nMethodsProspective cohort study of 1337 football players, staff and officials during a truncated football season (9 weeks) with a tailored infection control program based on preventive measures and regular SARS-CoV-2 PCR swab testing (every 3-5 days) combined with serology testing for immunity (every 4 weeks). Clinical symptoms in positive participants were recorded using a 26-item, Likert-scale-based scoring system.\n\nResultsDuring the study period, 85 subjects returned positive (cycle threshold (cT)[≤]30) or reactive (3030%), and comparatively stable rates among community-dwelling adults. Our findings substantiate reports suggesting that hospitalizations for nursing home residents with COVID-19 were low during the peak of the pandemics first wave in Canada, which may have contributed to the particularly high concentration of COVID-19 mortality in Ontarios nursing homes.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Kevin A Brown", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Nick Daneman", + "author_inst": "Department of Medicine, University of Toronto" + }, + { + "author_name": "Sarah A Buchan", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Adrienne K Chan", + "author_inst": "Department of Medicine, University of Toronto" + }, + { + "author_name": "Nathan M Stall", + "author_inst": "Department of Medicine, University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.05.20222596", "rel_title": "A lateral flow test detecting SARS-CoV-2 neutralizing antibodies", @@ -1094789,41 +1097830,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.07.20227512", - "rel_title": "Vitamin D - contrary to vitamin K - does not associate with clinical outcome in hospitalized COVID-19 patients", - "rel_date": "2020-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227512", - "rel_abs": "SARS-CoV-2 causes remarkably variable disease from asymptomatic individuals to respiratory insufficiency and coagulopathy. Vitamin K deficiency was recently found to associate with clinical outcome in a cohort of COVID-19 patients. Vitamin D has been hypothesized to reduce disease susceptibility by modulating inflammation, yet little is known about its role in disease severity. Considering the critical interaction between vitamin K and vitamin D in calcium and elastic fiber metabolism, we determined vitamin D status in the same cohort of 135 hospitalized COVID-19 patients by measuring blood 25(OH)D levels. We found no difference in vitamin D status between those with good and poor outcome (defined as intubation and/or death). Instead, we found vitamin D sufficient persons (25(OH)D >50 nmol/L) had accelerated elastic fiber degradation compared to those with mild deficiency (25(OH)D 25-50 nmol/L). Based on these findings, we hypothesize that vitamin D might have both favorable anti-inflammatory and unfavorable pro-calcification effects during COVID-19 and that vitamin K might compensate for the latter.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jona Walk", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - }, - { - "author_name": "Anton SM Dofferhoff", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - }, - { - "author_name": "Jody MW van den Ouweland", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - }, - { - "author_name": "Henny van Daal", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - }, - { - "author_name": "Rob Janssen", - "author_inst": "Canisius Wilhelmina Ziekenhuis" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.07.20201335", "rel_title": "Socio-economic disparities in social distancing during the COVID-19 pandemic in the United States", @@ -1095031,6 +1098037,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.11.09.374272", + "rel_title": "Single cell transcriptomic re-analysis of immune cells in bronchoalveolar lavage fluids reveals the correlation of B cell characteristics and disease severity of patients with SARS-CoV-2 infection", + "rel_date": "2020-11-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.09.374272", + "rel_abs": "The COVID-19 pandemic (SARS-CoV-2) is a global infectious disease with rapid spread. Some patients have severe symptoms and clinical signs caused by an excessive inflammatory response, which increases the risk of mortality. In this study, we reanalyzed scRNA-seq data of cells from bronchoalveolar lavage fluids of patients with COVID-19 with mild and severe symptoms, focusing on antibody-producing cells. In patients with severe disease, B cells seemed to be more activated and expressed more immunoglobulin genes compared with cells from patients with mild disease, and macrophages expressed higher levels of the TNF superfamily member B-cell activating factor but not of APRIL (a proliferation-inducing ligand). In addition, macrophages from patients with severe disease had increased pro-inflammatory features and pathways associated with Fc receptor-mediated signaling, compared with patients with mild disease. CCR2-positive plasma cells accumulated in patients with severe disease, probably because of increased CCL2 expression on macrophages from patients with severe disease. Together, these results support that different characteristics of B cells might affect the severity of COVID-19 infection.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Chae Won Kim", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Ji Eun Oh", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Heung Kyu Lee", + "author_inst": "Korea Advanced Institute of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.11.09.374603", "rel_title": "The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways", @@ -1096782,41 +1099815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.05.20226605", - "rel_title": "Alzheimer's and Parkinson's diseases predict different COVID-19 outcomes, a UK Biobank study", - "rel_date": "2020-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226605", - "rel_abs": "In December 2019, a coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began infecting humans causing a novel disease, coronavirus disease 19 (COVID-19). This was first described in the Wuhan province of the Peoples Republic of China. SARS-CoV-2 spread throughout the world causing a global pandemic. To date, thousands of cases of COVID-19 were reported in the United Kingdom, and over 45,000 patients have died. Some progress has been achieved in managing this disease, but the biological determinants of health, besides age, that affect COVID-19 infectivity and mortality are under scrutiny. Recent studies show that several medical conditions, including diabetes and hypertension, increase the risk of COVID-19 infection and death. The increased vulnerability of the elderly and those with comorbidities, together with the prevalence of neurodegenerative diseases with advanced age, led us to investigate the links between neurodegeneration and COVID-19. We analysed the primary health records of 13,338 UK individuals tested for COVID-19 between March and July 2020. We show that a pre-existing diagnosis of Alzheimers disease predicts the highest risk of COVID-19 infection and mortality among the elderly. In contrast, Parkinsons disease patients were found to be at increased risk of infection but not mortality from COVID-19. We conclude that there are disease-specific differences in COVID-19 susceptibility among patients affected by neurodegenerative disorders.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yizhou Yu", - "author_inst": "University ofCambridge" - }, - { - "author_name": "Marco Travaglio", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Rebeka Popovic", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Nuno Santos Leal", - "author_inst": "University of Cambridge" - }, - { - "author_name": "L. Miguel Martins", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.06.20227017", "rel_title": "Predicting the impact of disruptions in lymphatic filariasis elimination programmes due to the outbreak of coronavirus disease (COVID-19) and possible mitigation strategies", @@ -1097176,6 +1100174,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.11.06.20226969", + "rel_title": "Interventions targeting nonsymptomatic cases can be important to prevent local outbreaks: COVID-19 as a case-study", + "rel_date": "2020-11-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20226969", + "rel_abs": "During infectious disease epidemics, an important question is whether cases travelling to new locations will trigger local outbreaks. The risk of this occurring depends on the transmissibility of the pathogen, the susceptibility of the host population and, crucially, the effectiveness of surveillance in detecting cases and preventing onward spread. For many pathogens, transmission from presymptomatic and/or asymptomatic (together referred to as nonsymptomatic) infectious hosts can occur, making effective surveillance challenging. Here, using SARS-CoV-2 as a case-study, we show how the risk of local outbreaks can be assessed when nonsymptomatic transmission can occur. We construct a branching process model that includes nonsymptomatic transmission, and explore the effects of interventions targeting nonsymptomatic or symptomatic hosts when surveillance resources are limited. We consider whether the greatest reductions in local outbreak risks are achieved by increasing surveillance and control targeting nonsymptomatic or symptomatic cases, or a combination of both. We find that seeking to increase surveillance of symptomatic hosts alone is typically not the optimal strategy for reducing outbreak risks. Adopting a strategy that combines an enhancement of surveillance of symptomatic cases with efforts to find and isolate nonsymptomatic infected hosts leads to the largest reduction in the probability that imported cases will initiate a local outbreak.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Francesca Anne Lovell-Read", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Uri Obolski", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Christl Ann Donnelly", + "author_inst": "University of Oxford, Imperial College London" + }, + { + "author_name": "Robin Nicholas Thompson", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.05.20226738", "rel_title": "COVID-19 Wastewater Epidemiology: A Model to Estimate Infected Populations", @@ -1098664,101 +1101697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.11.04.20226191", - "rel_title": "Wastewater Analysis of SARS-CoV-2 as a Predictive Metric of Positivity Rate for a Major Metropolis", - "rel_date": "2020-11-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20226191", - "rel_abs": "Wastewater monitoring for SARS-CoV-2 has been suggested as an epidemiological indicator of community infection dynamics and disease prevalence. We report wastewater viral RNA levels of SARS-CoV-2 in a major metropolis serving over 3.6 million people geographically spread over 39 distinct sampling sites. Viral RNA levels were followed weekly for 22 weeks, both before, during, and after a major surge in cases, and simultaneously by two independent laboratories. We found SARS-CoV-2 RNA wastewater levels were a strong predictive indicator of trends in the nasal positivity rate two-weeks in advance. Furthermore, wastewater viral RNA loads demonstrated robust tracking of positivity rate for populations served by individual treatment plants, findings which were used in real-time to make public health interventions, including deployment of testing and education strike teams.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Lauren B Stadler", - "author_inst": "Rice University" - }, - { - "author_name": "Katherine Ensor", - "author_inst": "Rice University" - }, - { - "author_name": "Justin R Clark", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Prashant Kalvapalle", - "author_inst": "Rice University" - }, - { - "author_name": "Zachary W LaTurner", - "author_inst": "Rice University" - }, - { - "author_name": "Lilian Mojica", - "author_inst": "Houston Health Department" - }, - { - "author_name": "Austen L Terwilliger", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Yue Zhuo", - "author_inst": "Rice University" - }, - { - "author_name": "Priyanka Ali", - "author_inst": "Rice University" - }, - { - "author_name": "Vasanthi Avadhanula", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Roberto Bertolusso", - "author_inst": "Rice University" - }, - { - "author_name": "Tessa Crosby", - "author_inst": "Rice University" - }, - { - "author_name": "Haroldo Hernandez Santos", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Marielle Hollstein", - "author_inst": "Rice University" - }, - { - "author_name": "Kyle Weesner", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "David M Zong", - "author_inst": "Rice University" - }, - { - "author_name": "David Persse", - "author_inst": "Houston Health Department" - }, - { - "author_name": "Pedro A Piedra", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Anthony W Maresso", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Loren Hopkins", - "author_inst": "Houston Health Department" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.04.20226092", "rel_title": "Nowcasting and forecasting provincial-level SARS-CoV-2 case positivity using google search data in South Africa", @@ -1098982,6 +1101920,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.04.20226126", + "rel_title": "Post-acute COVID-19 syndrome negatively impacts health and wellbeing despite less severe acute infection", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20226126", + "rel_abs": "IntroductionOne of the noted features of COVID-19 is the spectrum of expressivity in symptoms among those with the disease, ranging from no or mild symptoms that may last a small number of days, to severe and/or longer lasting symptoms. It is emerging that many patients have long lasting symptoms, several months after initial infection with COVID-19. The aim of this research was to characterize post-acute COVID-19 syndrome (PACS).\n\nMethodsThis was a retrospective cross-sectional observational study. Participants were patients recovering from COVID-19 infection, enrolled in Mount Sinai Hospitals COVID-19 Precision Recovery Program (PRP). Inclusion criteria were confirmed or probable (based on World Health Organization criteria) initial diagnosis of COVID-19; post-acute COVID-19 syndrome (defined as experiencing symptoms > 6 weeks since acute symptom onset) and being currently enrolled in the PRP during the months of July and August 2020. Study survey data were collected using REDCap. Demographic data, COVID-19 clinical data and patient-reported outcomes for breathlessness (Medical Research Council Breathlessness Scale), fatigue and quality of life (EuroQoL 5D-5L) were collected.\n\nResults84 individuals with PACS were included. Symptoms persisted at mean (range) 151 (54 to 255) days. The most prevalent persistent symptoms were fatigue (92%), loss of concentration/memory (74%), weakness (68%), headache (65%) and dizziness (64%). Most participants reported increased levels of disability associated with breathlessness, increased fatigue and reduced quality of life.\n\nConclusionsPersistent symptoms following COVID-19 infection are prevalent, debilitating and appear to affect individuals regardless of acute infection severity or prior health status. More detailed research is required in order to identify specific symptom clusters associated with PACS, and to devise effective interventional strategies.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Laura Tabacof", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jenna Tosto-Mancuso", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jamie Wood", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mar Cortes", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Amy Kontorovich", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Dayna McCarthy", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Dahlia Rizk", + "author_inst": "Mount Sinai Beth Israel" + }, + { + "author_name": "Leila Nasr", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Erica Breyman", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nicki Mohammadi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Christopher Kellner", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "David Putrino", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rehabilitation medicine and physical therapy" + }, { "rel_doi": "10.1101/2020.11.04.20226076", "rel_title": "Platelet Activating Immune Complexes Identified in COVID-19 Associated Coagulopathy", @@ -1100593,29 +1103594,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.11.04.368449", - "rel_title": "Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes", - "rel_date": "2020-11-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.04.368449", - "rel_abs": "BackgroundDNA mismatches can affect the efficiency of PCR techniques if the intended target has mismatches in primers or probes regions. The accepted rule is that mismatches are detrimental as they reduce the hybridization temperatures, yet a more quantitative assessment is rarely performed.\n\nMethodsWe calculate the hybridization temperatures of primer/probe sets after aligning to SARS-COV-2, SARS-COV-1 and non-SARS genomes, considering all possible combinations of single, double and triple consecutive mismatches. We consider the mismatched hybridization temperature within a range of 5 {degrees}C to the fully matched reference temperature.\n\nResultsWe obtained the alignments of 19 PCR primers sets that were recently reported for the detection of SARS-CoV-2 and to 21665 SARS-CoV-2 genomes as well as 323 genomes of other viruses of the coronavirus family of which 10 are SARS-CoV-1. We find that many incompletely aligned primers become fully aligned to most of the SARS-CoV-2 when mismatches are considered. However, we also found that many cross-align to SARS-CoV-1 and non-SARS genomes.\n\nConclusionsSome primer/probe sets only align substantially to most SARS-CoV-2 genomes if mismatches are taken into account. Unfortunately, by the same mechanism, almost 75% of these sets also align to some SARS-CoV-1 and non-SARS viruses. It is therefore recommended to consider mismatch hybridization for the design of primers whenever possible, especially to avoid undesired cross-reactivity.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Pamella Miranda", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Gerald Weber", - "author_inst": "Universidade Federal de Minas Gerais" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.11.03.20225425", "rel_title": "Per capita COVID-19 Case Rates are Lower in U.S. Counties Voting more Heavily Democratic in the 2016 Presidential Election, except not in States with a Republican Governor and Legislature", @@ -1101003,6 +1103981,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2020.11.04.20225698", + "rel_title": "Early survey with bibliometric analysis on machine learning approaches in controlling coronavirus", + "rel_date": "2020-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20225698", + "rel_abs": "Background and ObjectiveThe COVID-19 pandemic has caused severe mortality across the globe with the USA as the current epicenter, although the initial outbreak was in Wuhan, China. Many studies successfully applied machine learning to fight the COVID-19 pandemic from a different perspective. To the best of the authors knowledge, no comprehensive survey with bibliometric analysis has been conducted on the adoption of machine learning for fighting COVID-19. Therefore, the main goal of this study is to bridge this gap by carrying out an in-depth survey with bibliometric analysis on the adoption of machine-learning-based technologies to fight the COVID-19 pandemic from a different perspective, including an extensive systematic literature review and a bibliometric analysis.\n\nMethodsA literature survey methodology is applied to retrieve data from academic databases, and a bibliometric technique is subsequently employed to analyze the accessed records. Moreover, the concise summary, sources of COVID-19 datasets, taxonomy, synthesis, and analysis are presented. The convolutional neural network (CNN) is found mainly utilized in developing COVID-19 diagnosis and prognosis tools, mostly from chest X-ray and chest computed tomography (CT) scan images. Similarly, a bibliometric analysis of machine-learning-based COVID-19-related publications in Scopus and Web of Science citation indexes is performed. Finally, a new perspective is proposed to solve the challenges identified as directions for future research. We believe that the survey with bibliometric analysis can help researchers easily detect areas that require further development and identify potential collaborators.\n\nResultsThe findings in this study reveal that machine-learning-based COVID-19 diagnostic tools received the most considerable attention from researchers. Specifically, the analyses of the results show that energy and resources are more dispensed toward COVID-19 automated diagnostic tools, while COVID-19 drugs and vaccine development remain grossly underexploited. Moreover, the machine-learning-based algorithm predominantly utilized by researchers in developing the diagnostic tool is CNN mainly from X-rays and CT scan images.\n\nConclusionsThe challenges hindering practical work on the application of machine-learning-based technologies to fight COVID-19 and a new perspective to solve the identified problems are presented in this study. We believe that the presented survey with bibliometric analysis can help researchers determine areas that need further development and identify potential collaborators at author, country, and institutional levels to advance research in the focused area of machine learning application for disease control.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Haruna Chiroma", + "author_inst": "National Yunlin University of Science and Technology" + }, + { + "author_name": "Absalom E Ezugwu", + "author_inst": "University of KwaZulu-Natal" + }, + { + "author_name": "Fatsuma Jauro", + "author_inst": "Ahmadu Bello University, Zaria" + }, + { + "author_name": "Mohammed A Al-Garadi", + "author_inst": "Emory University" + }, + { + "author_name": "Idris N Abdullahi", + "author_inst": "Ahmadu Bello University, Zaria" + }, + { + "author_name": "Liyana Shuib", + "author_inst": "University of Malaya" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.11.04.20225714", "rel_title": "Management of malaria in children under 5-years-old during COVID-19 pandemic in Sierra Leone: a lesson learned?", @@ -1102863,89 +1105880,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.10.30.20223230", - "rel_title": "SARS-CoV-2 Seroprevalence in a Cohort of Asymptomatic, RT-PCR Negative Croatian First League Football Players", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223230", - "rel_abs": "BackgroundDuring the COVID-19 pandemic the Croatian Football Federation has launched a new model of pre-season systematic examination of football players, emphasizing the diagnosis of asymptomatic SARS-CoV-2 infection and preventing further spread among the players.\n\nObjectivesThe aim of this study was to assess the prevalence and dynamics of SARS-CoV-2 IgA and IgG antibodies in the cohort of asymptomatic and SARS-CoV-2 PCR negative professional football players in the Croatian First Football League by using a commercial ELISA antibody assay in the paired serum samples taken 2 months apart.\n\nMethodsSerology testing was performed from May till July 2020 in a cohort of 305 asymptomatic football players and club staff members. RT-PCR for detection of SARS-CoV-2 from nasopharyngeal swabs was performed on three occasions, and Euroimmun ELISA for detection of IgA and IgG (S1 and NCP) antibodies was tested in paired serum samples in May and July.\n\nResultsAll RT-PCR results were negative. Sixty-one (20%) participants were reactive in one or two classes of antibodies at baseline and/or follow-up serology testing. IgA reactivity was found in 41 (13.4% [95% CI=10.7-17.7]) baseline sera and 42 (13.8% [95% CI=10.3-18.9]) follow-up sera. IgG to S1 protein was found in 6 (2% [95% CI=0.9-4.2]) participants at baseline and 1 (0.33% [95% CI=0.0006-1.83]) at follow-up. IgG to NCP was found in 2 (0.7% [95% CI=0.2-2.4]) participants at baseline and 8 (2.6% (95% CI=1.3-5.1]) participants at follow-up. Noticeable dynamics in the paired sera was observed in 18 (5.9%) participants (excluding borderline IgA results) or 32 (10.5%) (including IgA borderline results).\n\nConclusionVarious patterns of IgA and IgG reactivity were found in the paired serum samples. Based on serology dynamics we estimate that in 5.9%-10.5% of PCR negative football players asymptomatic exposure to SARS-CoV-2 during pandemics could not be excluded.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Adriana Vince", - "author_inst": "University Hospital for Infectious Diseases Dr. Fran Mihaljevic, Zagreb, Croatia School of Medicine University of Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Renata Zadro", - "author_inst": "St. Catherine Specialty Hospital, Zabok/Zagreb, Croatia" - }, - { - "author_name": "Zvonimir Sostar", - "author_inst": "Public Health Institute Dr. Andrija Stampar, Department of Microbiology, Zagreb, Croatia" - }, - { - "author_name": "Suncanica Ljubin Sternak", - "author_inst": "Public Health Institute Dr. Andrija Stampar, Department of Microbiology, Zagreb, Croatia School of Medicine University of Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Jasmina Vranes", - "author_inst": "Public Health Institute Dr. Andrija Stampar, Department of Microbiology, Zagreb, Croatia School of Medicine University of Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Vedrana Skaro", - "author_inst": "Institute for Anthropological Research, Centre for Applied Bioanthropology, Laboratory for Molecular Anthropology, Zagreb, Croatia Genos Ltd, DNA Laboratory, Z" - }, - { - "author_name": "Petar Projic", - "author_inst": "Institute for Anthropological Research, Centre for Applied Bioanthropology, Laboratory for Molecular Anthropology, Zagreb, Croatia Genos Ltd, DNA Laboratory, Z" - }, - { - "author_name": "Vilim Molnar", - "author_inst": "St. Catherine Specialty Hospital, Zabok/Zagreb, Croatia" - }, - { - "author_name": "Vid Matisic", - "author_inst": "St. Catherine Specialty Hospital" - }, - { - "author_name": "Bruno Barsic", - "author_inst": "School of Medicine University of Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Gordan Lauc", - "author_inst": "Genos Ltd, DNA Laboratory, Zagreb, Croatia University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia" - }, - { - "author_name": "Zvjezdana Lovric Makaric", - "author_inst": "Croatian Institute of Public Health, Zagreb, Croatia" - }, - { - "author_name": "Zoran Bahtijarevic", - "author_inst": "Childrens Hospital Zagreb, Zagreb, Croatia" - }, - { - "author_name": "Tomislav Vlahovic", - "author_inst": "Clinical Hospital Centre Sisters of Mercy, Clinic of Traumatology, Zagreb, Croatia" - }, - { - "author_name": "Sandra Sikic", - "author_inst": "Public Health Institute Dr. Andrija Stampar, Department of Microbiology, Zagreb, Croatia" - }, - { - "author_name": "Ozren Polasek", - "author_inst": "University of Split, Medical School, Split, Croatia" - }, - { - "author_name": "Dragan Primorac", - "author_inst": "St. Catherine Specialty Hospital, Zabok/Zagreb, Croatia Eberly College of Science, The Pennsylvania State University, University Park, PA, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "sports medicine" - }, { "rel_doi": "10.1101/2020.11.01.20217943", "rel_title": "CovidSIMVL - Agent-Based Modeling of Localized Transmission within a Heterogeneous Array of Locations: Motivation, Configuration and Calibration", @@ -1103165,6 +1106099,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.30.20223586", + "rel_title": "Lightweight Model For The Prediction of COVID-19 Through The Detection And Segmentation of Lesions in Chest CT Scans", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223586", + "rel_abs": "We introduce a lightweight Mask R-CNN model that segments areas with the Ground Glass Opacity and Consolidation in chest CT scans. The model uses truncated ResNet18 and ResNet34 nets with a single layer of Feature Pyramid Network as a backbone net, thus substantially reducing the number of the parameters and the training time compared to similar solutions using deeper networks. Without any data balancing and manipulations, and using only a small fraction of the training data, COVID-CT-Mask-Net classification model with 6.12M total and 600K trainable parameters derived from Mask R-CNN, achieves 91.35% COVID-19 sensitivity, 91.63% Common Pneumonia sensitivity, 96.98% true negative rate and 93.95% overall accuracy on COVIDx-CT dataset (21191 images). We also present a thorough analysis of the regional features critical to the correct classification of the image. The full source code, models and pretrained weights are available on https://github.com/AlexTS1980/COVID-CT-Mask-Net.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Aram Ter-Sarkisov", + "author_inst": "City, University of London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.10.31.20218958", "rel_title": "Concentration of the cellular material in the nasopharyngeal swabs increases the clinical sensitivity of SARS-CoV2 RT-PCR", @@ -1104393,65 +1107346,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.02.20224303", - "rel_title": "Randomized controlled trial of convalescent plasma therapy against standard therapy in patients with severe COVID-19 disease", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224303", - "rel_abs": "BackgroundConvalescent plasma (CP) therapy in COVID-19 disease has been suggested to improve clinical outcome in severe disease. This pilot study was designed to inform the design of a definitive phase 3 clinical trial.\n\nMethodsThis was a prospective, interventional and randomized open label pilot trial involving 40 patients with COVID-19 who were requiring oxygen therapy and who had radiological evidence of pneumonia. Twenty COVID-19 patients received two 200ml transfusions of convalescent patient CP over 24 hours were compared with 20 patients who received routine care alone. The primary outcome was the requirement for ventilation. The secondary outcomes were white blood cell count, lactate dehydrogenase (LDH), C-reactive protein (CRP), Troponin, Ferritin, D-Dimer, procalcitonin, mortality rate at 28 days.\n\nResultsThe CP group were a higher risk group with higher ferritin levels (p<0.05) though respiratory indices did not differ. The primary outcome measure - ventilation - was required in 6 controls and 4 patients on CP (risk ratio 0.67 95% CI 0.22 - 2.0, p=0.72); mean time on ventilation was 10.5 days in the control against 8.2 days in patients on CP (p=0.81). There were no differences in secondary measures at the end of the study. Two patients died in the control and one patient in the CP arm.\n\nConclusionThere were no significant differences in the primary or secondary outcome measures between CP and standard therapy though fewer patients required ventilation and for a shorter period of time. The study showed that CP therapy appears to be safe and it is feasible to perform a definitive phase 3 clinical trial using this study protocol.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Manaf AlQahtani", - "author_inst": "Bahrain National Taskforce to Combat COVID-19, Bahrain Defense Force Hospital, Bahrain" - }, - { - "author_name": "Abdulkarim Abdulrahman", - "author_inst": "Bahrain National Taskforce to Combat COVID-19, Mohammed bin Khalifa Cardiac Centre, Bahrain" - }, - { - "author_name": "Abdulrahman AlMadani", - "author_inst": "Bahrain Defence Force Hospital, Bahrain" - }, - { - "author_name": "Salman Yousif AlAli", - "author_inst": "Bahrain Defence Force Hospital, Bahrain" - }, - { - "author_name": "Alaa Mahmood Al Zamrooni", - "author_inst": "Salmaniya Medical Complex, Bahrain" - }, - { - "author_name": "Amal Hejab", - "author_inst": "Bahrain National Taskforce to Combat COVID-19" - }, - { - "author_name": "Pearl Wasif", - "author_inst": "Royal College of Surgeons in Ireland-Bahrain" - }, - { - "author_name": "Ronan Conroy", - "author_inst": "Royal College of Surgeons in Ireland, Dublin, Ireland" - }, - { - "author_name": "Stephen Atkin", - "author_inst": "Royal College of Surgeons in Ireland - Bahrain" - }, - { - "author_name": "Sameer Otoom", - "author_inst": "Royal College of Surgeons in Ireland-Bahrain" - }, - { - "author_name": "Manal Abduljalil AlSayed", - "author_inst": "Bahrain Defence Force Hospital, Bahrain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.31.20223776", "rel_title": "Cell phone mobility data reveals heterogeneity in stay-at-home behavior during the SARS-CoV-2 pandemic", @@ -1104779,6 +1107673,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.02.20221309", + "rel_title": "Seroprevalence of SARS-CoV-2 antibodies in Saint Petersburg, Russia: a population-based study", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20221309", + "rel_abs": "BackgroundEstimates from initial SARS-CoV-2 serological surveys were likely to be biased due to convenience sampling whereas large-scale population-based serosurveys could be biased due to non-response. This study aims to estimate the seroprevalence of SARS-CoV-2 infection in Saint Petersburg, Russia accounting for non-response bias.\n\nMethodsWe recruited a random sample of adults residing in St. Petersburg with random digit dialling. Computer-assisted telephone interview was followed by an invitation for an antibody test with randomized rewards for participation. Blood samples collected between May 27, 2020 and June 26, 2020 were assessed for anti-SARS-CoV-2 antibodies using two tests -- CMIA and ELISA. The seroprevalence estimates were corrected for non-response bias, test sensitivity, and specificity. Individual characteristics associated with seropositivity were assessed.\n\nFindings66,250 individuals were contacted, 6,440 adults agreed to be interviewed and were invited to participate in the serosurvey. Blood samples were obtained from 1038 participants. Naive seroprevalence corrected for test characteristics was 9.0% [95% CI 7.2-10.8] by CMIA and 10.8% [8.8-12.7] by ELISA. Correction for non-response bias decreased seroprevalence estimates to 7.4% [5.7-9.2] for CMIA and to 9.3% [7.4-11.2] for ELISA. The most pronounced decrease in non-response bias-corrected seroprevalence was attributed to the history of any illnesses in the past 3 months and COVID-19 testing. Besides that seroconversion was negatively associated with smoking status, self-reported history of allergies and changes in hand-washing habits.\n\nInterpretationThese results suggest that even low estimates of seroprevalence in Europes fourth-largest city can be an overestimation in the presence of non-response bias. Serosurvey design should attempt to identify characteristics that are associated both with participation and seropositivity. Further population-based studies are required to explain the lower seroprevalence in smokers and participant reporting allergies.\n\nFundingPolymetal International plc", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Anton Barchuk", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Dmitriy Skougarevskiy", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Kirill Titaev", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Daniil Shirokov", + "author_inst": "Clinic \"Scandinavia\" (LLC Ava-Peter)" + }, + { + "author_name": "Yulia Raskina", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Anastasia Novkunkskaya", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Petr Talantov", + "author_inst": "The Russian Academy of Sciences Commission for Counteracting the Falsification of Scientific Research" + }, + { + "author_name": "Artur Isaev", + "author_inst": "Human Stem Cells Institute" + }, + { + "author_name": "Ekaterina Pomerantseva", + "author_inst": "Center of Genetics and Reproductive Medicine GENETICO LLC" + }, + { + "author_name": "Svetlana Zhikrivetskaya", + "author_inst": "Center of Genetics and Reproductive Medicine GENETICO LLC" + }, + { + "author_name": "Lubov Barabanova", + "author_inst": "Clinic \"Scandinavia\" (LLC Ava-Peter)" + }, + { + "author_name": "Vadim Volkov", + "author_inst": "European University at St. Petersburg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.03.20225144", "rel_title": "Characteristics of those most vulnerable to employment changes during the COVID-19 pandemic: a nationally representative cross-sectional study in Wales", @@ -1106115,29 +1109072,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.11.03.20225227", - "rel_title": "Space-Time Covid-19 Bayesian SIR modeling in South Carolina", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20225227", - "rel_abs": "The Covid-19 pandemic has spread across the world since the beginning of 2020. Many regions have experienced its effects. The state of South Carolina in the USA has seen cases since early March 2020 and a primary peak in early April 2020. A lockdown was imposed on April 6th but lifting of restrictions started on April 24th. The daily case and death data as reported by NCHS (deaths) via the New York Times GitHUB repository have been analyzed and approaches to modeling of the data are presented. Prediction is also considered and the role of asymptomatic transmission is assessed as a latent unobserved effect. Two different time periods are examined and one step prediction is provided.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Andrew B Lawson", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Joanne Kim", - "author_inst": "Medical University of South Carolina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.30.20221440", "rel_title": "The relationship between anxiety, health, and potential stressors among adults in the United States during the COVID-19 pandemic", @@ -1106453,6 +1109387,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.03.20216580", + "rel_title": "Immune modulating drug MP1032 with SARS-CoV-2 antiviral activity in vitro: A potential multi-target approach for prevention and early intervention treatment of COVID-19.", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20216580", + "rel_abs": "At least since March 2020, the multiorgan disease COVID-19 has a firm grip on the world. Although most of the cases are mild, patients from risk populations could develop a cytokine storm, which is characterized by a systemic inflammatory response leading to acute respiratory distress syndrome and organ failure. The present paper will introduce the small molecule MP1032, describe its mode of action, and give rationale why it is a promising option for prevention/treatment of SARS-CoV-2-induced cytokine storm. MP1032 is a phase-pure anhydrous polymorph of 5-amino-2,3-dihydro-1,4-pthalazinedione sodium salt that exhibits good stability and bioavailability. The physiological action of MP1032 is based on a multi-target mechanism including localized, self-limiting antioxidant activities that were demonstrated in a model of lipopolysaccharide (LPS)-induced joint inflammation. Furthermore, immune-regulatory and PARP-1 modulating properties, coupled with antiviral effects against SARS-CoV-2 were shown in various cell models. Efficacy has been preclinically elucidated in LPS-induced endotoxemia, a model with excessively activated immune responses that shares many similarities to COVID-19. So far, during oral clinical development with three-months daily administrations, no serious adverse drug reactions occurred highlighting the outstanding safety profile of MP1032.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sara Schumann", + "author_inst": "MetrioPharm Deutschland GmbH" + }, + { + "author_name": "Astrid Kaiser", + "author_inst": "MetrioPharm Deutschland GmbH" + }, + { + "author_name": "Ferdinando Nicoletti", + "author_inst": "University of Catania" + }, + { + "author_name": "Katia Mangano", + "author_inst": "University of Catania" + }, + { + "author_name": "Paolo Fagone", + "author_inst": "University of Catania" + }, + { + "author_name": "Eduard van Wijk", + "author_inst": "Meluna Research" + }, + { + "author_name": "Yu Yan", + "author_inst": "Meluna Research" + }, + { + "author_name": "Petra Schulz", + "author_inst": "MetrioPharm Deutschland GmbH" + }, + { + "author_name": "Beate Ludescher", + "author_inst": "MetrioPharm Deutschland GmbH" + }, + { + "author_name": "Michael Niedermaier", + "author_inst": "MetrioPharm Deutschland GmbH" + }, + { + "author_name": "Joerg von Wegerer", + "author_inst": "MetrioPharm Deutschland GmbH" + }, + { + "author_name": "Pia Rauch", + "author_inst": "Friedrich-Alexander University Erlangen-Nuernberg" + }, + { + "author_name": "Christian Setz", + "author_inst": "Friedrich-Alexander University Erlangen-Nuernberg" + }, + { + "author_name": "Ulrich Schubert", + "author_inst": "Friedrich-Alexander University Erlangen-Nuernberg" + }, + { + "author_name": "Wolfgang Brysch", + "author_inst": "MetrioPharm AG" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2020.10.28.20220657", "rel_title": "Real-life performances of a novel antigen detection test on nasopharyngeal specimens for SARS-CoV-2 infection diagnosis: a prospective study", @@ -1107573,41 +1110582,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.29.20207167", - "rel_title": "Gastroenterological and Hepatic Manifestations of Patients with COVID-19, Prevalence, Mortality by Country, and Intensive Care Admission Rate: Systematic Review and Meta-analysis.", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20207167", - "rel_abs": "Background & AimsPatient infected with the SARS-COV2 usually report fever and respiratory symptoms. However, multiple gastrointestinal (GI) manifestations such as diarrhea and abdominal pain has been described. The aim of this study was to evaluate the prevalence of GI, liver function test (LFT) abnormalities, and mortality of COVID-19 patients.\n\nMethodsWe performed a systematic review and meta-analysis of published studies that included cohort of patients infected with SARS-COV2 from December 1st, 2019 to July 1st, 2020. We collected data from the cohort of patients with COVID-19 by conducting a literature search using PubMed, Embase, Scopus, and Cochrane according to the preferred reporting Items for Systematic Reviews and MetaAnalyses (PRISMA) guidelines. We analyzed pooled data on the prevalence of overall and individual gastrointestinal symptoms, LFTs abnormalities and performed subanalyses to investigate the relationship between gastrointestinal symptoms, geographic location, fatality, and ICU admission.\n\nResultsThe available data of 17,802 positive patients for SARS-COV2 from 120 studies were included in our analysis. The most frequent manifestations were diarrhea (13.3%, 95% CI 12-16), nausea (9.1%, 95% CI 9-13) and elevated LFTs (23.7%, 95% CI 21- 27). The overall and GI fatality were 7.2% (95% CI 6 -10), and 1% (95% CI 1- 4) respectively. Subgroup analysis showed non statistically significant associations between GI symptoms/LFTs abnormalities and ICU admissions (OR=3.41, 95% CI 0.87 - 13.4). The GI mortality rate was 0.58% in China and 3.5% in the United States (95% CI 2 - 5).\n\nConclusionDigestive symptoms and LFTs abnormalities are common in COVID-19 patients. Our subanalysis shows that the presence of gastrointestinal and liver manifestations does not appear to affect mortality, or ICU admission rate. However, the mortality rate was higher in the United States compared to China.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mohammad Shehab", - "author_inst": "Mubarak Hospital" - }, - { - "author_name": "Fatima Alrashed", - "author_inst": "MCPHS University" - }, - { - "author_name": "Sameera Shuaibi", - "author_inst": "Kuwait University" - }, - { - "author_name": "Dhuha Alajmi", - "author_inst": "Kuwait University" - }, - { - "author_name": "Alan Barkun", - "author_inst": "Mcgill University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2020.10.29.20215996", "rel_title": "''Necessity is the mother of invention'': Specialist palliative care service innovation and practice change in response to COVID-19. Results from a multi-national survey (CovPall)", @@ -1107839,6 +1110813,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.28.20221416", + "rel_title": "COVID-19 Active Surveillance Simulation Case Study - Health and Economic Impacts of Active Surveillance in a School Environment", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221416", + "rel_abs": "The COVID-19 pandemic has affected the lives of almost all human beings and has forced stay-at-home mandates across the world. Government and school officials are facing challenging decisions on how to start the new 2020/2021 school year. Almost every school system has chosen a remote learning model for the Fall of 2020 while many are facing financial and logistical challenges.\n\nIn this study, we explore the efficacy of an Active Surveillance testing model where a random number of students are tested daily for early detection of asymptomatic patients and for prevention of the infection among the student population. In addition to health impacts, we also analyze the financial impact of deploying the Active Surveillance system in schools while taking into consideration lost workdays of parents, hospitalization costs, and testing costs.\n\nUnder the given assumptions, initial modeling results indicate that low Active Surveillance testing rates (between 6-10% daily testing of student population) can help achieve low infection rates ([≤]10%) among students along with enforcing mitigation procedures, such as wearing masks and social distancing. Without enforcing mitigation procedures, the optimal Active Surveillance rate of 8-10% can also achieve ([≤]10%) infection rates among student population. The results also demonstrate that Active Surveillance can lower the financial burden of the pandemic by proactively lowering the infection rates among student populations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ali A Saad", + "author_inst": "Del Norte High School - San Diego" + }, + { + "author_name": "Malak Saad", + "author_inst": "Del Norte High School - San Diego" + }, + { + "author_name": "Emad M Boctor", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.28.20217778", "rel_title": "SARSeq, a robust and highly multiplexed NGS assay for parallel detection of SARS-CoV2 and other respiratory infections", @@ -1109634,113 +1112635,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.10.30.20215301", - "rel_title": "Remdesivir-based therapy improved recovery of patients with COVID-19 in the SARSTer multicentre, real-world study", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20215301", - "rel_abs": "BackgroundRemdesivir (RDV) is the only antiviral drug registered currently for treatment of COVID-19 after a few clinical trials with controversial results. The purpose of this study was to evaluate the effectiveness and safety of RDV in patients with COVID-19 in real world settings.\n\nMethodsPatients were selected from 1496 individuals included in the SARSTer national database; 122 of them received therapy with RDV and 211 were treated with lopinavir/ritonavir (LPV/r)-based therapy. The primary end-point of effectiveness was clinical improvement in the ordinal 8-point scale, which was defined as a 2-point decrease from baseline to 7, 14, 21 and 28 days of hospitalization. The secondary end-points of effectiveness included: death rate, rate of no clinical improvement within 28 days of hospitalization in the ordinal scale, rate of the need for constant oxygen therapy, duration of oxygen therapy, rate of the need for mechanical ventilation, total hospitalization time, and rate of positive RT PCR for SARS-CoV-2 after 30 days.\n\nFindingsSignificantly higher rates of clinical improvement, by 15% and 10% respectively, were observed after RDV treatment compared to LPV/r at days 21 and 28. The difference between regimens increased with worsening of oxygen saturation (SpO2) and depending on the baseline score from the ordinal scale. Statistically significant differences supporting RDV were also noted regarding the rate of no clinical improvement within 28 days of hospitalization and hospitalization duration in patients with baseline SpO2 [≤]90%. In the logistic regression model only the administration of remdesivir was independently associated with at least a 2-point improvement in the ordinal scale between baseline and day 21.\n\nInterpretationIn conclusion, data collected in this retrospective, observational, real world study supported use of remdesivir for treatment of SARS-CoV-2 infection particularly in patients with oxygen saturation [≤]95%.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Robert Flisiak", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Poland" - }, - { - "author_name": "Dorota Zarebska-Michaluk", - "author_inst": "Department of Infectious Diseases, Jan Kochanowski University, Kielce, Poland" - }, - { - "author_name": "Aleksandra Berkan-Kawinska", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Lodz, Lodz, Poland" - }, - { - "author_name": "Magdalena Tudrujek-Zdunek", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Lublin, Lublin, Poland" - }, - { - "author_name": "Magdalena Rogalska", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Bialystok, Poland" - }, - { - "author_name": "Anna Piekarska", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Lodz, Lodz, Poland" - }, - { - "author_name": "Dorota Kozielewicz", - "author_inst": "Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Poland" - }, - { - "author_name": "Krzysztof Klos", - "author_inst": "Department of Infectious Diseases and Allergology, Military Institute of Medicine, Warsaw, Poland" - }, - { - "author_name": "Marta Rorat", - "author_inst": "Department of Forensic Medicine, Wroclaw Medical University, Wroclaw, Poland & First Infectious Diseases Ward, Gromkowski Regional Specialist Hospital in Wrocla" - }, - { - "author_name": "Beata Bolewska", - "author_inst": "Department of Infectious Diseases, University of Medical Sciences, Poznan, Poland" - }, - { - "author_name": "Anna Szymanek-Pasternak", - "author_inst": "Department of Infectious Diseases and Hepatology, Wroclaw Medical University, Wroclaw, Poland" - }, - { - "author_name": "Wlodzimierz Mazur", - "author_inst": "Clinical Department of Infectious Diseases in Chorzow, Medical University of Silesia, Katowice, Poland" - }, - { - "author_name": "Beata Lorenc", - "author_inst": "Pomeranian Center of Infectious Diseases, Department of Infectious Diseases, Medical University of Gdansk, Gdansk, Poland" - }, - { - "author_name": "Regina Podlasin", - "author_inst": "Hospital of Infectious Diseases in Warsaw, Warsaw, Poland" - }, - { - "author_name": "Katarzyna Sikorska", - "author_inst": "Department of Tropical Medicine and Epidemiology, Medical University of Gdansk, Gdansk Poland" - }, - { - "author_name": "Barbara Oczko-Grzesik", - "author_inst": "Department of Infectious Diseases in Bytom, Medical University of Silesia, Katowice, Poland" - }, - { - "author_name": "Cezary Iwaszkiewicz", - "author_inst": "Department of Rheumatology and Osteoporosis, Jozef Strus Hospital in Poznan, Poland" - }, - { - "author_name": "Bartosz Szetela", - "author_inst": "Department of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Wroclaw Medical University, Wroclaw, Poland" - }, - { - "author_name": "Pawel Pabjan", - "author_inst": "Department of Infectious Diseases, Jan Kochanowski University, Kielce, Poland" - }, - { - "author_name": "Malgorzata Pawlowska", - "author_inst": "Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Poland" - }, - { - "author_name": "Krzysztof Tomasiewicz", - "author_inst": "Department of Infectious Diseases and Hepatology, Medical University of Lublin, Lublin, Poland" - }, - { - "author_name": "Joanna Polanska", - "author_inst": "Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland" - }, - { - "author_name": "Jerzy Jaroszewicz", - "author_inst": "Department of Infectious Diseases in Bytom, Medical University of Silesia, Katowice, Poland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.30.20222604", "rel_title": "Growth of respiratory droplets in cold and humid air", @@ -1110016,6 +1112910,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.30.20223180", + "rel_title": "Risk perceptions and preventive practices of COVID-19 among healthcare professionals in public hospitals in Ethiopia", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223180", + "rel_abs": "Healthcare professionals are at higher risk of contracting the novel coronavirus due to their work exposure in the healthcare settings. Practicing appropriate preventive measures to control COVID-19 infection is one of the most important interventions that healthcare workers are expected to use. The aim of this study was to assess the level of risk perception and practices of preventive measures of COVID-19 among health workers in Addis Ababa, Ethiopia. A hospital-based cross-sectional study was conducted from 9th to 26th June 2020 among healthcare professionals working at six public hospitals in Addis Ababa. Data were collected using a self-administered structured questionnaire. Frequency, percentage, and mean were used to summarize the data. A binary logistic regression analyses were performed to identify factors associated with risk perception about COVID-19. A total of 1,134 participants were surveyed. Wearing facemask (93%), hand washing for at least 20 seconds (93%), covering mouth and nose while coughing or sneezing (91%), and avoiding touching eyes, nose, and mouth (91%) were the commonly self-reported preventive practices. About 88% perceived that they were worried about the risk of becoming infected with coronavirus, and majority (91%) worried about the risk of infection to their family. The mean score of overall fear and worry of COVID-19 was 2.37 on a scale of 1 to 3. Respondents who ever provided clinical care to COVID-19 patients were more likely to report fear and worry (adjusted OR=1.34, 95% CI:1.02-1.91), however those who ever participated in Ebola or SARS outbreaks were less likely to report fear and worry due to COVID-19 crisis (adjusted OR=0.66, 95% CI:0.48-0.90). This study has revealed widespread practices of preventive measures and the highest perceived risk of COVID-19 among healthcare workers. Therefore, an effective risk communication intervention should be implemented to ensure the maintenance of appropriate practices during the current COVID-19 pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Wakgari Deressa", + "author_inst": "School of Public Health, College of Health Sciences, Addis Ababa University" + }, + { + "author_name": "Alemayehu Worku", + "author_inst": "School of Public Health, College of Health Sciences, Addis Ababa University" + }, + { + "author_name": "Workeabeba Abebe", + "author_inst": "Scool of Medicine, College of Health Sciences, Addis Ababa University" + }, + { + "author_name": "Muluken Gizaw", + "author_inst": "School of Public Health, College of Health Sciences, Addis Ababa University" + }, + { + "author_name": "Wondwossen Amogne", + "author_inst": "School of Medicine, College of Health Sciences, Addis Ababa University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.29.20221036", "rel_title": "Effect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States", @@ -1111452,29 +1114381,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.11.02.350439", - "rel_title": "Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning", - "rel_date": "2020-11-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.02.350439", - "rel_abs": "The COVID-19 pandemic has demonstrated the serious potential for novel zoonotic coronaviruses to emerge and cause major outbreaks. The immediate animal origin of the causative virus, SARS-CoV-2, remains unknown, a notoriously challenging task for emerging disease investigations. Coevolution with hosts leads to specific evolutionary signatures within viral genomes that can inform likely animal origins. We obtained a set of 650 spike protein and 511 whole genome nucleotide sequences from 225 and 187 viruses belonging to the family Coronaviridae, respectively. We then trained random forest models independently on genome composition biases of spike protein and whole genome sequences, including dinucleotide and codon usage biases in order to predict animal host (of nine possible categories, including human). In hold-one-out cross-validation, predictive accuracy on unseen coronaviruses consistently reached [~]73%, indicating evolutionary signal in spike proteins to be just as informative as whole genome sequences. However, different composition biases were informative in each case. Applying optimised random forest models to classify human sequences of MERS-CoV and SARS-CoV revealed evolutionary signatures consistent with their recognised intermediate hosts (camelids, carnivores), while human sequences of SARS-CoV-2 were predicted as having bat hosts (suborder Yinpterochiroptera), supporting bats as the suspected origins of the current pandemic. In addition to phylogeny, variation in genome composition can act as an informative approach to predict emerging virus traits as soon as sequences are available. More widely, this work demonstrates the potential in combining genetic resources with machine learning algorithms to address long-standing challenges in emerging infectious diseases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Liam Brierley", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Anna Fowler", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.11.01.363812", "rel_title": "Structural basis for repurpose and design of nucleoside drugs for treating COVID-19", @@ -1111790,6 +1114696,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.01.363739", + "rel_title": "Temporal patterns in the evolutionary genetic distance of SARS-CoV-2 during the COVID-19 pandemic", + "rel_date": "2020-11-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.01.363739", + "rel_abs": "BackgroundDuring the pandemic of coronavirus disease 2019 (COVID-19), the genetic mutations occurred in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cumulatively or sporadically. In this study, we employed a computational approach to identify and trace the emerging patterns of the SARS-CoV-2 mutations, and quantify accumulative genetic distance across different periods and proteins.\n\nMethodsFull-length human SARS-CoV-2 strains in United Kingdom were collected. We investigated the temporal variation in the evolutionary genetic distance defined by the Hamming distance since the start of COVID-19 pandemic.\n\nFindingsOur results showed that the SARS-CoV-2 was in the process of continuous evolution, mainly involved in spike protein (S protein), the RNA-dependent RNA polymerase (RdRp) region of open reading frame 1 (ORF1) and nucleocapsid protein (N protein). By contrast, mutations in other proteins were sporadic and genetic distance to the initial sequenced strain did not show an increasing trend.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jingzhi Lou", + "author_inst": "JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Shi Zhao", + "author_inst": "JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Lirong Cao", + "author_inst": "JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Zigui Chen", + "author_inst": "Department of Microbiology, the Chinese University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Renee WY Chan", + "author_inst": "Department of Paediatric, the Chinese University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Marc KC Chong", + "author_inst": "JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Benny CY Zee", + "author_inst": "JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Paul KS Chan", + "author_inst": "Department of Microbiology, the Chinese University of Hong Kong, Hong Kong SAR, China" + }, + { + "author_name": "Maggie H Wang", + "author_inst": "JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.11.02.364273", "rel_title": "D614G substitution enhances the stability of trimeric SARS-CoV-2 spike protein", @@ -1113062,81 +1116019,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.10.31.20223925", - "rel_title": "Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context", - "rel_date": "2020-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.31.20223925", - "rel_abs": "In October 2020, an outbreak of at least 50 COVID-19 cases was reported surrounding individuals employed at or visiting the White House. Here, we applied genomic epidemiology to investigate the origins of this outbreak. We enrolled two individuals with exposures linked to the White House COVID-19 outbreak into an IRB-approved research study and sequenced their SARS-CoV-2 infections. We find these viral sequences are identical to each other, but are distinct from over 190,000 publicly available SARS-CoV-2 genomes. These genomes fall as part of a lineage circulating in the USA since April or May 2020 and detected in Virginia and Michigan. Looking forwards, sequencing of additional community SARS-CoV-2 infections collected in the USA prior to October 2020 may shed further light on its geographic ancestry. In sequencing of SARS-CoV-2 infections collected after October 2020, it may be possible to identify infections that likely descend from the White House COVID-19 outbreak.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Trevor Bedford", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jennifer K. Logue", - "author_inst": "University of Washington" - }, - { - "author_name": "Peter D. Han", - "author_inst": "University of Washington" - }, - { - "author_name": "Caitlin R. Wolf", - "author_inst": "University of Washington" - }, - { - "author_name": "Chris D. Frazar", - "author_inst": "University of Washington" - }, - { - "author_name": "Benjamin Pelle", - "author_inst": "University of Washington" - }, - { - "author_name": "Erica Ryke", - "author_inst": "University of Washington" - }, - { - "author_name": "James Hadfield", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jover Lee", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Mark J Rieder", - "author_inst": "University of Washington" - }, - { - "author_name": "Deborah A. Nickerson", - "author_inst": "University of Washington" - }, - { - "author_name": "Christina M. Lockwood", - "author_inst": "University of Washington" - }, - { - "author_name": "Lea M. Starita", - "author_inst": "University of Washington" - }, - { - "author_name": "Helen Y. Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Jay Shendure", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.01.363788", "rel_title": "Discovery of five HIV nucleoside analog reverse-transcriptase inhibitors (NRTIs) as potent inhibitors against the RNA-dependent RNA polymerase (RdRp) of SARS-CoV and 2019-nCoV", @@ -1113336,6 +1116218,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.27.20220863", + "rel_title": "Retrospective in silico HLA predictions from COVID-19 patients reveal alleles associated with disease prognosis", + "rel_date": "2020-10-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220863", + "rel_abs": "BackgroundThe Human Leukocyte Antigen (HLA) gene locus plays a fundamental role in human immunity, and it is established that certain HLA alleles are disease determinants.\n\nMethodsBy combining the predictive power of multiple in silico HLA predictors, we have previously identified prevalent HLA class I and class II alleles, including DPA1*02:02, in two small cohorts at the COVID-19 pandemic onset. Since then, newer and larger patient cohorts with controls and associated demographic and clinical data have been deposited in public repositories. Here, we report on HLA-I and HLA-II alleles, along with their associated risk significance in one such cohort of 126 patients, including COVID-19 positive (n=100) and negative patients (n=26).\n\nResultsWe recapitulate an enrichment of DPA1*02:02 in the COVID-19 positive cohort (29%) when compared to the COVID-negative control group (Fishers exact test [FET] p=0.0174). Having this allele, however, does not appear to put this cohorts patients at an increased risk of hospitalization. Inspection of COVID-19 disease severity outcomes reveal nominally significant risk associations with A*11:01 (FET p=0.0078), C*04:01 (FET p=0.0087) and DQA1*01:02 (FET p=0.0121).\n\nConclusionsWhile enrichment of these alleles falls below statistical significance after Bonferroni correction, COVID-19 patients with the latter three alleles tend to fare worse overall. This is especially evident for patients with C*04:01, where disease prognosis measured by mechanical ventilation-free days was statistically significant after multiple hypothesis correction (Bonferroni p = 0.0023), and may hold potential clinical value.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Rene L Warren", + "author_inst": "BC Cancer, Genome Sciences Centre" + }, + { + "author_name": "Inanc Birol", + "author_inst": "BC Cancer, Genome Sciences Centre" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.10.27.20220921", "rel_title": "Estimates of the Value of Life Lost from COVID-19 in Ohio", @@ -1114780,145 +1117685,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.10.30.360115", - "rel_title": "PRAK-03202: A triple antigen VLP vaccine candidate against SARS CoV-2", - "rel_date": "2020-10-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.30.360115", - "rel_abs": "The rapid development of safe and effective vaccines against SARS CoV-2 is the need of the hour for the coronavirus outbreak. Here, we have developed PRAK-03202, the worlds first triple antigen VLP vaccine candidate in a highly characterized S. cerevisiae-based D-CryptTM platform, which induced SARS CoV-2 specific neutralizing antibodies in BALB/c mice. Immunizations using three different doses of PRAK-03202 induces antigen specific (Spike, envelope and membrane proteins) humoral response and neutralizing potential. PBMCs from convalescent patients, when exposed to PRAK-03202, showed lymphocyte proliferation and elevated IFN-{gamma} levels suggestive of conservation of epitopes and induction of T helper 1 (Th1)-biased cellular immune responses. These data support the clinical development and testing of PRAK-03202 for use in humans.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Saumyabrata Mazumder", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Ruchir Rastogi", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Avinash Undale", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Kajal Arora", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Nupur Mehrotra Arora", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Biswa Pratim Das Purkayastha", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Dilip Kumar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Abyson Joseph", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Bhupesh Mali", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Vidya Bhushan Arya", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Sriganesh Kalyanaraman", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Abhishek Mukherjee", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Aditi Gupta", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Swaroop Potdar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Sourav Singha Roy", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Deepak Parashar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Jeny Paliwal", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Sudhir Kumar Singh", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Aelia Naqvi", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Apoorva Srivastava", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Manglesh Kumar Singh", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Devanand Kumar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Sarthi Bansal", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Satabdi Rautray", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Indrajeet Singh", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Pankaj Fengade", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Bivekanand Kumar", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Manish Saini", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Kshipra Jain", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Reeshu Gupta", - "author_inst": "Premas Biotech Pvt Ltd" - }, - { - "author_name": "Prabuddha K Kundu", - "author_inst": "Premas Biotech Pvt Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.10.30.352914", "rel_title": "Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses", @@ -1115202,6 +1117968,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.28.359935", + "rel_title": "Global Absence and Targeting of Protective Immune States in Severe COVID-19.", + "rel_date": "2020-10-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.28.359935", + "rel_abs": "While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease. Examination of the serum from severe patients demonstrates that they uniquely produce antibodies with multiple patterns of specificity against interferon-stimulated cells and that those antibodies functionally block the production of the mild disease-associated ISG-expressing cells. Overzealous and auto-directed antibody responses pit the immune system against itself in many COVID-19 patients and this defines targets for immunotherapies to allow immune systems to provide viral defense.\n\nOne Sentence SummaryIn severe COVID-19 patients, the immune system fails to generate cells that define mild disease; antibodies in their serum actively prevents the successful production of those cells.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Alexis J Combes", + "author_inst": "UCSF" + }, + { + "author_name": "Tristan Courau", + "author_inst": "UCSF" + }, + { + "author_name": "Nicholas F Kuhn", + "author_inst": "UCSF" + }, + { + "author_name": "Kenneth H Hu", + "author_inst": "UCSF" + }, + { + "author_name": "Arja Ray", + "author_inst": "UCSF" + }, + { + "author_name": "William S Chen", + "author_inst": "UCSF" + }, + { + "author_name": "Simon J Clearly", + "author_inst": "UCSF" + }, + { + "author_name": "Nayvin W Chew", + "author_inst": "UCSF" + }, + { + "author_name": "Divyashree Kushnoor", + "author_inst": "UCSF" + }, + { + "author_name": "Gabriella C Reeder", + "author_inst": "UCSF" + }, + { + "author_name": "Alan Shen", + "author_inst": "UCSF" + }, + { + "author_name": "Jessica Tsui", + "author_inst": "UCSF" + }, + { + "author_name": "Kamir J Hiam-Galvez", + "author_inst": "UCSF" + }, + { + "author_name": "Priscila Munoz-Sandoval", + "author_inst": "UCSF" + }, + { + "author_name": "Wandi S Zhu", + "author_inst": "UCSF" + }, + { + "author_name": "David S Lee", + "author_inst": "UCSF" + }, + { + "author_name": "Yang Sun", + "author_inst": "UCSF" + }, + { + "author_name": "Ran You", + "author_inst": "UCSF" + }, + { + "author_name": "Melia Magnen", + "author_inst": "UCSF" + }, + { + "author_name": "Lauren Rodriguez", + "author_inst": "UCSF" + }, + { + "author_name": "Aleksandra Leligdowicz", + "author_inst": "UCSF" + }, + { + "author_name": "Colin R Zamecnik", + "author_inst": "UCSF" + }, + { + "author_name": "Rita P Loudermilk", + "author_inst": "UCSF" + }, + { + "author_name": "Michael R Wilson", + "author_inst": "UCSF" + }, + { + "author_name": "Chun J Ye", + "author_inst": "UCSF" + }, + { + "author_name": "Gabriela K Fragiadakis", + "author_inst": "UCSF" + }, + { + "author_name": "Mark R Looney", + "author_inst": "UCSF" + }, + { + "author_name": "Vincent Chan", + "author_inst": "UCSF" + }, + { + "author_name": "Alyssa Ward", + "author_inst": "UCSF" + }, + { + "author_name": "Sidney Carrillo", + "author_inst": "UCSF" + }, + { + "author_name": "Michael Matthay", + "author_inst": "UCSF" + }, + { + "author_name": "David J Erle", + "author_inst": "UCSF" + }, + { + "author_name": "Prescott G Woodruff", + "author_inst": "UCSF" + }, + { + "author_name": "Charles Langelier", + "author_inst": "UCSF" + }, + { + "author_name": "Kristen Kangelaris", + "author_inst": "UCSF" + }, + { + "author_name": "Carolyn M Hendrickson", + "author_inst": "UCSF" + }, + { + "author_name": "Carolyn Calfee", + "author_inst": "UCSF" + }, + { + "author_name": "Arjun Arkal Rao", + "author_inst": "UCSF" + }, + { + "author_name": "Matthew F Krummel", + "author_inst": "UCSF" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.28.359836", "rel_title": "Protective Effects of STI-2020 Antibody Delivered Post-Infection by the Intranasal or Intravenous Route in a Syrian Golden Hamster COVID-19 Model", @@ -1117538,33 +1120475,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.25.20218735", - "rel_title": "A multiagent coronavirus model with territorial vulnerability parameters", - "rel_date": "2020-10-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.25.20218735", - "rel_abs": "We developed a simple and user-friendly simulator called MD Corona that is based on a multiagent model and describes the transmission dynamics of coronavirus for a given location considering three setting parameters: population density, social-isolation rate, and effective transmission probability. The latter is represented by the Coronavirus Protection Index (CPI) - a measurement of a given territorys vulnerability to the coronavirus that includes characteristics of the health system and socioeconomic development as well as infrastructure. The dynamic model also relies on other real epidemiological parameters. The model is calibrated by using immunity surveys and provides accurate predictions and indications of the different spread dynamic mechanisms. Our simulation studies clearly demonstrate the existence of multiple epidemic curves in the same city due to different vulnerabilities to the virus across regions. And it elucidates the phenomenon of the epidemic slowing despite a reduction in social-distancing policies, understood as a consequence of \"local protection bubbles.\" The simulator can be used for scientific outreach purposes, bringing science closer to the general public in order to raise awareness and increase engagement about the effectiveness of social distancing in reducing the transmissibility of the virus, but also to support effective actions to mitigate the spread of the virus.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Patricia Magalhaes", - "author_inst": "University of Bristol" - }, - { - "author_name": "Jose Paulo Guedes Pinto", - "author_inst": "Federal University of ABC (UFABC)" - }, - { - "author_name": "Diana Maritza Segura-Angel", - "author_inst": "Army Aviation School" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.27.20219436", "rel_title": "Childhood asthma outcomes during the COVID-19 pandemic: Findings from the PeARL multi-national cohort.", @@ -1117956,6 +1120866,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.27.20211433", + "rel_title": "Early Tocilizumab Dosing is Associated with Improved Survival In Critically Ill Patients Infected With Sars-CoV-2", + "rel_date": "2020-10-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20211433", + "rel_abs": "BackgroundSARS-CoV-2 is a novel coronavirus that has rapidly expanded to become a pandemic, resulting in millions of deaths worldwide. The cytokine storm is caused by the release of inflammatory agents and results in a physiologic disruption. Tocilizumab is an IL-6 receptor antagonist with the ability to suppress the cytokine storm in critically ill patients infected with SARS-CoV-2.\n\nMethodsThis was a multi-center study of patients infected with SARS-CoV-2, admitted between 3/13/20 and 4/16/20, requiring mechanical ventilation. Parameters that were evaluated included age, sex, race, usage of steroids, inflammatory markers, and comorbidities. Early dosing was defined as a tocilizumab dose administered prior to or within one (1) day of intubation. Late dosing was defined as a dose administered greater than one (1) day after intubation. A control group that was treated only with standard of care, and without tocilizumab, was utilized for comparison (untreated).\n\nFindingsWe studied 118 patients who required mechanical ventilation. Eighty-one (81) received tocilizumab, compared to 37 who were untreated. Early tocilizumab therapy was associated with a statistically significant decrease in mortality as compared to patients who were untreated (p=0.003). Dosing tocilizumab late was associated with an increased mortality compared to the untreated group (p=0.006).\n\nInterpretationEarly tocilizumab administration was associated with decreased mortality in critically ill SARS-Co-V-2 patients, but a potential detriment was suggested by dosing later in a patients course.\n\nFundingThis work did not receive outside funding or sponsorship.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Russell Petrak", + "author_inst": "Metro Infectious DIsease Consultants" + }, + { + "author_name": "Nicholas Van Hise", + "author_inst": "Metro Infectious DIsease Consultants" + }, + { + "author_name": "Nathan Skorodin", + "author_inst": "Metro Infectious Disease Consultants" + }, + { + "author_name": "Robert Fliegelman", + "author_inst": "Metro Infectious Disease Consultants" + }, + { + "author_name": "Vishnu Chundi", + "author_inst": "Metro Infectious Disease Consultants" + }, + { + "author_name": "Vishal Didwania", + "author_inst": "Metro Infectious Disease Consultants" + }, + { + "author_name": "Alice Han", + "author_inst": "Metro Infectious Disease Consultants" + }, + { + "author_name": "Brian Harting", + "author_inst": "Metro Infectious Disease Consultants" + }, + { + "author_name": "David Hines", + "author_inst": "Metro Infectious Disease Consultants" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.27.20220640", "rel_title": "Characteristics and outcome profile of Hospitalized African COVID-19 patients: The Ethiopian Context", @@ -1119024,25 +1121985,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.10.23.20218461", - "rel_title": "Detection and Segmentation of Lesion Areas in Chest CT Scans For The Prediction of COVID-19", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218461", - "rel_abs": "In this paper we compare the models for the detection and segmentation of Ground Glass Opacity and Consolidation in chest CT scans. These lesion areas are often associated both with common pneumonia and COVID-19. We train a Mask R-CNN model to segment these areas with high accuracy using three approaches: merging masks for these lesions into one, deleting the mask for Consolidation, and using both masks separately. The best model achieves the mean average precision of 44.68% using MS COCO criterion for instance segmentation across all accuracy thresholds. The classification model, COVID-CT-Mask-Net, which learns to predict the presence of COVID-19 vs common pneumonia vs control, achieves the 93.88% COVID-19 sensitivity, 95.64% overall accuracy, 95.06% common pneumonia sensitivity and 96.91% true negative rate on the COVIDx-CT test split (21192 CT scans) using a small fraction of the training data. We also analyze the effect of Non-Maximum Suppression of overlapping object predictions, both on the segmentation and classification accuracy. The full source code, models and pretrained weights are available on https://github.com/AlexTS1980/COVID-CT-Mask-Net.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Aram Ter-Sarkisov", - "author_inst": "City, University of London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.24.20218727", "rel_title": "DNA methylation and gene expression pattern of ACE2 and TMPRSS2 genes in saliva samples of patients with SARS-CoV-2 infection", @@ -1119330,6 +1122272,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.24.20218701", + "rel_title": "Clinical characteristics of Severe Acute Respiratory Syndrome by COVID-19 in Indigenous of Brazil", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.24.20218701", + "rel_abs": "The new coronavirus (SARS-CoV-2) emerged in Wuhan in China in December 2019, causing severe pneumonias and deaths, soon in March 2020 it reached pandemic level, affecting several countries including Brazil. The disease was named COVID-19, with characteristics of most infected having mild and moderate symptoms and a part severe symptom. The disease has already reached 158 ethnic groups, which have high vulnerability and limited access to health services. The objective is to investigate the clinical and spatial characteristics of Severe Acute Respiratory Syndrome of COVID-19 in the indigenous peoples of Brazil. It is an epidemiological, cross-sectional, analytical ecological study, based on data from the OpenDataSUS platform from 01/01/2020 to 31/08/2020. Profile variables, signs and symptoms and risk factors/comorbidities. The data were analyzed by Bioestat 5.3. There were 1,207 cases and 470 deaths. Profile: male gender (59.48%) means age 53 years. Signs and symptoms: fever (74.23%), cough (77.71%), sore throat (35.62%), dyspnea (69.34%), respiratory discomfort (62.80%), O2 saturation <95% (56.42%); and associated with mortality: dyspnea (80.0%) and O2 saturation <95% (69.36%). Risk factors and comorbidities (45.89%) were associated with deaths (54.04%). Comorbidities: Chronic Cardiovascular Disease (18.97%) and Diabetes Mellitus (18.97%), and associated with deaths: Chronic Cardiovascular Disease (24.46%). Being admitted to the ICU has a risk of death in (OR-3.96-<0.0001-CI-2,913/5,383) followed by not being vaccinated against influenza (OR-1.85-<0.0001-CI-1,358/2,528). The public and health policies of Brazil should be directed to control the dissemination of COVID-19 in this population, that COVID-19 evolves in the same intensity, however, the indigenous have vulnerabilities that can increase the impact of the pan-demic in this population.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Daniele Melo Sardinha", + "author_inst": "Instituto Evandro Chagas" + }, + { + "author_name": "Karla VB LIMA", + "author_inst": "Universidade do Estado do Par" + }, + { + "author_name": "Ana LS Ferreira", + "author_inst": "Universidade do Estado do Par" + }, + { + "author_name": "Juliana CD Garcez", + "author_inst": "Universidade do Estado do Par" + }, + { + "author_name": "Thalyta MRL Ueno", + "author_inst": "Universidade do Estado do Par" + }, + { + "author_name": "Yan Correa Rodrigues", + "author_inst": "Universidade do Estado do Par" + }, + { + "author_name": "Anderson LS Santos", + "author_inst": "Universidade do Estado do Par" + }, + { + "author_name": "Rosane SP Loiola", + "author_inst": "Universidade Federal do Par" + }, + { + "author_name": "Ricardo JPS Guimaraes", + "author_inst": "Instituto Evandro Chagas" + }, + { + "author_name": "Luana NGC Lima", + "author_inst": "Instituto Evandro Chagas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.24.20218784", "rel_title": "Airborne Pathogens in a Heterogeneous World: Superspreading & Mitigation", @@ -1120542,29 +1123539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.20.20216085", - "rel_title": "COVIDTrach; a prospective cohort study of mechanically ventilated COVID-19 patients undergoing tracheostomy in the UK", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20216085", - "rel_abs": "PurposeCOVIDTrach is a UK multi-centre prospective cohort study project evaluating the outcomes of tracheostomy in patients with COVID-19 receiving mechanical ventilation. It also examines the incidence of SARS-CoV-2 infection among healthcare workers involved in the procedure.\n\nMethodAn invitation to participate was sent to all UK NHS departments involved in tracheostomy in COVID-19 patients. Data was entered prospectively and clinical outcomes updated via an online database (REDCap). Clinical variables were compared with outcomes using multivariable regression analysis, with logistic regression used to develop a prediction model for mortality. Participants recorded whether any operators tested positive for SARS-CoV-2 within two weeks of the procedure.\n\nResultsThe cohort comprised 1605 tracheostomy cases from 126 UK hospitals. The median time from intubation to tracheostomy was 15 days (IQR 11, 21). 285 (18%) patients died following the procedure. 1229 (93%) of the survivors had been successfully weaned from mechanical ventilation at censoring and 1049 (81%) had been discharged from hospital. Age, inspired oxygen concentration, PEEP setting, pyrexia, number of days of ventilation before tracheostomy, C-reactive protein and the use of anticoagulation and inotropic support independently predicted mortality. Six reports were received of operators testing positive for SARS-CoV-2 within two weeks of the procedure.\n\nConclusionsTracheostomy appears to be safe in mechanically ventilated patients with COVID-19 and to operators performing the procedure and we identified clinical indicators that are predictive of mortality.\n\nFundingThe COVIDTrach project is supported by the Wellcome Trust UCL COVID-19 Rapid Response Award and the National Institute for Health Research.\n\nTrial registrationThe study is registered with ClinicalTrials.Gov (NCT04572438).", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "- COVIDTrach", - "author_inst": "" - }, - { - "author_name": "Nick JI Hamilton", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2020.10.25.20219212", "rel_title": "Economic Losses Associated with COVID-19 Deaths in the United States", @@ -1120868,6 +1123842,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.25.20219030", + "rel_title": "High seroprevalence but short-lived immune response to SARS-CoV-2 infection in Paris", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.25.20219030", + "rel_abs": "Although the COVID-19 pandemic peaked in March/April 2020 in France, the prevalence of infection is barely known. Herein, we assessed using high-throughput methods the serological response against the SARS-CoV-2 virus of 1847 participants working in one institution in Paris.\n\nIn May-July 2020, 11% (95% CI: 9.7-12.6) of serums were positive for IgG against the SARS-CoV-2 N and S proteins and 9.5% (CI:8.2-11.0) were pseudo-neutralizer. The prevalence of immunization was 11.6% (CI:10.2-13.2) considering positivity in at least one assays. In 5% (CI:3.9-7.1) of RT-qPCR positive individuals, no systemic IgGs were detected. Among immune individuals, 21% had been asymptomatic. Anosmia and ageusia occurred in 52% of the IgG-positive individuals and in 3% of the negative ones. In contrast, 30% of the anosmia-ageusia cases were seronegative suggesting that the true prevalence of infection may reach 16.6%. In sera obtained 4-8 weeks after the first sampling anti-N and anti-S IgG titers and pseudo-neutralization activity declined by 31%, 17% and 53%, respectively with half-life of 35, 87 and 28 days, respectively.\n\nThe population studied is representative of active workers in Paris. The short lifespan of the serological systemic responses suggests an underestimation the true prevalence of infection.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Francois Anna", + "author_inst": "Theravectys, Paris, France" + }, + { + "author_name": "Sophie Goyard", + "author_inst": "Unit of Lymphocyte Cell Biology, Immunology Department, Institut Pasteur, Paris, France" + }, + { + "author_name": "Ana Ines Lalanne", + "author_inst": "Laboratoire d'Immunologie Clinique, Institut Curie, Paris, France." + }, + { + "author_name": "Fabien Nevo", + "author_inst": "Unit of Molecular Virology and Vaccinology, Virology Department, Institut Pasteur, Paris, France" + }, + { + "author_name": "Marion Gransagne", + "author_inst": "Innovation Laboratory: Vaccines, Institut Pasteur, Paris, France" + }, + { + "author_name": "Philippe Souque", + "author_inst": "Unit of Molecular Virology and Vaccinology, Virology Department, Institut Pasteur, Paris, France" + }, + { + "author_name": "Delphine Louis", + "author_inst": "Laboratoire d'Immunologie Clinique, Institut Curie, Paris, France" + }, + { + "author_name": "Veronique Gillon", + "author_inst": "Direction of the Clinical Research, Institut Curie, Paris, France" + }, + { + "author_name": "Isabelle Turbiez", + "author_inst": "Direction of the Clinical Research, Institut Curie, 75005, France" + }, + { + "author_name": "Francois-Clement Bidard", + "author_inst": "Centre d'Investigation Clinique en Biotherapie, Institut Curie (CIC-BT1428), Paris, France" + }, + { + "author_name": "Aline Gobillon", + "author_inst": "Biometry, Institut Curie, Paris, France" + }, + { + "author_name": "Alexia Savignoni", + "author_inst": "Biometry, Institut Curie, Paris, France" + }, + { + "author_name": "Maude Guillot-Delost", + "author_inst": "Centre d'Investigation Clinique en Biotherapie, Institut Curie (CIC-BT1428), Paris, France" + }, + { + "author_name": "Francois Dejardin", + "author_inst": "Production and Purification of Recombinant Proteins Technological Platform, Paris, France" + }, + { + "author_name": "Evelyne Dufour", + "author_inst": "Production and Purification of Recombinant Proteins Technological Platform, Paris, France" + }, + { + "author_name": "Stephane Petres", + "author_inst": "Production and Purification of Recombinant Proteins Technological Platform, Paris, France" + }, + { + "author_name": "Odile Richard-Le Goff", + "author_inst": "Unit of Antibody in Therapy and Pathology, Institut Pasteur, Paris, France" + }, + { + "author_name": "Zaineb Choucha", + "author_inst": "Innovation Laboratory: Vaccines, Institut Pasteur, Paris, France" + }, + { + "author_name": "Olivier Helynck", + "author_inst": "Unit of Chemistry and Biocatalysis, Institut Pasteur, UMR 3523 CNRS, Paris, France" + }, + { + "author_name": "Yves L Janin", + "author_inst": "Unit of Chemistry and Biocatalysis, Institut Pasteur, UMR 3523 CNRS, Paris, France" + }, + { + "author_name": "Nicolas Escriou", + "author_inst": "Innovation Laboratory: Vaccines, Institut Pasteur, Paris, France" + }, + { + "author_name": "Pierre Charneau", + "author_inst": "Unit of Molecular Virology and Vaccinology, Virology Department, Institut Pasteur, Paris, France" + }, + { + "author_name": "Franck Perez", + "author_inst": "Unit of Cell Biology and Cancer, Institut Curie" + }, + { + "author_name": "Thierry ROSE", + "author_inst": "Unit of Lymphocyte Cell Biology, Immunology Department, Institut Pasteur, Paris, France" + }, + { + "author_name": "Olivier Lantz", + "author_inst": "Laboratoire d'Immunologie Clinique, Institut Curie, Paris, France." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.25.20219055", "rel_title": "Saliva is a promising alternative specimen for the detection of SARS-CoV-2 in children and adults", @@ -1122096,93 +1125185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.10.26.20219600", - "rel_title": "Head-to-head comparison of SARS-CoV-2 antigen-detecting rapid test with self-collected anterior nasal swab versus professional-collected nasopharyngeal swab", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219600", - "rel_abs": "BackgroundTwo antigen-detecting rapid diagnostic tests (Ag-RDTs) are now approved through the WHO Emergency Use Listing procedure and can be performed at the point-of-care. However, both tests use nasopharyngeal (NP) swab samples. NP swab samples must be collected by trained healthcare personnel with protective equipment and are frequently perceived as uncomfortable by patients.\n\nMethodsThis was a manufacturer-independent, prospective diagnostic accuracy study with comparison of a supervised, self-collected anterior nose (AN) swab sample with a professional-collected NP swab sample, using a WHO-listed SARS-CoV-2 Ag-RDT, STANDARD Q COVID-19 Ag Test (SD Biosensor), which is also being distributed by Roche. The reference standard was RT-PCR from an oro-/nasopharyngeal swab sample. Percent positive and negative agreement as well as sensitivity and specificity were calculated.\n\nResultsAmong the 289 participants, 39 (13.5%) tested positive for SARS-CoV-2 by RT-PCR. The positive percent agreement of the two different sampling techniques for the Ag-RDT was 90.6% (CI 75.8-96.8). The negative percent agreement was 99.2% (CI 97.2-99.8). The Ag-RDT with AN sampling showed a sensitivity of 74.4% (29/39 PCR positives detected; CI 58.9-85.4) and specificity of 99.2% (CI 97.1-99.8) compared to RT-PCR. The sensitivity with NP sampling was 79.5% (31/39 PCR positives detected; CI 64.5-89.2) and specificity was 99.6% (CI 97.8-100). In patients with high viral load (>7.0 log 10 RNA SARS-CoV2/swab), the sensitivity of the Ag-RDT with AN sampling was 96% and 100% with NP sampling.\n\nConclusionSupervised self-sampling from the anterior nose is a reliable alternative to professional nasopharyngeal sampling using a WHO-listed SARS-CoV-2 Ag-RDT. Considering the ease-of-use of Ag-RDTs, self-sampling and potentially patient self-testing at home may be a future use case.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Andreas K. Lindner", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Olga Nikolai", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Franka Kausch", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Mia Wintel", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Franziska Hommes", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Maximilian Gertler", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Lisa Kr\u00fcger", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Mary Gaeddert", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Frank Tobian", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Federica Lainati", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Lisa K\u00f6ppel", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany." - }, - { - "author_name": "Joachim Seybold", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Medical Dire" - }, - { - "author_name": "Victor M Corman", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "J\u00f6rg Hofmann", - "author_inst": "Labor Berlin - Charit\u00e9 Vivantes GmbH, Berlin, Germany" - }, - { - "author_name": "Jilian Sacks", - "author_inst": "Foundation for Innovative New Diagnostics, Geneva, Switzerland" - }, - { - "author_name": "Frank Mockenhaupt", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Claudia M. Denkinger", - "author_inst": "Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.27.20220541", "rel_title": "A Scalable Saliva-based, Extraction-free RT-LAMP Protocol for SARS-Cov-2 Diagnosis", @@ -1122630,6 +1125632,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.26.20219725", + "rel_title": "Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219725", + "rel_abs": "BackgroundThe prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into its spread in the community, the likelihood of reinfection and potential for some level of population immunity.\n\nMethodsPrevalence of antibody positivity in England, UK (REACT2) with three cross-sectional surveys between late June and September 2020. 365104 adults used a self-administered lateral flow immunoassay (LFIA) test for IgG. A laboratory comparison of LFIA results to neutralization activity in panel of sera was performed.\n\nResultsThere were 17,576 positive tests over the three rounds. Antibody prevalence, adjusted for test characteristics and weighted to the adult population of England, declined from 6.0% [5.8, 6.1], to 4.8% [4.7, 5.0] and 4.4% [4.3, 4.5], a fall of 26.5% [-29.0, -23.8] over the three months of the study. There was a decline between rounds 1 and 3 in all age groups, with the highest prevalence of a positive result and smallest overall decline in positivity in the youngest age group (18-24 years: -14.9% [-21.6, -8.1]), and lowest prevalence and largest decline in the oldest group (75+ years: -39.0% [-50.8, -27.2]); there was no change in antibody positivity between rounds 1 and 3 in healthcare workers (+3.45% [-5.7, +12.7]).\n\nThe decline from rounds 1 to 3 was largest in those who did not report a history of COVID-19, (-64.0% [-75.6, -52.3]), compared to -22.3% ([-27.0, -17.7]) in those with SARS-CoV-2 infection confirmed on PCR.\n\nDiscussionThese findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Helen Ward", + "author_inst": "Imperial College London" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Imperial College" + }, + { + "author_name": "Christina J Atchison", + "author_inst": "Imperial College London" + }, + { + "author_name": "Matthew Whitaker", + "author_inst": "Imperial College London" + }, + { + "author_name": "Joshua Elliott", + "author_inst": "Imperial College London" + }, + { + "author_name": "Maya Moshe", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jonathan C Brown", + "author_inst": "Imperial College London" + }, + { + "author_name": "Barney Flower", + "author_inst": "Imperial College London" + }, + { + "author_name": "Anna Daunt", + "author_inst": "Imperial College London" + }, + { + "author_name": "Kylie E. C. Ainslie", + "author_inst": "Imperial College London" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Steven Riley", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Elliott", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.27.20220277", "rel_title": "Transmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study", @@ -1124350,29 +1127431,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.22.20217554", - "rel_title": "Extending the range of symptoms in a Bayesian Network for the Predictive Diagnosis of COVID-19", - "rel_date": "2020-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20217554", - "rel_abs": "Emerging digital technologies have taken an unprecedented position at the forefront of COVID-19 management. This paper extends a previous Bayesian network designed to predict the probability of COVID-19 infection, based on a patients profile. The structure and prior probabilities have been amalgamated from the knowledge of peer-reviewed articles. The network accounts for demographics, behaviours and symptoms, and can mathematically identify multivariate combinations with the highest risk. Potential applications include patient triage in healthcare systems or embedded software for contact-tracing apps. Specifically, this paper extends the set of symptoms that are a marker for COVID-19 infection and the differential diagnosis of other conditions with similar presentations.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rachel Butcher", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Norman Fenton", - "author_inst": "Queen Mary University of London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.22.20217430", "rel_title": "Covid-19 and Socioeconomic Factors: Cross-country Evidence", @@ -1124560,6 +1127618,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.22.20217513", + "rel_title": "Measuring the Impact of Exposure to COVID-19 Vaccine Misinformation on Vaccine Intent in the UK and US", + "rel_date": "2020-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20217513", + "rel_abs": "The successful development and widespread acceptance of a SARS-CoV-2 vaccine will be a major step in fighting the pandemic, yet obtaining high uptake will be a challenging task, worsened by online misinformation. To help inform successful COVID-19 vaccination campaigns in the UK and US, we conducted a survey to quantify how online misinformation impacts COVID-19 vaccine uptake intent and identify socio-economic groups that are most at-risk of non-vaccination and most susceptible to online misinformation. Here, we report findings from nationally representative surveys in the UK and the US conducted in September 2020. We show that recent misinformation around a COVID-19 vaccine induces a fall in vaccination intent among those who would otherwise \"definitely\" vaccinate by 6.4 (3.8, 9.0) percentages points in the UK and 2.4 (0.1, 5.0) in the US, with larger decreases found in intent to vaccinate to protect others. We find evidence that socio-econo-demographic, political, and trust factors are associated with low intent to vaccinate and susceptibility to misinformation: notably, older age groups in the US are more susceptible to misinformation. We find evidence that scientific-sounding misinformation relating to COVID-19 and vaccines COVID-19 vaccine misinformation lowers vaccination intent, while corresponding factual information does not. These findings reveal how recent COVID-19 misinformation can impact vaccination rates and suggest pathways to robust messaging campaigns.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sahil Loomba", + "author_inst": "Imperial College London" + }, + { + "author_name": "Alex de Figueiredo", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Simon Piatek", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Kristen de Graaf", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Heidi J Larson", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.22.20217414", "rel_title": "Forecasting the spread of COVID-19 pandemic in Bangladesh using ARIMA model", @@ -1125728,53 +1128821,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.10.21.20216804", - "rel_title": "Predictors of PTSD, depression and anxiety in UK frontline health and social care workers during COVID-19.", - "rel_date": "2020-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216804", - "rel_abs": "BackgroundStudies have shown that working in frontline healthcare roles during epidemics and pandemics was associated with PTSD, depression, anxiety, and other mental health disorders.\n\nObjectivesThe objectives of this study were to identify demographic, work-related and other predictors for clinically significant PTSD, depression, and anxiety during the COVID-19 pandemic in UK frontline health and social care workers (HSCWs), and to compare rates of distress across different groups of HCSWs working in different roles and settings.\n\nMethodsA convenience sample (n=1194) of frontline UK HCSWs completed an online survey during the first wave of the pandemic (27 May - 23 July 2020). Participants worked in UK hospitals, nursing or care homes and other community settings. PTSD was assessed using the International Trauma Questionnaire (ITQ); Depression was assessed using the Patient Health Questionnaire-9 (PHQ-9); Anxiety was assessed using the Generalized Anxiety Disorder Scale (GAD-7).\n\nResultsNearly 58% of respondents met the threshold for clinically significant PTSD, anxiety or depression, and symptom levels were high across occupational groups and settings. Logistic regression analyses found that participants who were concerned about infecting others, who felt they could not talk with their managers, who reported feeling stigmatised and who had not had reliable access to personal protective equipment (PPE) were more likely to meet criteria for a clinically significant mental disorder. Being redeployed during the pandemic, and having had COVID were associated with higher odds for PTSD. Higher household income was associated with reduced odds for a mental disorder.\n\nConclusionsThis study identified predictors of clinically significant distress during COVID-19 and highlights the need for reliable access to PPE and further investigation of barriers to communication between managers and staff.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Talya Greene", - "author_inst": "University of Haifa" - }, - { - "author_name": "Jasmine Harju-Seppanen", - "author_inst": "University College London" - }, - { - "author_name": "Mariam Adjeniji", - "author_inst": "University College London" - }, - { - "author_name": "Charlotte Steel", - "author_inst": "University College London" - }, - { - "author_name": "Nick Grey", - "author_inst": "Sussex Partnership NHS Foundation Trust" - }, - { - "author_name": "Chris R Brewin", - "author_inst": "University College London" - }, - { - "author_name": "Michael A Bloomfield", - "author_inst": "University College London" - }, - { - "author_name": "Jo Billings", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.10.21.20217406", "rel_title": "Social and Psychiatric Effects of COVID-19 Pandemic and Distance Learning On High School Students: A Cross-Sectional Web-Based Survey Comparing Turkey and Denmark", @@ -1125962,6 +1129008,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.23.353177", + "rel_title": "Dysregulation of Pulmonary Responses in Severe COVID-19", + "rel_date": "2020-10-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.23.353177", + "rel_abs": "Patients with coronavirus disease 2019 (COVID-19) predominantly have a respiratory tract infection with various symptoms and high mortality is associated with respiratory failure second to severe disease. The risk factors leading to severe disease remain unclear. Here, we reanalyzed a published single-cell RNA-Seq (scRNA-Seq) dataset and found that bronchoalveolar lavage fluid (BALF) of patients with severe disease compared to those with mild disease contained decreased TH17 type cells, decreased IFNA1 expressing cells with lower expression of toll-like receptor 7 (TLR7) and TLR8, increased IgA expressing B cells, and increased hyperactive epithelial cells (and/or macrophages) expressing matrix metalloproteinases (MMPs), Hyaluronan synthase 2 (HAS2), and Plasminogen activator inhibitor-1 (PAI-1), which may together contribute to the pulmonary pathology in severe COVID-19. We propose IFN-I (and TLR7/TLR8) and PAI-1 as potential biomarkers to predict the susceptibility to severe COVID19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Dandan Wu", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Xuexian Yang", + "author_inst": "University of New Mexico" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.21.348854", "rel_title": "Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut", @@ -1127286,97 +1130355,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.21.20216820", - "rel_title": "Seroprevalence of SARS-CoV-2 IgG antibodies in two regions of Estonia (KoroSero-EST-1)", - "rel_date": "2020-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216820", - "rel_abs": "BackgroundIn Estonia, during the first wave of COVID-19 total number of cases confirmed by PCR was 13.3/10,000, similar in most regions, including capital Tallinn, but in the hotspot of Estonian epidemic, an island Saaremaa, the cumulative incidence was 166.1/10,000.\n\nAimWe aimed to determine the prevalence of SARS-CoV-2 IgG antibodies in these two regions, symptoms associated with infection and factors associated with antibody concentrations.\n\nMethodsParticipants were selected using stratified (formed by age decades) random sampling and recruited by general practitioners. IgG were determined from sera by four assays. Symptoms of acute respiratory illness associated with seropositivity were analyzed by multiple correspondence analysis, antibody concentrations by multiple linear regression.\n\nResultsTotal of 3608 individual were invited and 1960 recruited From May 8 to July 31, 2020. Seroprevalence was 1.5% (95% confidence interval (CI) 0.9-2.5) and 6.3% (95% CI 5.0-7.9), infection fatality rate 0.1% (95% CI 0.0-0.2) and 1.3% (95% CI 0.4-2.1) in Tallinn and Saaremaa, respectively. Of seropositive subjects 19.2% (14/73) had acute respiratory illness. Fever, diarrhea and the absence of cough and runny nose were associated with seropositivity in individuals aged 50 or more years. IgG concentrations were higher if fever, difficulty breathing, shortness of breath, chest pain or diarrhea was present, or hospitalization required.\n\nConclusionSimilarly to other European countries the seroprevalence of SARS-CoV-2 in Estonia was low even in the hotspot region Saaremaa suggesting that majority of population is still susceptible to SARS-CoV-2. Focusing only on respiratory symptoms may delay accurate diagnosis of SARS-CoV-2 infection.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Piia Jogi", - "author_inst": "Tartu University Hospital" - }, - { - "author_name": "Hiie Soeorg", - "author_inst": "University of Tartu" - }, - { - "author_name": "Diana Ingerainen", - "author_inst": "Family doctor center Jarveotsa" - }, - { - "author_name": "Mari Soots", - "author_inst": "Family doctor center Kuressaare" - }, - { - "author_name": "Freddy Lattekivi", - "author_inst": "University of Tartu" - }, - { - "author_name": "Paul Naaber", - "author_inst": "SYNLAB Eesti" - }, - { - "author_name": "Karolin Toompere", - "author_inst": "University of Tartu" - }, - { - "author_name": "Part Peterson", - "author_inst": "University of Tartu" - }, - { - "author_name": "Liis Haljasmagi", - "author_inst": "University of Tartu" - }, - { - "author_name": "Eva Zusinaite", - "author_inst": "University of Tartu" - }, - { - "author_name": "Hannes Vaas", - "author_inst": "Tartu University Hospital" - }, - { - "author_name": "Merit Pauskar", - "author_inst": "University of Tartu" - }, - { - "author_name": "Arina Shablinskaja", - "author_inst": "University of Tartu" - }, - { - "author_name": "Katrin Kaarna", - "author_inst": "University of Tartu" - }, - { - "author_name": "Heli Paluste", - "author_inst": "Ministry of Social Affairs of the Republic of Estonia" - }, - { - "author_name": "Kai Kisand", - "author_inst": "University of Tartu" - }, - { - "author_name": "Marje Oona", - "author_inst": "University of Tartu" - }, - { - "author_name": "Riina Janno", - "author_inst": "Tartu University Hospital" - }, - { - "author_name": "Irja Lutsar", - "author_inst": "University of Tartu" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.21.20216895", "rel_title": "Superspreading Events Without Superspreaders: Using High Attack Rate Events to Estimate N o forAirborne Transmission of COVID-19", @@ -1127572,6 +1130550,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.21.20216721", + "rel_title": "Patterns of Multimorbidity and Risk of Severe SARS-CoV-2 Infection: an observational study in the U.K.", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216721", + "rel_abs": "BackgroundPre-existing comorbidities have been linked to SARS-CoV-2 infection but evidence is sparse on the importance and pattern of multimorbidity (2 or more conditions) and severity of infection indicated by hospitalisation or mortality. We aimed to use a multimorbidity index developed specifically for COVID-19 to investigate the association between multimorbidity and risk of severe SARS-CoV-2 infection.\n\nMethodsWe used data from the UK Biobank linked to laboratory confirmed test results for SARS-CoV-2 infection and mortality data from Public Health England between March 16 and July 26, 2020. By reviewing the current literature on COVID-19 we derived a multimorbidity index including: 1) angina; 2) asthma; 3) atrial fibrillation; 4) cancer; 5) chronic kidney disease; 6) chronic obstructive pulmonary disease; 7) diabetes mellitus; 8) heart failure; 9) hypertension; 10) myocardial infarction; 11) peripheral vascular disease; 12) stroke. Adjusted logistic regression models were used to assess the association between multimorbidity and risk of severe SARS-CoV-2 infection (hospitalisation or death). Potential effect modifiers of the association were assessed: age, sex, ethnicity, deprivation, smoking status, body mass index, air pollution, 25-hydroxyvitamin D, cardiorespiratory fitness, high sensitivity C-reactive protein.\n\nResultsAmong 360,283 participants, the median age was 68 [range, 48-85] years, most were White (94.5%), and 1,706 had severe SARS-CoV-2 infection. The prevalence of multimorbidity was more than double in those with severe SARS-CoV-2 infection (25%) compared to those without (11%), and clusters of several multimorbidities were more common in those with severe SARS-CoV-2 infection. The most common clusters with severe SARS-CoV-2 infection were stroke with hypertension (79% of those with stroke had hypertension); diabetes and hypertension (72%); and chronic kidney disease and hypertension (68%). Multimorbidity was independently associated with a greater risk of severe SARS-CoV-2 infection (adjusted odds ratio 1.91 [95% confidence interval 1.70, 2.15] compared to no multimorbidity). The risk remained consistent across potential effect modifiers, except for greater risk among men.\n\nConclusionThe risk of severe SARS-CoV-2 infection is higher in individuals with multimorbidity, indicating the need to target research and resources in people with SARS-CoV-2 infection and multimorbidity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yogini V Chudasama", + "author_inst": "University of Leicester" + }, + { + "author_name": "Francesco Zaccardi", + "author_inst": "University of Leicester" + }, + { + "author_name": "Clare L Gillies", + "author_inst": "University of Leicester" + }, + { + "author_name": "Cameron Razieh", + "author_inst": "University of Leicester" + }, + { + "author_name": "Thomas Yates", + "author_inst": "University of Leicester" + }, + { + "author_name": "David E Kloecker", + "author_inst": "University of Leicester" + }, + { + "author_name": "Alex V Rowlands", + "author_inst": "University of Leicester" + }, + { + "author_name": "Melanie J Davies", + "author_inst": "University of Leicester" + }, + { + "author_name": "Nazrul Islam", + "author_inst": "University of Oxford" + }, + { + "author_name": "Samuel Seidu", + "author_inst": "University of Leicester" + }, + { + "author_name": "Nita G Forouhi", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.21.20216705", "rel_title": "The impact of COVID-19 on Long Term Care Facilities (LTCFs) of an Italian Province: a cohort study and a retrospective analysis of observed vs. expected mortality", @@ -1128856,37 +1131897,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.10.22.328864", - "rel_title": "Databiology Lab CORONAHACK: Collection of Public COVID-19 Data", - "rel_date": "2020-10-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.22.328864", - "rel_abs": "COVID-19 has had an unprecedented global impact in health and economy affecting millions of persons world-wide. To support and enable a collaborative response from the global research communities, we created a data collection for different public sources for anonymized patient clinical data, imaging datasets, molecular data as nucleotide and protein sequences for the SARS-CoV-2 virus, reports of count of cases and deaths per city/country, and other economic indicators in Databiology Lab (https://www.lab.databiology.net/) where researchers could access these data assets and use the hundreds of available open source bioinformatic applications to analyze them. These data assets are regularly updated and was used in a successful virtual 3-day hackathon organized by Databiology Ltd and Mindstream-AI where hundreds of attendees to work collaboratively to analyze these data collections.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Juan Caballero Perez", - "author_inst": "Databiology Ltd" - }, - { - "author_name": "Carlos de Blas Perez", - "author_inst": "Databiology Ltd" - }, - { - "author_name": "Felipe Leza Alvarez", - "author_inst": "Databiology Ltd" - }, - { - "author_name": "Jose Manuel Caballero Contreras", - "author_inst": "Databiology Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.10.22.349522", "rel_title": "Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites", @@ -1129222,6 +1132232,37 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.10.19.20215483", + "rel_title": "Deep learning segmentation model for automated detection of the opacity regions in the chest X-rays of the Covid-19 positive patients and the application for disease severity", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20215483", + "rel_abs": "PurposeThe pandemic of Covid-19 has caused tremendous losses to lives and economy in the entire world. The machine learning models have been applied to the radiological images of the Covid-19 positive patients for disease prediction and severity assessment. However, a segmentation model for detecting the opacity regions like haziness, ground-glass opacity and lung consolidation from the Covid-19 positive chest X-rays is still lacking.\n\nMethodsThe recently published collection of the radiological images for a rural population in United States had made the development of such a model a possibility, for the high quality images and consistent clinical measurements. We manually annotated 221 chest X-ray images with the lung fields and the opacity regions and trained a segmentation model for the opacity region using the Unet framework and the Resnet18 backbone. In addition, we applied the percentage of the opacity region over the area of the total lung fields for predicting the severity of patients.\n\nResultsThe model has a good performance regarding the overlap between the predicted and the manually labelled opacity regions. The performance is comparable for both the testing data set and the validation data set which comes from very diverse sources. However, careful manual examinations by experienced radiologists show mistakes in the predictions, which could be caused by the anatomical complexities. Nevertheless, the percentage of the opacity region can predict the severity of the patients well in regards to the ICU admissions and mortality.\n\nConclusionIn view of the above, our model is a successful first try in the development of a segmentation model for the opacity regions for the Covid-19 positive chest X-rays. However, additional work is needed before a robust model can be developed for the ultimate goal of the implementations in the clinical setting.\n\nModel and supporting materials can be found in https://github.com/haimingt/opacity_segmentation_covid_chest_X_ray.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Haiming Tang", + "author_inst": "Mercury Data Science" + }, + { + "author_name": "Nanfei Sun", + "author_inst": "University of Houston, Clear Lake" + }, + { + "author_name": "Yi Li", + "author_inst": "Fox Chase Cancer Center" + }, + { + "author_name": "Haoran Xia", + "author_inst": "Independent researcher" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.10.19.20215426", "rel_title": "Early prognostication of COVID-19 to guide hospitalisation versus outpatient monitoring using a point-of-test risk prediction score", @@ -1130485,101 +1133526,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.20.20213116", - "rel_title": "Prevalence of SARS-CoV-2 antibodies in France: results from nationwide serological surveillance", - "rel_date": "2020-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20213116", - "rel_abs": "BackgroundAssessment of cumulative incidence of SARS-CoV-2 infections is critical for monitoring the course and the extent of the epidemic. As asymptomatic or mild cases were typically not captured by surveillance data in France, we implemented nationwide serological surveillance. We present estimates for prevalence of anti-SARS-CoV-2 antibodies in the French population and the proportion of infected individuals who developed potentially protective neutralizing antibodies throughout the first epidemic wave.\n\nMethodsWe performed serial cross-sectional sampling of residual sera over three periods: prior to (9-15 March), during (6-12 April) and following (11-17 May) a nationwide lockdown. Each sample was tested for anti-SARS-CoV-2 IgG antibodies targeting the Nucleoprotein and Spike using two Luciferase-Linked ImmunoSorbent Assays, and for neutralising antibodies using a pseudo-neutralisation assay. We fitted a general linear mixed model of seropositivity in a Bayesian framework to derive prevalence estimates stratified by age, sex and region.\n\nFindingsIn total, sera from 11 021 individuals were analysed. Nationwide seroprevalence of SARS-CoV-2 antibodies was estimated at 0.41% [0.05-0.88] mid-March, 4.14% [3.31-4.99] mid-April and 4.93% [4.02-5.89] mid-May. Approximately 70% of seropositive individuals had detectable neutralising antibodies. Seroprevalence was higher in regions where circulation occurred earlier and was more intense. Seroprevalence was lowest in children under 10 years of age (2.72% [1.10-4.87]).\n\nInterpretationSeroprevalence estimates confirm that the nationwide lockdown substantially curbed transmission and that the vast majority of the French population remains susceptible to SARS-CoV-2. Low seroprevalence in school age children suggests limited susceptibility and/or transmissibility in this age group. Our results show a clear picture of the progression of the first epidemic wave and provide a framework to inform the ongoing public health response as viral transmission is picking up again in France and globally.\n\nFundingSante publique France.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Stephane Le Vu", - "author_inst": "Sante publique France" - }, - { - "author_name": "Gabrielle Jones", - "author_inst": "Sante publique France" - }, - { - "author_name": "Francois Anna", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Thierry Rose", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean-Baptiste Richard", - "author_inst": "Sante publique France" - }, - { - "author_name": "Sibylle Bernard-Stoecklin", - "author_inst": "Sante publique France" - }, - { - "author_name": "Sophie Goyard", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Caroline Demeret", - "author_inst": "Institut pasteur" - }, - { - "author_name": "Olivier Helynck", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Corinne Robin", - "author_inst": "Cerba Healthcare Division" - }, - { - "author_name": "Virgile Monnet", - "author_inst": "Eurofins-Biomnis" - }, - { - "author_name": "Louise Perrin de Facci", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Marie-Noelle Ungeheuer", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Lucie Leon", - "author_inst": "Sante publique France" - }, - { - "author_name": "Yvonnick Guillois", - "author_inst": "Sante publique France" - }, - { - "author_name": "Laurent Filleul", - "author_inst": "Sante publique France" - }, - { - "author_name": "Pierre Charneau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Daniel Levy-Bruhl", - "author_inst": "Sante publique France" - }, - { - "author_name": "Sylvie van der Werf", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Harold Noel", - "author_inst": "Sante publique France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.20.20215863", "rel_title": "Cognitive deficits in people who have recovered from COVID-19 relative to controls: An N=84,285 online study", @@ -1130959,6 +1133905,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.21.347690", + "rel_title": "Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP", + "rel_date": "2020-10-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.21.347690", + "rel_abs": "The RNA polymerase inhibitor, favipiravir, is currently in clinical trials as a treatment for infection with SARS-CoV-2, despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 [A]. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Katerina Naydenova", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Kyle W Muir", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Long-Fei Wu", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Ziguo Zhang", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Francesca Coscia", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Mathew J Peet", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Pablo Castro-Hartmann", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "Pu Qian", + "author_inst": "Thermo Fischer Scientific" + }, + { + "author_name": "Kasim Sader", + "author_inst": "Thermo Fischer Scientific" + }, + { + "author_name": "Kyle Dent", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Dari Kimanius", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "John D Sutherland", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Jan Lowe", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "David Barford", + "author_inst": "MRC Laboratory of Molecular Biology" + }, + { + "author_name": "Christopher J Russo", + "author_inst": "MRC Laboratory of Molecular Biology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.10.21.349225", "rel_title": "Restriction of SARS-CoV-2 Replication by Targeting Programmed -1 Ribosomal Frameshifting In Vitro", @@ -1132031,53 +1135052,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.10.15.20213371", - "rel_title": "Impact of SARS-CoV-2 on Seasonal Respiratory Viruses: A Tale of Two Large Metropolitan Centers in the United States", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20213371", - "rel_abs": "To assess the impact of the SARS-CoV-2 pandemic on seasonal respiratory viruses, absolute case counts and viral reproductive rates from 2019-2020 were compared against previous seasons. Our findings suggest that the public health measures implemented to reduce SARS-CoV-2 transmission significantly reduced the transmission of other respiratory viruses.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Amy C Sherman", - "author_inst": "Division of Infectious Diseases, Brigham and Women's Hospital" - }, - { - "author_name": "Ahmed Babiker", - "author_inst": "Division of Infectious Diseases, Emory University School of Medicine" - }, - { - "author_name": "Andrew J Sieben", - "author_inst": "Emory University" - }, - { - "author_name": "Alexander Pyden", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center" - }, - { - "author_name": "James Steinberg", - "author_inst": "Division of Infectious Diseases, Emory University School of Medicine" - }, - { - "author_name": "Colleen S Kraft", - "author_inst": "Division of Infectious Diseases, Emory University School of Medicine" - }, - { - "author_name": "Katia Koelle", - "author_inst": "Department of Biology, Emory University" - }, - { - "author_name": "Sanjat Kanjilal", - "author_inst": "Division of Infectious Diseases, Brigham and Women's Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.15.20213512", "rel_title": "COVID-19 neutralizing antibodies predict disease severity and survival", @@ -1132597,6 +1135571,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.10.15.20213645", + "rel_title": "A Comparative Analysis of System Features Used in the TREC-COVID Information Retrieval Challenge", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20213645", + "rel_abs": "The COVID-19 pandemic has resulted in a rapidly growing quantity of scientific publications from journal articles, preprints, and other sources. The TREC-COVID Challenge was created to evaluate information retrieval methods and systems for this quickly expanding corpus. Based on the COVID-19 Open Research Dataset (CORD-19), several dozen research teams participated in over 5 rounds of the TREC-COVID Challenge. While previous work has compared IR techniques used on other test collections, there are no studies that have analyzed the methods used by participants in the TREC-COVID Challenge. We manually reviewed team run reports from Rounds 2 and 5, extracted features from the documented methodologies, and used a univariate and multivariate regression-based analysis to identify features associated with higher retrieval performance. We observed that fine-tuning datasets with relevance judgments, MS-MARCO, and CORD-19 document vectors was associated with improved performance in Round 2 but not in Round 5. Though the relatively decreased heterogeneity of runs in Round 5 may explain the lack of significance in that round, fine-tuning has been found to improve search performance in previous challenge evaluations by improving a systems ability to map relevant queries and phrases to documents. Furthermore, term expansion was associated with improvement in system performance, and the use of the narrative field in the TREC-COVID topics was associated with decreased system performance in both rounds. These findings emphasize the need for clear queries in search. While our study has some limitations in its generalizability and scope of techniques analyzed, we identified some IR techniques that may be useful in building search systems for COVID-19 using the TREC-COVID test collections.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jimmy Chen", + "author_inst": "OHSU" + }, + { + "author_name": "William Hersh", + "author_inst": "Oregon Health & Science University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.10.15.20213553", "rel_title": "Treatment with human umbilical cord-derived mesenchymal stem cells for COVID-19 patients with lung damage: a randomised, double-blind, placebo controlled phase 2 trial", @@ -1133785,69 +1136782,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2020.10.18.20214221", - "rel_title": "Structural and metabolic brain abnormalities in COVID-19 patients with sudden loss of smell", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.18.20214221", - "rel_abs": "ObjectivesSudden loss of smell is a very common symptom of coronavirus disease 19 (COVID-19). This study characterizes the structural and metabolic cerebral correlates of dysosmia in patients with COVID-19.\n\nMethodsStructural brain magnetic resonance imaging (MRI) and positron emission tomography with [18F]-fluorodeoxyglucose (FDG-PET) were prospectively acquired simultaneously on a hybrid PET-MR in twelve patients (2 males, 10 females, mean age: 42.6 years, age range: 23-60 years) with sudden dysosmia and positive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on nasopharyngeal swab specimens. FDG-PET data were analysed using a voxel-based approach and compared with that of a group of healthy subjects.\n\nResultsBilateral blocking of the olfactory cleft was observed in six patients, while subtle olfactory bulb asymmetry was found in three patients. No MRI signal abnormality downstream of the olfactory tract was observed. Heterogeneous (decrease or increase) glucose metabolism abnormalities were observed in core olfactory and high-order neocortical areas. A modulation of regional cerebral glucose metabolism by the severity and the duration of COVID-19-related dysosmia was disclosed using correlation analyses.\n\nConclusionsThis PET-MR study shows that sudden loss of smell in COVID-19 is not related to central involvement due to SARS-CoV-2 neuroinvasiveness. Loss of smell is associated with heterogeneous cerebral metabolic changes in core olfactory and high-order cortical areas likely related to combined processes of deafferentation and active functional reorganisation secondary to the lack of olfactory stimulation.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Maxime Niesen", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Nicola Trotta", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Antoine Noel", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Tim Coolen", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Georges Fayad", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Gil Leurkin-Sterk", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Isabelle Delpierre", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Sophie Henrard", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Niloufar Sadeghi", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Jean-Christophe Goffard", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Serge Goldman", - "author_inst": "CUB Hopital Erasme" - }, - { - "author_name": "Xavier De Ti\u00e8ge", - "author_inst": "CUB Hopital Erasme" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.10.17.20214429", "rel_title": "SARS-CoV-2 infection among patients with multiple sclerosis; A cross-sectional study", @@ -1133991,6 +1136925,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.17.20214205", + "rel_title": "Composition of the immunoglobulin G glycome associates with the severity of COVID-19", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.17.20214205", + "rel_abs": "A large variation in the severity of disease symptoms is one of the key open questions in COVID-19 pandemics. The fact that only a small subset of people infected with SARS-CoV-2 develop severe disease suggests that there have to be some predisposing factors, but biomarkers that reliably predict disease severity have not been found so far. Since overactivation of the immune system is implicated in a severe form of COVID-19 and the IgG glycosylation is known to be involved in the regulation of different immune processes, we evaluated the association of inter-individual variation in IgG N-glycome composition with the severity of COVID-19. The analysis of 166 severe and 167 mild cases from hospitals in Spain, Italy and Portugal revealed statistically significant differences in the composition of the IgG N-glycome. The most notable difference was the decrease in bisecting N-acetylglucosamine (GlcNAc) in severe patients from all three cohorts. IgG galactosylation was also lower in severe cases in all cohorts, but the difference in galactosylation was not statistically significant after correction for multiple testing. To our knowledge, this is the first study exploring IgG N-glycome variability in COVID-19 severity.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Tea Petrovic", + "author_inst": "Genos Glycoscience Research Laboratory" + }, + { + "author_name": "Ines Alves", + "author_inst": "Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal" + }, + { + "author_name": "Dario Bugada", + "author_inst": "Emergency and Intensive Care Department, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy" + }, + { + "author_name": "Julio Pascual", + "author_inst": "Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain" + }, + { + "author_name": "Frano Vuckovic", + "author_inst": "Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia" + }, + { + "author_name": "Andrea Skelin", + "author_inst": "Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia" + }, + { + "author_name": "Joana Gaifem", + "author_inst": "Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal" + }, + { + "author_name": "Judit Villar", + "author_inst": "Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain" + }, + { + "author_name": "Manuel M Vicente", + "author_inst": "Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal" + }, + { + "author_name": "Angela Fernandes", + "author_inst": "Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal" + }, + { + "author_name": "Ana M Dias", + "author_inst": "Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal" + }, + { + "author_name": "Ivan-Christian Kurolt", + "author_inst": "University Hospital for Infectious Diseases \"Dr. Fran Mihaljevic\", Zagreb, Croatia" + }, + { + "author_name": "Alemka Markotic", + "author_inst": "University Hospital for Infectious Diseases Dr. Fran Mihaljevic, Zagreb, Croatia" + }, + { + "author_name": "Dragan Primorac", + "author_inst": "St. Catharine Hospital, Zagreb" + }, + { + "author_name": "Adriana Soares", + "author_inst": "Internal Medicine Department, Hospital Beatriz Angelo, Loures, Portugal" + }, + { + "author_name": "Luis Malheiro", + "author_inst": "Medical Faculty, University of Porto, Porto, Portugal" + }, + { + "author_name": "Irena Trbojevic-Akmacic", + "author_inst": "Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia" + }, + { + "author_name": "Miguel Abreu", + "author_inst": "Institute of Biomedical Sciences of Abel Salazar, University of Porto, Porto, Portugal" + }, + { + "author_name": "Rui Sarmento e Castro", + "author_inst": "Institute of Biomedical Sciences of Abel Salazar, University of Porto, Porto, Portugal" + }, + { + "author_name": "Silvia Bettinelli", + "author_inst": "Biobank Unit, ASST Papa Giovanni XXIII, Bergamo, Italy" + }, + { + "author_name": "Annapaola Callegaro", + "author_inst": "Biobank Unit, ASST Papa Giovanni XXIII, Bergamo, Italy" + }, + { + "author_name": "Marco Arosio", + "author_inst": "Biobank Unit, ASST Papa Giovanni XXIII, Bergamo, Italy" + }, + { + "author_name": "Lorena Sangiorgio", + "author_inst": "Biobank Unit, ASST Papa Giovanni XXIII, Bergamo, Italy" + }, + { + "author_name": "Luca Lorini", + "author_inst": "Emergency and Intensive Care Department, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy" + }, + { + "author_name": "Xavier Castells", + "author_inst": "Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain" + }, + { + "author_name": "Juan P Horcajada", + "author_inst": "Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain" + }, + { + "author_name": "Salome Pinho", + "author_inst": "Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal" + }, + { + "author_name": "Massimo Allegri", + "author_inst": "Pain Service, Policlinico of Monza Hospital, 20090 Monza, Italy" + }, + { + "author_name": "Clara Barrios", + "author_inst": "Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain" + }, + { + "author_name": "Gordan Lauc", + "author_inst": "University of Zagreb" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.16.20214171", "rel_title": "Face masks to prevent transmission of COVID-19: a systematic review and meta-analysis", @@ -1135423,37 +1138492,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.10.18.344622", - "rel_title": "An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants", - "rel_date": "2020-10-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.18.344622", - "rel_abs": "The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE22.v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain (RBD) followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. Variant N501Y in the RBD, which has emerged in a rapidly spreading lineage (B.1.1.7) in England, enhances affinity for wild type ACE2 20-fold but remains tightly bound to engineered sACE22.v2.4. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kui K Chan", - "author_inst": "Orthogonal Biologics, Inc." - }, - { - "author_name": "Timothy JC Tan", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Krishna K Narayanan", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Erik Procko", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.10.19.343954", "rel_title": "Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium", @@ -1135873,6 +1138911,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.14.20212167", + "rel_title": "Anxiety Levels among Healthcare Professionals during Covid-19 Pandemic: A Multifactorial Study", + "rel_date": "2020-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212167", + "rel_abs": "The current study focuses on psychological stress level among doctors, estimated by calculating anxiety score. For the assessment of anxiety levels, the GAD-7 scale was used. Chi-Square test and Odd ratios were calculated among the exposed and not exposed groups involved in the management of COVID-19 patients. Results revealed increased anxiety levels in the exposed group. Besides, the availability of personal protective equipments and stress from the family to quit the job were the substantial contributing factors that increased anxiety. Based on the results, it is proposed that the concern administrative authorities should consider these findings to facilitate medical healthcare professionals.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Arif Malik", + "author_inst": "Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore-Pakistan" + }, + { + "author_name": "Muhammad Mansoor Hafeez", + "author_inst": "The University of Lahore" + }, + { + "author_name": "Muhammad Asim Rana", + "author_inst": "Bahria International Hospital, Lahore" + }, + { + "author_name": "Sulayman Waquar", + "author_inst": "Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore-Pakistan" + }, + { + "author_name": "rabail alam", + "author_inst": "Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore-Pakistan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.10.16.20213298", "rel_title": "Systematic review of reviews of symptoms and signs of COVID-19 in children and adolescents", @@ -1137008,77 +1140081,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.14.20212415", - "rel_title": "CoViD-19, learning from the past: A wavelet and cross-correlation analysis of the epidemic dynamics looking to emergency calls and Twitter trends in Italian Lombardy region", - "rel_date": "2020-10-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212415", - "rel_abs": "The first case of Coronavirus Disease 2019 in Italy was detected on February the 20th in Lombardy region. Since that date, Lombardy has been the most affected Italian region by the epidemic, and its healthcare system underwent a severe overload during the outbreak. From a public health point of view, therefore, it is fundamental to provide healthcare services with tools that can reveal possible new health system stress periods with a certain time anticipation, which is the main aim of the present study. Moreover, the sequence of law decrees to face the epidemic and the large amount of news generated in the population feelings of anxiety and suspicion. Considering this whole complex context, it is easily understandable how people \"overcrowded\" social media with messages dealing with the pandemic, and emergency numbers were overwhelmed by the calls. Thus, in order to find potential predictors of possible new health system overloads, we analysed data both from Twitter and emergency services comparing them to the daily infected time series at a regional level. Particularly, we performed a wavelet analysis in the time-frequency plane, to finely discriminate over time the anticipation capability of the considered potential predictors. In addition, a cross-correlation analysis has been performed to find a synthetic indicator of the time delay between the predictor and the infected time series. Our results show that Twitter data are more related to social and political dynamics, while the emergency calls trends can be further evaluated as a powerful tool to potentially forecast new stress periods. Since we analysed aggregated regional data, and taking into account also the huge geographical heterogeneity of the epidemic spread, a future perspective would be to conduct the same analysis on a more local basis.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Bruno Alessandro Rivieccio", - "author_inst": "Department of Laboratory Medicine, Division of Anatomic Pathology, Niguarda Hospital, Milan, Italy" - }, - { - "author_name": "Alessandra Micheletti", - "author_inst": "Department of Environmental Science and Policy, University of Milan, Milan, Italy" - }, - { - "author_name": "Manuel Maffeo", - "author_inst": "Department of Biomedical Sciences for Health, University of Milan, Milan, Italy" - }, - { - "author_name": "Matteo Zignani", - "author_inst": "Department of Computer Science, University of Milan, Milan, Italy" - }, - { - "author_name": "Alessandro Comunian", - "author_inst": "Department of Earth Sciences, University of Milan, Milan, Italy" - }, - { - "author_name": "Federica Nicolussi", - "author_inst": "Department of Economics, Management and Quantitative Methods & Data Science Research Center, University of Milan, Milan, Italy" - }, - { - "author_name": "Silvia Salini", - "author_inst": "Department of Economics, Management and Quantitative Methods & Data Science Research Center, University of Milan, Milan, Italy" - }, - { - "author_name": "Giancarlo Manzi", - "author_inst": "Department of Economics, Management and Quantitative Methods & Data Science Research Center, University of Milan, Milan, Italy" - }, - { - "author_name": "Francesco Auxilia", - "author_inst": "Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; ASST FBF-Sacco, Milan, Italy" - }, - { - "author_name": "Mauro Giudici", - "author_inst": "Department of Earth Sciences, University of Milan, Milan, Italy" - }, - { - "author_name": "Giovanni Naldi", - "author_inst": "Department of Environmental Science and Policy, University of Milan, Milan, Italy" - }, - { - "author_name": "Sabrina Gaito", - "author_inst": "Department of Computer Science, University of Milan, Milan, Italy" - }, - { - "author_name": "Silvana Castaldi", - "author_inst": "Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Fondazione IRCCS Ca Granda Ospedale Maggiore, Milan, Italy" - }, - { - "author_name": "Elia Biganzoli", - "author_inst": "Department of Clinical Sciences and Community Health & Data Science Research Center, University of Milan, Milan, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.14.20212555", "rel_title": "Multi-organ impairment in low-risk individuals with long COVID", @@ -1137410,6 +1140412,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.16.342410", + "rel_title": "Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro", + "rel_date": "2020-10-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.16.342410", + "rel_abs": "The SARS-COV-2 pandemic and the global spread of coronavirus disease 2019 (COVID-19) urgently calls for efficient and safe antiviral treatment strategies. A straightforward approach to speed up drug development at lower costs is drug repurposing. Here we investigated the therapeutic potential of targeting the host- SARS-CoV-2 interface via repurposing of clinically licensed drugs and evaluated their use in combinatory treatments with virus- and host-directed drugs. We tested the antiviral potential of repurposing the antifungal itraconazole and the antidepressant fluoxetine on the production of infectious SARS-CoV-2 particles in the polarized Calu-3 cell culture model and evaluated the added benefit of a combinatory use of these host-directed drugs with remdesivir, an inhibitor of viral RNA polymerase. Drug treatments were well-tolerated and potent impaired viral replication was observed with all drug treatments. Importantly, both itraconazole-remdesivir and fluoxetine-remdesivir combinations inhibited the production of infectious SARS-CoV-2 particles > 90% and displayed synergistic effects in commonly used reference models for drug interaction. Itraconazole-Remdesivir and Fluoxetine-Remdesivir combinations are promising therapeutic options to control SARS-CoV-2 infection and severe progression of COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ursula Rescher", + "author_inst": "Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation, University of Muenster" + }, + { + "author_name": "Sebastian Schloer", + "author_inst": "Institute of Medical Biochemistry, Center for Molecular Biology of Inflammation, University of Muenster" + }, + { + "author_name": "Linda Brunotte", + "author_inst": "Institute of Molecular Virology, Center for Molecular Biology of Inflammation, Muenster University" + }, + { + "author_name": "Angeles Mecate-Zambrano", + "author_inst": "Institute of Molecular Virology, Center for Molecular Biology of Inflammation, Muenster University" + }, + { + "author_name": "Shuyu Zheng", + "author_inst": "Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki" + }, + { + "author_name": "Jing Tang", + "author_inst": "Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki" + }, + { + "author_name": "Stephan Ludwig", + "author_inst": "Institute of Molecular Virology, Center for Molecular Biology of Inflammation, University of Muenster" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.10.16.339937", "rel_title": "Peptide vaccine candidate mimics the heterogeneity of natural SARS-CoV-2 immunity in convalescent humans and induces broad T cell responses in mice models", @@ -1138754,57 +1141799,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.10.15.339838", - "rel_title": "Inhibition of SARS-CoV-2 viral entry in vitro upon blocking N- and O-glycan elaboration", - "rel_date": "2020-10-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.15.339838", - "rel_abs": "The Spike protein of SARS-CoV-2, its receptor binding domain (RBD), and its primary receptor ACE2 are extensively glycosylated. The impact of this post-translational modification on viral entry is yet unestablished. We expressed different glycoforms of the Spike-protein and ACE2 in CRISPR-Cas9 glycoengineered cells, and developed corresponding SARS-CoV-2 pseudovirus. We observed that N- and O-glycans had only minor contribution to Spike-ACE2 binding. However, these carbohydrates played a major role in regulating viral entry. Blocking N-glycan biosynthesis at the oligomannose stage using both genetic approaches and the small molecule kifunensine dramatically reduced viral entry into ACE2 expressing HEK293T cells. Blocking O-glycan elaboration also partially blocked viral entry. Mechanistic studies suggest multiple roles for glycans during viral entry. Among them, inhibition of N-glycan biosynthesis enhanced Spike-protein proteolysis. This could reduce RBD presentation on virus, lowering binding to host ACE2 and decreasing viral entry. Overall, chemical inhibitors of glycosylation may be evaluated for COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Qi Yang", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Thomas A. Hughes", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Anju Kelkar", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Xinheng Yu", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Kai Cheng", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Sheldon J. Park", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "We-Chiao Huang", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Jonathan F. Lovell", - "author_inst": "State University of New York, Buffalo, NY, USA" - }, - { - "author_name": "Sriram Neelamegham", - "author_inst": "State University of New York, Buffalo, NY, USA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.10.14.339952", "rel_title": "Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung", @@ -1139156,6 +1142150,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.15.340604", + "rel_title": "Quantitative Assays Reveal Cell Fusion at Minimal Levels of SARS-CoV-2 Spike Protein and Fusion-from-Without", + "rel_date": "2020-10-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.15.340604", + "rel_abs": "Cell entry of the pandemic virus SARS-CoV-2 is mediated by its spike protein S. As main antigenic determinant, S protein is in focus of antibody-based prophylactic and therapeutic strategies. Besides particle-cell fusion, S mediates fusion between infected and uninfected cells resulting in syncytia formation. Here we present quantitative assay systems covering not only particle-cell and cell-cell fusion, but also demonstrating fusion-from-without (FFWO), the formation of syncytia induced by S-containing viral particles in absence of newly synthesized S protein. Based on complementation of split {beta}-galactosidase and virus-like-particles (VLPs) displaying S protein, this assay can be performed at BSL-1. All three assays provided readouts with a high dynamic range and signal-to-noise ratios covering several orders of magnitude. The data obtained confirm the enhancing effect of trypsin and overexpression of angiotensin-converting enzyme 2 (ACE2) on membrane fusion. Neutralizing antibodies as well as sera from convalescent patients inhibited particle-cell fusion with high efficiency. Cell-cell fusion, in contrast, was only moderately inhibited despite requiring much lower levels of S protein, which were below the detection limit of flow cytometry and Western blot. The data indicate that syncytia formation as a pathological consequence in tissues of Covid-19 patients can proceed at low levels of S protein and may not be effectively prevented by antibodies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Samuel A. Theuerkauf", + "author_inst": "Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Langen, Germany" + }, + { + "author_name": "Alexander Michels", + "author_inst": "Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Langen, Germany" + }, + { + "author_name": "Vanessa Riechert", + "author_inst": "Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Langen, Germany" + }, + { + "author_name": "Thorsten J. Maier", + "author_inst": "Division Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institut, Langen, Germany" + }, + { + "author_name": "Egbert Flory", + "author_inst": "Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany" + }, + { + "author_name": "Klaus Cichutek", + "author_inst": "Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Langen, Germany" + }, + { + "author_name": "Christian J. Buchholz", + "author_inst": "Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Langen, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.14.339986", "rel_title": "A Common Methodological Phylogenomics Framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones", @@ -1140168,49 +1143205,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.13.20211797", - "rel_title": "Use of antivirals and antibiotics for COVID-19 in Mexico City: A Real-World Multicenter Cohort Study", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20211797", - "rel_abs": "AimTo evaluate all-cause mortality risk in patients with laboratory-confirmed COVID-19 in Mexico City treated with repurposed antivirals and antibiotics.\n\nMethodsThis real-world retrospective cohort study contemplated 395,343 patients evaluated for suspected COVID-19 between February 24 and September 14, 2020 in 688 primary-to-tertiary medical units in Mexico City. Patients were included with a positive RT-PCR for SARS-CoV-2; those receiving unspecified antivirals, excluded; and antivirals prescribed in <30 patients, eliminated. Survival and mortality risks were determined for patients receiving antivirals, antibiotics, both, or none.\n\nResults136,855 patients were analyzed; mean age 44.2 (SD:16.8) years; 51.3% were men. 16.6% received antivirals (3%), antibiotics (10%), or both (3.6%). Antivirals studied were Oseltamivir (n=8414), Amantadine (n=319), Lopinavir-Ritonavir (n=100), Rimantadine (n=61), Zanamivir (n=39), and Acyclovir (n=36). Survival with antivirals (73.7%, p<0.0001) and antibiotics (85.8%, p<0.0001) was lower than no antiviral/antibiotic (93.6%). After multivariable adjustment, increased risk of death occurred with antivirals (HR=1.72, 95%CI:1.61-1.84) in ambulatory (HR=4.7, 95%CI:3.94-5.62) and non-critical (HR=2.03, 95%CI:1.86-2.21) patients. Oseltamivir increased mortality risk in the general population (HR=1.72, 95%CI:1.61-1.84), ambulatory (HR=4.79, 95%CI:4.01-5.75), non-critical (HR=2.05, 95%CI:1.88-2.23), and pregnancy (HR=8.35, 95%CI:1.77-39.30); as well as hospitalized (HR=1.13, 95%CI:1.01-1.26) and critical patients (HR:1.22, 95%CI:1.05-1.43) after propensity score-matching. Antibiotics were a risk factor in general population (HR=1.13, 95%CI:1.08-1.19) and pediatrics (HR=4.22, 95%CI:2.01-8.86), but a protective factor in hospitalized (HR=0.81, 95%CI:0.77-0.86) and critical patients (HR=0.67, 95%CI:0.63-0.72).\n\nConclusionsNo significant benefit for repurposed antivirals was observed; oseltamivir was associated with increased mortality. Antibiotics increased mortality risk in the general population but may increase survival in hospitalized and critical patients.\n\nWHAT IS ALREADY KNOWNO_LICurrent recommendations for using repurposed antivirals and antibiotics for COVID-19 are conflicting.\nC_LIO_LIFew antivirals (i.e. lopinavir-ritonavir) have been shown to provide no additional benefit for COVID-19 in clinical trials; other antivirals may be having widespread use in real-world settings without formal assessment in clinical trials.\nC_LIO_LIReal-world use of repurposed antivirals and antibiotics for COVID-19 in population-based studies have not been performed; important populations have been left largely understudied (ambulatory patients, pregnant women, and pediatrics).\nC_LI\n\nWHAT THIS STUDY ADDSO_LIThis is the first real-world observational study evaluating amantadine, rimantadine, zanamivir, and acyclovir for COVID-19; no registered studies to evaluate these drugs exist. Only one study has evaluated risk of death for oseltamivir. Lopinavir-ritonavir have been previously evaluated in clinical trials.\nC_LIO_LIRepurposed antivirals and antibiotics were commonly prescribed in 688 ambulatory units and hospitals of Mexico City despite unclear recommendations for their use out of clinical trials.\nC_LIO_LIOseltamivir was associated with increased mortality risk; other repurposed antivirals (zanamivir, amantadine, rimantadine, and acyclovir) had no significant and consistent impact on mortality. Antibiotics were associated with increased mortality risk in the general population but may increase survival in hospitalized and critical patients.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Javier Mancilla-Galindo", - "author_inst": "Unidad de Investigacion UNAM-INC, Instituto Nacional de Cardiologia Ignacio Chavez" - }, - { - "author_name": "Jorge Oscar Garcia-Mendez", - "author_inst": "Departamento de Posgrado y Educacion Medica Continua, Instituto Nacional de Cancerologia." - }, - { - "author_name": "Jessica Marquez-Sanchez", - "author_inst": "Departamento de Infectologia, Instituto Nacional de Pediatria" - }, - { - "author_name": "Rodrigo Estefano Reyes-Casarrubias", - "author_inst": "Facultad de Medicina, Universidad Nacional Autonoma de Mexico." - }, - { - "author_name": "Eduardo Aguirre-Aguilar", - "author_inst": "Departamento de Atencion Institutcional Continua y Urgencias, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Hector Isaac Rocha-Gonzalez", - "author_inst": "Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional" - }, - { - "author_name": "Ashuin Kammar-Garcia", - "author_inst": "Departamento de Atencion Institucional Continua y Urgencias, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.10.13.20178483", "rel_title": "Automated chest radiograph diagnosis: A Twofer for tuberculosis and Covid-19", @@ -1140554,6 +1143548,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.10.12.20211573", + "rel_title": "Preventing COVID-19 spread in closed facilities by regular testing of employees - an efficient intervention in long-term care facilities and prisons", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211573", + "rel_abs": "BackgroundDifferent levels of control measures were introduced to contain the global COVID-19 pandemic, many of which have been controversial, particularly the comprehensive use of diagnostic tests. Regular testing of high-risk individuals (pre-existing conditions, older than 60 years of age) has been suggested by public health authorities. The WHO suggested the use of routine screening of residents, employees, and visitors of long-term care facilities (LTCF) to protect the resident risk group. Similar suggestions have been made by the WHO for other closed facilities including incarceration facilities (e.g., prisons or jails), wherein parts of the U.S., accelerated release of approved inmates is taken as a measure to mitigate COVID-19.\n\nMethods and findingsHere, the simulation model underlying the pandemic preparedness tool CovidSim 1.1 (http://covidsim.eu/) is extended to investigate the effect of regularly testing of employees to protect immobile resident risk groups in closed facilities. The reduction in the number of infections and deaths within the risk group is investigated. Our simulations are adjusted to reflect the situation of LTCFs in Germany, and incarceration facilities in the U.S.\n\nCOVID-19 spreads in closed facilities due to contact with infected employees even under strict confinement of visitors in a pandemic scenario without targeted protective measures. Testing is only effective in conjunction with targeted contact reduction between the closed facility and the outside world - and will be most inefficient under strategies aiming for herd immunity. The frequency of testing, the quality of tests, and the waiting time for obtaining test results have noticeable effects. The exact reduction in the number of cases depends on disease prevalence in the population and the levels of contact reductions. Testing every 5 days with a good quality test and a processing time of 24 hours can lead up to a 40% reduction in the number of infections. However, the effects of testing vary substantially among types of closed facilities and can even be counterproductive in U.S. IFs.\n\nConclusionsThe introduction of COVID-19 in closed facilities is unavoidable without a thorough screening of persons that can introduce the disease into the facility. Regular testing of employees in closed facilities can contribute to reducing the number of infections there, but is only meaningful as an accompanying measure, whose economic benefit needs to be assessed carefully.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Henri Christian Junior Tsoungui Obama", + "author_inst": "Hochschule Mittweida" + }, + { + "author_name": "Nessma Adil Mahmoud Yousif", + "author_inst": "Hochschule Mittweida" + }, + { + "author_name": "Looli Hassan Mohamed Alawam Nemer", + "author_inst": "AIMS Cameroon" + }, + { + "author_name": "Pierre Marie Ngougoue Ngougoue", + "author_inst": "Hochschule Mittweida" + }, + { + "author_name": "Gideon Akumah Ngwa", + "author_inst": "University of Buea" + }, + { + "author_name": "Miranda Teboh-Ewungkem", + "author_inst": "Lehigh University" + }, + { + "author_name": "Kristan Schneider", + "author_inst": "Hochschule Mittweida" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.10.13.20211524", "rel_title": "From more testing to smart testing: data-guided SARS-CoV-2 testing choices", @@ -1142046,41 +1145083,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.13.20211839", - "rel_title": "Measurement of small droplet aerosol concentrations in public spaces using handheld particle counters", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20211839", - "rel_abs": "We investigate the role of aerosols in the transmission of SARS-CoV-2 in public spaces. Direct measurement of aerosol concentrations however has proven technically difficult; we propose the use of handheld particle counters as a novel and easily applicable method to measure aerosol concentrations. This allow us to perform measurements in typical public spaces, each differing in volume, number of people and ventilation rate. These data are used to estimate the relation between aerosol persistence time and the risk of infection with SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "G Aernout Somsen", - "author_inst": "Cardiology Centers of the Netherlands" - }, - { - "author_name": "Cees van Rijn", - "author_inst": "Institute of Physics, University of Amsterdam" - }, - { - "author_name": "Stefan Kooy", - "author_inst": "Instute of Physics, University of Amsterdam" - }, - { - "author_name": "Reinout A Bem", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Daniel Bonn", - "author_inst": "Institute of Physics, University of Amsterdam" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.13.20211904", "rel_title": "Background and concurrent factors predicting non-adherence to public health preventive measures during the chronic phase of the COVID-19 pandemic", @@ -1142376,6 +1145378,133 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.14.335893", + "rel_title": "Co-infection of influenza A virus enhances SARS-CoV-2 infectivity", + "rel_date": "2020-10-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.14.335893", + "rel_abs": "The upcoming flu season in the northern hemisphere merging with the current COVID-19 pandemic raises a potentially severe threat to public health. Through experimental co-infection of IAV with either pseudotyped or SARS-CoV-2 live virus, we found that IAV pre-infection significantly promoted the infectivity of SARS-CoV-2 in a broad range of cell types. Remarkably, increased SARS-CoV-2 viral load and more severe lung damage were observed in mice co-infected with IAV in vivo. Moreover, such enhancement of SARS-CoV-2 infectivity was not seen with several other viruses probably due to a unique IAV segment as an inducer to elevate ACE2 expression. This study illustrates that IAV has a special nature to aggravate SARS-CoV-2 infection, and prevention of IAV is of great significance during the COVID-19 pandemic.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Lei Bai", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Yongliang Zhao", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Jiazhen Dong", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Simeng Liang", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Ming Guo", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Xinjin Liu", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Xin Wang", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Zhixiang Huang", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Xiaoyi Sun", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Zhen Zhang", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Lianghui Dong", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Qianyun Liu", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Yucheng Zheng", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Danping Niu", + "author_inst": "Wuhan University" + }, + { + "author_name": "Min Xiang", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Kun Song", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Jiajie Ye", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Wenchao Zheng", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Zhidong Tang", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Mingliang Tang", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Yu Zhou", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Chao Shen", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Ming Dai", + "author_inst": "Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Li Zhou", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Yu Chen", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Huan Yan", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Ke Lan", + "author_inst": "State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China" + }, + { + "author_name": "Ke Xu", + "author_inst": "Wuhan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.13.338541", "rel_title": "Simple rapid in vitro screening method for SARS-CoV-2 anti-virals that identifies potential cytomorbidity-associated false positives", @@ -1143507,65 +1146636,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.09.20208876", - "rel_title": "Using an Agent-Based Model to Assess K-12 School Re-openings Under Different COVID-19 Spread Scenarios - United States, School Year 2020/21", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20208876", - "rel_abs": "School-age children play a key role in the spread of airborne viruses like influenza due to the prolonged and close contacts they have in school settings. As a result, school closures and other non-pharmaceutical interventions were recommended as the first line of defense in response to the novel coronavirus pandemic (COVID-19). Assessing school reopening scenarios is a priority for states, administrators, parents, and children in order to balance educational disparities and negative population impacts of COVID-19. To address this challenge, we used an agent-based model that simulates communities across the United States including daycares, primary, and secondary schools to quantify the relative health outcomes of reopening schools. We explored different reopening scenarios including remote learning, in-person school, and several hybrid options that stratify the student population into cohorts (also referred to as split cohort) in order to reduce exposure and disease spread. In addition, we assessed the combined impact of reduced in-person attendance in workplaces (e.g., through differing degrees of reliance on telework and/or temporary workplace closings) and school reopening scenarios to quantify the potential impact of additional transmission pathways contributing to COVID-19 spread. Scenarios where split cohorts of students return to school in non-overlapping formats resulted in significant decreases in the clinical attack rate (i.e., the percentage of symptomatic individuals), potentially by as much as 75%. These split cohort scenarios have impacts which are only modestly lesser than the most impactful 100% distance learning scenario. Split cohort scenarios can also significantly avert the number of cases-approximately 60M and 28M-depending on the scenario, at the national scale over the simulated eight-month period. We found the results of our simulations to be highly dependent on the number of workplaces assumed to be open for in-person business, as well as the initial level of COVID-19 incidence within the simulated community. Our results show that reducing the number of students attending school leads to better health outcomes, and the split cohort option enables part-time in-classroom education while substantially reducing risk. The results of this study can support decisions regarding optimal school reopening strategies that at the population level balance education and the negative health outcomes of COVID-19.\n\nDisclaimerThis work was sponsored by the United States Centers for Disease Control and Prevention. Los Alamos National Laboratory, an affirmative action/equal opportunity employer, is operated by Triad National Security, LLC, for the National Nuclear Security Administration of the United States Department of Energy under contract # 19FED1916814CKC. Approved for public release: LA-UR-20-27982.\n\nThe findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention or Los Alamos National Laboratory.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Timothy C. Germann", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Manhong Z. Smith", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Lori Dauelsberg", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Geoffrey Fairchild", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Terece Turton", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Morgan E. Gorris", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Chrysm Watson Ross", - "author_inst": "University of New Mexico and Los Alamos National Laboratory" - }, - { - "author_name": "James P. Ahrens", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Daniel D. Hemphill", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Carrie Manore", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Sara Y Del Valle", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.10.20210427", "rel_title": "Mathematical Modeling of COVID-19 pandemic in the African continent", @@ -1144161,6 +1147231,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.10.10.20210591", + "rel_title": "Predicting mortality of individual COVID-19 patients: A multicenter Dutch cohort", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20210591", + "rel_abs": "ObjectiveDevelop and validate models that predict mortality of SARS-CoV-2 infected patients admitted to the hospital.\n\nDesignRetrospective cohort study\n\nSettingA multicenter cohort across ten Dutch hospitals including patients from February 27 to June 8 2020.\n\nParticipantsSARS-CoV-2 positive patients (age [≥] 18) admitted to the hospital.\n\nMain Outcome Measures21-day mortality evaluated by the area under the receiver operatory curve (AUC), sensitivity, specificity, positive predictive value and negative predictive value. The predictive value of age was explored by comparison with age-based rules used in practice and by excluding age from analysis.\n\nResults2273 patients were included, of whom 516 had died or discharged to palliative care within 21 days after admission. Five feature sets, including premorbid, clinical presentation and laboratory & radiology values, were derived from 80 features. Additionally, an ANOVA-based data-driven feature selection selected the ten features with the highest F-values: age, number of home medications, urea nitrogen, lactate dehydrogenase, albumin, oxygen saturation (%), oxygen saturation is measured on room air, oxygen saturation is measured on oxygen therapy, blood gas pH and history of chronic cardiac disease. A linear logistic regression (LR) and non-linear tree-based gradient boosting (XGB) algorithm fitted the data with an AUC of 0.81 (95% confidence interval 0.77 to 0.85) and 0.82 (0.79 to 0.85), respectively, using the ten selected features. Both models outperformed age-based decision rules used in practice (AUC of 0.69, 0.65 to 0.74 for age > 70). Furthermore, performance remained stable when excluding age as predictor (AUC of 0.78, 0.75 to 0.81)\n\nConclusionBoth models showed excellent performance and had better test characteristics than age-based decision rules, using ten admission features readily available in Dutch hospitals. The models hold promise to aid decision making during a hospital bed shortage.", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Maarten C Ottenhoff", + "author_inst": "Maastricht University" + }, + { + "author_name": "Lucas A Ramos", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Wouter Potters", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Marcus LF Janssen", + "author_inst": "Maastricht University" + }, + { + "author_name": "Deborah Hubers", + "author_inst": "Maastricht University" + }, + { + "author_name": "Dan Pina-Fuentes", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Rajat Thomas", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Iwan CC van der Horst", + "author_inst": "Maastricht University Medical Center" + }, + { + "author_name": "Christian Herff", + "author_inst": "Maastricht University" + }, + { + "author_name": "Pieter Kubben", + "author_inst": "Maastricht University Medical Center" + }, + { + "author_name": "Paul WG Elbers", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Henk A Marquering", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Max Welling", + "author_inst": "University of Amsterdam" + }, + { + "author_name": "Shi Hu", + "author_inst": "University of Amsterdam" + }, + { + "author_name": "Suat Simsek", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Martijn D de Kruif", + "author_inst": "Zuyderland Medical Center" + }, + { + "author_name": "Tom Dorman", + "author_inst": "Zuyderland Medical Center" + }, + { + "author_name": "Lucas M Fleuren", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Michiel Schinkel", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Peter G Noordzij", + "author_inst": "St Antonius Hospital" + }, + { + "author_name": "Joop P van den Bergh", + "author_inst": "VieCuri Medical Centre" + }, + { + "author_name": "Caroline E Wyers", + "author_inst": "VieCuri Medical Centre" + }, + { + "author_name": "David TP Buis", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Joost Wiersinga", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Ella HC van den Hout", + "author_inst": "Northwest Clinics" + }, + { + "author_name": "Auke C Reidinga", + "author_inst": "Martini ziekenhuis" + }, + { + "author_name": "Daisy Rusch", + "author_inst": "Martini ziekenhuis" + }, + { + "author_name": "Kim CE Sigaloff", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Renee A Douma", + "author_inst": "Flevoziekenhuis" + }, + { + "author_name": "Lianne de Haan", + "author_inst": "Flevoziekenhuis" + }, + { + "author_name": "Egill A Fridgeirsson", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Niels C Gritters van de Oever", + "author_inst": "Treant Zorggroep" + }, + { + "author_name": "Roger JMW Rennenberg", + "author_inst": "Maastricht University Medical Center" + }, + { + "author_name": "Guido van Wingen", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Marcel JH Aries", + "author_inst": "Maastricht University Medical Center" + }, + { + "author_name": "Martijn Beudel", + "author_inst": "Amsterdam University Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.09.20203430", "rel_title": "Gargle-Direct: Extraction-Free Detection of SARS-CoV-2 using Real-time PCR (RT-qPCR) of Saline Gargle Rinse Samples", @@ -1145729,57 +1148958,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.08.20208785", - "rel_title": "Rapid and Low-cost Sampling for Detection of Airborne SARS-CoV-2 in Dehumidifier Condensate", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20208785", - "rel_abs": "Airborne spread of COVID-19 by infectious aerosol is all but certain. However, easily implemented approaches to assess the actual environmental threat are currently unavailable. We present a simple approach with the potential to rapidly provide information about the prevalence of SARS-CoV-2 in the atmosphere at any location. We used a portable dehumidifier as a readily available and affordable tool to collect airborne virus in the condensate. The dehumidifiers were deployed in selected locations of a hospital ward with patients reporting flu like symptoms which could possibly be due to COVID-19 over three separate periods of one week. Samples were analyzed frequently for both virus envelope protein and SARS-CoV-2 RNA. In several samples across separate deployments, condensate from dehumidifiers tested positive for the presence of SARS-CoV-2 antigens and confirmed using two independent assays. RNA was detected, but not attributable to SARS-CoV-2. Our results point to a facile pool testing method to sample air in any location in the world and assess the presence and concentration of the infectious agent in order to obtain quantitative risk assessment of exposure, designate zones as hot spots and minimize the need for individual testing which may often be time consuming, expensive and laborious.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Parikshit Moitra", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Maha Alafeef", - "author_inst": "University ofMaryland School of Medicine and University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Ketan Dighe", - "author_inst": "University ofMaryland Baltimore County and University of Maryland School of Medicine" - }, - { - "author_name": "Priyanka Ray", - "author_inst": "University of Maryland Baltimore County and University of Maryland School of Medicine" - }, - { - "author_name": "James Chang", - "author_inst": "University of maryland Medical Center" - }, - { - "author_name": "Sai Sathish Ramamurthy", - "author_inst": "University of Maryland Baltimore County and Sri Sathya Sai Insistute of Higher Learning" - }, - { - "author_name": "Xudong Ge", - "author_inst": "University of Maryland Baltimore County" - }, - { - "author_name": "Dipanjan Pan", - "author_inst": "University of Maryland baltimore County and University of Maryland School of Medicine" - }, - { - "author_name": "Govind Rao", - "author_inst": "UMBC" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.08.20208991", "rel_title": "Covid Pandemic Analysis using Regression", @@ -1145930,6 +1149108,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.09.20209601", + "rel_title": "Cleaning and Re-Use of cobas(R) 6800/8800 Processing Plates for the SARS-CoV-2 Assay", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209601", + "rel_abs": "Real-time reverse transcription polymerase chain reaction (rRT-PCR) is the primary method used for the detection and diagnosis of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since SARS-CoV-2s entrance into the United States, numerous clinical laboratories and in vitro diagnostic companies have developed rRT-PCR assays, some requiring specialized materials and reagents. One such assay includes the cobas(R) SARS-CoV-2 Qualitative Assay for use on the cobas(R) 6800/8800 (Roche Molecular Systems, Inc.). Since initiation of this assay at our facility, our ability to run testing at full capacity has been limited due to restricted supply of the omni cobas(R) Processing Plate (Product Number 05534917001), a 96 deep well plate used for all sample processing and total nucleic acid extraction via MagNA Pure magnetic beads. To work around this limiting factor, we have successfully designed and tested a cleaning protocol utilizing the widely available laboratory resources of bleach, ethyl-alcohol and autoclaving, for omni cobas(R) Processing Plate re-use.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "R Matthew Sperling", + "author_inst": "Indiana University Health" + }, + { + "author_name": "Ryan F Relich", + "author_inst": "Indiana University School of Medicine" + }, + { + "author_name": "Bryan H Schmitt", + "author_inst": "Indiana University School of Medicine" + }, + { + "author_name": "Drew Bell", + "author_inst": "Indiana University School of Medicine" + }, + { + "author_name": "Lauren A Cooper", + "author_inst": "Indiana University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.10.11.20210831", "rel_title": "The SIR model estimates incorrectly the basic reproduction number for the covid-19 epidemic", @@ -1147190,29 +1150403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.08.20209064", - "rel_title": "Social Distancing with Movement Restrictions and the Effective Replication Number of COVID-19: Multi-Country Analysis Based on Phone Mobility Data", - "rel_date": "2020-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209064", - "rel_abs": "Linking phone mobility data to the effective replication number (Rt) could help evaluation of the impact of social distancing on the coronavirus disease 2019 (COVID-19) spread and estimate the time lag (TL) needed for the effect of movement restrictions to appear. We used a time-series analysis to discover how patterns of five indicators of mobility data relate to changes in Rt of 125 countries distributed over three groups based on Rt-mobility correlation. Group 1 included 71 countries in which Rt correlates negatively with residential and positively with other mobility indicators. Group 2 included 25 countries showing an opposite correlation pattern to Group 1. Group 3 included the 29 remaining countries. We chose the best-fit TL based on forecast and linear regression models. We used linear mixed models to evaluate how mobility indicators and the stringency index (SI) relate with Rt. SI reflects the strictness of governmental responses to COVID-19. With a median of 14 days, TLs varied across countries as well as across groups of countries. There was a strong negative correlation between SI and Rt in most countries belonging to Group 1 as opposed to Group 2. SI (units of 10%) associated with decreasing Rt in Group 1 [{beta} -0.15, 95% CI -0.15 - (-0.14)] and Group 3 [-0.05, -0.07 - (-0.03)], whereas, in Group 2, SI associated with increasing Rt (0.13, 0.11 - 0.16). Mobile phone mobility data could contribute evaluations of the impact of social distancing with movement restrictions on the spread of the COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mounir Ould Setti", - "author_inst": "University of Eastern Finland" - }, - { - "author_name": "Ari Voutilainen", - "author_inst": "University of Eastern Finland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.10.20210492", "rel_title": "Transmission of SARS-CoV-2 from Children and Adolescents", @@ -1147608,6 +1150798,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.11.335406", + "rel_title": "Unsupervised explainable AI for simultaneous molecular evolutionary study of forty thousand SARS-CoV-2 genomes", + "rel_date": "2020-10-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.11.335406", + "rel_abs": "Unsupervised AI (artificial intelligence) can obtain novel knowledge from big data without particular models or prior knowledge and is highly desirable for unveiling hidden features in big data. SARS-CoV-2 poses a serious threat to public health and one important issue in characterizing this fast-evolving virus is to elucidate various aspects of their genome sequence changes. We previously established unsupervised AI, a BLSOM (batch-learning SOM), which can analyze five million genomic sequences simultaneously. The present study applied the BLSOM to the oligonucleotide compositions of forty thousand SARS-CoV-2 genomes. While only the oligonucleotide composition was given, the obtained clusters of genomes corresponded primarily to known main clades and internal divisions in the main clades. Since the BLSOM is explainable AI, it reveals which features of the oligonucleotide composition are responsible for clade clustering. The BLSOM has powerful image display capabilities and enables efficient knowledge discovery about viral evolutionary processes.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Toshimichi Ikemura", + "author_inst": "Nagahama Institute of Bio-Science and Technology" + }, + { + "author_name": "Kennosuke Wada", + "author_inst": "Nagahama Institute of Bio-Science and Technology" + }, + { + "author_name": "Yoshiko Wada", + "author_inst": "Nagahama Institute of Bio-Science and Technology" + }, + { + "author_name": "Yuki Iwasaki", + "author_inst": "Nagahama Institute of Bio-Science and Technology" + }, + { + "author_name": "Takashi Abe", + "author_inst": "Faculty of Engineering, Niigata University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.10.12.335513", "rel_title": "Alternate primers for whole-genome SARS-CoV-2 sequencing", @@ -1149056,85 +1152281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.07.20208645", - "rel_title": "Low zinc levels at clinical admission associates with poor outcomes in COVID-19", - "rel_date": "2020-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208645", - "rel_abs": "BackgroundBiomarkers to predict Coronavirus disease-19 (COVID-19) outcome early at infection are urgently needed to improve prognosis and treatment. Zinc balances immune responses and also has a proven direct antiviral action against some viruses. Importantly, zinc deficiency (ZD) is a common condition in elderly and individuals with chronic diseases, two groups with more severe COVID-19 outcomes. We hypothesize that serum zinc content (SZC) influences COVID-19 disease progression and thus might represent a useful biomarker.\n\nMethodsWe run a retrospective observational study with 249 COVID-19 patients admitted in Hospital del Mar. We have studied COVID-19 severity and progression attending to SZC at admission. In parallel we have studied SARS-CoV2 replication in the Vero E6 cell line modifying zinc concentrations.\n\nFindingsOur study demonstrates a correlation between serum zinc levels and COVID-19 outcome. Serum zinc levels lower than 50 {micro}g/dl at admission correlated with worse clinical presentation, longer time to reach stability and higher mortality. Our in vitro results indicate that low zinc levels favor viral expansion in SARS-CoV2 infected cells.\n\nInterpretationSZC is a novel biomarker to predict COVID-19 outcome. We encourage performing randomized clinical trials to study zinc supplementation as potential prophylaxis and treatment with people at risk of zinc deficiency.\n\nFundingSpanish Ministry of Science and Innovation, \"Maria de Maeztu\" Programme for Units of Excellence in R&D and Secretaria dUniversitats i Recerca del Departament dEconomia i Coneixement of the Generalitat de Catalunya. Instituto Carlos III Fondos de Investigaciones Sanitarias (FIS), CIBER on Frailty and Healthy Ageing and FEDER funds", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Marina Vogel", - "author_inst": "Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Marc Tallo-Parra", - "author_inst": "Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Victor Herrera-Fernandez", - "author_inst": "Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Gemma Perez-Vilaro", - "author_inst": "Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Miguel Chillon", - "author_inst": "Department of Biochemistry and Molecular Biology and Institute of Neurosciences, Edifici H, Universitat Autonoma de Barcelona, E-08193, Bellaterra, Spain." - }, - { - "author_name": "Xavier Nogues", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Internal Medicine, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERFES" - }, - { - "author_name": "Silvia Gomez-Zorrilla", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Inmaculada Lopez-Montesinos", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Judit Villar", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Maria Luisa Sorli-Redo", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Juan Pablo Horcajada", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Natalia Garcia-Giralt", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - }, - { - "author_name": "Julio Pascual", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Nephrology, Hospital del Mar, Autonomous University of Barcelona, Spain." - }, - { - "author_name": "Juana Diez", - "author_inst": "Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Ruben Vicente", - "author_inst": "Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain." - }, - { - "author_name": "Robert Guerri-Fernandez", - "author_inst": "Institut Mar d'Investigacions Mediques, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar, Autonomous University of Barcelona, Spain; CIBERF" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.06.20208025", "rel_title": "Enoxaparin is associated with lower rates of thrombosis, kidney injury, and mortality than Unfractionated Heparin in hospitalized COVID patients", @@ -1149350,6 +1152496,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.08.20209510", + "rel_title": "Global projections of potential lives saved from COVID-19 through universal mask use", + "rel_date": "2020-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209510", + "rel_abs": "BACKGROUNDSocial distancing mandates (SDM) have reduced health impacts from COVID-19 but also resulted in economic downturns that have led many nations to relax SDM. Until deployment of an efficacious and equitable vaccine, intervention options to reduce COVID-19 mortality and minimize restrictive SDM are sought by society.\n\nMETHODSA susceptible-exposed-infectious-recovered (SEIR) deterministic transmission model was parameterized with data on reported deaths, cases, and select covariates to predict infections and deaths from COVID-19 through March 01, 2021. We explore three scenarios: a \"non-adaptive\" scenario where neither mask use or SDM adapt to changing conditions, a \"reference\" where current national levels of mask use are maintained and SDM reintroduced when deaths rise, and an increase in mask use to 95% coverage levels (\"universal mask\"). We reviewed published studies to set priors on the magnitude of reduction in transmission through increasing mask use.\n\nRESULTSMask use was estimated at 59.0% of people globally on October 19, 2020. Universal mask use could avert 733,310 deaths (95% UI 385,981 to 1,107,759) between October 27, 2020 and March 01, 2021, the difference between the predicted 2.95 million deaths (95% UI 2.70 to 3.35) in the reference scenario and 2.22 million deaths (95% UI 2.00 to 2.45) in the universal mask scenario over this time period.\n\nCONCLUSIONSThe cumulative toll of the COVID-19 pandemic could be substantially reduced by the universal adoption of masks before the availability of a vaccine. This low-cost, low-barrier policy, whether customary or mandated, has enormous health benefits with presumed marginal economic costs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Emmanuela Gakidou", + "author_inst": "IHME" + }, + { + "author_name": "- IHME COVID-19 Forecasting Team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.10.20210484", "rel_title": "Development of wastewater pooled surveillance of SARS-CoV-2 from congregate living settings", @@ -1150774,65 +1153943,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.07.20207282", - "rel_title": "COVID-19, Type-2 Diabetes, and Associated Health Outcomes in China: Results from a Nationwide Survey of 10,545 Adults", - "rel_date": "2020-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20207282", - "rel_abs": "ObjectiveThis study examined the associations between type-2 diabetes (T2DM) and self-reported/familial COVID-19 infection and investigated health-related outcomes among those with diabetes during Chinas nationwide quarantine.\n\nMethodsThe 2020 China COVID-19 Survey was administered anonymously via social media (WeChat) across China. It was completed by 10,545 adults in all of mainland Chinas 31 provinces. The survey consisted of 74 items covering sociodemographic characteristics, preventive measures for COVID-19, lifestyle behaviors, and health-related outcomes during the period of quarantine. Regression models examined associations among study variables, adjusting for covariates.\n\nResultsDiabetes was associated with a six-fold increased risk of reporting COVID-19 infection among respondents or their family members. Among patients with diabetes, individuals who rarely wore masks had double the risk of suspected COVID-19 infection compared with those who always wore masks, with an inverse J-shaped relationship between face mask wearing and suspected COVID-19 infection. People with T2DM tended to have both poor knowledge of COVID-19 and poor compliance with preventive measures, despite perceiving a high risk of personal infection (40.0% among respondents reporting T2DM and 8.0% without T2DM). Only 54-55% of these respondents claimed to consistently practice preventive measures, including wearing face masks. Almost 60% of those with T2DM experienced food or medication shortages during the quarantine period, which was much higher than those without T2DM. Importantly, respondents who experienced medication shortages reported a 63% higher COVID-19 infection rate.\n\nConclusionsT2DM was associated with an increased risk of self-reported personal and family member COVID-19 infection, which is mitigated by consistent use of face masks.\n\nFundingThe project is supported in part by research grants from the China Medical Board (Grant number: 16-262), the National Key Research and Development Program of China (Grant Number: 2017YFC0907200 & 2017YFC0907201), the University Alliance of the Silk Road (Grant number: 2020LMZX002), and Xian Jiaotong University Global Health Institute.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSDuring the COVID-19 pandemic, it has become increasingly clear that the risk factors for initial infection and subsequent poor health outcomes include, but are not limited to, social vulnerability, economic status, older age, and obesity. While community-wide masking has been recommended by the World Health Organization to control COVID-19, its overall effectiveness has not been clearly evaluated.\n\nAdded value of this studyThrough an anonymous survey disseminated and promoted through WeChat, the largest social media platform in China, we sought to understand the impact of COVID-19 on the health, wellbeing, and health-related behaviors of adults in China. Specifically, this study examined how individuals with chronic diseases managed the threat, including their COVID-19 related knowledge, attitudes, and adherence to preventive measures such as wearing face masks, and their disease-related self-care.\n\nImplications of the available evidenceThis study demonstrates that type-2 diabetes mellitus is associated with an increased risk of COVID-19 infection, which is mitigated by consistent use of face masks.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Zumin Shi", - "author_inst": "Human Nutrition Department, College of Health Sciences, QU Health, Qatar University, Doha, Qatar" - }, - { - "author_name": "Alice Yan", - "author_inst": "Center for Advancing Population Science, Division of General Internal Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA" - }, - { - "author_name": "Paul Zimmet", - "author_inst": "Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia" - }, - { - "author_name": "Xiaoming Sun", - "author_inst": "Global Health Institute, School of Public Health, Xian Jiaotong University Health Science Center, Xian, China" - }, - { - "author_name": "Nayla Cristina do Vale Moreira", - "author_inst": "Faculty of Medicine, Federal University of Ceara (FAMED-UFC), Brazil" - }, - { - "author_name": "Lawrence J Cheskin", - "author_inst": "Department of Nutrition and Food Studies, George Mason University, Fairfax, VA 220030, USA" - }, - { - "author_name": "Liming Wang", - "author_inst": "National Center for Chronic and Non-communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" - }, - { - "author_name": "Weidong Qu", - "author_inst": "Centers for Water and Health, Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fu" - }, - { - "author_name": "Hong Yan", - "author_inst": "School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China" - }, - { - "author_name": "Akhtar Hussain", - "author_inst": "Faculty of Health Sciences, Nord University, Norway; International Diabetes Federation. 166 Chaussee de La Hulpe B-1170, Brussels, Belgium" - }, - { - "author_name": "Youfa Wang", - "author_inst": "Global Health Institute, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.07.20208280", "rel_title": "A high-throughput microfluidic nano-immunoassay for detecting anti-SARS-CoV-2 antibodies in serum or ultra-low volume dried blood samples", @@ -1151051,6 +1154161,121 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.10.08.332544", + "rel_title": "Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant.", + "rel_date": "2020-10-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.08.332544", + "rel_abs": "The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. With an increased infection and transmission rate, it is imperative to determine whether antibodies induced against the D614 isolate may cross-neutralize against the G614 variant. In this report, profiling of the anti-SARS-CoV-2 humoral immunity reveals similar neutralization profiles against both S protein variants, albeit waning neutralizing antibody capacity at the later phase of infection. These findings provide further insights towards the validity of current immune-based interventions.\n\nIMPORTANCERandom mutations in the viral genome is a naturally occurring event that may lead to enhanced viral fitness and immunological resistance, while heavily impacting the validity of licensed therapeutics. A single point mutation from aspartic acid (D) to glycine (G) at position 614 of the SARS-CoV-2 spike (S) protein, termed D614G, has garnered global attention due to the observed increase in transmissibility and infection rate. Given that a majority of the developing antibody-mediated therapies and serological assays are based on the S antigen of the original Wuhan reference sequence, it is crucial to determine if humoral immunity acquired from the original SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against the novel prevailing D614G variant.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Cheryl Yi-Pin Lee", + "author_inst": "Singapore Immunology Network, A*STAR" + }, + { + "author_name": "Siti Naqiah Amrun", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Rhonda Sin-Ling Chee", + "author_inst": "Singapore Immunology Network, A*STAR" + }, + { + "author_name": "Yun Shan Goh", + "author_inst": "Singapore Immunology Network, A*STAR" + }, + { + "author_name": "Tze Minn Mak", + "author_inst": "National Public Health Laboratory, National Centre for Infectious Diseases" + }, + { + "author_name": "Sophie Octavia", + "author_inst": "Ministry of Health" + }, + { + "author_name": "Nicholas Yeo", + "author_inst": "Singapore Immunology Network A*STAR" + }, + { + "author_name": "Zi Wei Chang", + "author_inst": "Singapore Immunology Network-A*STAR" + }, + { + "author_name": "Matthew Zirui Tay", + "author_inst": "Singapore Immunology Network, A*STAR" + }, + { + "author_name": "Anthony Torres", + "author_inst": "Singapore Immunology Network, A*STAR" + }, + { + "author_name": "Guillaume Carissimo", + "author_inst": "Singapore Immunology Network, A*STAR" + }, + { + "author_name": "Chek Meng Poh", + "author_inst": "Singapore Immunology Network-BMSI-A*STAR" + }, + { + "author_name": "Siew-Wai Fong", + "author_inst": "Singapore Immunology Network, A*STAR" + }, + { + "author_name": "Bei Wang", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Sandy Lee", + "author_inst": "Singapore Immunology Network, A*STAR" + }, + { + "author_name": "Barnaby Young", + "author_inst": "National Centre for Infectious Diseases" + }, + { + "author_name": "Seow Yen Tan", + "author_inst": "Changi General Hospital" + }, + { + "author_name": "Yee Sin Leo", + "author_inst": "National Centre for Infectious Disease" + }, + { + "author_name": "David Chien Boon Lye", + "author_inst": "National Centre of Infectious Diseases" + }, + { + "author_name": "Raymond TP Lin", + "author_inst": "National Centre for Infectious Diseases" + }, + { + "author_name": "Sebastian Maurer-Stroh", + "author_inst": "Bioinformatics Institute" + }, + { + "author_name": "Bernett T. K. Lee", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Cheng-I Wang", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Laurent Renia", + "author_inst": "Singapore Immunology Network-BMSI-A*STAR" + }, + { + "author_name": "Lisa F. P. Ng", + "author_inst": "Singapore Immunology Network" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.08.332452", "rel_title": "Possible transmission flow of SARS-CoV-2 based on ACE2 features", @@ -1152251,125 +1155476,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.05.20206730", - "rel_title": "Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya", - "rel_date": "2020-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20206730", - "rel_abs": "We generated 274 SARS-CoV-2 genomes from samples collected during the early phase of the Kenyan pandemic. Phylogenetic analysis identified 8 global lineages and at least 76 independent SARS-CoV-2 introductions into Kenyan coast. The dominant B.1 lineage (European origin) accounted for 82.1% of the cases. Lineages A, B and B.4 were detected from screened individuals at the Kenya-Tanzania border or returning travellers but did not lead to established transmission. Though multiple lineages were introduced in coastal Kenya within three months following the initial confirmed case, none showed extensive local expansion other than cases characterised by lineage B.1, which accounted for 45 of the 76 introductions. We conclude that the international points of entry were important conduits of SARS-CoV-2 importations. We speculate that early public health responses prevented many introductions leading to established transmission, but nevertheless a few undetected introductions were sufficient to give rise to an established epidemic.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "George Githinji", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Zaydah R deLaurent", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Khadija Said Mohamed", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Donwilliams O Omuoyo", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Peter M Macharia", - "author_inst": "Population Health Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya" - }, - { - "author_name": "John M Morobe", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Edward Otieno", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Samson M Kinyanjui", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Ambrose Agweyu", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Eric Maitha", - "author_inst": "Department of Health, Kilifi county" - }, - { - "author_name": "Ben Kitole", - "author_inst": "Department of Health, Kilifi county" - }, - { - "author_name": "Thani Suleiman", - "author_inst": "Department of Health, Mombasa county" - }, - { - "author_name": "Mohamed Mwakinangu", - "author_inst": "Department of Health, Kwale county" - }, - { - "author_name": "John Nyambu", - "author_inst": "Department of Health, Taita Taveta county" - }, - { - "author_name": "John Otieno", - "author_inst": "Department of Health, Lamu county" - }, - { - "author_name": "Barke Salim", - "author_inst": "Department of Health, Tana River county" - }, - { - "author_name": "Kadondi Kasera", - "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" - }, - { - "author_name": "John Kiiru", - "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" - }, - { - "author_name": "Rashid Aman", - "author_inst": "Ministry of Health, Government of Kenya, Nairobi, Kenya" - }, - { - "author_name": "Edwine Barasa", - "author_inst": "Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya" - }, - { - "author_name": "George Warimwe", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Philip Bejon", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Benjamin Tsofa", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Lynette Isabella Ochola-Oyier", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "D James Nokes", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Charles N Agoti", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.02.20205674", "rel_title": "Mental health symptoms in a cohort of hospital healthcare workers following the first peak of the Covid-19 pandemic in the United Kingdom.", @@ -1152593,6 +1155699,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.05.20206664", + "rel_title": "Antibody reactivity to SARS-CoV-2 in adults from the Vancouver metropolitan area, Canada", + "rel_date": "2020-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20206664", + "rel_abs": "BackgroundQuantifying antibody reactivity against multiple SARS-CoV-2 antigens at the population level may help understand individual differences in COVID-19 severity. Pre-existing low antibody cross-reactivity may be particularly prevalent among childcare providers, including pediatric health care workers (HCW) who may be more exposed to circulating coronaviruses.\n\nMethodsCross-sectional study that included adults in the Vancouver area in British Columbia (BC), Canada, between May 17 and June 19, 2020. SARS-CoV-2 seroprevalence was ascertained by measuring total SARS-CoV-2 IgG/M/A antibodies against a recombinant spike (S1) protein and adjusted for bias due to false-positive and false-negative test results. A novel, high sensitivity multiplex assay was also used to profile IgG against four SARS-CoV-2 antigens, SARS-CoV and four circulating coronaviruses.\n\nFindingsAmong 276 participants (71% HCW), three showed evidence of direct viral exposure, yielding an adjusted seroprevalence of 0.60% [95%CI 0% - 2.71%], with no difference between HCW and non-HCW, or between paediatric and adult HCW. Among the 273 unexposed individuals, 7.3% [95%CI 4.5% - 11.1%], 48.7 [95%CI 42.7% - 54.8%] and 82.4% [95%CI 77.4% - 86.7%] showed antibody reactivity against SARS-CoV-2 RBD, N or Spike proteins, respectively. SARS-CoV-2 reactivity did not significantly correlate with age, sex, did not significantly differ between HCW and non-HCW (prevalence 1.0% vs 1.0%; P=1.00) and between pediatric and adult HCW (0.7% vs 1.6%; P=0.54), and modestly correlated with reactivity to circulating coronaviruses (Spearman rho range: 0.130 to 0.224 for 7 significant (FDR 5%), out of 16 correlations, from 36 correlations tested).\n\nInterpretationA substantial proportion of individuals showed low, but detectable antibody reactivity against SARS-CoV-2 antigens in this population despite low evidence of direct SARS-CoV-2 exposure.\n\nFundingNIAID/NIH", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Abdelilah Majdoubi", + "author_inst": "BC Children Hospital Research Institute, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Christina Michalski", + "author_inst": "BC Children Hospital Research Institute, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Sarah E O'Connell", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, Maryland 20892, Unite" + }, + { + "author_name": "Sarah Dada", + "author_inst": "BC Children Hospital Research Institute, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Sandeep Narpala", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, Maryland 20892, Unite" + }, + { + "author_name": "Jean Gelinas", + "author_inst": "Department of Anesthesiology, Surrey Memorial Hospital, Surrey, British Columbia, Canada" + }, + { + "author_name": "Disha Mehta", + "author_inst": "Department of Anesthesiology, Surrey Memorial Hospital, Surrey, British Columbia, Canada Department of Department of Anesthesiology, Pharmacology and Therapeut" + }, + { + "author_name": "Claire Cheung", + "author_inst": "BC Children Hospital Research Institute, Department of Pediatrics, University of British Columbia, Vancouver, Canada" + }, + { + "author_name": "Manjula Basappa", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, Maryland 20892, Unite" + }, + { + "author_name": "Aaron C Liu", + "author_inst": "BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Matthias Gorges", + "author_inst": "BC Children Hospital Research Institute, Department of Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, B" + }, + { + "author_name": "Vilte E Barakauskas", + "author_inst": "Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Jennifer Mehalko", + "author_inst": "National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc" + }, + { + "author_name": "Dominic Esposito", + "author_inst": "National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc" + }, + { + "author_name": "Inna Sekirov", + "author_inst": "British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Agatha N Jassem", + "author_inst": "British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada" + }, + { + "author_name": "David M Goldfarb", + "author_inst": "BC Children Hospital Research Institute, Department of Pediatrics, Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, University" + }, + { + "author_name": "Daniel C Douek", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, Maryland 20892, Unite" + }, + { + "author_name": "Adrian B McDermott", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, Maryland 20892, Unite" + }, + { + "author_name": "Pascal M Lavoie", + "author_inst": "BC Children Hospital Research Institute, Vancouver, British Columbia, Canada" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.06.20207878", "rel_title": "The potential impact of intervention strategies on COVID-19 transmission in Malawi: A mathematical modelling study", @@ -1153965,41 +1157166,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.10.04.20206680", - "rel_title": "Serological testing in addition to PCR screening for the re-opening of American colleges and universities: potential for cost-savings without compromising pandemic mitigation", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.04.20206680", - "rel_abs": "ImportanceThe addition of a serological testing could reduce the overall testing costs of a PCR-based SARS-CoV-2 testing reopening plan for colleges/universities in the United States, without compromising the efficacy of the testing plan.\n\nObjectivesTo determine whether a college/university reopening SARS-CoV-2 testing plan that includes serological testing can be cost-saving compared to a PCR-only testing.\n\nDesign, Setting, and ParticipantsWe assessed costs of serological testing in addition to PCR testing under various scenarios of university sizes (2000, 10,000, and 40,000) and epidemic conditions (initial antibody prevalence 2.5-15%; cumulative SARS-CoV-2 incidence during the school year 5-30%) of SARS-CoV-2 in the United States. We estimated total testing costs and relative percentage of cost-savings of different screening (i.e. targeted/ universal) and testing (i.e. in-sourcing/out-sourcing) scenarios between September 2020-May 2021.\n\nMain Outcomes and MeasuresTesting costs of serological testing and PCR testing, Relative percentage of cost saving by including serology testing in addition to PCR testing.\n\nResultsIncluding baseline serology testing alongside routine regular PCR testing can reduce total test volumes and related costs throughout the school year. While the total testing cost is likely much lower if regular PCR testing is insourced compared to outsourced ($5 million vs $34 million for university size 10,000), including serologic testing could achieve the up to 20% cost-savings relative to PCR testing alone. The insourcing of serological testing when PCR testing is insourced can achieve greater cost-savings under high initial antibody prevalence (>5%) and cumulative incidence throughout the school year (>10%) at medium and large sized universities. If PCR testing is outsourced, however, the inclusion of serological testing becomes always preferred in most university sizes and epidemic conditions.\n\nConclusions and RelevanceWhile regular PCR testing alone is the preferred strategy for containing epidemics, including serology testing may help achieve cost-savings if outbreaks are anticipated, or if baseline seropositivity is high.\n\nKey Points (96/100)O_ST_ABSQuestionC_ST_ABSCan the addition of a serological testing reduce the overall testing costs of a PCR-based SARS-CoV-2 testing reopening plan for universities in the United States?\n\nFindingsThis costing study suggested that inclusion of serological testing in addition to outsourced PCR testing as part of a university re-opening strategy could achieve cost savings of up to 20%. The amount of savings, or additional costs, is dependent on insourcing or outsourcing of testing, epidemic conditions and university size.\n\nMeaningThe relative cost-savings depend strongly on whether PCR and/or serology are being insourced or outsourced, university sizes and cumulative incidence.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Youngji Jo", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Ruby Singh", - "author_inst": "Boston University" - }, - { - "author_name": "Gabriella Rao", - "author_inst": "Boston University" - }, - { - "author_name": "Sandro Galea", - "author_inst": "Boston University" - }, - { - "author_name": "Brooke E Nichols", - "author_inst": "Boston University School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.10.05.20206920", "rel_title": "Development of a customised data management system for a COVID-19-adapted colorectal cancer pathway", @@ -1154163,6 +1157329,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.04.20206466", + "rel_title": "Rapid SARS-CoV-2 antigen detection by immunofluorescence - a new tool to detect infectivity", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.04.20206466", + "rel_abs": "The evaluated SARS-CoV-2 antigen rapid fluorescence immunoassays reliably identified patients within the first 5 days of symptom onset, when respiratory secretions carried high viral loads. This high performance suggests that these tests might play an important role for future PCR-independent strategies to detect early or infective cases.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Lorena Porte", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Paulette Legarraga", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Mirentxu Iruretagoyena", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Valeska Vollrath", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Gabriel Pizarro", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Jos\u00e9 Manuel Munita", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Rafael Araos", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Thomas Weitzel", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.03.20206375", "rel_title": "Renin Angiotensin System Inhibition and Susceptibility and Outcomes from COVID-19: A Systematic Review and Meta-analysis of 69,200 COVID-19 Patients", @@ -1155283,85 +1158496,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.03.20206128", - "rel_title": "Characteristics and outcomes of hospitalized adults with COVID-19 in Nepal: a multicenter, prospective cohort study", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20206128", - "rel_abs": "IntroductionThere is limited data on clinical course and outcomes of hospitalized adults with COVID-19 in Nepal. Thus, it is imperative to characterize the features of this disease in the domestic context.\n\nMethodologyWe identified all adult patients with laboratory-confirmed COVID-19 admitted to five different hospitals in Nepal from June 15 to July 15, 2020. We collected epidemiological, socio-cultural and clinicopathologic data, and stratified the patients based on their symptom status.\n\nResultsThe study included 220 patients with an overall median age of 31.5 (25-37) years, and 181 (82.3%) were males. 159 (72.3%) were asymptomatic, and 163 (74.1%) were imported cases. Of 217 patients with the available data, 110 (50.7%) reported their annual household income less than 2000 US dollars, and 122 (56.2%) practiced Pranayama (yogic rhythmic breathing techniques) regularly. Eight patients (3.6%) required supplemental oxygen and two patients (0.9%) died. None of the patients who practiced Pranayama regularly required supplemental oxygen. Compared to asymptomatic patients, symptomatic patients had greater proportion of females (31.1% vs. 12.6%, p=0.001), imported cases (85.2% vs. 69.8%, p=0.02), illiterates (26.8% vs. 12.1%, p=0.01), alcohol users (43.3% vs. 24.5%, p=0.01), patients feeling stigmatized by society (45.8% vs. 22.6%, p=0.001), and had higher platelet count (253x 109/L vs. 185x109/L, p=0.02).\n\nConclusionsMost cases were imported, asymptomatic young males, with very few deaths. Pranayama practice was associated with protection against severe COVID-19, but more data is needed to substantiate this. The association of platelets count with symptom status in the Nepalese population needs further exploration.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ashok Chaudhary", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Uday Narayan Singh", - "author_inst": "Narayani Hospital,Birgunj, Nepal" - }, - { - "author_name": "Pramod Paudel", - "author_inst": "Bharatpur Hospital, Bharatpur, Nepal" - }, - { - "author_name": "Niresh Thapa", - "author_inst": "Karnali Academy of Health Sciences, Jumla, Nepal" - }, - { - "author_name": "Kamal Khadka", - "author_inst": "Rapti Provincial Hospital, Tulsipur, Nepal" - }, - { - "author_name": "Prameshwar Kumar Sah", - "author_inst": "Narayani Hospital, Birgunj, Nepal" - }, - { - "author_name": "Sher Bahadur Kamar", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Jagadish Joshi", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Kamar Hasan Ansari", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Shree Ram Tiwari", - "author_inst": "Bharatpur Hospital, Bharatpur, Nepal" - }, - { - "author_name": "Sarbesh Sharma", - "author_inst": "Rapti Provincial Hospital, Tulsipur, Nepal" - }, - { - "author_name": "Sanjay Kumar Jaiswal", - "author_inst": "Anamnagar Diagnostic Center and Polyclinic, Kathmandu, Nepal" - }, - { - "author_name": "Ramesh Joshi", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - }, - { - "author_name": "Samikchya Baskota", - "author_inst": "Anamnagar Diagnostic Center and Polyclinic, Kathmandu, Nepal" - }, - { - "author_name": "Arjun Prasad Tiwari", - "author_inst": "Karnali Academy of Health Sciences, Jumla, Nepal" - }, - { - "author_name": "Hem Raj Pandey", - "author_inst": "Seti Provincial Hospital, Dhangadhi, Nepal" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.06.20207662", "rel_title": "Which factors should be included in triage? An online survey of the attitudes of the UK general public to pandemic triagedilemmas", @@ -1155565,6 +1158699,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.06.20207589", + "rel_title": "Epidemic characteristics of respiratory viruses in hospitals in a Chinese city during the SARS-CoV-2 epidemic", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207589", + "rel_abs": "The SARS-CoV-2 virus first broke out in China in early 2020. The early symptoms of COVID-19 are similar to those of influenza. Therefore, during the epidemic, patients with similar symptoms will be tested for multiple pathogens at the same time. In order to control the spread of SARS-CoV-2, China has taken many measures. Under this special situation, have the types and epidemic characteristics of respiratory viruses changed? The nucleic acid test results of influenza A virus, influenza B virus and respiratory syncytial virus, as well as the antibody test results of 8 common respiratory viruses of Jinan Central Hospital were collected before and after the occurrence of SARS-CoV-2, and age distribution and time distribution characteristics were statisticed. Furthermore the epidemiological characteristics of this new virus before and after the SARS-CoV-2 epidemic was compared. In the early stage of the SARS-CoV-2 epidemic, influenza A, influenza B and respiratory syncytial virus nucleic acid test samples were large, and the positive rate of the three viruses was high. After that, the sample size and positive rate decreased significantly. No co-infection of SARS-CoV-2 and other viruses was found in our hospital. The sample size before the SARS-CoV-2 outbreak was larger than that after the outbreak, but the positive rate of the outbreak was lower than that after the outbreak. And the infection rate of children decreased in the middle and late stages of the epidemic. This is because since January 23, in order to prevent the spread of the new crown epidemic, my country has adopted measures such as wearing masks, not gathering together, and quarantining at home. This not only prevents the spread of the new crown virus, but also prevents the common respiratory tract. The spread of the virus has reduced the incidence of residents.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Weihua Yang", + "author_inst": "Jinan central hospital affiliated to shandong first medical university" + }, + { + "author_name": "Jian Chen", + "author_inst": "Department of Chinese Medicine, Jinan central hospital affiliated to Shandong university" + }, + { + "author_name": "Mingjie Xu", + "author_inst": "Department of clinical laboratory, Jinan central hospital affiliated to Shandong first medical university" + }, + { + "author_name": "Jun Wang", + "author_inst": "Department of clinical laboratory, Jinan central hospital affiliated to Shandong first medical university" + }, + { + "author_name": "Huanjie Li", + "author_inst": "Department of clinical laboratory, Jinan central hospital affiliated to Shandong first medical university" + }, + { + "author_name": "Yunshan Wang", + "author_inst": "Department of clinical laboratory, Jinan central hospital affiliated to Shandong first medical university;Shandong province key lab of tumor target molecule, Ji" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.27.20189548", "rel_title": "An in-depth investigation of the safety and immunogenicity of an inactivated SARS-CoV-2 vaccine", @@ -1156829,41 +1160002,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.04.325266", - "rel_title": "Reference ontology and database annotation of the COVID-19 Open Research Dataset (CORD-19)", - "rel_date": "2020-10-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.04.325266", - "rel_abs": "The COVID-19 Open Research Dataset (CORD-19) was released in March 2020 to allow the machine learning and wider research community to develop techniques to answer scientific questions on COVID-19. The dataset consists of a large collection of scientific literature, including over 100,000 full text papers. Annotating training data to normalise variability in biological entities can improve the performance of downstream analysis and interpretation. To facilitate and enhance the use of the CORD-19 data in these applications, in late March 2020 we performed a comprehensive annotation process using named entity recognition tool, TERMite, along with a number of large reference ontologies and vocabularies including domains of genes, proteins, drugs and virus strains. The additional annotation has identified and tagged over 45 million entities within the corpus made up of 62,746 unique biomedical entities. The latest updated version of the annotated data, as well as older versions, is made openly available under GPL-2.0 License for the community to use at: https://github.com/SciBiteLabs/CORD19", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Oliver Giles", - "author_inst": "SciBite" - }, - { - "author_name": "Rachael Huntley", - "author_inst": "SciBite" - }, - { - "author_name": "Anneli Karlsson", - "author_inst": "SciBite" - }, - { - "author_name": "Jane Lomax", - "author_inst": "SciBite" - }, - { - "author_name": "James Malone", - "author_inst": "SciBite" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.10.03.20205278", "rel_title": "Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19", @@ -1157191,6 +1160329,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.02.20206045", + "rel_title": "Safety and efficacy of pharmacotherapy used for the management of COVID 19: A systematic review and meta-analysis of randomized control trials", + "rel_date": "2020-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20206045", + "rel_abs": "BackgroundCOVID-19 is a novel coronavirus, which is highly contagious and a threat to human health, spreading across nearly 235 countries, affecting 33.8 million and causing 1.01 million fatalities as of 22 September 2020. Researchers have invested tremendous efforts to develop vaccines or effective drug therapy but have not yet been fruitful. Hence, we planned to conduct this systematic review and meta-analysis to supplement the readers with comprehensive data and credible information on the safety and efficacyof essential pharmacotherapy during the pharmacological management of COVID-19.\n\nMethodsTheprotocol will be designed based on the updated PRISMA-P 2015 guidelines. An elaborate search of electronic databases such as PubMed/Medline, Web of Science, Scopus, The Cochrane Library, ClinicalTrials.gov, Google Scholar, Medrxiv and other potential databases for articles published during January 2020 to 10 October 2020 is planned to be conducted. Following this,randomized control trials published in English language that assess the safety and efficacy of pharmacotherapy versusplacebo or standard of care or usual care will be evaluated for inclusion. The primary outcomes will include time to clinical recovery and the probability for the negative conversion of COVID-19. Secondary outcomes will quantifythe proportion of patients relieved of symptoms, the all-cause mortality, morbidity, detection of viral RNA, time needed to achieve a negative viral load, ordinal scale changes, ventilatorand oxygen requirements,length of hospital stayand the incidence of adverse and serious adverse events.RevMan V.5.3 computer software packages will be utilised to conduct an accurate statistical analysis of the study. Thebinary random-effects model will be used at a 95 % confidence interval to estimate the weighted effect size ofdichotomous data and continuous data studies. The results of statistical analysis will be considered statistically significant whena p-value <0.05 is attained.\n\nResultsSelected studies will be used to evaluate the safety and efficacy of pharmacotherapy used during the management of the novel COVID-19.\n\nConclusionThis study will be a qualitative and quantitative pool of comprehensive evidence regarding the safety and efficacy of pharmacotherapy on COVID-19.\n\nPROSPERO registrationCRD42020205433", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Sujit Kumar Sah", + "author_inst": "Department of Pharmacy Practice, JSS College of pharmacy, JSS Academy of Higher Education and Research, SS Nagar, Mysuru-570015 Karnataka, India" + }, + { + "author_name": "Krishna Undela", + "author_inst": "Associate Professor\t Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Guwahati, Assam, India" + }, + { + "author_name": "Dr. Sharad Chand", + "author_inst": "NGSMIPS, Nitte (Deemed to be University)" + }, + { + "author_name": "Madhan Ramesh", + "author_inst": "Professor & Head Department of Pharmacy Practice, JSS College of pharmacy JSS Academy of Higher Education and Research, SS Nagar, Mysuru-570015" + }, + { + "author_name": "Subramanian R", + "author_inst": "Department of Rheumatology & Immunology, JSS Medical College & Hospital JSS Academy of Higher Education and Research, SS Nagar, Mysuru-570015" + }, + { + "author_name": "Oliver Joel Gona", + "author_inst": "Department of Pharmacy Practice, JSS College of pharmacy JSS Academy of Higher Education and Research, SS Nagar, Mysuru-570015" + }, + { + "author_name": "Sophia M. George", + "author_inst": "Department of Pharmacy Practice, NGSM Institute of Pharmaceutical Sciences, Paneer, Nitte (Deemed to be University), Deralakatte, Mangaluru- 575018." + }, + { + "author_name": "Nandakumar UP", + "author_inst": "Department of Pharmacy Practice, NGSM Institute of Pharmaceutical Sciences, Paneer, Nitte (Deemed to be University), Deralakatte, Mangaluru- 575018." + }, + { + "author_name": "Santosh Aryal", + "author_inst": "District Coordinator, The Leprosy Mission Nepal, Sunsari and Morang Nepal" + }, + { + "author_name": "Niharika P", + "author_inst": "Department of Pharmacy Practice, TVM College of Pharmacy, Ballari-583101 Karnataka, India" + }, + { + "author_name": "C.S. Shastry", + "author_inst": "Department of Pharmacy Practice, NGSM Institute of Pharmaceutical Sciences, Paneer, Nitte (Deemed to be University), Deralakatte, Mangaluru- 575018." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.02.20205708", "rel_title": "Antigen-based testing but not real-time PCR correlates with SARS-CoV-2 virus culture.", @@ -1158731,77 +1161928,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.01.20205310", - "rel_title": "Prognostic accuracy of MALDI mass spectrometric analysis of plasma in COVID-19", - "rel_date": "2020-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20205310", - "rel_abs": "PurposeSARS-CoV-2 infection poses a global public health problem. There is a critical need for improvements in the noninvasive prognosis of COVID-19. We hypothesized that matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS) analysis combined with bottom-up proteomic analysis of plasma proteins might identify features to predict high and low risk cases of COVID-19.\n\nPatients and MethodsWe used MALDI-TOF MS to analyze plasma small proteins and peptides isolated using C18 micro-columns from a cohort containing a total of 117 cases of high (hospitalized) and low risk (outpatients) cases split into training (n = 88) and validation sets (n= 29). The plasma protein/peptide fingerprint obtained was used to train the algorithm before validation using a blinded test cohort.\n\nResultsSeveral sample preparation, MS and data analysis parameters were optimized to achieve an overall accuracy of 85%, sensitivity of 90%, and specificity of 81% in the training set. In the blinded test set, this signature reached an overall accuracy of 93.1%, sensitivity of 87.5%, and specificity of 100%. From this signature, we identified two distinct regions in the MALDI-TOF profile belonging to the same proteoforms. A combination of 1D SDS-PAGE and quantitative bottom-up proteomic analysis allowed the identification of intact and truncated forms of serum amyloid A-1 and A-2 proteins. Conclusions: We found a plasma proteomic profile that discriminates against patients with high and low risk COVID-19. Proteomic analysis of C18-fractionated plasma may have a role in the noninvasive prognosis of COVID-19. Further validation will consolidate its clinical utility.\n\nKey messageO_ST_ABSWhat is the key question?C_ST_ABSDo individuals infected with SARS-CoV-2 harboring different degree of disease severity have a plasma protein profile that differentiate them and predict the COVID-19 outcome?\n\nWhat is the bottom line?In a series of 117 patients with COVID-19 divided in hospitalized (60) and outpatients (57), differential expression of serum amyloid A-1 (SAA1) and A-2 (SAA2) predict their outcome.\n\nWhy read on?The high mortality rate in SARS-CoV-2 infected individuals requires accurate markers for predicting COVID-19 severity. Plasma levels of SAA1 and SAA2 indicate higher risk of hospitalization and can be used to improve COVID-19 monitoring and therapy.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Lucas Cardoso Lazari", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Fabio de Rose Ghilardi", - "author_inst": "Instituto de Medicina Tropical, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Livia Rosa-Fernandes", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Diego M Assis", - "author_inst": "Bruker do Brasil, Atibaia, Sao Paulo, Brazil" - }, - { - "author_name": "Jose Carlos Nicolau", - "author_inst": "Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil" - }, - { - "author_name": "Veronica Feijoli Santiago", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Talia F Dalcoquio", - "author_inst": "Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil" - }, - { - "author_name": "Claudia Blanes Angeli", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Adriadne Justi Bertolin", - "author_inst": "Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil" - }, - { - "author_name": "Claudio Romero Farias Marinho", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Carsten Wrenger", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Edison Luiz Durigon", - "author_inst": "Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Rinaldo Focaccia Siciliano", - "author_inst": "Heart Institute (InCor), University of Sao Paulo Medical School, Sao Paulo, Brazil" - }, - { - "author_name": "Giuseppe Palmisano", - "author_inst": "Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.30.20204719", "rel_title": "Corticosteroid pulses for hospitalized patients with COVID-19. Effects on mortality and in-hospital stay.", @@ -1159049,6 +1162175,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.10.01.20205112", + "rel_title": "COVID-19 Pandemic in University Hospital: Is There an Effect on The Medical Interns?", + "rel_date": "2020-10-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20205112", + "rel_abs": "IntroductionCoronavirus Disease 2019 (COVID-19) pandemic has disrupted the current healthcare system and carries a major impact to the healthcare workers (HCW). University Malaya Medical Centre (UMMC) has been selected as one of the centres in managing COVID-19 cases in Malaysia. Many HCW including the medical interns, are directly or indirectly involved in the management.\n\nMethodsThis is a cross-sectional, pilot study to determine the impact of the pandemic on UMMC medical interns. A survey which comprises 37-items was used. Data are analysed by Ordinal Logistic Regression Analysis.\n\nResultsOur study shows that medical interns are tired (p = 0.014), starving (p = 0.004), have inadequate exercises (p = 0.004) and burdened with heavy workload (p=0.023) during pandemic period. Many are depressed (p = 0.043), scared to work (p = 0.03), and worried of getting infected (p < 0.05). Some quarrel with their colleagues (p < 0.05), losing contact with friends (p = 0.022) and feel that it will be beneficial to have a peer support group (p = 0.027).\n\nConclusionIn summary, the impact of COVID-19 amongst medical interns is significant and their overall well-being should be protected without jeopardising their training.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "WeiHonn Lim", + "author_inst": "University Malaya Medical Centre" + }, + { + "author_name": "Li Ying Teoh", + "author_inst": "University Malaya Medical Centre" + }, + { + "author_name": "Kanesh Kumaran Seevalingam", + "author_inst": "University Malaya Medical Centre" + }, + { + "author_name": "Shanggar Kuppusamy", + "author_inst": "University of Malaya Medical Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.10.01.20205120", "rel_title": "Biomathematical models for genetic diversity analyses in complete genomes of SARS-CoV-2", @@ -1160505,65 +1163662,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.09.30.317818", - "rel_title": "SARS-CoV-2 Spike protein promotes hyper-inflammatory response that can be ameliorated by Spike-antagonistic peptide and FDA-approved ER stress and MAP kinase inhibitors in vitro", - "rel_date": "2020-10-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.30.317818", - "rel_abs": "SARS-CoV-2 infection causes an inflammatory cytokine storm and acute lung injury. Currently there are no effective antiviral and/or anti-inflammatory therapies. Here we demonstrate that 2019 SARS-CoV-2 spike protein subunit 1 (CoV2-S1) induces high levels of NF-{kappa}B activations, production of pro-inflammatory cytokines and mild epithelial damage, in human bronchial epithelial cells. CoV2-S1-induced NF-{kappa}B activation requires S1 interaction with human ACE2 receptor and early activation of endoplasmic reticulum (ER) stress, and associated unfolded protein response (UPR), and MAP kinase signalling pathways. We developed an antagonistic peptide that inhibits S1-ACE2 interaction and CoV2-S1-induced productions of pro-inflammatory cytokines. The existing FDA-approved ER stress inhibitor, 4-phenylburic acid (4-PBA), and MAP kinase inhibitors, trametinib and ulixertinib, ameliorated CoV2-S1-induced inflammation and epithelial damage. These novel data highlight the potentials of peptide-based antivirals for novel ACE2-utilising CoVs, while repurposing existing drugs may be used as treatments to dampen elevated inflammation and lung injury mediated by SARS-CoV-2.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alan C-Y. Hsu", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Guoqiang Wang", - "author_inst": "Department of Pathogen Biology, College of Basic Medical Science, Jilin University, Changchun 130021, China." - }, - { - "author_name": "Andrew T. Reid", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Punnam Chander Veerati", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Prabuddha S. Pathinayake", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Katie Daly", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Jemma R. Mayall", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Philip M. Hansbro", - "author_inst": "Centenary UTS Centre for Inflammation, Centenary Institute, New South Wales 2050, Australia" - }, - { - "author_name": "Jay C. Horvat", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - }, - { - "author_name": "Fang Wang", - "author_inst": "Department of Pathogen Biology, College of Basic Medical Science, Jilin University, Changchun 130021, China." - }, - { - "author_name": "Peter A. Wark", - "author_inst": "Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, New South Wales 2305, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.09.30.320903", "rel_title": "SARS-CoV-2 viral budding and entry can be modeled using virus-like particles", @@ -1160775,6 +1163873,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.28.20203489", + "rel_title": "Mental health of undocumented college students during the COVID-19 pandemic", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20203489", + "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has caused a surge in mental health problems across the United States, and some reports suggest a more severe impact for racial and ethnic minorities. The present study was conducted to gain a preliminary understanding of the mental health consequences of the COVID-19 pandemic specifically for dreamers, i.e., undocumented immigrants who entered the U.S. as minors. A population of about 150 dreamers currently enrolled at a public university in Delaware were invited to participate in an online survey. The survey contained questions about demographics, mental health, academics, immigration, COVID-19 infection, and unemployment, in addition to mental health screens for anxiety (GAD-7), depression (PHQ-9), and stress (PSS-10). In total, 109 dreamers completed the survey. We observed remarkably high clinical levels of anxiety and depression: 47% of the dreamers met the clinical cutoff for anxiety, 63% met the cutoff for depression, and 67% (2 in 3) met the cutoff for anxiety and/or depression. Rates of anxiety and depression in our sample were significantly higher than those recently reported for college students overall, suggesting that dreamers may be experiencing a more severe mental health impact of the COVID-19 pandemic. We also found that pandemic-induced concerns about finances, COVID-19 infection, immigration, and unemployment (among other factors) were associated with greater anxiety, stress, and depression among the dreamers in our sample. The present findings are consistent with recent predictions by social scientists that the COVID-19 pandemic would have a disproportionately negative impact on the mental health of undocumented immigrants.\n\nHighlightsO_LINearly half the dreamers (47%) met the clinical cutoff for anxiety, and 62% met the clinical cutoff for depression.\nC_LIO_LI2 in 3 dreamers met the clinical cutoff for anxiety and/or depression.\nC_LIO_LIThe percentage of dreamers meeting the cutoff for anxiety (47%) and depression (63%) were significantly higher than observed for college students overall during the pandemic (31% and 41%, respectively).\nC_LIO_LIThe percentage of dreamers meeting the cutoff for anxiety was also significantly higher than previously observed for undocumented college students in a 2015 survey (35%).\nC_LIO_LI60% of dreamers said the pandemic had a serious negative impact on their mental health, while 90% said the pandemic made them more anxious about finances.\nC_LIO_LI90% of dreamers said the pandemic made it harder for them to concentrate on coursework, and 2 in 3 said pandemic-related anxiety hurt their academic performance.\nC_LIO_LIAbout 1 in 3 dreamers are \"extremely worried\" that the pandemic will prevent them from achieving their academic and professional goals.\nC_LIO_LI76% of dreamers said the pandemic increased their fears of DACA termination.\nC_LIO_LI10% of dreamers said they or an immediate family member suspected COVID-19 infection at some point but did not get tested for fear of detainment or deportation.\nC_LIO_LIAbout 1 in 5 dreamers said they would be \"extremely worried\" to seek treatment or have a family member seek treatment for COVID-19 due to fears of detainment or deportation.\nC_LIO_LIDreamers who reported one or both parents lost their job due to the pandemic had significantly greater anxiety and depression scores and were more likely to meet clinical cutoffs for anxiety and depression.\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jarid Goodman", + "author_inst": "Delaware State University" + }, + { + "author_name": "Sharron Xuanren Wang", + "author_inst": "Delaware State University" + }, + { + "author_name": "Rubi A Guadarrama Ornelas", + "author_inst": "Delaware State University" + }, + { + "author_name": "Marina Hernandez Santana", + "author_inst": "Delaware State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.09.28.20202796", "rel_title": "COVID-19 Related Deaths Among Doctors In India", @@ -1162199,97 +1165328,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.30.20194290", - "rel_title": "Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test", - "rel_date": "2020-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20194290", - "rel_abs": "ObjectivesWe evaluated widely-used SARS-CoV-2 serological tests and their potential association with virus neutralization test (VNT) in a cohort of mild COVID-19 patients.\n\nMethodsA total of 439 specimens were longitudinally collected from 76 healthcare workers with RT-PCR-confirmed mild COVID-19. Nine serological assays developed by leading global companies (Abbott, DiaSorin, Siemens, Bio-Rad, Wantai, bioMerieux, Euroimmun) were assessed. For each test the sensitivity to detect SARS-CoV-2 antibodies was determined weekly after symptom onset. Correlation and concordance were assessed using the Spearman and Cohens Kappa coefficients, respectively. Positive percent agreement and negative percent agreement (NPA) with the VNT were also determined.\n\nResultsThe Wantai Total Ab assay targeting the receptor binding domain (RBD) within the S protein presented the best sensitivity at different times during the course of disease. The best correlation between antibody level and neutralizing antibody titer was found with the Euroimmun S1-based IgA assay (Spearman coefficient [95%CI]: 0.71 [0.61-0.79]). A moderate concordance (Kappa [95%CI]: 0.43[0.23-0.63]) as well as the lowest NPA (33%) was found between the Wantai Total Ab assay and the VNT. Compared to the Wantai Total Ab assay, other total Ab or IgG assays targeting the S or the RBD (bioMerieux, DiaSorin, Siemens,) were more concordant with the VNT (Kappa>0.7 for the three tests) and had a higher NPA (range: 90% to 97%).\n\nConclusionsAlthough some assays presented a better concordance with VNT than others, the present findings emphasize that commercialized serological tests including those targeting the RBD cannot substitute VNT for the assessment of functional antibody response.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Antonin Bal", - "author_inst": "Hospices civils de Lyon" - }, - { - "author_name": "Bruno Pozzetto", - "author_inst": "Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France" - }, - { - "author_name": "Mary-Anne Trabaud", - "author_inst": "HCL" - }, - { - "author_name": "Vanessa Escuret", - "author_inst": "HCL" - }, - { - "author_name": "Muriel Rabilloud", - "author_inst": "HCL" - }, - { - "author_name": "Carole Langlois-jacques", - "author_inst": "HCL" - }, - { - "author_name": "Adele Paul", - "author_inst": "HCL" - }, - { - "author_name": "Nicolas Guibert", - "author_inst": "HCL" - }, - { - "author_name": "Constance d'Aubarede", - "author_inst": "HCL" - }, - { - "author_name": "Amelie Massardier", - "author_inst": "HCL" - }, - { - "author_name": "Nicole Fabien", - "author_inst": "HCL" - }, - { - "author_name": "David Goncalves", - "author_inst": "HCL" - }, - { - "author_name": "Andre Boibieux", - "author_inst": "HCL" - }, - { - "author_name": "Florence Morfin", - "author_inst": "HCL" - }, - { - "author_name": "Virginie Pitiot", - "author_inst": "HCL" - }, - { - "author_name": "Francois Gueyffier", - "author_inst": "HCL" - }, - { - "author_name": "Bruno Lina", - "author_inst": "HCL" - }, - { - "author_name": "Jean Baptiste Fassier", - "author_inst": "HCL" - }, - { - "author_name": "Sophie Assant", - "author_inst": "HCL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.30.20201830", "rel_title": "Geospatial Analysis of Individual and Community-Level Socioeconomic Factors Impacting SARS-CoV-2 Prevalence and Outcomes", @@ -1162473,6 +1165511,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.29.20204172", + "rel_title": "The Challenge of Forecasting Demand of Medical Resources and Supplies During a Pandemic: A Comparative Evaluation of Three Surge Calculators for COVID-19", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20204172", + "rel_abs": "Ever since the World Health Organization (WHO) declared the new coronavirus disease 2019 (COVID-19) as a pandemic, there has been a public health debate concerning medical resources and supplies including hospital beds, intensive care units (ICU), ventilators, and Protective Personal Equipment (PPE). Forecasting COVID-19 dissemination has played a key role in informing healthcare professionals and governments on how to manage overburdened healthcare systems. However, forecasting during the pandemic remained challenging and sometimes highly controversial. Here, we highlight this challenge by performing a comparative evaluation for the estimations obtained from three COVID-19 surge calculators under different social distancing approaches, taking Lebanon as a case study. Despite discrepancies in estimations, the three surge calculators used herein agree that there will be a relative shortage in the capacity of medical resources and a significant surge in PPE demand as the social distancing policy is removed. Our results underscore the importance of implementing containment interventions including social distancing in alleviating the demand for medical care during the COVID-19 pandemic in the absence of any medication or vaccine. It is said that \"All models are wrong, but some are useful,\" in this paper we highlight that it is even more useful to employ several models.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Amina A. Kamar", + "author_inst": "American University of Beirut-AUB" + }, + { + "author_name": "Noel Maalouf", + "author_inst": "American University of Beirut" + }, + { + "author_name": "Eveline Hitti", + "author_inst": "American University of Beirut" + }, + { + "author_name": "Ghada El Eid", + "author_inst": "American University of Beirut" + }, + { + "author_name": "Hussain A Ismaeel", + "author_inst": "American University of Beirut" + }, + { + "author_name": "Imad H. Elhajj", + "author_inst": "American University of Beirut" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.28.20202028", "rel_title": "SARS-CoV-2 viral load peaks prior to symptom onset: a systematic review and individual-pooled analysis of coronavirus viral load from 66 studies", @@ -1164289,41 +1167366,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.28.20203190", - "rel_title": "Predictors of symptomatic laboratory-confirmed SARS-COV-2 reinfection", - "rel_date": "2020-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20203190", - "rel_abs": "ObjectiveTo identify factors predicting symptomatic laboratory-positive SARS-COV-2 reinfection.\n\nMethodWe conducted a nationwide retrospective cohort study and data from 99,993 confirmed cases of COVID-19 were analyzed.\n\nResultsThe overall risk of reinfection (28 or more elapsed days between both episodes onset) was 0.21%, and older subjects and those with mild primary disease were at reduced risk of reinfection. Healthcare workers and immunosuppressed or renal patients had at greater risk of SARS-COV-2 reinfection.\n\nConclusionsIf replicated in other populations, these results may be useful to prioritize efforts focusing on the reduction of SARS-COV-2 spread and the related burden.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "EFREN MURILLO-ZAMORA", - "author_inst": "INSTITUTO MEXICANO DEL SEGURO SOCIAL" - }, - { - "author_name": "CARLOS M HERNANDEZ-SUAREZ", - "author_inst": "UNIVERSIDAD DE COLIMA" - }, - { - "author_name": "AGUSTIN LUGO-RADILLO", - "author_inst": "CONACYT-FACULTAD DE MEDICINA Y CIRUGIA, UNIVERSIDAD AUTONOMA BENITO JUAREZ DE OAXACA" - }, - { - "author_name": "FELIPE AGUILAR-SOLLANO", - "author_inst": "UNIVERSIDAD DE COLIMA. PROGRAMA DE MAESTRIA EN CIENCIAS MEDICAS." - }, - { - "author_name": "OLIVER MENDOZA-CANO", - "author_inst": "UNIVERSIDAD DE COLIMA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.29.20203760", "rel_title": "Which early indicator allows for a better understanding of the evolution of the COVID-19 epidemic in France?", @@ -1164455,6 +1167497,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.28.20202937", + "rel_title": "The potential contribution of face coverings to the control of SARS-CoV-2 transmission in schools and broader society in the UK: a modelling study", + "rel_date": "2020-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20202937", + "rel_abs": "Recent findings suggest that an adequate test-trace-isolate (TTI) strategy is needed to prevent a secondary COVID-19 wave with the reopening of society in the UK. Here we assess the potential importance of mandatory masks in the parts of community and in secondary schools. We show that, assuming current TTI levels, adoption of masks in secondary schools in addition to community settings can reduce the size of a second wave, but will not prevent it; more testing of symptomatic people, tracing and isolating of their contacts is also needed. To avoid a second wave, with masks mandatory in secondary schools and in certain community settings, under current tracing levels, 68% or 46% of those with symptomatic infection would need to be tested if masks effective coverage were 15% or 30% respectively, compared to 76% and 57% if masks are mandated in community settings but not secondary schools.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jasmina Panovska-Griffiths", + "author_inst": "UCL" + }, + { + "author_name": "Cliff C Kerr", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "William Waites", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Robyn Margaret Stuart", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Dina Mistry", + "author_inst": "Institute for Disease Modelling" + }, + { + "author_name": "Derek Foster", + "author_inst": "Rethink Priorities" + }, + { + "author_name": "Daniel J Klein", + "author_inst": "Institute for Disease Modelling" + }, + { + "author_name": "Russell M Viner", + "author_inst": "UCL Great Ormond St. Institute of Child Health" + }, + { + "author_name": "Chris Bonell", + "author_inst": "LSHTM" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.29.20203646", "rel_title": "Tracking WhatsApp behaviors during a crisis: A longitudinal observation of messaging activities during the COVID-19 pandemic", @@ -1165659,113 +1168752,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.25.20201921", - "rel_title": "Improved Sensitivity, Safety, and Rapidity of COVID-19 Tests by Replacing Viral Storage Solution with Lysis Buffer", - "rel_date": "2020-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201921", - "rel_abs": "Conducting numerous, rapid, and reliable PCR tests for SARS-CoV-2 is essential for our ability to monitor and control the current COVID-19 pandemic.\n\nHere, we tested the sensitivity and efficiency of SARS-CoV-2 detection in clinical samples collected directly into a mix of lysis buffer and RNA preservative, thus inactivating the virus immediately after sampling.\n\nWe tested 79 COVID-19 patients and 20 healthy controls. We collected two samples (nasopharyngeal swabs) from each participant: one swab was inserted into a test tube with Viral Transport Medium (VTM), following the standard guideline used as the recommended method for sample collection; the other swab was inserted into a lysis buffer supplemented with nucleic acid stabilization mix (coined NSLB).\n\nWe found that RT-qPCR tests of patients were significantly more sensitive with NSLB sampling, reaching detection threshold 2.1{+/-}0.6 (Mean{+/-}SE) PCR cycles earlier then VTM samples from the same patient. We show that this improvement is most likely since NSLB samples are not diluted in lysis buffer before RNA extraction. Re-extracting RNA from NSLB samples after 72 hours at room temperature did not affect the sensitivity of detection, demonstrating that NSLB allows for long periods of sample preservation without special cooling equipment. We also show that swirling the swab in NSLB and discarding it did not reduce sensitivity compared to retaining the swab in the tube, thus allowing improved automation of COVID-19 tests. Overall, we show that using NSLB instead of VTM can improve the sensitivity, safety, and rapidity of COVID-19 tests at a time most needed.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Oran Erster", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel" - }, - { - "author_name": "Omer Shkedi", - "author_inst": "Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel" - }, - { - "author_name": "Gil Benedek", - "author_inst": "Hadassah Medical Center, Jerusalem, Israel" - }, - { - "author_name": "Eyal Zilber", - "author_inst": "Department of Internal Medicine, Sheba Medical Center, Tel Hashomer, Israel" - }, - { - "author_name": "Itay Varkovitzky", - "author_inst": "Directorate of Defense Research & Development, Israeli Ministry of Defense, Israel" - }, - { - "author_name": "Rachel Shirazi", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel" - }, - { - "author_name": "Dorit Oriya Shorka", - "author_inst": "Hadassah Medical Center, Jerusalem, Israel" - }, - { - "author_name": "Yuval Cohen", - "author_inst": "Directorate of Defense Research & Development, Israeli Ministry of Defense, Israel" - }, - { - "author_name": "Tzahi Bar", - "author_inst": "Independent Researcher, Israel" - }, - { - "author_name": "Rafi Yechieli", - "author_inst": "Independent Researcher, Israel" - }, - { - "author_name": "Michal Tepperberg Oikawa", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel" - }, - { - "author_name": "Dana Venkert", - "author_inst": "Department of Neurobiology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel" - }, - { - "author_name": "Michal Linial", - "author_inst": "Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel" - }, - { - "author_name": "Esther Oiknine-Djian", - "author_inst": "Hadassah Medical Center, Jerusalem, Israel" - }, - { - "author_name": "Michal Mandelboim", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; School of Public Health, Sackler" - }, - { - "author_name": "Zvi Livneh", - "author_inst": "Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel" - }, - { - "author_name": "Gilat Shenhav-Saltzman", - "author_inst": "Department of Internal Medicine, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; School of Public Health, Sackler" - }, - { - "author_name": "Dana Wolf", - "author_inst": "Hadassah Medical Center, Jerusalem, Israel" - }, - { - "author_name": "Moran Szwarcwort-Cohen", - "author_inst": "Virology Laboratory, Rambam Health Care Campus, Haifa, Israel" - }, - { - "author_name": "Orna Mor", - "author_inst": "Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, P.O. Box 5265601, Ramat-Gan, Israel; School of Public Health, Sackler" - }, - { - "author_name": "Yair Lewis", - "author_inst": "Navina AI Medical Technologies, Tel Aviv, Israel" - }, - { - "author_name": "Danny Zeevi", - "author_inst": "Department of Biotechnology, Hadassah Academic College, Jerusalem, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.26.20201814", "rel_title": "Evolution of COVID-19 cases in selected low- and middle-income countries: past the herd immunity peak?", @@ -1165917,6 +1168903,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.09.26.20202382", + "rel_title": "Estimation of the fraction of COVID-19 infected people in U.S. states and countries worldwide", + "rel_date": "2020-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.26.20202382", + "rel_abs": "Since the beginning of the COVID-19 pandemic, daily counts of confirmed cases and deaths have been publicly reported in real-time to control the virus spread. However, substantial undocumented infections have obscured the true prevalence of the virus. A machine learning framework was developed to estimate time courses of actual new COVID-19 cases and current infections in 50 countries and 50 U.S. states from reported test results and deaths, as well as published epidemiological parameters. Severe under-reporting of cases was found to be universal. Our framework projects for countries like Belgium, Brazil, and the U.S. [~]10% of the population has been once infected. In the U.S. states like Louisiana, Georgia, and Florida, more than 4% of the population is estimated to be currently infected, as of September 3, 2020, while in New York the fraction is 0.12%. The estimation of the actual fraction of currently infected people is crucial for any definition of public health policies, which up to this point may have been misguided by the reliance on confirmed cases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jungsik Noh", + "author_inst": "UT Southwestern Medical Center" + }, + { + "author_name": "Gaudenz Danuser", + "author_inst": "UT Southwestern Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.26.20202051", "rel_title": "Sleep apnoea is a risk factor for severe COVID-19", @@ -1167377,37 +1170386,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.09.25.20194431", - "rel_title": "The Use of Psychoactive Substances in the Context of the Covid-19 Pandemic in Brazil", - "rel_date": "2020-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20194431", - "rel_abs": "BackgroundThe protocols for mitigating the transmission of Covid-19 seem to be a trigger for the use of psychoactive substances, as an individuals adaptive response to support this new way of being in the world. Objective: To investigate the use of psychoactive substances in the context of the Covid-19 pandemic in Brazil. Method: A cross-sectional and prospective observational study, undertaken in a virtual environment. An online survey was developed and employed through Google Forms to collect data. The survey was made available to participants on social networks, Facebook@, Whatsapp@, and Instagram@, linked to the research group, during the period 06/15/2020 to 07/15/2020. 1,145 individuals participated in the research. Results: The average age of the participants was 37 years old. They were mostly female, white, Brazilians, with a higher education level, with occupations in the health field, and had religion. They either maintained their family income or suffered a small income decrease. Moreover, they informed that they were caring for social isolation. The most used substances before and after the beginning of the Covid-19 pandemic were alcohol, tobacco, marijuana, although the use of these substances decreased (P< 0.001). Approximately 32% of the participants started using psychoactive substances in this period. Among them, most individuals started by their own initiative. Conclusions: For a better understanding of the pattern use of psychoactive substances during the Covid-19 pandemic and the adverse effects on human behavior and mental disorders, careful longitudinal studies must be developed, due to the great interest in the knowledge of adaptive responses when peoples lives are at risk.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Cesar Augusto Trinta Weber", - "author_inst": "Centro de Estudos Jose de Barros Falcao" - }, - { - "author_name": "Ingridi Teixeira Monteiro", - "author_inst": "Centro de Estudos Jose de Barros Falcao" - }, - { - "author_name": "Julia Medeiros Gehrke", - "author_inst": "Centro de Estudos Jose de Barros Falcao" - }, - { - "author_name": "Wagner Silva de Souza", - "author_inst": "Centro de Estudos Jose de Barros Falcao" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.09.25.20201616", "rel_title": "COVID-19 in Youth Soccer", @@ -1167723,6 +1170701,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.25.20201889", + "rel_title": "Prioritising COVID-19 vaccination in changing social and epidemiological landscapes", + "rel_date": "2020-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201889", + "rel_abs": "BackgroundDuring the COVID-19 pandemic, authorities must decide which groups to prioritise for vaccination. These decision will occur in a constantly shifting social-epidemiological landscape where the success of large-scale non-pharmaceutical interventions (NPIs) like physical distancing requires broad population acceptance.\n\nMethodsWe developed a coupled social-epidemiological model of SARS-CoV-2 transmission. Schools and workplaces are closed and re-opened based on reported cases. We used evolutionary game theory and mobility data to model individual adherence to NPIs. We explored the impact of vaccinating 60+ year-olds first; <20 year-olds first; uniformly by age; and a novel contact-based strategy. The last three strategies interrupt transmission while the first targets a vulnerable group. Vaccination rates ranged from 0.5% to 4.5% of the population per week, beginning in January or July 2021.\n\nFindingsCase notifications, NPI adherence, and lockdown periods undergo successive waves during the simulated pandemic. Vaccination reduces median deaths by 32% - 77% (22% - 63%) for January (July) availability, depending on the scenario. Vaccinating 60+ year-olds first prevents more deaths (up to 8% more) than transmission-interrupting strategies for January vaccine availability across most parameter regimes. In contrast, transmission-interrupting strategies prevent up to 33% more deaths than vaccinating 60+ year-olds first for July availability, due to higher levels of natural immunity by that time. Sensitivity analysis supports the findings.\n\nInterpretationFurther research is urgently needed to determine which populations can benefit from using SARS-CoV-2 vaccines to interrupt transmission.\n\nFundingOntario Ministry of Colleges and Universities.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWhether to vaccinate individuals who cause the most transmission or those who are at highest risk of death is relevant to prioritizing COVID-19 vaccination. We searched PubMed and medRxiv for the terms COVID19, vaccin*, model, and priorit* up to September 24, 2020, with no date or language restrictions. We identified 4 papers on mathematical models of COVID-19 vaccine prioritization that explored the conditions under which different age groups should be vaccinated first. We did not find any coupled social-epidemiological models that capture feedback between social dynamics and epidemic trajectories.\n\nAdded value of this studyThe dynamic interaction between SARS-CoV-2 epidemics and the population response through scalable non-pharmaceutical interventions will continue to play a large role in the course of the pandemic, both before and after vaccines become available. Hence, social-epidemiological models may be useful. Our social-epidemiological model identifies the conditions under which COVID-19 deaths can be reduced most effectively by prioritizing older individuals first, versus other strategies designed to interrupt transmission. We explore how the best vaccination strategy varies depending on a wide range of socio-epidemiological and vaccine program parameters. We identify clear and interpretable conditions under which using COVID-19 vaccines to interrupt transmission can reduce mortality most effectively.\n\nImplications of all the available evidenceSeroprevalence surveys before the onset of vaccination could measure population-level SARS-CoV-2 immunity. In populations where seropositivity is high due to previous waves, vaccinating to interrupt transmission may reduce deaths more effectively than targeting older individuals. More research is urgently required to evaluate how to prioritise vaccination in populations that have experienced one or more waves of COVID-19.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Peter Jentsch", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Madhur Anand", + "author_inst": "University of Guelph" + }, + { + "author_name": "Chris T Bauch", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.25.20201269", "rel_title": "Quantitative, Epitope-specific, Serological Screening of COVID-19 Patients Using a Novel Multiplexed Array-based Immunoassay Platform", @@ -1168963,41 +1171968,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.23.20200410", - "rel_title": "Review of clinical characteristics and laboratory findings of COVID-19 in children-Systematic review and Meta-analysis", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20200410", - "rel_abs": "OBJECTIVE: To conduct a systematic review and meta-analysis to assess the prevalence of various clinical symptoms and laboratory findings of COVID-19 in children. METHODS: PubMed, MEDLINE, and SCOPUS databases were searched to include studies conducted between January 1, 2020, and July 15, 2020 which reported data about clinical characteristics and laboratory findings in laboratory-confirmed diagnosis of COVID-19 in pediatric patients. Random effects meta-analysis using generalized linear mixed models was used to estimate the pooled prevalence. RESULTS: The most prevalent symptom of COVID-19 in children was 46.17% (95%CI 39.18-53.33%), followed by cough (40.15%, 95%CI 34.56-46.02%). Less common symptoms were found to be dyspnea, vomiting, nasal congestion/rhinorrhea, diarrhea, sore throat/pharyngeal congestion, headache, and fatigue. The prevalence of asymptomatic children was 17.19% (95%CI 11.02-25.82%). The most prevalent laboratory findings in COVID-19 children were elevated Creatinine Kinase (26.86%, 95%CI 16.15-41.19%) and neutropenia (25.76%, 95%CI 13.96-42.58%). These were followed by elevated LDH, thrombocytosis, lymphocytosis, neutrophilia, elevated D Dimer, Elevated CRP, elevated ESR, leukocytosis, elevated AST and leukopenia. There was a low prevalence of elevated ALT and lymphopenia in children with COVID- 19. CONCLUSIONS AND RELEVANCE: This study provides estimates of the pooled prevalence of various symptoms and laboratory findings of COVID-19 in the pediatric population.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Harmeet K Kharoud", - "author_inst": "Division of Epidemiology, School of Public Health, University of Minnesota, MN, USA" - }, - { - "author_name": "Rizwana Asim", - "author_inst": "Fatima Jinnah Medical University, Lahore, Pakistan" - }, - { - "author_name": "Lianne Siegel", - "author_inst": "Division of Biostatistics, School of Public Health, University of Minnesota" - }, - { - "author_name": "Lovepreet Chahal", - "author_inst": "School of Health Science Kwantlen Polytechnic University, Surrey, Canada" - }, - { - "author_name": "Gagan Deep Singh", - "author_inst": "Department of Internal Medicine, University of Connecticut, CT, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.23.20198713", "rel_title": "Suitability of Two Rapid Lateral Flow Immunochromatographic Assays for Predicting SARS-CoV-2 Neutralizing Activity of Sera", @@ -1169465,6 +1172435,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.24.20200543", + "rel_title": "Evidence for and level of herd immunity against SARS-CoV-2 infection: the ten-community study", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20200543", + "rel_abs": "BackgroundQatar experienced a large severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic that disproportionately affected the craft and manual workers (CMWs) who constitute 60% of the population. This study aimed to investigate level of immunity in communities within this population as well as infection exposure required to achieve herd immunity.\n\nMethodsAnti-SARS-CoV-2 seropositivity was assessed in ten CMW communities between June 21 and September 9, 2020. PCR positivity, infection positivity (antibody and/or PCR positive), and infection severity rate were also estimated. Associations with anti-SARS-CoV-2 positivity were investigated using regression analyses.\n\nResultsStudy included 4,970 CMWs who were mostly men (95.0%) and <40 years of age (71.5%). Seropositivity ranged from 54.9% (95% CI: 50.2-59.4%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean seropositivity across all communities was 66.1% (95% CI: 61.5-70.6%). PCR positivity ranged from 0.0% to 10.5% (95% CI: 7.4-14.8%) in the different CMW communities. Pooled mean PCR positivity was 3.9% (95% CI: 1.6-6.9%). Median cycle threshold (Ct) value was 34.0 (range: 15.8-37.4)--majority (79.5%) of PCR-positive individuals had Ct value >30 indicative of earlier rather than recent infection. Infection positivity (antibody and/or PCR positive) ranged from 62.5% (95% CI: 58.3-66.7%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean infection positivity was 69.5% (95% CI: 62.8-75.9%). Only five infections were ever severe and one was ever critical--an infection severity rate of 0.2% (95% CI: 0.1-0.4%).\n\nConclusionsBased on an extended range of epidemiological measures, active infection is rare in these communities with limited if any sustainable infection transmission for clusters to occur. At least some CMW communities in Qatar have reached or nearly reached herd immunity for SARS-CoV-2 infection at a proportion of ever infection of 65-70%.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Houssein H. Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "Moza Abdellatif Hassan Abdulla", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Abdul Badi Abou-Samra", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Jameela Ali A.A. Al Ajmi", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Nasser Ali Asad Al-Ansari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ahmed Al-Mohammed", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Naema Hassan Abdulla Al Molawi", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Huda Mohamad Al Naomi", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Reham Awni El Kahlout", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Imtiaz Gillani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Naseer Ahmad Masoodi", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anil George Thomas", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanaa Nafady-Hego", + "author_inst": "Hamad Medical Corporation and Microbiology and Immunology Department, Faculty of Medicine, Assiut University" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Nourah B M Younes", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Hadi M. Yassine", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed G. Al Kuwari", + "author_inst": "Primary Health Care Corporation, Doha, Qatar" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Sheikh Mohammad Al Thani", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.24.20201061", "rel_title": "Quantifying the impact of quarantine duration on COVID-19 transmission", @@ -1170561,45 +1173670,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.24.20201301", - "rel_title": "Psychological preparedness for pandemic (COVID-19) management: Perceptions of nurses and nursing students in India", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20201301", - "rel_abs": "IntroductionThe growing COVID-19 pandemic has posed a great threat to millions of people worldwide. Nurses and nursing students are an important group of health professionals who are most likely to face many challenges in this unprecedented scenario. The present study aimed at exploring the perception of nurses and nursing students regarding psychological preparedness for the pandemic (COVID-19) management.\n\nMaterials & MethodsThe study employed a quantitative cross-sectional online survey research design. Purposive sampling was used with an attempt to represent the entire nurses (i.e. nursing officers, nurse administrators and nursing teachers) and nursing students group of India. The survey link was shared to their email ID and they were invited to participate in the study. Data were collected using Psychological Preparedness for Disaster Threat Scale (PPDTS)-Modified, General Self Efficacy (GSE) Scale, Optimism Scale and Brief Resilient Coping Scale (BRS). Totally 685 responses were received and 676 forms were completed which were analyzed using SPSS software (version 24).\n\nResultsThe mean age of the subjects was 31.72 (SD=9.58) years. Around 20% of the subjects previously had some kind of psychological training and 4% of the subjects had taken care of persons with COVID-19. Findings revealed that mean score for PPDTS, GSE, BRCS and Optimism was 73.44 (SD=10.82, 33.19 (SD=5.23), 16.79 (SD=2.73) and 9.61 (SD=2.26) respectively indicating that the subjects had moderate level of psychological preparedness, self-efficacy and resilience but higher level of optimism. Psychological preparedness, self-efficacy, optimism and resilience were positively correlated to each other. Self-efficacy, optimism, and resilience emerged as predictors of psychological preparedness.\n\nConclusionThe findings suggested that self-efficacy, optimism and resilience can be considered as predictors for psychological preparedness in pandemic management. Appropriate training could influence self-efficacy while programs addressing resilience and coping may strengthen psychological preparedness which can help in further management of ongoing pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sailaxmi Gandhi", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Maya Sahu", - "author_inst": "National Institute of Mental Health & Neuro Sciences" - }, - { - "author_name": "Radhakrishnan Govindan", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Prasanthi Nattala", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Paulomi M Sudhir", - "author_inst": "National Institute of Mental Health and Neurosciences" - }, - { - "author_name": "Rathi Balachandran", - "author_inst": "Ministry of Health & Family Welfare, Government of India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nursing" - }, { "rel_doi": "10.1101/2020.09.24.20201228", "rel_title": "Outcomes associated with SARS-CoV-2 viral clades in COVID-19", @@ -1170995,6 +1174065,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.24.312553", + "rel_title": "SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial derived cells and cardiomyocytes", + "rel_date": "2020-09-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.24.312553", + "rel_abs": "Coronaviruses are adept at evading host antiviral pathways induced by viral double-stranded RNA, including interferon (IFN) signaling, oligoadenylate synthetase-ribonuclease L (OAS-RNase L), and protein kinase R (PKR). While dysregulated or inadequate IFN responses have been associated with severe coronavirus infection, the extent to which the recently emerged SARS-CoV-2 activates or antagonizes these pathways is relatively unknown. We found that SARS-CoV-2 infects patient-derived nasal epithelial cells, present at the initial site of infection, induced pluripotent stem cell-derived alveolar type 2 cells (iAT2), the major cell type infected in the lung, and cardiomyocytes (iCM), consistent with cardiovascular consequences of COVID-19 disease. Robust activation of IFN or OAS-RNase L is not observed in these cell types, while PKR activation is evident in iAT2 and iCM. In SARS-CoV-2 infected Calu-3 and A549ACE2 lung-derived cell lines, IFN induction remains relatively weak; however activation of OAS-RNase L and PKR is observed. This is in contrast to MERS-CoV, which effectively inhibits IFN signaling as well as OAS-RNase L and PKR pathways, but similar to mutant MERS-CoV lacking innate immune antagonists. Remarkably, both OAS-RNase L and PKR are activated in MAVS knockout A549ACE2 cells, demonstrating that SARS-CoV-2 can induce these host antiviral pathways despite minimal IFN production. Moreover, increased replication and cytopathic effect in RNASEL knockout A549ACE2 cells implicates OAS-RNase L in restricting SARS-CoV-2. Finally, while SARS-CoV-2 fails to antagonize these host defense pathways, which contrasts with other coronaviruses, the IFN signaling response is generally weak. These host-virus interactions may contribute to the unique pathogenesis of SARS-CoV-2.\n\nSignificanceSARS-CoV-2 emergence in late 2019 led to the COVID-19 pandemic that has had devastating effects on human health and the economy. Early innate immune responses are essential for protection against virus invasion. While inadequate innate immune responses are associated with severe COVID-19 diseases, understanding of the interaction of SARS-CoV-2 with host antiviral pathways is minimal. We have characterized the innate immune response to SARS-CoV-2 infections in relevant respiratory tract derived cells and cardiomyocytes and found that SARS-CoV-2 activates two antiviral pathways, oligoadenylate synthetase-ribonuclease L (OAS-RNase L), and protein kinase R (PKR), while inducing minimal levels of interferon. This in contrast to MERS-CoV which inhibits all three pathways. Activation of these pathways may contribute to the distinctive pathogenesis of SARS-CoV-2.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Yize Li", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "David Renner", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Courtney E Comar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jillian Whelan", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Hanako Reyes", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Fabian Leonardo Cardenas-Diaz", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Rachel Truitt", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Li Hui Tan", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Beihua Dong", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Konstantinos Dionysios Alysandratose", + "author_inst": "Boston University" + }, + { + "author_name": "Jesse Huang", + "author_inst": "Boston University" + }, + { + "author_name": "James N Palmer", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Nithin D Adappa", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Michael A Kohanski", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Darrell N Kotton", + "author_inst": "Boston University" + }, + { + "author_name": "Robert H Silverman", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Wenli Yang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Edward Morrisey", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Noam Cohen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Susan R Weiss", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.24.312769", "rel_title": "Cyclooxgenase-2 is induced by SARS-CoV-2 infection but does not affect viral entry or replication", @@ -1172307,105 +1175472,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2020.09.22.308965", - "rel_title": "Cross-reactive serum and memory B cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection", - "rel_date": "2020-09-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.22.308965", - "rel_abs": "Pre-existing immune responses to seasonal endemic coronaviruses could have profound consequences for antibody responses to SARS-CoV-2, either induced in natural infection or through vaccination. Such consequences are well established in the influenza and flavivirus fields. A first step to establish whether pre-existing responses can impact SARS-CoV-2 infection is to understand the nature and extent of cross-reactivity in humans to coronaviruses. We compared serum antibody and memory B cell responses to coronavirus spike (S) proteins from pre-pandemic and SARS-CoV-2 convalescent donors using a series of binding and functional assays. We found weak evidence of pre-existing SARS-CoV-2 cross-reactive serum antibodies in pre-pandemic donors. However, we found stronger evidence of pre-existing cross-reactive memory B cells that were activated on SARS-CoV-2 infection. Monoclonal antibodies (mAbs) isolated from the donors showed varying degrees of cross-reactivity with betacoronaviruses, including SARS and endemic coronaviruses. None of the cross-reactive mAbs were neutralizing except for one that targeted the S2 subunit of the S protein. The results suggest that pre-existing immunity to endemic coronaviruses should be considered in evaluating antibody responses to SARS-CoV-2.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Ge Song", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Wan-ting He", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Sean Callaghan", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Fabio Anzanello", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Deli Huang", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "James Ricketts", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Jonathan L. Torres", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Nathan Beutler", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Linghang Peng", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Sirena Vargas", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Jon Cassell", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Mara Parren", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Linlin Yang", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Caroline Ignacio", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "Davey M. Smith", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "James E. Voss", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "David Nemazee", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Andrew B. Ward", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Thomas Rogers", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "Dennis R. Burton", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Raiees Andrabi", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.09.23.309948", "rel_title": "Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK", @@ -1172773,6 +1175839,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.09.20.20198531", + "rel_title": "Puerto Rico Health System Resilience After Hurricane Maria: Implications for Disaster Preparedness in the COVID-19 Era", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20198531", + "rel_abs": "Background: Every year, Puerto Rico faces a hurricane season fraught with potentially catastrophic structural, emotional and health consequences. In 2017, Puerto Rico was hit by Hurricane Maria, the largest natural disaster to ever affect the island. Several studies have estimated the excess morbidity and mortality following Hurricane Maria in Puerto Rico, yet no study has comprehensively examined the underlying health system weaknesses contributing to the deleterious health outcomes. Methods: A qualitative case study was conducted to assess the ability of the UPR health system to provide patient care in response to Hurricane Maria. An established five key resilience framework and inductive analysis was used to identify factors that affected health system resilience. Thirteen Emergency Medicine Physicians, Family Medicine Physicians, and Hospital Administrators in a University of Puerto Rico (UPR) Community Hospital were interviewed as part of our study. Results: Of the five key resiliency components, three domains were notably weak with respect to UPR resiliency. Prior to the Hurricane, key personnel at the UPR hospital were unaware of the limited capacity of back-up generators at hospitals and were ill-prepared to transfer ICU patients to appropriate hospitals. Post Hurricane, the hospital faced self-regulation challenges when triaging the provision of Hurricane-related emergency services with delivering core health services, in particular for patients with chronic conditions. Finally, during and after the Hurricane, integration of patient care coordination between the UPR hospital ambulances, neighboring hospitals, and national and state government was suboptimal. The two remaining resiliency factors, addressing diverse needs and system adaptiveness in a time of crisis, were seen as strengths. Conclusions: Hurricane Maria exposed weaknesses in the Puerto Rican health system, notably the lack of awareness about the limited capacity of backup generators, poor patient care coordination, and interruption of medical care for patients with chronic conditions. As in other countries, the current COVID epidemic is taxing the capacity of the Puerto Rico health system, which could increase the likelihood of another health system collapse should another hurricane hit the island. Therefore, a resilience framework is a useful tool to help health systems identify areas of improvement in preparation for possible natural disasters.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Christopher Rios", + "author_inst": "Stanford University" + }, + { + "author_name": "Emilia Ling", + "author_inst": "Stanford University" + }, + { + "author_name": "Ralph Rivera Gutierrez", + "author_inst": "University of Puerto Rico Medical Science Campus" + }, + { + "author_name": "Juan Gonzalez", + "author_inst": "University of Puerto Rico Medical Science Campus" + }, + { + "author_name": "Janine Bruce", + "author_inst": "Stanford University" + }, + { + "author_name": "Michele Barry", + "author_inst": "Stanford University" + }, + { + "author_name": "Vinicio de Jesus Perez", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.21.20198887", "rel_title": "The effect of COVID-19 on the economy: evidence from an early adopter of localized lockdowns", @@ -1174117,25 +1177226,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.20.20198283", - "rel_title": "Exponential distribution of large excess death rates in Europe during the COVID-19 outbreak in the spring of 2020", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20198283", - "rel_abs": "Excess death rates E during the spring of 2020 are computed in N = 540 level 3 European territorial units for statistics --NUTS3 in Belgium (40), France (96), Italy (110), Netherlands (44), Spain (50), Sweden(21) and United Kingdom (179)-- from 2020 provisional week deaths, the population numbers for 2020, and observations in previous years (reference or baseline), all of them obtained from Eurostat web page.\n\nExcess death rates are classified in three tiers. Largest 27 excess death rates (tier 1, E > 1721x 10-6) were distributed exponentially with empirical complementary cumulative distribution function (empirical survival function) S following S {propto} 2-E/{varepsilon} with{varepsilon} 1 = 958(42) x 10-6. Tier 2 (the next 52 largest excess death rates, E < 1142 x 10-6 also distributed exponentially with{varepsilon} 2 = 379.5(89) x10-6. Tier 3 (smallest 460 excess death rates) were distributed normally.\n\nThe results suggests that when, within some regions, the outbreak is above a threshold, interaction with neighbouring region become less relevant and the outcomes --excess death rates-- become exponentially distributed as it happens with independent events.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jose Maria Martin-Olalla", - "author_inst": "Universidad de Sevilla" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.22.20198275", "rel_title": "Knowledge, Attitude and Practice towards COVID-19 among people in Bangladesh during the pandemic: a cross-sectional study.", @@ -1174539,6 +1177629,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.20.20198242", + "rel_title": "First quarter chronicle of COVID-19: an attempt to measure governments response", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20198242", + "rel_abs": "The crisis caused by COVID-19 revealed the global unpreparedness for handling the impact of a pandemic. In this paper, we present a first quarter chronicle of COVID-19 in Hubei China, Italy and Spain, specifically their infection speed, death and fatality rates. By fitting distributions to these rates, we look for the effectiveness of government measures during the pandemic through a number of statistical approaches.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sule Sahin", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Maria del Carmen Boado-Penas", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Corina Constantinescu", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Julia Eisenberg", + "author_inst": "TU Wien" + }, + { + "author_name": "Kira Henshaw", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Maoqi Hu", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Jing Wang", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Wei Zhu", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.09.20.20198143", "rel_title": "Resuming assisted reproduction services during COVID-19 Pandemic: An Indian experience", @@ -1176079,145 +1179216,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.23.308239", - "rel_title": "The COVID-19 PHARMACOME: Rational Selection of Drug Repurposing Candidates from Multimodal Knowledge Harmonization", - "rel_date": "2020-09-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.23.308239", - "rel_abs": "The SARS-CoV-2 pandemic has challenged researchers at a global scale. The scientific communitys massive response has resulted in a flood of experiments, analyses, hypotheses, and publications, especially in the field of drug repurposing. However, many of the proposed therapeutic compounds obtained from SARS-CoV-2 specific assays are not in agreement and thus demonstrate the need for a singular source of COVID-19 related information from which a rational selection of drug repurposing candidates can be made. In this paper, we present the COVID-19 PHARMACOME, a comprehensive drug-target-mechanism graph generated from a compilation of 10 separate disease maps and sources of experimental data focused on SARS-CoV-2 / COVID-19 pathophysiology. By applying our systematic approach, we were able to predict the synergistic effect of specific drug pairs, such as Remdesivir and Thioguanosine or Nelfinavir and Raloxifene, on SARS-CoV-2 infection. Experimental validation of our results demonstrate that our graph can be used to not only explore the involved mechanistic pathways, but also to identify novel combinations of drug repurposing candidates.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Bruce T Schultz", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - }, - { - "author_name": "Andrea Zaliani", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "Christian Ebeling", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - }, - { - "author_name": "Jeanette Reinshagen", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "Denisa Bojkova", - "author_inst": "Institute of Medical Virology" - }, - { - "author_name": "Vanessa Lage-Rupprecht", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - }, - { - "author_name": "Reagon Karki", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Soeren Lukassen", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Yojana Gadiya", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing" - }, - { - "author_name": "Neal Giri Ravindra", - "author_inst": "Yale University" - }, - { - "author_name": "Sayoni Das", - "author_inst": "PrecisionLife Ltd." - }, - { - "author_name": "Shounak Baksi", - "author_inst": "Causality BioModels Pvt Ltd" - }, - { - "author_name": "Daniel Domingo-Fernandez", - "author_inst": "Fraunhofer SCAI" - }, - { - "author_name": "Manuel Lentzen", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Mark Strivens", - "author_inst": "PrecisionLife Ltd." - }, - { - "author_name": "Tamara Raschka", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Jindrich Cinatl Jr.", - "author_inst": "Klinikum der Goethe-Universitaet" - }, - { - "author_name": "Lauren Nicole DeLong", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Philip Gribbon", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "Gerd Geisslinger", - "author_inst": "Fraunhofer Cluster of Excellence for Immune Mediated Diseases" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "David van Dijk Jr.", - "author_inst": "Yale University" - }, - { - "author_name": "Steve Gardner", - "author_inst": "PrecisionLife Ltd" - }, - { - "author_name": "Alpha Tom Kodamullil", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - }, - { - "author_name": "Holger Froehlich", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Manuel Peitsch", - "author_inst": "Philip Morris International" - }, - { - "author_name": "Marc Jacobs", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)" - }, - { - "author_name": "Julia Hoeng", - "author_inst": "Philip Morris International (Switzerland)" - }, - { - "author_name": "Roland Eils", - "author_inst": "Charite Universitaetsmedizin Berlin & Berlin Institute of Health (BIH)" - }, - { - "author_name": "Carsten Claussen", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology IME" - }, - { - "author_name": "Martin Hofmann-Apitius", - "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing SCAI" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.09.18.20197582", "rel_title": "Ruling In and Ruling Out COVID-19: Computing SARS-CoV-2 Infection Risk From Symptoms, Imaging and Test Data.", @@ -1176469,6 +1179467,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.09.19.20198028", + "rel_title": "An improved method to estimate the effective reproduction number of the COVID-19 pandemic: lessons from its application in Greece", + "rel_date": "2020-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.19.20198028", + "rel_abs": "IntroductionMonitoring the time-varying effective reproduction number Rt is crucial for assessing the evolution of the COVID-19 pandemic. We present an improved method to estimate Rt and its application to routine surveillance data from Greece.\n\nMethodsOur method extends that of Cori et al (2013), adding Bayesian imputation of missing symptom onset dates, imputation of infection times using an external estimate of the incubation period, and an adjustment for reporting delay. To facilitate its use, we provide an R software package named \"bayEStim\". We applied the method to COVID-19 surveillance data from Greece, and examined the resulting Rt estimates in relation to control measures applied, in order to assess their effectiveness. We also associated Rt, as a measure of transmissibility, to population mobility as recorded in Google data and to ambient temperature. We used a serial interval between 4 and 7.5 days, and a median incubation period of 5.1 days.\n\nResultsIn Greece Rt fell rapidly as the first control measures were introduced, dropping below 1 at least a week before a full lockdown came into effect. In mid-July Rt started increasing again, as increased mobility associated with tourism activity was observed. Each 10% of increase in relative mobility increased Rt by 8.1% (95% CrI 6.1-10.2%), whereas each unit celsius of temperature increase decreased Rt by 4.6% (95% CrI 5.4-13.7%).\n\nConclusionsMobility patterns significantly affect Rt. Most of the reduction in COVID-19 transmissibility in Greece occurred already before the lockdown, likely as a result of decreased population mobility. Lower viral transmissibility in summer does not appear sufficient to counterbalance the increased mobility due to tourism. Monitoring Rt is an essential component of COVID-19 surveillance, and it is crucial for correctly assessing the effect of control measures.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Theodore Lytras", + "author_inst": "Department of Medicine, School of Medicine, European University Cyprus, Nicosia, Cyprus" + }, + { + "author_name": "Vana Sypsa", + "author_inst": "Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Demosthenes Panagiotakos", + "author_inst": "School of Health Science and Education, Harokopio University, Athens, Greece" + }, + { + "author_name": "Sotirios Tsiodras", + "author_inst": "4th Department of Internal Medicine, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.19.20197996", "rel_title": "Quantifying the Effects of Social Distancing on theSpread of COVID-19", @@ -1177765,33 +1180794,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.09.22.308098", - "rel_title": "Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation", - "rel_date": "2020-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.22.308098", - "rel_abs": "BackgroundThe SARS-CoV-2 pandemic urges for cheap, reliable, and rapid technologies for disinfection and decontamination. One frequently proposed method is UV-C irradiation. However, UV-C doses necessary to achieve inactivation of high-titer SARS-CoV-2 are poorly defined.\n\nMethodsUsing a box and two handheld systems designed to decontaminate objects and surfaces we evaluated the efficacy of 254 nm UV-C treatment to inactivate surface dried SARS-CoV-2.\n\nResultsDrying for two hours did not have a major impact on the infectivity of SARS-CoV-2, indicating that exhaled virus in droplets or aerosols stays infectious on surfaces at least for a certain amount of time. Short exposure of high titer surface dried virus (3-5*10^6 IU/ml) with UV-C light (16 mJ/cm2) resulted in a total inactivation of SARS-CoV-2. Dose-dependency experiments revealed that 3.5 mJ/cm2 were still effective to achieve a > 6-log reduction in viral titers whereas 1.75 mJ/cm2 lowered infectivity only by one order of magnitude.\n\nConclusionsOur results demonstrate that SARS-CoV-2 is rapidly inactivated by relatively low doses of UV-C irradiation. Furthermore, the data reveal that the relationship between UV-C dose and log-viral titer reduction of surface residing SARS-CoV-2 is non-linear. In the context of UV-C-based technologies used to disinfect surfaces, our findings emphasize the necessity to assure sufficient and complete exposure of all relevant areas by integrated UV-C doses of at least 3.5 mJ/cm2 at 254 nm. Altogether, UV-C treatment is an effective non-chemical possibility to decontaminate surfaces from high-titer infectious SARS-CoV-2.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Natalia Ruetalo", - "author_inst": "Institiute for Medical Virology, University Hospital Tuebingen, Germany" - }, - { - "author_name": "Ramona Businger", - "author_inst": "Institiute for Medical Virology, University Hospital Tuebingen, Germany" - }, - { - "author_name": "Michael Schindler", - "author_inst": "Institiute for Medical Virology, University Hospital Tuebingen, Germany" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.22.308023", "rel_title": "Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain.", @@ -1178038,6 +1181040,97 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.22.307975", + "rel_title": "Mass cytometry and artificial intelligence define CD169 as a specific marker of SARS-CoV2-induced acute respiratory distress syndrome", + "rel_date": "2020-09-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.22.307975", + "rel_abs": "Acute respiratory distress syndrome (ARDS) is the main complication of COVID-19, requiring admission to Intensive Care Unit (ICU). Despite recent immune profiling of COVID-19 patients, to what extent COVID-19-associated ARDS specifically differs from other causes of ARDS remains unknown, To address this question, we built 3 cohorts of patients categorized in COVID-19negARDSpos, COVID-19posARDSpos, and COVID-19posARDSneg, and compared their immune landscape analyzed by high-dimensional mass cytometry on peripheral blood followed by artificial intelligence analysis. A cell signature associating S100A9/calprotectin-producing CD169pos monocytes, plasmablasts, and Th1 cells was specifically found in COVID-19posARDSpos, unlike COVID-19negARDSpos patients. Moreover, this signature was shared by COVID-19posARDSneg patients, suggesting severe COVID-19 patients, whatever they experienced or not ARDS, displayed similar immune dysfunctions. We also showed an increase in CD14posHLA-DRlow and CD14lowCD16pos monocytes correlated to the occurrence of adverse events during ICU stay. Our study demonstrates that COVID-19-associated ARDS display a specific immune profile, and might benefit from personalized therapy in addition to standard ARDS management.\n\nOne Sentence SummaryCOVID-19-associated ARDS is biologically distinct from other causes of ARDS.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Mikael Roussel", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Juliette Ferrant", + "author_inst": "Univ Rennes 1" + }, + { + "author_name": "Florian Reizine", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Simon Le Gallou", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Joelle Dulong", + "author_inst": "Univ Rennes 1" + }, + { + "author_name": "Sarah Carl", + "author_inst": "Scailyte" + }, + { + "author_name": "Mathieu Lesouhaitier", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Murielle Gregoire", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Nadine Bescher", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Clotilde Verdy", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Maelle Latour", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Isabelle Bezier", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Marie Cornic", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Simon Leonard", + "author_inst": "Univ Rennes 1" + }, + { + "author_name": "Jean Feuillard", + "author_inst": "CHU Limoges" + }, + { + "author_name": "Vijay Tiwari", + "author_inst": "Scailyte" + }, + { + "author_name": "Jean Marc Tadie", + "author_inst": "CHU Rennes" + }, + { + "author_name": "Michel Cogne", + "author_inst": "Univ Rennes1" + }, + { + "author_name": "Karin Tarte", + "author_inst": "Univ Rennes 1" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.22.20199240", "rel_title": "Knowledge, attitudes and practices of COVID 19 among Medical Laboratory Professionals in Zambia", @@ -1179290,53 +1182383,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.09.18.302901", - "rel_title": "SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism", - "rel_date": "2020-09-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.18.302901", - "rel_abs": "The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious virus that underlies the current COVID-19 pandemic. SARS-CoV-2 is thought to disable various features of host immunity and cellular defense. The SARS-CoV-2 nonstructural protein 1 (Nsp1) is known to inhibit host protein translation and could be a target for antiviral therapy against COVID-19. However, how SARS-CoV-2 circumvents this translational blockage for the production of its own proteins is an open question. Here, we report a bipartite mechanism of SARS-CoV-2 Nsp1 which operates by: (1) hijacking the host ribosome via direct interaction of its C-terminal domain (CT) with the 40S ribosomal subunit and (2) specifically lifting this inhibition for SARS-CoV-2 via a direct interaction of its N-terminal domain (NT) with the 5 untranslated region (5 UTR) of SARS-CoV-2 mRNA. We show that while Nsp1-CT is sufficient for binding to 40S and inhibition of host protein translation, the 5 UTR of SARS-CoV-2 mRNA removes this inhibition by binding to Nsp1-NT, suggesting that the Nsp1-NT-UTR interaction is incompatible with the Nsp1-CT-40S interaction. Indeed, lengthening the linker between Nsp1-NT and Nsp1-CT of Nsp1 progressively reduced the ability of SARS-CoV-2 5 UTR to escape the translational inhibition, supporting that the incompatibility is likely steric in nature. The short SL1 region of the 5 UTR is required for viral mRNA translation in the presence of Nsp1. Thus, our data provide a comprehensive view on how Nsp1 switches infected cells from host mRNA translation to SARS-CoV-2 mRNA translation, and that Nsp1 and 5 UTR may be targeted for anti-COVID-19 therapeutics.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ming Shi Sr.", - "author_inst": "Harbin Institute of Technology" - }, - { - "author_name": "Longfei Wang", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School" - }, - { - "author_name": "Pietro Fontana", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School" - }, - { - "author_name": "Setu Vora", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School," - }, - { - "author_name": "Ying Zhang", - "author_inst": "Program in Cellular and Molecular Medicine, Boston Childrens Hospital" - }, - { - "author_name": "Tian-Min Fu", - "author_inst": "Department of Biological Chemistry and Pharmacology, The Ohio State University" - }, - { - "author_name": "Judy Lieberman", - "author_inst": "Program in Cellular and Molecular Medicine, Boston Childrens Hospital" - }, - { - "author_name": "Hao Wu", - "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.09.18.304493", "rel_title": "An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2.", @@ -1179548,6 +1182594,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.09.14.20194605", + "rel_title": "Strict lockdown versus flexible social distance strategy for COVID-19 disease: a cost-effectiveness analysis", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20194605", + "rel_abs": "ObjectivesTo balance the costs and effects comparing a strict lockdown versus a flexible social distancing strategy for societies affected by Coronavirus-19 Disease (COVID-19).\n\nDesignCost-effectiveness analysis.\n\nParticipantsWe used societal data and COVID-19 mortality rates from the public domain.\n\nInterventionsThe intervention was a strict lockdown strategy that has been followed by Denmark. Reference strategy was flexible social distancing policy as was applied by Sweden. We derived mortality rates from COVID-19 national statistics, assumed the expected life years lost from each COVID-19 death to be 11 years and calculated lost life years until 31st August 2020. Expected economic costs were derived from gross domestic productivity (GDP) statistics from each countrys official statistics bureau and forecasted GDP. The incremental financial costs of the strict lockdown were calculated by comparing Sweden with Denmark using externally available market information. Calculations were projected per one million inhabitants. In sensitivity analyses we varied the total cost of the lockdown (range -50% to +100%).\n\nMain outcome measureFinancial costs per life years saved.\n\nResultsIn Sweden, the number of people who died with COVID-19 was 577 per million inhabitants, resulting in an estimated 6,350 life years lost per million inhabitants. In Denmark, where a strict lockdown strategy was installed for months, the number of people dying with COVID-19 was on average 111 per million, resulting in an estimated 1,216 life years per million inhabitants lost. The incremental costs of strict lockdown to save one life year was US$ 137,285, and higher in most of the sensitivity analyses.\n\nConclusionsComparisons of public health interventions for COVID-19 should take into account life years saved and not only lost lives. Strict lockdown costs more than US$ 130,000 per life year saved. As our all our assumptions were in favour of strict lockdown, a flexible social distancing policy in response to COVID19 is defendable.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ben W. Mol", + "author_inst": "Monash University" + }, + { + "author_name": "Jonathan Karnon", + "author_inst": "Flinders University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.09.12.20193375", "rel_title": "A comparative study and application of modified SIR and Logistic models at Municipal Corporation level database of CoViD-19 in India", @@ -1180796,45 +1183865,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.15.20194944", - "rel_title": "COVID-19 pandemic increased the magnitude of mortality risks associated with cold temperature in Italy: A nationwide time-stratified case-crossover study", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194944", - "rel_abs": "Abstract Backgrounds: The coronavirus disease 2019 (COVID-19) pandemic and some containment measures have changed many people lives and behaviours. Whether the pandemic could change the association between cold temperature and mortality remains unknown. Objectives: We aimed to assess whether the association between cold temperature and all-cause mortality in the pandemic period has changed compared to non-COVID-19 period (2015-2019) in Italy. Methods: We collected daily all-cause mortality data and meteorological data for 107 Italian provinces from 1, January 2015 to 31, May 2020. A time-stratified case-crossover design with the distributed lag non-linear model was used to examine the association between cold temperature and all-cause mortality during the first three months (from March to May in 2020) of the COVID-19 outbreak and the same months in 2015-2019. Results: The relative risk (RR) of all-cause mortality at extreme cold temperature (2.5th percentile of temperature at 3 {degrees}C) in comparison with the minimum mortality temperature (24 {degrees}C) was 4.75 [95% confidence interval (CI): 3.90-5.79] in the pandemic period, which is more than triple higher than RR [1.41 (95%CI: 1.33-1.50)] in the same months during 2015-2019. The shift in cold-mortality association was particularly significant for people aged 65-74 years [RR (95%CI): 5.98 (3.78-9.46) in 2020 versus 1.29 (1.10-1.51) in 2015-2019], 75-84 years [5.25 (3.79-7.26) versus 1.40 (1.25-1.56)], and [≥] 85 years [5.03 (3.90-6.51) versus 1.52 (1.39-1.66)], but not significant for those aged 0-64 years [1.95 (1.17-3.24) versus 1.24 (1.05-1.48)]. Conclusion: The findings suggest that the COVID-19 pandemic enhanced the risk of cold temperature on mortality in Italy, particularly among the elderly people. Further studies are warranted to understand the exact mechanism when detailed data are available.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Wenhua Yu", - "author_inst": "Monash University" - }, - { - "author_name": "Rongbin Xu", - "author_inst": "Monash Unviersity" - }, - { - "author_name": "Tingting Ye", - "author_inst": "Monash University" - }, - { - "author_name": "Chunlei Han", - "author_inst": "Binzhou Medical University" - }, - { - "author_name": "Shanshan Li", - "author_inst": "Monash University" - }, - { - "author_name": "Yuming Guo", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.15.20191957", "rel_title": "Adherence to the test, trace and isolate system: results from a time series of 21 nationally representative surveys in the UK (the COVID-19 Rapid Survey of Adherence to Interventions and Responses study)", @@ -1181350,6 +1184380,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.15.20195263", + "rel_title": "Clinical Thrombosis Rate was not Increased in a Cohort of Cancer Patients with COVID-19", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20195263", + "rel_abs": "Increased rates of thromboembolic events (TE) have been reported in patients with coronavirus disease (COVID-19), even without prior predisposition to thrombosis. D-dimer levels have been shown to positively correlate with disease severity and mortality, leading to adoption of new empiric anticoagulation protocols by many centers.\n\nWe aimed to assess whether COVID-19 further increased the risk of TE events in a cancer population who tested positive for COVID-19 at Montefiore Medical Center, Bronx, NY.\n\nThe electronic medical records of 218 cancer patients were retrospectively reviewed up to April 10th, 2020. Work-up of thrombosis was done by the primary team upon clinical or laboratory suspicion. All imaging studies reports, within 20 days of COVID-19 positive test, were reviewed for presence of new arterial or venous thrombosis. Mortality was assessed up to one month since positive COVID-19 test result.\n\nTwelve patients (5.5%) were found to have new arterial (N=6, 50%) or venous (N=6, 50%) thrombosis. Five patients (41.7%) had history of prior TE events. Incidence of deep venous thrombosis and pulmonary embolism was 1.8% and 0.5%, respectively. Arterial events occurred in the brain (66.7%), aorta (16.7%) and coronary arteries (16.7%). Median time from COVID test was 8 days (IQR, 1.5 - 11.3). Five patients (41.7%) had received either prophylactic or therapeutic anticoagulation for a median 2 days (IQR, 1 - 5). Median peak D-dimer within 36 hours of the TE event was 9.8 mcg/mL (N=4 patients, IQR, 1.7 - 18.3). Mortality did not differ significantly between the patients with new TE events vs those without; mortality 41.7% vs 37.4%, respectively, p=0.77. Empiric anticoagulation did not improve mortality.\n\nFifty percent of all TE events were arterial. The overall TE rate of 5.5% in the cancer population was not higher than the risk of general population. Our findings support the need for larger studies in the COVID-19+ cancer population.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Phaedon D Zavras", + "author_inst": "Department of Medicine, Jacobi Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA" + }, + { + "author_name": "Vikas Mehta", + "author_inst": "Department of Otorhinolaryngology, Head & Neck Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA" + }, + { + "author_name": "Sanjay Goel", + "author_inst": "Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA" + }, + { + "author_name": "Henny H. Billett", + "author_inst": "Division of Hematology, Department of Medical Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.15.20193862", "rel_title": "COVID-19 Case-Age Distribution: Correction for Differential Testing by Age", @@ -1182794,105 +1185855,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.16.20196071", - "rel_title": "COVID-19 and human milk: SARS-CoV-2, antibodies, and neutralizing capacity", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20196071", - "rel_abs": "Background: It is not known whether SARS-CoV-2 can be transmitted from mother to infant during breastfeeding, and if so whether the benefits of breastfeeding outweigh this risk. This study was designed to evaluate 1) if SARS-CoV-2 RNA can be detected in milk and on the breast of infected women, 2) concentrations of milk-borne anti-SARS-CoV-2 antibodies, and 3) the capacity of milk to neutralize SARS-CoV-2 infectivity. Methods: We collected 37 milk samples and 70 breast swabs (before and after breast washing) from 18 women recently diagnosed with COVID-19. Samples were analyzed for SARS-CoV-2 RNA using RT-qPCR. Milk was also analyzed for IgA and IgG specific for the nucleocapsid protein, receptor binding domain (RBD), S2 subunit of the spike protein of SARS-CoV-2, as well as 2 seasonal coronaviruses using ELISA; and for its ability to neutralize SARS-CoV-2. Results: We did not detect SARS-CoV-2 RNA in any milk sample. In contrast, SARS-CoV-2 RNA was detected on several breast swabs, although only one was considered conclusive. All milk contained SARS-CoV-2-specific IgA and IgG, and levels of anti-RBD IgA correlated with SARS-CoV-2 neutralization. Strong correlations between levels of IgA and IgG to SARS-CoV-2 and seasonal coronaviruses were noted. Conclusions: Our data do not support maternal-to-child transmission of SARS-CoV-2 via milk; however, risk of transmission via breast skin should be further evaluated. Importantly, milk produced by infected mothers is a source of anti-SARS-CoV-2 IgA and IgG and neutralizes SARS-CoV-2 activity. These results support recommendations to continue breastfeeding during mild-to-moderate maternal COVID-19 illness.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Ryan M Pace", - "author_inst": "University of Idaho" - }, - { - "author_name": "Janet E Williams", - "author_inst": "University of Idaho" - }, - { - "author_name": "Kirsi M J\u00e4rvinen", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Mandy B Belfort", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Christina DW Pace", - "author_inst": "University of Idaho" - }, - { - "author_name": "Kimberly A Lackey", - "author_inst": "University of Idaho" - }, - { - "author_name": "Alexandra C Gogel", - "author_inst": "University of Idaho" - }, - { - "author_name": "Phuong Nguyen-Contant", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Preshetha Kanagaiah", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Theresa Fitzgerald", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Rita Ferri", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Bridget Young", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Casey Rosen-Carole", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Nichole Diaz", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Courtney Meehan", - "author_inst": "Washington State University" - }, - { - "author_name": "Beatrice Caffe", - "author_inst": "Washington State University" - }, - { - "author_name": "Mark Y Sangster", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "David J Topham", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Mark A McGuire", - "author_inst": "University of Idaho" - }, - { - "author_name": "Antti Seppo", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Michelle K McGuire", - "author_inst": "University of Idaho" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.16.20195446", "rel_title": "High-throughput quantitation of SARS-CoV-2 antibodies in a single-dilution homogeneous assay", @@ -1183208,6 +1186170,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.09.18.20196980", + "rel_title": "Relations between demographic, geographic, and environmental statistics, and the spread of novel coronavirus disease (COVID-19) in Italy", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.18.20196980", + "rel_abs": "BACKGROUND: Since January 2020, the COVID-19 pandemic has raged around the world, causing nearly a million deaths and hundreds of severe economic crises. In this scenario, Italy has been one of the most affected countries. OBJECTIVE: This study investigated significant correlations between COVID-19 cases and demographic, geographical, and environmental statistics of each Italian region from February 26 to August 12, 2020. We further investigated the link between the spread of SARS-CoV-2 and particulate matter (PM) 2.5 and 10 concentrations before the lockdown in Lombardy. METHODS: All demographic data were obtained from the AdminStat Italia website, and geographic data were from the Il Meteo website. The collection frequency was one week. Data on PM2.5 and PM10 average daily concentrations were collected from previously published articles. We used Pearson's coefficients to correlate the quantities that followed a normal distribution, and Spearman's coefficient to correlate quantities that did not follow a normal distribution. RESULTS: We found significant strong correlations between COVID-19 cases and population number in 60.0% of the regions. We also found a significant strong correlation between the spread of SARS-CoV-2 in the various regions and their latitude, and with the historical averages (last 30 years) of their minimum temperatures. We identified a significant strong correlation between the number of COVID-19 cases until August 12 and the average daily concentrations of PM2.5 in Lombardy until February 29, 2020. No significant correlation with PM10 was found in the same periods. However, we found that 40 g/m^3 for PM2.5 and 50 g/m^3 PM10 are plausible thresholds beyond which particulate pollution clearly favors the spread of SARS-CoV-2. CONCLUSION: Since SARS-CoV-2 is correlated with historical minimum temperatures and PM10 and 2.5, health authorities are urged to monitor pollution levels and to invest in precautions for the arrival of autumn. Furthermore, we suggest creating awareness campaigns for the recirculation of air in enclosed places and to avoid exposure to the cold. KEYWORDS: COVID-19, Italy, Pandemic, Epidemiology, Coronavirus-2019", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alessandro Rovetta", + "author_inst": "Mensana srls, Via Moro Aldo 5, Brescia (IT)" + }, + { + "author_name": "Lucia Castaldo", + "author_inst": "Mensana srls, Via Moro Aldo 5, Brescia (IT)" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.18.20197160", "rel_title": "Apparent reductions in COVID-19 Case Fatality Rates reflect changes in average age of those testing positive.", @@ -1184488,113 +1187473,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.09.17.20194860", - "rel_title": "High-risk exposure without personal protective equipment and infection with SARS-CoV-2 in healthcare workers: results of the CoV-CONTACT prospective cohort", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20194860", - "rel_abs": "Objective: We aimed to estimate the risk of infection in Healthcare workers (HCWs) following a high-risk exposure without personal protective equipment (PPE). Methods: We conducted a prospective cohort in HCWs who had a high-risk exposure to SARS-CoV-2-infected subject without PPE. Daily symptoms were self-reported for 30 days, nasopharyngeal swabs for SARS-CoV-2 RT-PCR were performed at inclusion and at days 3, 5, 7 and 12, SARS-CoV-2 serology was assessed at inclusion and at day 30. Confirmed infection was defined by positive RT-PCR or seroconversion, and possible infection by one general and one specific symptom for two consecutive days. Results: Between February 5th and May 30th, 2020, 154 HCWs were enrolled within 14 days following one high-risk exposure to either a hospital patient (70/154; 46.1%) and/or a colleague (95/154; 62.5%). At day 30, 25.0% had a confirmed infection (37/148; 95%CI, 18.4%; 32.9%), and 43.9% (65/148; 95%CI, 35.9%; 52.3%) had a confirmed or possible infection. Factors independently associated with confirmed or possible SARS-CoV-2 infection were being a pharmacist or administrative assistant rather than being from medical staff (adjusted OR (aOR)=3.8, CI95%=1.3;11.2, p=0.01), and exposure to a SARS-CoV-2-infected patient rather than exposure to a SARS-CoV-2-infected colleague (aOR=2.6, CI95%=1.2;5.9, p=0.02). Among the 26 HCWs with a SARS-CoV-2-positive nasopharyngeal swab, 7 (26.9%) had no symptom at the time of the RT-PCR positivity. Conclusions: The proportion of HCWs with confirmed or possible SARS-CoV-2 infection was high. There were less occurrences of high-risk exposure with patients than with colleagues, but those were associated with an increased risk of infection.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Sarah Tubiana", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Charles Burdet", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Nadhira Houhou", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Michael Thy", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Pauline Manchon", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Francois Blanquart", - "author_inst": "Universite de Paris, INSERM; College de France, France" - }, - { - "author_name": "Charlotte Charpentier", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Jeremie Guedj", - "author_inst": "Universite de Paris, INSERM, France" - }, - { - "author_name": "Loubna Alavoine", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Sylvie Behillil", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Anne Leclercq", - "author_inst": "APHP, Paris, France" - }, - { - "author_name": "Jean-Christophe Lucet", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Yazdan Yazdanpanah", - "author_inst": "APHP; Universite de Paris, INSERM, Paris, France" - }, - { - "author_name": "Mickael Attia", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Caroline Demeret", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Thierry Rose", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Julia A Bielicki", - "author_inst": "University of Basel Children's Hospital, Basel, Switzerland" - }, - { - "author_name": "Patricia Bruijning-Verhagen", - "author_inst": "University Medical Center Utrecht,Utrecht, The Netherlands" - }, - { - "author_name": "Herman Goossens", - "author_inst": "University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Diane Descamps", - "author_inst": "APHP; Universite de Paris, Paris, France" - }, - { - "author_name": "Sylvie van der Werf", - "author_inst": "Institut Pasteur, Paris, France" - }, - { - "author_name": "Bruno Lina", - "author_inst": "Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France" - }, - { - "author_name": "Xavier Duval", - "author_inst": "APHP; Universite de Paris, Paris, France" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.18.20195669", "rel_title": "How do the general population behave with facemasks to prevent COVID-19 in the community?", @@ -1185034,6 +1187912,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.17.20196469", + "rel_title": "Renin-angiotensin system inhibitors and susceptibility to COVID-19 in patients with hypertension: a propensity score-matched cohort study in primary care", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196469", + "rel_abs": "Introduction A significant proportion of patients with Coronavirus Disease-19 (COVID-19) have hypertension and are treated with renin-angiotensin system (RAS) inhibitors, namely angiotensin-converting enzyme I inhibitors (ACE inhibitors) or angiotensin II type-1 receptor blockers (ARBs). These medications have been postulated to influence susceptibility to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The objective of this study was to assess a possible association between prescription of RAS inhibitors and the incidence of COVID-19 and all-cause mortality. Methods We conducted a propensity-score matched cohort study to assess the incidence of COVID-19 among patients with hypertension who were prescribed ACE inhibitors or ARBs compared to patients treated with calcium channel blockers (CCBs) in a large UK-based primary care database (The Health Improvement Network). We estimated crude incidence rates for confirmed/suspected COVID-19 among those prescribed ACE inhibitors, ARBs and CCBs. We used a Cox proportional hazards model to produce adjusted hazard ratios for COVID-19 comparing patients prescribed ACE inhibitors or ARBs to those prescribed CCBs. We further assessed all-cause mortality as a secondary outcome and a composite of accidents, trauma or fractures as a negative control outcome to assess for residual confounding. Results In the propensity score matched analysis, 83 of 18,895 users (0.44%) of ACE inhibitors developed COVID-19 over 8,923 person-years, an incidence rate of 9.3 per 1000 person-years. 85 of 18,895 (0.45%) users of CCBs developed COVID-19 over 8,932 person-years, an incidence rate of 9.5 per 1000 person-years. The adjusted hazard ratio for suspected/confirmed COVID-19 for users of ACE inhibitors compared to CCBs was 0.92 (95% CI 0.68 to 1.26). 79 out of 10,623 users (0.74%) of ARBs developed COVID-19 over 5010 person-years, an incidence rate of 15.8 per 1000 person-years, compared to 11.6 per 1000 person-years among users of CCBs. The adjusted hazard ratio for suspected/confirmed COVID-19 for users of ARBs compared to CCBs was 1.38 (95% CI 0.98 to 1.95). There were no significant associations between use of ACE inhibitors or ARBs and all-cause mortality, compared to use of CCBs. We found no evidence of significant residual confounding with the negative control analysis. Conclusion Current use of ACE inhibitors was not associated with the risk of suspected or confirmed COVID-19 whereas use of ARBs was associated with a statistically non-significant 38% relative increase in risk compared to use of CCBs. However, no significant associations were observed between prescription of either ACE inhibitors or ARBs and all-cause mortality during the peak of the pandemic.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Shamil Haroon", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Anuradhaa Subramanian", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Jennifer Cooper", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Astha Anand", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Krishna Gokhale", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Nathan Byne", + "author_inst": "Cegedim Health Data, Cegedim Rx, London, UK" + }, + { + "author_name": "Samir Dhalla", + "author_inst": "Cegedim Health Data, Cegedim Rx, London, UK" + }, + { + "author_name": "Dionisio Acosta-Mena", + "author_inst": "Cegedim Health Data, Cegedim Rx, London, UK" + }, + { + "author_name": "Thomas Taverner", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Kelvin Okoth", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Jingya Wang", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Joht Singh Chandan", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Christopher Sainsbury", + "author_inst": "University of Birmingham and Department of Diabetes, Gartnavel General Hospital, NHS Greater Glasgow and Clyde, UK" + }, + { + "author_name": "Dawit Tefra Zemedikun", + "author_inst": "University of Birmingham" + }, + { + "author_name": "G Neil Thomas", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Dhruv Parekh", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Tom Marshall", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Elizabeth Sapey", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Nicola J Adderley", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Krishnarajah Nirantharakumar", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.17.20197087", "rel_title": "The Peak of COVID-19 in India", @@ -1186594,61 +1189567,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.09.16.300459", - "rel_title": "The flexibility of ACE2 in the context of SARS-CoV-2 infection", - "rel_date": "2020-09-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.300459", - "rel_abs": "The COVID-19 pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine developments efforts are underway, many questions remain outstanding on the mechanism of SARS-CoV-2 viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and entry in the cell. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular Spike glycoprotein and at the receptor binding domain-receptor interface, suggesting a role in infection. Here, we perform all-atom molecular dynamics simulations of the glycosylated, full-length membrane-bound ACE2 receptor, in both an apo and spike receptor binding domain (RBD) bound state, in order to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix, while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer, and suggests a mechanical contribution of the host receptor towards the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can be exploited for the rational design of effective SARS-CoV-2 therapeutics.\n\nStatement of SignificanceAs the host receptor of SARS-CoV-2, ACE2 has been the subject of extensive structural and antibody design efforts in aims to curtail COVID-19 spread. Here, we perform molecular dynamics simulations of the homodimer ACE2 full-length structure to study the dynamics of this protein in the context of the cellular membrane. The simulations evidence exceptional plasticity in the protein structure due to flexible hinge motions in the head-transmembrane domain linker region and helix mobility in the membrane, resulting in a varied ensemble of conformations distinct from the experimental structures. Our findings suggest a dynamical contribution of ACE2 to the spike glycoprotein shedding required for infection, and contribute to the question of stoichiometry of the Spike-ACE2 complex.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Emilia P. Barros", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Lorenzo Casalino", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Zied Gaieb", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Abigail C Dommer", - "author_inst": "UC San Diego" - }, - { - "author_name": "Yuzhang Wang", - "author_inst": "State University of New York" - }, - { - "author_name": "Lucy Fallon", - "author_inst": "State University of New York" - }, - { - "author_name": "Lauren Raguette", - "author_inst": "State University of New York" - }, - { - "author_name": "Kellon Belfon", - "author_inst": "State University of New York" - }, - { - "author_name": "Carlos L. Simmerling", - "author_inst": "SUNY at Stony Brook" - }, - { - "author_name": "Rommie E. Amaro", - "author_inst": "UC San Diego" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.09.16.299537", "rel_title": "Mouse model for testing SARS-CoV-2 antivirals: Pharmacokinetics", @@ -1187040,6 +1189958,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.16.297366", + "rel_title": "Bromelain Inhibits SARS-CoV-2 Infection in VeroE6 Cells", + "rel_date": "2020-09-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.297366", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The initial interaction between Transmembrane Serine Protease 2 (TMPRSS2) primed SARS-CoV-2 spike (S) protein and host cell receptor angiotensin-converting enzyme 2 (ACE-2) is a pre-requisite step for this novel coronavirus pathogenesis. Here, we expressed a GFP-tagged SARS-CoV-2 S-Ectodomain in Tni insect cells. That contained sialic acid-enriched N- and O-glycans. Surface resonance plasmon (SPR) and Luminex assay showed that the purified S-Ectodomain binding to human ACE-2 and immunoreactivity with COVID-19 positive samples. We demonstrate that bromelain (isolated from pineapple stem and used as a dietary supplement) treatment diminishes the expression of ACE-2 and TMPRSS2 in VeroE6 cells and dramatically lowers the expression of S-Ectodomain. Importantly, bromelain treatment reduced the interaction between S-Ectodomain and VeroE6 cells. Most importantly, bromelain treatment significantly diminished the SARS-CoV-2 infection in VeroE6 cells. Altogether, our results suggest that bromelain or bromelain rich pineapple stem may be used as an antiviral against COVID-19.\n\nHighlights\n\nO_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC=\"FIGDIR/small/297366v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@b7afb0org.highwire.dtl.DTLVardef@16f8185org.highwire.dtl.DTLVardef@1a07df8org.highwire.dtl.DTLVardef@1ae33fa_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIBromelain inhibits / cleaves the expression of ACE-2 and TMPRSS2\nC_LIO_LIBromelain cleaves / degrades SARS-CoV-2 spike protein\nC_LIO_LIBromelain inhibits S-Ectodomain binding and SARS-CoV-2 infection\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Satish Sagar", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Ashok Kumar Rathinavel", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "William E. Lutz", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Lucas R Struble", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Surender Khurana", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Andy T Schnaubelt", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Nitish K Mishra", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Chittibabu Guda", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Mara J Broadhurst", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "St Patrick Reid", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Kenneth W Bayles", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Gloria E.O Borgstahl", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Prakash Radhakrishnan", + "author_inst": "University of Nebraska Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.16.300483", "rel_title": "Evaluation of nafamostat mesylate safety and inhibition of SARS-CoV-2 replication using a 3-dimensional human airway epithelia model", @@ -1188288,73 +1191273,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.14.20194472", - "rel_title": "SARS-CoV-2 in wastewater settled solids is associated with COVID-19 cases in a large urban sewershed", - "rel_date": "2020-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20194472", - "rel_abs": "Wastewater-based epidemiology (WBE) may be useful for informing public health response to viral diseases like COVID-19 caused by SARS-CoV-2. We quantified SARS-CoV-2 RNA in wastewater influent and primary settled solids in two wastewater treatment plants to inform the pre-analytical and analytical approaches, and to assess whether influent or solids harbored more viral targets. The primary settled solids samples resulted in higher SARS-CoV-2 detection frequencies than the corresponding influent samples. Likewise, SARS-CoV-2 RNA was more readily detected in solids using one-step digital droplet (dd)RT-PCR than with two-step RT-QPCR and two-step ddRT-PCR, likely owing to reduced inhibition with the one-step ddRT-PCR assay. We subsequently analyzed a longitudinal time series of 89 settled solids samples from a single plant for SARS-CoV-2 RNA as well as coronavirus recovery (bovine coronavirus) and fecal strength (pepper mild mottle virus, PMMoV) controls. SARS-CoV-2 RNA targets N1 and N2 concentrations correlate positively and significantly with COVID-19 clinical confirmed case counts in the sewershed. Together, the results demonstrate that measuring SARS-CoV-2 RNA concentrations in settled solids may be a more sensitive approach than measuring SARs-CoV-2 in influent.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Katherine Graham", - "author_inst": "Stanford University" - }, - { - "author_name": "Stephanie Loeb", - "author_inst": "Stanford University" - }, - { - "author_name": "Marlene Wolfe", - "author_inst": "Stanford University" - }, - { - "author_name": "David Catoe", - "author_inst": "SLAC National Accelerator Laboratory" - }, - { - "author_name": "Nasa Sinnott-Armstrong", - "author_inst": "Stanford University" - }, - { - "author_name": "Sooyeol Kim", - "author_inst": "Stanford University" - }, - { - "author_name": "Kevan Yamahara", - "author_inst": "Monterey Bay Aquarium Research Institute" - }, - { - "author_name": "Lauren Sassoubre", - "author_inst": "University of San Francisco" - }, - { - "author_name": "Lorelay Mendoza", - "author_inst": "Stanford University" - }, - { - "author_name": "Laura Roldan-Hernandez", - "author_inst": "Stanford University" - }, - { - "author_name": "Linlin Li", - "author_inst": "County of Santa Clara Public Health Department" - }, - { - "author_name": "Krista Wigginton", - "author_inst": "University of Michigan" - }, - { - "author_name": "Alexandria Boehm", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.14.20191759", "rel_title": "SARS-CoV-2 N-antigenemia: A new alternative to nucleic acid amplification techniques", @@ -1188790,6 +1191708,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.15.296228", + "rel_title": "The Anti-histamine Azelastine, Identified by Computational Drug Repurposing, Inhibits SARS-CoV-2 Infection in Reconstituted Human Nasal Tissue In Vitro", + "rel_date": "2020-09-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.15.296228", + "rel_abs": "BackgroundThe COVID-19 pandemic is an enormous threat for healthcare systems and economies worldwide that urgently demands effective preventive and therapeutic strategies. Unlike the development of vaccines and new drugs specifically targeting SARS-CoV-2, repurposing of approved or clinically tested drugs can provide an immediate solution.\n\nMethodsWe applied a novel computational approach to search among approved and clinically tested drugs from the DrugBank database. Candidates were selected based on Shannon entropy homology and predefined activity profiles of three small molecules with proven anti-SARS-CoV activity and a published data set. Antiviral activity of a predicted drug, azelastine, was tested in vitro in SARS-CoV-2 infection assays with Vero E6 monkey kidney epithelial cells and reconstituted human nasal tissue. The effect on viral replication was assessed by quantification of viral genomes by droplet digital PCR.\n\nFindingsThe computational approach with four independent queries identified major drug families, most often and in overlapping fashion anti-infective, anti-inflammatory, anti-hypertensive, anti-histamine and neuroactive drugs. Azelastine, an histamine 1 receptor-blocker, was predicted in multiple screens, and based on its attractive safety profile and availability in nasal formulation, was selected for experimental testing. Azelastine significantly reduced cytopathic effect and SARS-CoV-2 infection of Vero E6 cells with an EC50 of [~]6 M both in a preventive and treatment setting. Furthermore, azelastine in a commercially available nasal spray tested at 5-fold dilution was highly potent in inhibiting viral propagation in SARS-CoV-2 infected reconstituted human nasal tissue.\n\nInterpretationsAzelastine, an anti-histamine, available in nasal sprays developed against allergic rhinitis may be considered as a topical prevention or treatment of nasal colonization with SARS-CoV-2. As such, it could be useful in reducing viral spread and prophylaxis of COVID-19. Ultimately, its potential benefit should be proven in clinical studies.\n\nFundingprovided by the Hungarian government to the National Laboratory of Virology and by CEBINA GmbH.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Robert Konrat", + "author_inst": "Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria" + }, + { + "author_name": "Henrietta Papp", + "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Valeria Szijarto", + "author_inst": "CEBINA (Central European Biotech Incubator and Accelerator) GmbH, Karl-Farkas-Gasse 22, A-1030 Vienna, Austria" + }, + { + "author_name": "Tanja Gesell", + "author_inst": "Calyxha Biotechnologies GmbH, Karl-Farkas-Gasse 22, A-1030 Vienna, Austria" + }, + { + "author_name": "Gabor Nagy", + "author_inst": "CEBINA (Central European Biotech Incubator and Accelerator) GmbH, Karl-Farkas-Gasse 22, A-1030 Vienna, Austria" + }, + { + "author_name": "Monika Madai", + "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Safia Zeghbib", + "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Anett Kuczmog", + "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Zsofia Lanszki", + "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Zsuzsanna Helyes", + "author_inst": "Department of Pharmacology and Pharmacotherapy, Medical School & Szentagothai Research Center, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Gabor Kemenesi", + "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Ferenc Jakab", + "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary" + }, + { + "author_name": "Eszter Nagy", + "author_inst": "CEBINA (Central European Biotech Incubator and Accelerator) GmbH, Karl-Farkas-Gasse 22, A-1030 Vienna, Austria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.15.297846", "rel_title": "Emergence and expansion of highly infectious spike:D614G mutant SARS-CoV-2 in central India", @@ -1189910,125 +1192895,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.09.13.20193581", - "rel_title": "Rapid, accurate, nucleobase detection using FnCas9", - "rel_date": "2020-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193581", - "rel_abs": "Rapid detection of pathogenic sequences or variants in DNA and RNA through a point-of-care diagnostic approach is valuable for accelerated clinical prognosis as has been witnessed during the recent COVID-19 outbreak. Traditional methods relying on qPCR or sequencing are difficult to implement in settings with limited resources necessitating the development of accurate alternative testing strategies that perform robustly. Here, we present FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that employs a direct Cas9 based enzymatic readout for detecting nucleotide sequences and identifying nucleobase identity without the requirement of trans-cleavage activity of reporter molecules. We demonstrate that FELUDA is 100% accurate in detecting single nucleotide variants (SNVs) including heterozygous carriers of a mutation and present a simple design strategy in the form of a web-tool, JATAYU, for its implementation. FELUDA is semi quantitative, can be adapted to multiple signal detection platforms and can be quickly designed and deployed for versatile applications such as infectious disease outbreaks like COVID-19. Using a lateral flow readout within 1h, FELUDA shows 100% sensitivity and 97% specificity across all range of viral loads in clinical samples. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection at home.\n\nSingle sentence summaryA method to identify nucleotide sequence or nucleobase identity using FnCas9 and its implementation in the rapid and accurate diagnosis of SARS-CoV-2", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Mohd. Azhar", - "author_inst": "CSIR Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Rhythm Phutela", - "author_inst": "CSIR Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Manoj Kumar", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Asgar Hussain Ansari", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Riya Rauthan", - "author_inst": "CSIR Institute of Genomics and Integrative Biology, New Delhi" - }, - { - "author_name": "Sneha Gulati", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Namrata Sharma", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Dipanjali Sinha", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Saumya Sharma", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Sunaina Singh", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Sundaram Acharya", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Deepanjan Paul", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Poorti Kathpalia", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Meghali Aich", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Paras Sehgal", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Gyan Ranjan", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Rahul C Bhoyar", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "- Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium", - "author_inst": "" - }, - { - "author_name": "Khushboo Singhal", - "author_inst": "CSIR-Institute of Genomics & Integrative Biology, New Delhi" - }, - { - "author_name": "Harsha Lad", - "author_inst": "CSIR-Sickle Cell Anemia Mission Laboratory, Chhattisgarh Institute of Medical Sciences, Bilaspur 495001, Chhattisgarh, India" - }, - { - "author_name": "Pradeep Kumar Patra", - "author_inst": "CSIR-Sickle Cell Anemia Mission Laboratory, Chhattisgarh Institute of Medical Sciences, Bilaspur 495001, Chhattisgarh, India" - }, - { - "author_name": "Govind Makharia", - "author_inst": "All India Institute of Medical Sciences, Ansari Nagar East, New Delhi 110029, India" - }, - { - "author_name": "Giriraj Ratan Chandak", - "author_inst": "CSIR-Center for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telengana 500007" - }, - { - "author_name": "Bala Pesala", - "author_inst": "CSIR-Central Electronics Engineering Research Institute, Chennai, India" - }, - { - "author_name": "Debojyoti Chakraborty", - "author_inst": "CSIR Institute of Genomics & Integrative Biology" - }, - { - "author_name": "Souvik Maiti", - "author_inst": "CSIR Institute of Genomics & Integrative Biology, New Delhi" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.09.13.20193722", "rel_title": "Sensing of COVID-19 Antibodies in Seconds via Aerosol Jet Printed Three Dimensional Electrodes", @@ -1190296,6 +1193162,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.13.20193508", + "rel_title": "Slight reduction in SARS-CoV-2 exposure viral load due to masking results in a significant reduction in transmission with widespread implementation", + "rel_date": "2020-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193508", + "rel_abs": "Masks are a vital tool for limiting SARS-CoV-2 spread in the population. Here we utilize a mathematical model to assess the impact of masking on transmission within individual transmission pairs and at the population level. Our model quantitatively links mask efficacy to reductions in viral load and subsequent transmission risk. Our results reinforce that the use of masks by both a potential transmitter and exposed person substantially reduces the probability of successful transmission, even if masks only lower exposure viral load by [~]50%. Slight increases in mask adherence and/or efficacy above current levels would reduce the effective reproductive number (Re) substantially below 1, particularly if implemented comprehensively in potential super-spreader environments. Our model predicts that moderately efficacious masks will lower exposure viral load 10-fold among people who get infected despite masking, potentially limiting infection severity. Because peak viral load tends to occur pre-symptomatically, we also identify that antiviral therapy targeting symptomatic individuals is unlikely to impact transmission risk. Instead, antiviral therapy would only lower Re if dosed as post-exposure prophylaxis and if given to [~]50% of newly infected people within 3 days of an exposure. These results highlight the primacy of masking relative to other biomedical interventions under consideration for limiting the extent of the COVID-19 pandemic prior to widespread implementation of a vaccine.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ashish Goyal", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Daniel B Reeves", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "E Fabian Cardozo Ojeda", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Bryan T Mayer", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Joshua T Schiffer", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.09.20191031", "rel_title": "A dual antigen ELISA allows the assessment of SARS-CoV-2 antibody seroprevalence in a low transmission setting", @@ -1191444,41 +1194345,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.11.20193052", - "rel_title": "Adapting Lot Quality Assurance Sampling to accommodate imperfect tests: application to COVID-19 serosurveillance in Haiti", - "rel_date": "2020-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20193052", - "rel_abs": "Background: Lot Quality Assurance Sampling (LQAS), a tool used for monitoring health indicators in low resource settings resulting in \"high\" or \"low\" classifications, assumes that determination of the trait of interest is perfect. This is often not true for diagnostic tests, with imperfect sensitivity and specificity. Here, we develop Lot Quality Assurance Sampling for Imperfect Tests (LQAS-IMP) to address this issue and apply it to a COVID-19 serosurveillance study in Haiti. Development: As part of the standard LQAS procedure, the user specifies allowable classification errors for the system, which is defined by a sample size and decision rule. We show that when an imperfect diagnostic test is used, the classification errors are larger than specified. We derive a modified procedure, LQAS-IMP, that accounts for the sensitivity and specificity of a diagnostic test to yield correct classification errors. Application: At Zanmi Lasante health facilities in Haiti, the goal was to assess the prior circulation of COVID-19 among healthcare workers (HCWs) using a limited number of antibody tests. As the COVID-19 antibody tests were known to have imperfect diagnostic accuracy, we used the LQAS-IMP procedure to define valid systems for sampling at eleven hospitals in Haiti. Conclusions: The LQAS-IMP procedure accounts for imperfect sensitivity and specificity in system design; if the accuracy of a test is known, the use of LQAS-IMP extends LQAS to applications for indicators that are based on laboratory tests, such as COVID-19 antibodies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Isabel R Fulcher", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Mary Clisbee", - "author_inst": "Zanmi Lasante" - }, - { - "author_name": "Wesler Lambert", - "author_inst": "Zanmi Lasante" - }, - { - "author_name": "Fernet Renand Leandre", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Bethany Hedt-Gauthier", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.11.20192401", "rel_title": "Anakinra and Intravenous IgG versus Tocilizumab in the Treatment of COVID-19 Pneumonia", @@ -1191714,6 +1194580,209 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.12.293498", + "rel_title": "Discovery of a Novel Inhibitor of Coronavirus 3CL Protease as a Clinical Candidate for the Potential Treatment of COVID-19", + "rel_date": "2020-09-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.12.293498", + "rel_abs": "COVID-19 caused by the SARS-CoV-2 virus has become a global pandemic. 3CL protease is a virally encoded protein that is essential across a broad spectrum of coronaviruses with no close human analogs. The designed phosphate prodrug PF-07304814 is metabolized to PF-00835321 which is a potent inhibitor in vitro of the coronavirus family 3CL pro, with selectivity over human host protease targets. Furthermore, PF-00835231 exhibits potent in vitro antiviral activity against SARS-CoV-2 as a single agent and it is additive/synergistic in combination with remdesivir. We present the ADME, safety, in vitro, and in vivo antiviral activity data that supports the clinical evaluation of this compound as a potential COVID-19 treatment.", + "rel_num_authors": 47, + "rel_authors": [ + { + "author_name": "Britton Boras", + "author_inst": "Pfizer" + }, + { + "author_name": "Rhys M Jones", + "author_inst": "Pfizer" + }, + { + "author_name": "Brandon J Anson", + "author_inst": "Purdue" + }, + { + "author_name": "Dan Arenson", + "author_inst": "Pfizer" + }, + { + "author_name": "Lisa Aschenbrenner", + "author_inst": "Pfizer" + }, + { + "author_name": "Malina A Bakowski", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Nathan Beutler", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Joseph Binder", + "author_inst": "Pfizer" + }, + { + "author_name": "Emily Chen", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Heather Eng", + "author_inst": "Pfizer" + }, + { + "author_name": "Jennifer Hammond", + "author_inst": "Pfizer" + }, + { + "author_name": "Robert Hoffman", + "author_inst": "Pfizer" + }, + { + "author_name": "Eugene P Kadar", + "author_inst": "Pfizer" + }, + { + "author_name": "Robert Kania", + "author_inst": "Pfizer" + }, + { + "author_name": "Emi Kimoto", + "author_inst": "Pfizer" + }, + { + "author_name": "Melanie G Kirkpatrick", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Lorraine Lanyon", + "author_inst": "Pfizer" + }, + { + "author_name": "Emma K. Lendy", + "author_inst": "Purdue" + }, + { + "author_name": "Jonathan R. Lillis", + "author_inst": "Pfizer" + }, + { + "author_name": "Suman A. Luthra", + "author_inst": "Pfizer" + }, + { + "author_name": "Chunlong Ma", + "author_inst": "University of Arizona" + }, + { + "author_name": "Stephen Noell", + "author_inst": "Pfizer" + }, + { + "author_name": "R. Scott Obach", + "author_inst": "Pfizer" + }, + { + "author_name": "Kevin Ogilvie", + "author_inst": "Pfizer" + }, + { + "author_name": "Dafydd Owen", + "author_inst": "Pfizer" + }, + { + "author_name": "Martin Pettersson", + "author_inst": "Pfizer" + }, + { + "author_name": "Mattew R. Reese", + "author_inst": "Pfizer" + }, + { + "author_name": "Thomas Rogers", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Michelle I Rossulek", + "author_inst": "Pfizer" + }, + { + "author_name": "Jean G Sathish", + "author_inst": "Pfizer" + }, + { + "author_name": "Claire Steppan", + "author_inst": "Pfizer" + }, + { + "author_name": "Martyn Ticehurst", + "author_inst": "Pfizer" + }, + { + "author_name": "Lawrence W. Updyke", + "author_inst": "Pfizer" + }, + { + "author_name": "Yuao Zhu", + "author_inst": "Pfizer" + }, + { + "author_name": "Jun Wang", + "author_inst": "University of Arizona" + }, + { + "author_name": "Arnab K Chatterjee", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Andrew D Mesecar", + "author_inst": "Purdue University" + }, + { + "author_name": "Annaliesa S. Anderson", + "author_inst": "Pfizer" + }, + { + "author_name": "Charlotte Allerton", + "author_inst": "Pfizer" + }, + { + "author_name": "Matthew Frieman", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Stuart Weston", + "author_inst": "University of Maryland, School of Medicine" + }, + { + "author_name": "Marisa E. McGrath", + "author_inst": "University of Maryland" + }, + { + "author_name": "James Logue", + "author_inst": "University of Maryland" + }, + { + "author_name": "Robert E. Haupt", + "author_inst": "University of Maryland" + }, + { + "author_name": "Holly Hammond", + "author_inst": "University of Maryland" + }, + { + "author_name": "Stephen Mason", + "author_inst": "Pfizer" + }, + { + "author_name": "Norimitsu Shirai", + "author_inst": "Pfizer" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.09.12.294066", "rel_title": "SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike", @@ -1193050,29 +1196119,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.10.20192120", - "rel_title": "Estimating the global reduction in transmission and rise in detection capacity of the novel coronavirus SARS-CoV-2 in early 2020", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192120", - "rel_abs": "To better control the SARS-CoV-2 pandemic, it is essential to quantify the impact of control measures and the fraction of infected individuals that are detected. To this end we developed a deterministic transmission model based on the renewal equation and fitted the model to daily case and death data in the first few months of 2020 in 79 countries and states, representing more than 4 billions individuals. Based on a region-specific infected fatality ratio, we inferred the time-varying probability of case detection and the time-varying decline in transmissiblity. The model was validated by the good correlation between the predicted total number of infected and that found in serosurveys; and most importantly by the strong correlation between the inferred probability of detection and the number of daily tests per inhabitant, with 50% detection achieved with 0.003 daily tests per inhabitants. Most of the decline in transmission was explained by the reductions in transmissibility (social distancing), which avoided 107 deaths in the regions studied over the first four months of 2020. In contrast, symptom-based testing and isolation was not an efficient way to control the spread of the disease, as a large part of transmission happens before symptoms and only a small fraction of infected individuals was typically detected. We developed a phenomenological model to link the number of daily tests with the probability of detection and verified the prediction that increasing test capacity increases the probability of detection less than proportionally. Together these results suggest that little control can be achieved by symptom-based testing and isolation alone.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Antoine Belloir", - "author_inst": "Ecole Polytechnique" - }, - { - "author_name": "Francois Blanquart", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.10.20191841", "rel_title": "The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample", @@ -1193320,6 +1196366,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.10.20190793", + "rel_title": "The impact of asthma on mental health & wellbeing during COVID-19 lockdown", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20190793", + "rel_abs": "IntroductionThe global SARS CoV2 pandemic resulted in social isolation measures with unintended negative impacts, particularly on mental health. We hypothesised that people with asthma are likely to be more vulnerable to worse mental health during lockdown.\n\nMethodsWe examined COVID-19 surveys (completed April/May 2020), nested within two generations of the Avon Longitudinal Study of Parents and Children (ALSPAC): index-generation ALSPAC-G1 (n= 2942, mean age=28) and the parents generation ALSPAC-G0 (n=3737, mean age=59). We used Poisson and logistic regression models to estimate the effect of asthma on wellbeing, anxiety and depression, and factors related to COVID-19 and lockdown. Models were adjusted for validated pre-pandemic measures of mental health and socio-economic factors.\n\nResultsAsthma was associated with a 13% increase in depression score in ALSPAC-G1 (p=0.005) and 15% increase in ALSPAC-G0 (p=0.05) compared to participants without asthma, anxiety scores increased by 14% in ALSPAC-G1 (p=0.005) and by 16% in ALSPAC-G0 (p=0.02). Asthma was associated with a similar increase of anxiety and depression scores during COVID-19 in both generations (Z test p values >0.80).\n\nDiscussionPeople with asthma have worse mental health & wellbeing during lockdown compared to people without asthma. Although the effect of asthma on mental health is of similar magnitude between the generations, younger participants with asthma declined to lower levels of mental health despite reporting less symptoms, COVID-19 infection and self-isolation. This has important implications given repeated lockdowns. Young people with asthma should be closely monitored and supported to mitigate the impact of lockdown on their mental health.\n\nKey Messages\n\nWhat is the question?What is the impact of asthma on mental health & wellbeing during COVID-19 pandemic?\n\nWhat is the bottom line?People living with asthma report worse wellbeing, anxiety and depression in lockdown compared to those without asthma, the effect is not entirely explained by pre-existing mental health problems, physical symptoms or COVID-19 infections.\n\nWhy read on?Young people living with asthma are more likely to report concerns about susceptibility to COVID 19 and job security. The negative impact of asthma on length of self-isolation, suspected COVID and symptoms appears greater in older people with asthma.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Daniel H Higbee", + "author_inst": "University of Bristol. Academic Respiratory Unit, Southmead" + }, + { + "author_name": "George Nava", + "author_inst": "Academic Respiratory Unit, Southmead Hospital" + }, + { + "author_name": "Alex S F Kwong", + "author_inst": "University of Bristol, University of Edinburgh" + }, + { + "author_name": "James W Dodd", + "author_inst": "University of Bristol. Academic Respiratory Unit, Southmead Hospital." + }, + { + "author_name": "Raquel Granell", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.09.09.20191395", "rel_title": "Increased prolonged sitting in rheumatoid arthritis patients during the COVID-19 pandemic: a within-subjects, accelerometer-based study", @@ -1194684,77 +1197765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.09.11.20192591", - "rel_title": "Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192591", - "rel_abs": "Background It is almost nine months, still there is no sign to stop the spreading of the COVID-19 pandemic. Rapid and early detection of the virus is the master key to cease the rapid spread and break the human transmission chain. There are very few studies in search of an alternate and convenient diagnostic tool which can substitute nasopharyngeal swab (NPS) specimen for detection of SARS-CoV-2. We aimed to analyse the comparison and agreement between the feasibility of using the saliva in comparison to NPS for diagnosis of SARS-CoV-2. Methods A total number of 74 patients were enrolled for this study. We analysed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. We used real time quantitative polymerase chain reaction (RT-qPCR), gene sequencing for the detection and determination SARS-CoV-2 specific genes. Phylogenetic tree was constructed to establish the isolation of viral RNA from saliva. We use Bland-Altman model to identify the agreement between two sampling methods. Findings This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Bland-Altman analysis produces relatively smaller bias and high agreement between these specimen tools. Phylogenetic analysis with the RdRp and Spike gene confirmed the presence of SARS-CoV-2 in the saliva samples. Interpretation: In conclusion, our study highlights that saliva represents a promising tool in COVID-19 diagnosis and would reduce the exposure risk of frontline health workers which is one of biggest concern in primary healthcare settings.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Dr. Debdutta Bhattacharya", - "author_inst": "ICMR - Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Debaprasad Parai", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Usha Kiran Rout", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Rashmi Ranjan Nanda", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Srikanta Kanungo", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Girish Chandra Dash", - "author_inst": "ICMR-Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Subrat Kumar Palo", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Siddharth Giri", - "author_inst": "ICMR- Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Hari Ram Choudhary", - "author_inst": "ICMR- Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Jaya Singh Kshatri", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Jyotirmayee Turuk", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Bijay Mishra", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Saroj Dash", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - }, - { - "author_name": "Dr. Sanghamitra Pati", - "author_inst": "ICMR- Regional Medical Research Centre, Bhubaneswar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.10.20192260", "rel_title": "Evaluating ten commercially-available SARS-CoV-2 rapid serological tests using the STARD (Standards for Reporting of Diagnostic Accuracy Studies) method.", @@ -1195010,6 +1198020,173 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.11.292631", + "rel_title": "A key linear epitope for a potent neutralizing antibody to SARS-CoV-2 S-RBD", + "rel_date": "2020-09-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.11.292631", + "rel_abs": "The spread of SARS-CoV-2 confers a serious threat to the public health without effective intervention strategies1-3. Its variant carrying mutated Spike (S) protein D614G (SD614G) has become the most prevalent form in the current global pandemic4,5. We have identified a large panel of potential neutralizing antibodies (NAbs) targeting the receptor-binding domain (RBD) of SARS-CoV-2 S6. Here, we focused on the top 20 potential NAbs for the mechanism study. Of them, the top 4 NAbs could individually neutralize both authentic SARS-CoV-2 and SD614G pseudovirus efficiently. Our epitope mapping revealed that 16/20 potent NAbs overlapped the same steric epitope. Excitingly, we found that one of these potent NAbs (58G6) exclusively bound to a linear epitope on S-RBD (termed as 58G6e), and the interaction of 58G6e and the recombinant ACE2 could be blocked by 58G6. We confirmed that 58G6e represented a key site of vulnerability on S-RBD and it could positively react with COVID-19 convalescent patients plasma. We are the first, as far as we know, to provide direct evidences of a linear epitope that can be recognized by a potent NAb against SARS-CoV-2 S-RBD. This study paves the way for the applications of these NAbs and the potential safe and effective vaccine design.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Tingting Li", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "XiaoJian Han", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Yingming Wang", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Chenjian Gu", + "author_inst": "Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, F" + }, + { + "author_name": "Jianwei Wang", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Chao Hu", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Shenglong Li", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Kai Wang", + "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University" + }, + { + "author_name": "Feiyang Luo", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Jingjing Huang", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Yingyi Long", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Shuyi Song", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Wang Wang", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Jie Hu", + "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University" + }, + { + "author_name": "Ruixin Wu", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Song Mu", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Yanan Hao", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Qian Chen", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Fengxia Gao", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Meiying Shen", + "author_inst": "Department of Breast Surgery, Harbin Medical University Cancer Hospital" + }, + { + "author_name": "Shunhua Long", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Fang Gong", + "author_inst": "Department of Pediatrics, Yongchuan Hospital Affiliated to Chongqing Medical University" + }, + { + "author_name": "Luo Li", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Yang Wu", + "author_inst": "Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, F" + }, + { + "author_name": "Wei Xu", + "author_inst": "Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, F" + }, + { + "author_name": "Xia Cai", + "author_inst": "Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, F" + }, + { + "author_name": "Di Qu", + "author_inst": "Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, F" + }, + { + "author_name": "Zhenghong Yuan", + "author_inst": "Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, F" + }, + { + "author_name": "Qingzhu Gao", + "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University" + }, + { + "author_name": "Guiji Zhang", + "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University" + }, + { + "author_name": "Changlong He", + "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University" + }, + { + "author_name": "Yaru Nai", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Kun Deng", + "author_inst": "Department of laboratory, The Third Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Li Du", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + }, + { + "author_name": "Ni Tang", + "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University" + }, + { + "author_name": "Youhua Xie", + "author_inst": "Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, F" + }, + { + "author_name": "Ailong Huang", + "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University" + }, + { + "author_name": "Aishun Jin", + "author_inst": "Department of Immunology, College of Basic Medicine, Chongqing Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.11.293183", "rel_title": "Molecular Characterization, Phylogenetic and Variation Analyzes of SARS-CoV-2 strains in Turkey", @@ -1196110,53 +1199287,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.08.20189555", - "rel_title": "The Impact of COVID-19 Pandemic on The Preventive Services in Qatar", - "rel_date": "2020-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20189555", - "rel_abs": "BackgroundIn March 2020, Qatar started reporting increased numbers of COVID-19 cases. At that stage, containment measures were put in place. The health authority in Qatar developed an emergency action plan to respond to the outbreak with the Primary Health Care as the main component of that response and suspended all non-urgent services including preventive health services. The aim of the retrospective analysis to measure the Impact of COVID 19 on the preventive services provided in Qatar.\n\nMethodsA retrospective data analysis was conducted for all the preventive services utilization volume across the 27 PHCC health centers from the 1st of January 2017 to the 31st of July 2020.\n\nResultsWith 17,012 no-show appointments, well-baby and Immunization services utilization demonstrated a reduction of 40% in May and started to come back to volumes higher than expected in June. The number of cancelled appointments for breast cancer and colorectal cancer screening programs were 3,481 and 5,854 respectively. The expected volumes demand has dropped by 100% in comparison to 2017 demand. Wellness services only met 20% of its projected utilization in April, however, the services picked up in June.\n\nConclusionThese findings will guide the public health policymakers to understand the effects COVID-19 on preventive services and the risk of having an increased number of outbreaks for childhood communicable disease, cancer cases with delayed diagnosis due to the screening services suspension. In addition, the plan will address the increased number of sedately behavior due to the services reduced utilization of wellness services.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ahmad Haj Bakri", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Mohamed Ghaith Al-Kuwari", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Mariam Ali Abdulmalik", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Hamad Rashid Al-Mudahka", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Wadha Ahmed Al-Baker", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Shaikha Sami Abushaikha", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Mujeeb Chettiyam Kandy", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "John Gibb", - "author_inst": "Primary Health Care Corporation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.09.20188482", "rel_title": "Adherence to COVID-19 pandemic prescribed recommendations, source of information and lockdown psychological impact of Nigeria social media users", @@ -1196344,6 +1199474,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.07.286344", + "rel_title": "Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease", + "rel_date": "2020-09-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.07.286344", + "rel_abs": "The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of Mpro, a cysteine protease, have been determined, facilitating structure-based drug design. Mpro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41-Cys145, Mpro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nu-cleophile Cys145 have been debated in previous studies of SARS-CoV Mpro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 Mpro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of Mpro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an -ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N{delta} (HD) and N{epsilon} (HE) protonation of His41 and His164, respectively, the -ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 Mpro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Anna Pavlova", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Diane L. Lynch", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Laura Zanetti-Polzi", + "author_inst": "CNR Institute of Nanoscience" + }, + { + "author_name": "Micholas Dean Smith", + "author_inst": "The University of Tennessee, Knoxville" + }, + { + "author_name": "Chris Chipot", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Daniel W. Kneller", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Andrey Kovalevsky", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Leighton Coates", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Andrei A. Golosov", + "author_inst": "Novartis Institutes for BioMedical Research" + }, + { + "author_name": "Callum J. Dickson", + "author_inst": "Novartis Institutes for BioMedical Research" + }, + { + "author_name": "Camilo Velez-Vega", + "author_inst": "Novartis Institutes for BioMedical Research" + }, + { + "author_name": "Jos\u00e9 S. Duca", + "author_inst": "Novartis Institutes for BioMedical Research" + }, + { + "author_name": "Josh V. Vermaas", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Yui Tik Pang", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Atanu Acharya", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Jerry M Parks", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Jeremy C. Smith", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "James C. Gumbart", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.09.10.288548", "rel_title": "Susceptibility of domestic swine to experimental infection with SARS-CoV-2", @@ -1197872,49 +1201089,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.07.20189860", - "rel_title": "Ongoing natural selection drives the evolution of SARS-CoV-2 genomes", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20189860", - "rel_abs": "SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively through world populations since its first outbreak in late December, 2019. Whether the transmissibility and pathogenicity of SARS-CoV-2 is actively evolving, and driven by adaptation to the new host and environments is still unknown. Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend, and providing guidance for disease control and treatments. Interrogating 22,078 SARS-CoV-2 genome sequences of 84 countries, we demonstrate with convincing evidence that (i) SARS-CoV-2 genomes are overall conserved under purifying selection. (ii) Ongoing positive selection is actively driving the evolution of specific genes. Notably, genes related to coronavirus infection and host immune system defense are under adaptive evolution while genes related to viral RNA replication, transcription and translation are under purifying selection. A spatial and temporal landscape of 54 critical mutants is constructed based on their divergence among viral haplotype clusters, of which multiple mutants potentially conferring viral transmissibility, infectivity and virulence of SARS-CoV-2 are highlighted.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Qi Liu", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Shilei Zhao", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Yali Hou", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Wenmin Zhao", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Yimin Bao", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Yongbiao Xue", - "author_inst": "Beijing Institute of Genomics, CAS" - }, - { - "author_name": "Hua Chen", - "author_inst": "Beijing Institute of Genomics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.07.20189597", "rel_title": "COVID-19 control across urban-rural gradients", @@ -1198086,6 +1201260,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.09.08.20190488", + "rel_title": "Comparative evaluation of six immunoassays for the detection of antibodies against SARS-CoV-2", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190488", + "rel_abs": "ObjectivesSerologic techniques can serve as a complement to diagnose SARS-CoV-2 infection. The objective of our study was to compare the diagnostic performance of six immunoassays to detect antibodies against SARS-CoV-2: three lateral flow immunoassays (LFAs), one ELISA and two chemiluminescence assays (CLIAs).\n\nMethodsWe evaluated three LFAs (Alltest, One Step and SeroFlash), one ELISA (Dia.Pro) and 34 two CLIAs (Elecsys and COV2T). To assess the specificity, 60 pre-pandemic sera were 35 used. To evaluate the sensitivity, we used 80 serum samples from patients with 36 positive PCR for SARS-CoV-2. Agreement between techniques was evaluated using the kappa score (k).\n\nResultsAll immunoassays showed a specificity of 100% except for SeroFlash (96.7%). Overall sensitivity was 61.3%, 73.8%, 67.5%, 85.9%, 88.0% and 92.0% for Alltest, One Step, SeroFlash, Dia.Pro, Elecsys and COV2T, respectively. Sensitivity increased throughout the first two weeks from the onset of symptoms, reaching sensitivities over 85% from 14 days for all LFAs, being One Step the most sensitive (97.6%), followed by SeroFlash (95.1%). Dia.Pro, Elecsys and COV2T showed sensitivities over 97% from 14 days, being 100% for COV2T. One Step showed the best agreement results among LFAs, showing excellent agreement with Dia.Pro (agreement=94.2%, k=0.884), COV2T (99.1%, k=0.981) and Elecsys (97.3%, k=0.943). Dia.Pro, COV2T and Elecsys also showed excellent agreement between them.\n\nConclusionOne Step, Dia.Pro, Elecsys and COV2T obtained the best diagnostic performanc e results. All these techniques showed a specificity of 100% and sensitivities over 97% from 14 days after the onset of symptoms, as well as excellent levels of agreement.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Felipe Perez-Garcia", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Ramon Perez-Tanoira", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Maria Esther Iglesias", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Juan Romanyk", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Teresa Arroyo", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Pena Gomez-Herruz", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Rosa Gonzalez", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Juan Cuadros-Gonzalez", + "author_inst": "Hospital Universitario Principe de Asturias" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.09.20191213", "rel_title": "Airborne contamination of COVID-19 in hospitals: a scoping review of the current evidence.", @@ -1199294,97 +1202515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.08.20190496", - "rel_title": "Systematic profiling of SARS-CoV-2 specific IgG epitopes at single amino acid resolution", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190496", - "rel_abs": "SARS-CoV-2 specific IgG responses play critical roles for patients to recover from COVID-19, in-depth dissecting of the IgG responses on systems level is of great interest. Herein, we adopted a newly developed high-throughput epitope mapping technology (AbMap), analyzed 55 COVID-19 convalescent sera and 226 antibody samples enriched by specific proteins or peptides from these sera. We revealed three areas that are rich of IgG epitopes, two are on Spike protein but outside of RBD, and one is on Nucleocapsid protein. We identified 29 significant epitopes on Spike protein, from two of these significant epitopes, two critical epitope residues were found, i. e., D936 and P1263, which are highly related to the infectivity of SARS-CoV-2 In summary, we provided the first global map of IgG binding epitopes for SARS-CoV-2 at single amino acid resolution. This map will facilitate the precise development of therapeutic antibodies and vaccines.\n\nHIGHLIGHTSO_LIA map of SARS-CoV-2 specific IgG binding epitopes at single amino acid resolution\nC_LIO_LITwo areas outside of RBD that are rich of significant epitopes were identified\nC_LIO_LIOne area rich of significant epitopes was determined on Nucleocapsid protein\nC_LIO_LITwo critical epitope residues (D936 and P1263) on Spike protein are highly related to the infectivity of SARS-CoV-2\nC_LI", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Huan Qi", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Ming-liang Ma", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Jeremy Jiang", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Jian-ya Ling", - "author_inst": "Shandong University" - }, - { - "author_name": "Ling-yun Chen", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Hai-nan Zhang", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Dan-yun Lai", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Yang Li", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Zi-wen Guo", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Chuang-sheng Hu", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Shu-juan Guo", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Qing-feng Meng", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Yan Ren", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Wei Wang", - "author_inst": "Foshan Fourth Hospital" - }, - { - "author_name": "Xiao Yang", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Foshan Fourth Hospital" - }, - { - "author_name": "Xiao-dong Zhao", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Hua Li", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Sheng-ce Tao", - "author_inst": "Shanghai Jiao Tong University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.09.20191239", "rel_title": "COVID-19 Transmission Within Danish Households: A Nationwide Study from Lockdown to Reopening", @@ -1199668,6 +1202798,57 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.09.08.272328", + "rel_title": "Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2", + "rel_date": "2020-09-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.08.272328", + "rel_abs": "Thrombosis has been one of the complications of the Coronavirus disease of 2019 (COVID-19), often associated with poor prognosis. There is a well-recognized link between coagulation and inflammation, however, the extent of thrombotic events associated with COVID-19 warrants further investigation. Poly(A) Binding Protein Cytoplasmic 4 (PABPC4), Serine/Cysteine Proteinase Inhibitor Clade G Member 1 (SERPING1) and Vitamin K epOxide Reductase Complex subunit 1 (VKORC1), which are all proteins linked to coagulation, have been shown to interact with SARS proteins. We computationally examined the interaction of these with SARS-CoV-2 proteins and, in the case of VKORC1, we describe its binding to ORF7a in detail. We examined the occurrence of variants of each of these proteins across populations and interrogated their potential contribution to COVID-19 severity. Potential mechanisms by which some of these variants may contribute to disease are proposed. Some of these variants are prevalent in minority groups that are disproportionally affected by severe COVID-19. Therefore, we are proposing that further investigation around these variants may lead to better understanding of disease pathogenesis in minority groups and more informed therapeutic approaches.\n\nAuthor summaryIncreased blood clotting, especially in the lungs, is a common complication of COVID-19. Infectious diseases cause inflammation which in turn can contribute to increased blood clotting. However, the extent of clot formation that is seen in the lungs of COVID-19 patients suggests that there may be a more direct link. We identified three human proteins that are involved indirectly in the blood clotting cascade and have been shown to interact with proteins of SARS virus, which is closely related to the novel coronavirus. We examined computationally the interaction of these human proteins with the viral proteins. We looked for genetic variants of these proteins and examined how these variants are distributed across populations. We investigated whether variants of these genes could impact severity of COVID-19. Further investigation around these variants may provide clues for the pathogenesis of COVID-19 particularly in minority groups.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "David Holcomb", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Aikaterini Alexaki", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Nancy Hernandez", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Kyle Laurie", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Jacob Kames", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Nobuko Hamasaki-Katagiri", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Anton A. Komar", + "author_inst": "Cleveland State University" + }, + { + "author_name": "Michael DiCuccio", + "author_inst": "National Center of Biotechnology Information" + }, + { + "author_name": "Chava Kimchi-Sarfaty", + "author_inst": "US Food and Drug Administration" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.09.09.287987", "rel_title": "Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing", @@ -1201232,33 +1204413,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "orthopedics" }, - { - "rel_doi": "10.1101/2020.09.06.20189258", - "rel_title": "Superspreaders and High Variance Infectious Diseases", - "rel_date": "2020-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.06.20189258", - "rel_abs": "(Dated: September 6, 2020)\n\nA well-known characteristic of pandemics such as COVID-19 is the high level of transmission heterogeneity in the infection spread: not all infected individuals spread the disease at the same rate and some individuals (superspreaders) are responsible for most of the infections. To quantify this phenomenon requires the analysis of the effect of the variance and higher moments of the infection distribution. Working in the framework of stochastic branching processes, we derive an approximate analytical formula for the probability of an outbreak in the high variance regime of the infection distribution, verify it numerically and analyze its regime of validity in various examples. We show that it is possible for an outbreak not to occur in the high variance regime even when the basic reproduction number R0 is larger than one and discuss the implications of our results for COVID-19 and other pandemics.\n\nPACS numbers: 87.10.+e", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shmuel Safra", - "author_inst": "Tel Aviv university" - }, - { - "author_name": "Yaron Oz", - "author_inst": "Tel Aviv university" - }, - { - "author_name": "Ittai Rubinstein", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.04.20188110", "rel_title": "Modelling the transmission of infectious diseases inside hospital bays: implications for Covid-19", @@ -1202622,6 +1205776,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.06.20189266", + "rel_title": "Multiscale statistical physics of the Human-SARS-CoV-2 interactome", + "rel_date": "2020-09-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.06.20189266", + "rel_abs": "Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID-19 and providing ground for drug repurposing strategies. However, our knowledge of (dis)similarities between this one and other viral agents is still very limited. Here we compare the novel coronavirus PPI network against 45 known viruses, from the perspective of statistical physics. Our results show that classic analysis such as percolation is not sensitive to the distinguishing features of viruses, whereas the analysis of biochemical spreading patterns allows us to meaningfully categorize the viruses and quantitatively compare their impact on human proteins. Remarkably, when Gibbsian-like density matrices are used to represent each systems state, the corresponding macroscopic statistical properties measured by the spectral entropy reveals the existence of clusters of viruses at multiple scales. Overall, our results indicate that SARS-CoV-2 exhibits similarities to viruses like SARS-CoV and Influenza A at small scales, while at larger scales it exhibits more similarities to viruses such as HIV1 and HTLV1.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Arsham Ghavasieh", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Sebastiano Bontorin", + "author_inst": "Universita' degli Studi di Trento and Fondazione Bruno Kessler" + }, + { + "author_name": "Oriol Artime", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Manlio De Domenico", + "author_inst": "Fondazione Bruno Kessler" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.07.286666", "rel_title": "UVA radiation could be a significant contributor to sunlight inactivation of SARS-CoV-2", @@ -1204186,29 +1207371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.04.20188326", - "rel_title": "Variations in state-level SARS-COV-2 testing recommendations in the United States, March-July 2020", - "rel_date": "2020-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188326", - "rel_abs": "BackgroundState health departments have been responsible for prioritizing and allocating SARS-CoV-2 tests and vaccines. Testing and vaccination recommendations in the United States varied by state and over time, as did vaccine rollouts, COVID-19 cases, and estimates of excess mortality.\n\nMethodsWe compiled data about COVID-19 testing, cases, and deaths, and excess pneumonia + influenza + COVID-19 deaths to assess relationships between testing recommendations, per capita tests performed, epidemic intensity, and excess mortality during the early months of the COVID-19 pandemic in the United States. We compiled further data about state-level SARS-CoV-2 vaccination policies and doses administered during the early months of the vaccine rollout.\n\nResultsAs of July 2020, 16 states recommended testing asymptomatic members of the general public. The rate of COVID-19 tests reported in each state correlated with more inclusive testing recommendations and with higher epidemic intensity. Higher per capita testing was associated with more complete reporting of COVID-19 deaths, which is a fundamental requirement for analyzing the pandemic. Testing per capita during the first three months was associated with vaccination per capita in the first three months of rollout. Per capita vaccine doses in each state were not associated with adherence to national guidelines.\n\nConclusionsReported deaths due to COVID-19 likely represent an undercount of the true burden of the pandemic. States that struggled with testing rollout have also frequently struggled with vaccine rollout. Coordinated, consistent guidelines for COVID-19 testing and vaccine administration should be a high priority for state and national health systems.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Stephanie R Perniciaro", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Daniel M Weinberger", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.04.20188359", "rel_title": "COVID-19 superspreading in cities versus the countryside", @@ -1204412,6 +1207574,221 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.09.05.20188458", + "rel_title": "The association between COVID-19 and preterm delivery: A cohort study with a multivariate analysis", + "rel_date": "2020-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.05.20188458", + "rel_abs": "Structured AbstractO_ST_ABSObjectiveC_ST_ABSTo determine whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the cause of COVID-19 disease) exposure in pregnancy, compared to non-exposure, is associated with infection-related obstetric morbidity.\n\nDesign and settingThroughout Spain, 45 hospitals took part in universal screening of pregnant women going into labour using polymerase-chain-reaction (PCR) for COVID-19 since late March 2020.\n\nMethodsThe cohort of exposed and unexposed pregnancies was followed up until 6-weeks post-partum. Multivariate logistic regression analysis, adjusting for known confounding variables, determined the adjusted odds ratio (aOR) with 95% confidence intervals (95% CI) of the association of COVID-19 exposure, compared to non-exposure, with infection-related obstetric outcomes.\n\nMain outcome measuresPreterm delivery (primary), premature rupture of membranes and neonatal intensive care unit admissions.\n\nResultsIn the cohort of 1,009 screened pregnancies, 246 were COVID-19 positive. Compared to non-exposure, COVID-19 exposure increased the odds of preterm birth (34 vs 51, 13.8% vs 6.7%, aOR 2.12, 95% CI 1.32-3.36, p = 0.002), premature rupture of membranes at term (39 vs 75, 15.8% vs 9.8%, aOR 1.70, 95% CI 1.11-2.57, p = 0.013) and neonatal intensive care unit admissions (23 vs 18, 9.3% vs 2.4%, aOR 4.62, 95% CI 2.43 - 8.94, p< 0.001).\n\nConclusionThis first prospective cohort study demonstrated that pregnant women infected with SARS- CoV-2 have more infection-related obstetric morbidity. This hypothesis merits evaluation of a causal association in further research.", + "rel_num_authors": 50, + "rel_authors": [ + { + "author_name": "- SPANISH OBSTETRIC EMERGENCY GROUP", + "author_inst": "" + }, + { + "author_name": "Oscar Martinez Perez", + "author_inst": "Puerta de Hierro University Hospital" + }, + { + "author_name": "Pilar Prats Rodriguez", + "author_inst": "Hospital Universitari Dexeus Grupo Quironsalud. Barcelona" + }, + { + "author_name": "Marta Muner Hernandez", + "author_inst": "Hospital Universitario La Paz. Madrid" + }, + { + "author_name": "Maria Begona Encinas Pardilla", + "author_inst": "Hospital Universitario Puerta de Hierro.Madrid" + }, + { + "author_name": "Noelia Perez Perez", + "author_inst": "Hospital Clinico San Carlos.Madrid" + }, + { + "author_name": "Maria Rosa Vila Hernandez", + "author_inst": "Hospital de Santa Caterina.Girona" + }, + { + "author_name": "Ana Villalba Yarza", + "author_inst": "Hospital Universitario de Salamanca" + }, + { + "author_name": "Olga Nieto Velasco", + "author_inst": "Hospital Universitario Quironsalud Madrid" + }, + { + "author_name": "Pablo G Del Barrio Fernandez", + "author_inst": "Hospital Universitario de Getafe.Madrid" + }, + { + "author_name": "Laura Forcen Acebal", + "author_inst": "Hospital Universitario Doce de Octubre.Madrid" + }, + { + "author_name": "Carmen M Orizales Lago", + "author_inst": "Hospital Universitario Severo Ochoa.Leganes.Madrid." + }, + { + "author_name": "Alicia Martinez Varea", + "author_inst": "Hospital Universitario La Fe.Valencia" + }, + { + "author_name": "Begona Munoz Abellana", + "author_inst": "Hospital Sant Joan de Reus. Tarragona" + }, + { + "author_name": "Maria Suarez Arana", + "author_inst": "Hospital Regional Universitario de Malaga" + }, + { + "author_name": "Raquel Gonzalez Seoane", + "author_inst": "Hospital Universitario de Ferrol.A Coruna" + }, + { + "author_name": "Clara Martinez Diago", + "author_inst": "Hospital Universitario de Girona Doctor Josep Trueta.Girona" + }, + { + "author_name": "Esther Canedo Carballeira", + "author_inst": "Complejo Hospitalario A Coruna" + }, + { + "author_name": "Macarena Alferez Alvarez Mallo", + "author_inst": "HM Hospitales" + }, + { + "author_name": "Cristina Casanova Pedraz", + "author_inst": "Hospital Universitario de Torrejon. Torrejon de Ardoz. Madrid" + }, + { + "author_name": "Onofre Alomar Mateu", + "author_inst": "Hospital de Inca.Mallorca" + }, + { + "author_name": "Cristina Lesmes Heredia", + "author_inst": "Hospital Parc Tauli.Sabadell.Barcelona" + }, + { + "author_name": "Juan Carlos Wizner de Alva", + "author_inst": "Hospital San Pedro Alcantara.Caceres" + }, + { + "author_name": "Ruth Bernardo Vega", + "author_inst": "Hospital Universitario Rio Hortega.Valladolid" + }, + { + "author_name": "Montserrat Macia Badia", + "author_inst": "Hospital Arnau de Vilanova.Lleida" + }, + { + "author_name": "Cristina Alvarez Colomo", + "author_inst": "Hospital Clinico Universitario de Valladolid" + }, + { + "author_name": "Antonio Sanchez Munoz", + "author_inst": "Hospital General Universitario de Ciudad Real" + }, + { + "author_name": "Laia Pratcorona Alicart", + "author_inst": "Hospital Universitari Germans Trias i Pujol.Badalona.Barcelona" + }, + { + "author_name": "Ruben Alonso Saiz", + "author_inst": "Hospital Universitario de Burgos" + }, + { + "author_name": "Monica Lopez Rodriguez", + "author_inst": "Hospital Universitario de Tarragona Juan XXIII" + }, + { + "author_name": "Maria Carmen Barbancho Lopez", + "author_inst": "Hospital Universitario Infanta Sofia.Madrid" + }, + { + "author_name": "Marta Meca Casbas", + "author_inst": "Hospital de Poniente.Almeria" + }, + { + "author_name": "Oscar Vaquerizo Ruiz", + "author_inst": "Hospital Universitario de Cabuenes.Gijon.Asturias" + }, + { + "author_name": "Eva Moran Antolin", + "author_inst": "Hospital Universitario Son Espases.Mallorca" + }, + { + "author_name": "Maria Jose Nunez Valera", + "author_inst": "Hospital Virgen de la Luz.Cuenca" + }, + { + "author_name": "Camino Fernandez Fernandez", + "author_inst": "Complejo Asistencial de Leon" + }, + { + "author_name": "Albert Tubau Navarra", + "author_inst": "Hospital de Son Llatzer.Mallorca" + }, + { + "author_name": "Alejandra M Cano Garcia", + "author_inst": "Hospital del Tajo.Aranjuez.Madrid" + }, + { + "author_name": "Carmen Baena Luque", + "author_inst": "Hospital Infanta Margarita.Cabra, Cordoba" + }, + { + "author_name": "Susana Soldevilla Perez", + "author_inst": "Hospital Jerez de la Frontera.Cadiz" + }, + { + "author_name": "Irene Gastaca Abasolo", + "author_inst": "Hospital Universitario Araba Txagorritxu.Araba" + }, + { + "author_name": "Jose Adanez Garcia", + "author_inst": "Hospital Universitario Central de Asturias" + }, + { + "author_name": "Maria Teulon Gonzalez", + "author_inst": "Hospital Universitario de Fuenlabrada.Madrid" + }, + { + "author_name": "Alberto Puertas Prieto", + "author_inst": "Hospital Universitario Virgen de las Nieves" + }, + { + "author_name": "Rosa Ostos", + "author_inst": "Hospital Universitario Virgen de Valme.Sevilla" + }, + { + "author_name": "Maria del Pilar Guadix Martin", + "author_inst": "Hospital Universitario Virgen Macarena.Sevilla" + }, + { + "author_name": "Monica Catalina Coello", + "author_inst": "Hospital Virgen de la Concha.Zamora" + }, + { + "author_name": "Maria Luisa De la Cruz Conti", + "author_inst": "Fundacion Investigacion Biomedica.Hospital U Puerta de Hierro.Madrid" + }, + { + "author_name": "Africa Cano Aguilar", + "author_inst": "Hospital Universitario San Cecilio.IBS Granada" + }, + { + "author_name": "Jose A Sainz Bueno", + "author_inst": "Hospital Viamed, Grupo Chacon. Sevilla" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2020.09.04.20188516", "rel_title": "The timing of COVID-19 transmission", @@ -1205576,61 +1208953,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.03.20187377", - "rel_title": "Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study", - "rel_date": "2020-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187377", - "rel_abs": "BackgroundDiagnostic testing forms a major part of the UKs response to the current COVID-19 pandemic with tests offered to people with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK.\n\nMethodsIn this analysis of the Bug Watch prospective community cohort study, we estimated the incidence of cough or fever in England in 2018-2019. We then estimated the COVID-19 diagnostic testing rates required in the UK for baseline cough or fever cases for the period July 2020-June 2021. This was explored for different rates of the population requesting tests and four second wave scenarios and then compared to current national capacity.\n\nResultsThe baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020.\n\nConclusionsOur results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UKs response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Max T Eyre", - "author_inst": "Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK; Liverpool School of Tropical Med" - }, - { - "author_name": "Rachel Burns", - "author_inst": "Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK" - }, - { - "author_name": "Victoria Kirkby", - "author_inst": "Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK" - }, - { - "author_name": "Catherine Smith", - "author_inst": "Institute of Health Informatics, University College London, London, NW1 2DA, UK" - }, - { - "author_name": "Spiros Denaxas", - "author_inst": "Institute of Health Informatics, University College London, London, NW1 2DA, UK; Health Data Research UK, London, NW1 2DA, UK; The Alan Turing Institute, London" - }, - { - "author_name": "Vincent Nguyen", - "author_inst": "Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK; Institute of Epidemiology and Health Care" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "Institute of Epidemiology and Health Care, University College London, London, WC1E 7HB, UK" - }, - { - "author_name": "Laura Shallcross", - "author_inst": "Institute of Health Informatics, University College London, London, NW1 2DA, UK" - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "Institute of Health Informatics, University College London, London, NW1 2DA, UK; Faculty of Epidemiology and Population Health, London School of Hygiene and Tro" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "Centre of Public Health Data Science, Institute of Health Informatics, University College London, London, NW1 2DA, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.03.20187336", "rel_title": "Household Secondary Attack Rate in Gandhinagar district of Gujarat state from Western India", @@ -1205882,6 +1209204,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.04.20187922", + "rel_title": "Viable virus aerosol propagation by PAP circuit leak and mitigation with a ventilated patient hood: a model for improving health care worker safety in the COVID-19 pandemic", + "rel_date": "2020-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20187922", + "rel_abs": "BackgroundNosocomial transmission of SARS-CoV-2 has been a major cause of morbidity and mortality in the COVID-19 pandemic. Emerging evidence suggests patients auto-emit aerosols containing viable respiratory viruses. These aerosols could be further propagated when patients undergo certain treatments including continuous positive airway pressure (PAP) therapy. This study aimed to assess the degree of viable virus propagated from mask leak in a PAP circuit and the mitigation of virus propagation by an air filter combined with a plastic canopy.\n\nMethodsBacteriophage PhiX174 (108copies/mL) was nebulised into a custom PAP circuit within a non-vented clinical room. Mask leak was systematically varied to allow 0, 7, 21, 28 and 42 L/min at the mask interface. Plates containing Escherichia coli host assessed the degree of viable virus (via plaque forming unit) settling on surfaces around the room. In order to contain virus spread, the efficacy of a simple, low-cost ventilated headboard, created from a plastic tarpaulin hood and a high efficiency particulate air (HEPA) filter was tested.\n\nFindingsIncreasing mask leak was associated with virus contamination in a dose response manner ({chi}2 = 58.24, df = 4, p< 0.001). Clinically relevant levels of leak ([≥]21 L/min) were associated with virus counts equivalent to using PAP with a standard vented mask. The highest frequency of viruses was detected on surfaces 1m from the leak source, however, viable viruses were recorded on all plates (up to 3.86m from source). A plastic hood with HEPA filtration significantly reduced viable viruses on all plates. HEPA exchange rates of 170 and 470m3/hr eradicated all evidence of virus contamination.\n\nInterpretationMask leak from PAP circuits may be a major source of environmental contamination and nosocomial spread of infectious respiratory diseases. Subclinical levels of leak should be treated as an infectious risk. Cheap and low-cost patient hoods with HEPA filtration are an effective countermeasure.\n\nFundingNational Health and Medical Research Council of Australia (1139745).\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSNosocomial spread of SARS-CoV-2 results in increased infection rates among healthcare workers compared to the general population. Those workers involved in the delivery of non-invasive ventilation are at higher risk based on evidence from previous SARS outbreaks. However, little is known about virus aerosol spread and environmental contamination from respiratory interventions like non-invasive ventilation, which is one of few life-saving treatments for COVID-19 patients. We therefore searched through PubMed with no language restrictions from inception to August 21, 2020 using the search terms ([NIV] or [non-invasive ventilation] or [noninvasive ventilation] or [CPAP] or [continuous positive airways pressure] or [PAP] or [positive airways pressure]) and ([aerosol spread] or [aerosol dispersion] or [aerosol generation]). The search returned 130 publications of which 28 related to the generation or spread of aerosols. Of the 28 related papers, 17 were consensus or opinion papers, 4 were reviews and 7 were original research papers. All previous studies investigating aerosol propagation with respiratory interventions utilised particle sizers or smoke visualisation techniques. These methodological limitations mean that particles are counted or visualised close to the aerosol source and reveal little about wider aerosol spread. Furthermore, they ignore the inherent biological aspects of viral aerosol dispersion in that the aerosol needs to contain viable virus in order to be infectious. It has not been directly established that clinical respiratory interventions are capable of propagating viable virus aerosol and no attempt has been made to systematically quantify the degree of environmental contamination from viable virus aerosol escaping from non-invasive ventilation circuits. There are no current studies informing us as to the effectiveness of air filtration interventions at mitigating environmental contamination with viable virus aerosol escaping from non-invasive ventilation circuits.\n\nAdded value of this studyOur study quantifies the degree of viable virus aerosol spread from clinically relevant levels of noninvasive ventilator circuit mask leak, and demonstrates a risk mitigation strategy using a hood and air-purifier at completely eliminating viable virus aerosol environmental contamination. We developed a viable virus aerosol model utilising bacteriophage PhiX174 which is similar in size to SARS-CoV-2 and is harmless to humans. Through nebulising a solution of PhiX174 into a custom ventilation circuit with controllable mask leak settings, we were able to demonstrate that increasing circuit leak was associated with environmental virus contamination in a dose response manner (p< 0.001). Even sub-clinically apparent levels of circuit leak (< 7L/min) were associated with detectable virus propagation up to 3.86 metres from the leak source. Deployment of a hood and air-purifier setup as described by the United States Centres for Disease Control and Prevention, completely eliminated environmental virus contamination from viral aerosol dispersion.\n\nImplications of all the available evidenceNon-invasive ventilator circuit mask leak can propagate live virus containing aerosol and can lead to extensive environmental contamination up to 3.86 metres from the leak source, even at levels of leak that would be difficult to detect clinically. This raises important safety considerations for open wards delivering non-invasive ventilatory support and could explain the noted increased risk of nosocomial SARS infections in healthcare workers delivering non-invasive ventilation treatment. Point of emission air filtration with simple hood and air-purifier completely eliminates environmental contamination with viable virus and could be readily deployed to protect health care workers in the COVID-19 pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Shane A Landry", + "author_inst": "Department of Physiology, Monash University" + }, + { + "author_name": "Jeremy Barr", + "author_inst": "Monash University" + }, + { + "author_name": "Martin MacDonald", + "author_inst": "Monash Lung and Sleep" + }, + { + "author_name": "Dinesh Subedi", + "author_inst": "Monash University" + }, + { + "author_name": "Darren Mansfield", + "author_inst": "Monash Lung and Sleep" + }, + { + "author_name": "Garun Hamilton", + "author_inst": "Monash Lung and Sleep" + }, + { + "author_name": "Bradley Edwards", + "author_inst": "Monash University" + }, + { + "author_name": "Simon Joosten", + "author_inst": "Monash Lung and Sleep" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.09.03.20187732", "rel_title": "Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2", @@ -1207166,45 +1210535,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.01.20186395", - "rel_title": "Age-dependence of healthcare interventions for SARS-CoV-2 infection in Ontario, Canada", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20186395", - "rel_abs": "BackgroundPatient age is the most salient clinical indicator of risk from COVID-19. Age-specific distributions of known SARS-CoV-2 infections and COVID-19-related deaths are available for most countries. However, relatively little attention has been given to the age distributions of hospitalizations and serious healthcare interventions administered to COVID-19 patients. We examined these distributions in Ontario, Canada, in order to quantify the age-related impacts of COVID-19, and to identify potential risks should the healthcare system become overwhelmed with COVID-19 patients in the future.\n\nMethodsWe analysed known SARS-CoV-2 infection records from the integrated Public Health Information System (iPHIS) and the Toronto Public Health Coronavirus Rapid Entry System (CORES) between 23 January 2020 and 17 June 2020 (N = 30,546), and estimated the age distributions of hospitalizations, ICU admissions, intubations, and ventilations. We quantified the probability of hospitalization given known SARS-CoV-2 infection, and of survival given COVID-19-related hospitalization.\n\nResultsThe distribution of COVID-19-related hospitalizations peaks with a wide plateau covering ages 54-90, whereas deaths are sharply concentrated in very old ages, with a maximum at age 90. The estimated probability of hospitalization given known SARS-CoV-2 infection reaches a maximum of 32.0% at age 75 (95% CI 27.5%-36.7%). The probability of survival given COVID-19-related hospitalization is uncertain for children (due to small sample size), and near 100% for adults younger than 40. After age 40, survival of hospitalized COVID-19 patients declines substantially; for example, a hospitalized 50-year-old patient has a 90.4% chance of surviving COVID-19 (95% CI 81.9%-95.7%).\n\nInterpretationConcerted efforts to control the spread of SARS-CoV-2 have kept prevalence of the virus low in the population of Ontario. The healthcare system has not been overstretched, yet the probability of survival given hospitalization for COVID-19 has been lower than is generally recognized for patients over 40. If prevalence of the virus were to increase and healthcare capacities were to be exceeded, survival of individuals in the broad age range requiring acute care would be expected to decrease, potentially expanding the distribution of COVID-19-related deaths toward younger ages.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Irena Papst", - "author_inst": "Cornell University" - }, - { - "author_name": "Michael Li", - "author_inst": "McMaster University" - }, - { - "author_name": "David Champredon", - "author_inst": "University of Western Ontario" - }, - { - "author_name": "Benjamin M Bolker", - "author_inst": "McMaster University" - }, - { - "author_name": "Jonathan Dushoff", - "author_inst": "McMaster University" - }, - { - "author_name": "David J D Earn", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.01.20185280", "rel_title": "SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence.", @@ -1207484,6 +1210814,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.09.01.20186288", + "rel_title": "A model assessing potential benefits of isolation and mass testing on COVID-19: the case of Nigeria", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20186288", + "rel_abs": "We consider a model with mass testing and isolation mimicking the current policies implemented in Nigeria and use the Nigerian daily cumulative cases to calibrate the model to obtain the optimal mass testing and isolation levels. Mathematical analysis was done and important thresholds such the peak size relation and final size relation were obtained. Global stability analysis of the disease-free equilibrium indicated that COVID-19 can be eradicated provided that [Formula] and unstable otherwise. Results from simulations revealed that an increase in mass testing and reduction of transmission from isolated individuals are associated with benefits of increasing detected cases, lowering peaks of symptomatic cases, increase in self-isolating cases, decrease in cumulative deaths and decrease in admissions into monitored isolation facilities in the case of Nigeria.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Faraimunashe Chirove", + "author_inst": "University of Johannesburg" + }, + { + "author_name": "Chinwendu Emilian Madubueze", + "author_inst": "University of Agriculture, Makurdi" + }, + { + "author_name": "Zviiteyi Chazuka", + "author_inst": "Chinhoyi University of Technology, Zimbabwe" + }, + { + "author_name": "Sunday Casmir Madubueze", + "author_inst": "Dalhatu Araf Specialist Hospital, Department of Family Medicine, Lafia, Nigeria." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.01.20184937", "rel_title": "The clinical course of COVID-19 in the outpatient setting: a prospective cohort study", @@ -1208752,29 +1212113,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.02.20186676", - "rel_title": "Estimating the number of COVID-19 cases being introduced into British Higher Education Institutions during Autumn 2020", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186676", - "rel_abs": "It is estimated that 81% of the 163 UK Higher Educational Institutes (HEIs) have more than a 50% chance of having at least one COVID-19 case arriving on campus when considering all staff and students. Across all HEIs it is estimated that there will be a total of approximately 700 COVID-19 cases (95% CI: 640 - 750) arriving on campus of which 380 are associated from UK students, 230 from international and 90 from staff. This assumes all students will return to campus and that student numbers and where they come from are similar to previous years. According to the current UK government guidance approximately 237,370 students arriving on campus will be required to quarantine because they come from countries outwith designated travel corridors. Assuming quarantining is 100% efficient this will potentially reduce the overall number of cases by approximately 20% to 540 (95% CI: 500 - 590). Universities must plan for COVID-19 cases to arrive on campus and facilitate mitigations to reduce the spread of disease. It is likely that the first two weeks will be crucial to stop spread of introduced cases. Following that, the risk of introduction of new cases onto campus will be from interactions between students, staff and the local community as well as students travelling off campus for personal, educational or recreational reasons.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Francisco Perez-Reche", - "author_inst": "University of Aberdeen" - }, - { - "author_name": "Norval Strachan", - "author_inst": "University of Aberdeen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.01.20182873", "rel_title": "Effects of Public Health Interventions on the Epidemiological Spread During the First Wave of the COVID-19 Outbreak in Thailand", @@ -1209058,6 +1212396,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.02.20186528", + "rel_title": "Vaccination for some childhood diseases may impact the outcome of covid-19 infections", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186528", + "rel_abs": "BackgroundCOVID-19 found the world in a state of unpreparedness. While research efforts to develop a vaccine are on-going, others have suggested the use of available vaccines to boost innate immunity.\n\nObjectiveWe analysed three databases: UNICEF Immunization Coverage, Worldometer Corona Virus Updates and World Bank List of Economies to establish the association, if any, between vaccination for various diseases and COVID-19 death rates and recoveries across world economies.\n\nResultsMean percentage death rates were lower in countries that vaccinated for Hepatitis-B birth dose (2.53% vs 3.79%, p = 0.001), Bacille Calmette-Guerin Vaccine (2.93% vs 5.10%, p = 0.025) and Inactivated Polio Vaccine 1st dose (2.8% vs 4.01%, p = 0.022) than those which did not report vaccination. In high income countries, a significant negative correlation with death rates was observed with vaccination for Measles-containing vaccine 2nd dose (r = -0.290, p = 0.032), Rubella-containing vaccine 1st dose (r = -0.325, p = 0.015), Hepatitis B 3rd dose (r = -0.562, p = 3.3 x10-5), Inactivated Polio vaccine 1st dose (r = -0.720, p = 0.008). Inactivated Polio Vaccine 1st dose and Measles-containing vaccine 2nd dose also correlated with better recoveries. In Low Income countries, only Rubella-containing vaccine correlated with lower deaths while Yellow fever vaccine was associated with poorer recoveries.\n\nConclusionOur analysis corroborates the potential benefit of vaccination and warrant further research to explore the rationale for repurposing other vaccines to fight COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Irene Gobe", + "author_inst": "University of Botswana" + }, + { + "author_name": "Garesego F Koto", + "author_inst": "University of Botswana" + }, + { + "author_name": "Kesaobaka Molebatsi", + "author_inst": "University of Botswana" + }, + { + "author_name": "Margaret Mokomane", + "author_inst": "University of Botswana" + }, + { + "author_name": "Ishmael Kasvosve", + "author_inst": "University of Botswana" + }, + { + "author_name": "Modisa S Motswaledi", + "author_inst": "University of Botswana" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.02.20187021", "rel_title": "Impact of universal masking in health care and community on SARS-CoV-2 spread", @@ -1210242,49 +1213619,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.30.20184705", - "rel_title": "Analyzing inherent biases in SARS-CoV-2 PCR and serological epidemiologic metrics", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20184705", - "rel_abs": "BackgroundProspective observational data show that infected persons with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain polymerase chain reaction (PCR) positive for a prolonged duration, and that detectable antibodies develop slowly with time. We aimed to analyze how these effects can bias key epidemiological metrics used to track and monitor SARS-CoV-2 epidemics.\n\nMethodsAn age-structured mathematical model was constructed to simulate progression of SARS-CoV-2 epidemics in populations. PCR testing to diagnose infection and cross-sectional surveys to measure seroprevalence were also simulated. Analyses were conducted on simulated outcomes assuming a natural epidemic time course and an epidemic in presence of interventions.\n\nResultsThe prolonged PCR positivity biased the epidemiological measures. There was a lag of 10 days between the true epidemic peak and the actually-observed peak. Prior to epidemic peak, PCR positivity rate was 2-fold higher than that based only on current active infection, and half of those tested positive by PCR were in the prolonged PCR positivity stage after infection clearance. Post epidemic peak, PCR positivity rate poorly predicted true trend in active infection. Meanwhile, the prolonged PCR positivity did not appreciably bias estimation of the basic reproduction number R0. The time delay in development of detectable antibodies biased measured seroprevalence. The actually-observed seroprevalence substantially underestimated true prevalence of ever infection, with the underestimation being most pronounced around epidemic peak.\n\nConclusionsCaution is warranted in interpreting PCR and serological testing data, and any drawn inferences need to factor the effects of the investigated biases for an accurate assessment of epidemic dynamics.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Monia Makhoul", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar" - }, - { - "author_name": "Farah Abou-Hijleh", - "author_inst": "Department of Public Health, College of Health Sciences, Academic Quality Affairs Office, QU Health, Qatar University, Doha, Qatar" - }, - { - "author_name": "Shaheen Seedat", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar" - }, - { - "author_name": "Ghina R Mumtaz", - "author_inst": "Department of Epidemiology and Population Health, American University of Beirut, Beirut, Lebanon" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar" - }, - { - "author_name": "Houssein Ayoub", - "author_inst": "Department of Mathematics, Statistics, and Physics, College of Arts and Sciences, Qatar University, Doha, Qatar" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.29.20184135", "rel_title": "Modeling the combined effect of digital exposure notification and non-pharmaceutical interventions on the COVID-19 epidemic in Washington state", @@ -1210532,6 +1213866,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.29.20184382", + "rel_title": "Are COVID-19 proximity tracing apps working under real-world conditions? Indicator development and assessment of drivers for app (non-)use", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184382", + "rel_abs": "Digital proximity tracing (DPT) apps have been released to mitigate SARS-CoV-2 transmission, but it remains unclear how their effectiveness should be monitored. The aim of this study was to formalize indicators for measuring the fulfillment of assumptions for appropriate proximity tracing app functioning.\n\nSix indicators were developed to monitor the SwissCovid app functioning and effectiveness in the Swiss population. Using official statistics and survey data, we calculated indicator values and examined socio-demographic factors associated with the SwissCovid app utilization. Indicators show that 1 in 3 adults in Switzerland have downloaded the app. However, only 15% of new cases also triggered DPT-app notifications, and indicators also reveal ignored app notifications. In the full survey sample (n=2098), higher monthly household income or being a non-smoker were associated with higher SwissCovid app uptake; older age or having a non-Swiss nationality with a lower uptake. In a subsample including more detailed information (n=701), high trust in health authorities was associated with higher SwissCovid app uptake.\n\nThe indicators help to monitor key drivers of DPT-apps effectiveness and hint to non-compliance issues. Streamlining procedures, removing technical hurdles, and communicating the usefulness of DPT-apps are crucial to promote uptake, compliance, and ultimately effectiveness of DPT-apps for pandemic mitigation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Viktor von Wyl", + "author_inst": "University of Zurich" + }, + { + "author_name": "Marc Hoeglinger", + "author_inst": "Zurich University of Applied Sciences" + }, + { + "author_name": "Chloe Sieber", + "author_inst": "University of Zurich" + }, + { + "author_name": "Marco Kaufmann", + "author_inst": "University of Zurich" + }, + { + "author_name": "Andre Moser", + "author_inst": "University of Zurich" + }, + { + "author_name": "Miquel Serra-Burriel", + "author_inst": "University of Zurich" + }, + { + "author_name": "Tala Ballouz", + "author_inst": "University of Zurich" + }, + { + "author_name": "Dominik Menges", + "author_inst": "University of Zurich" + }, + { + "author_name": "Anja Frei", + "author_inst": "University of Zurich" + }, + { + "author_name": "Milo Puhan", + "author_inst": "University of Zurich" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.29.20184283", "rel_title": "Relation of Doubling Time and Reproduction Number with Testing Rate for Corona Infections in India", @@ -1212116,57 +1215505,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.31.20185017", - "rel_title": "First snap-shot meta-analysis to estimate the prevalence of serum antibodies to SARS-CoV-2 in humans", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185017", - "rel_abs": "BackgroundCOVID-19 is arguably the number-one public health concern worldwide, and efforts are now escalating to control its spread.\n\nObjectiveIn this study, we undertake a meta-analysis to estimate the global and regional anti-SARS-CoV-2 seroprevalence rates in humans and assess whether seroprevalence associates with geographical, climatic and socio-demographic factors.\n\nData sourcesWe systematically reviewed PubMed, Scopus, Embase, medRxiv and bioRxiv for peer-reviewed articles or preprints (up to 14 August 2020).\n\nStudy eligibility criteriaPopulation-based studies describing prevalence of anti-SARS-CoV-2 serum antibodies in general people.\n\nParticipantsgeneral people who were tested for prevalence of anti-SARS-CoV-2 serum antibodies.\n\nInterventionsThere were no interventions.\n\nMethodsWe used random-effects model to estimate pooled seroprevalence, and then extrapolated these findings to the global population (for 2020). Sub-group and meta-regression analyses explored potential sources of heterogeneity in the data and relationships between seroprevalence and socio-demographic, geographical and climatic factors.\n\nResultsIn total, 47 serological studies involving 399,265 people from 23 countries met the inclusion criteria. The pooled seroprevalence of SARS-CoV-2 in general people was estimated at 3.38% (95% CI, 3.05%-3.72%; 15,879/399,265). On a regional basis, we determined seroprevalence estimates of 5.27% (3.97-6.57%) in Northern Europe; 4.41% (2.20-6.61%) in Southern Europe; 4.41% (3.03- 5.79%) in North America; 3.17% (1.96-4.38%) in Western Europe; 2.02% (1.56-2.49%) in the Eastern Asia; and 1.45% (0.95-1.94%) in South America. Extrapolating to the 2020 world population, we estimated that 263,565,606 individuals had been exposed or infected with SARS-CoV-2 at the first wave of the pandemic. A significantly higher seroprevalence was related to higher income levels and human development indices, higher geographical latitudes and lower mean environmental temperatures.\n\nInterpretationThis study reinforces that SARS-CoV-2 infection is a very rapidly-spreading communicable disease and calls for routine surveys to constantly monitor temporal changes in seroprevalence around the globe.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ali Rostami", - "author_inst": "Babol University of Medical Science" - }, - { - "author_name": "Mahdi Sepidarkish", - "author_inst": "Babol University of Medical Sciences" - }, - { - "author_name": "Mariska Leeflang", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Seyed Mohammad Riahi", - "author_inst": "Birjand University of Medical Sciences" - }, - { - "author_name": "Malihe Nourollahpour Shiadeh", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Sahar Esfandyari", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Ali H Mokdad", - "author_inst": "University of Washington" - }, - { - "author_name": "Peter J. Hotez", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Robin B. Gasser", - "author_inst": "The University of Melbourne" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.31.20185587", "rel_title": "Health and economic effects of COVID-19 control in Australia: Modelling and quantifying the payoffs of hard versus soft lockdown", @@ -1212478,6 +1215816,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.31.20185082", + "rel_title": "Outcome of SARS-CoV-2 infection linked to MAIT cell activation and cytotoxicity: evidence for an IL-18 dependent mechanism", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185082", + "rel_abs": "Immune system dysfunction is paramount in Coronavirus disease 2019 (COVID-19) severity and fatality rate. Mucosal-Associated Invariant T (MAIT) cells are innate-like T cells involved in mucosal immunity and protection against viral infections. Here, we studied the immune cell landscape, with emphasis on MAIT cells, in a cohort of 182 patients including patients at various stages of disease activity. A profound decrease of MAIT cell counts in blood of critically ill patients was observed. These cells showed a strongly activated and cytotoxic phenotype that positively correlated with circulating pro-inflammatory cytokines, notably IL-18. MAIT cell alterations markedly correlated with disease severity and patient mortality. SARS-CoV-2-infected macrophages activated MAIT cells in a cytokine-dependent manner involving an IFN-dependent early phase and an IL-18-induced later phase. Therefore, altered MAIT cell phenotypes represent valuable biomarkers of disease severity and their therapeutic manipulation might prevent the inflammatory phase involved in COVID-19 aggravation.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "H\u00e9lo\u00efse Flament", + "author_inst": "Immunological Dysfunction Unit, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France ; University of Paris, Center fo" + }, + { + "author_name": "Matthieu Rouland", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "Lucie Beaudoin", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "Amine Toubal", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "L\u00e9o Bertrand", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "Samuel Lebourgeois", + "author_inst": "Department of Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evo" + }, + { + "author_name": "Zouriatou Gouda", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "Camille Rousseau", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "Pauline Soulard", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "Maria Hurtado-Nedelec", + "author_inst": "Immunological Dysfunction Unit, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France ; University of Paris, Center fo" + }, + { + "author_name": "Sandrine Luce", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "Karine Bailly", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "Muriel Andrieu", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France." + }, + { + "author_name": "Christian Boitard", + "author_inst": "Department of Diabetology, Assistance Publique-Hopitaux de Paris, Cochin University Hospital, Paris, France." + }, + { + "author_name": "Ana\u00efs Vallet-Pichard", + "author_inst": "Department of Hepatology, Assistance Publique-Hopitaux de Paris, Cochin University Hospital, Paris, France." + }, + { + "author_name": "Jean-Francois Gautier", + "author_inst": "Department of Diabetes and Endocrinology, Lariboisiere Hospital, AP-HP, Paris, France." + }, + { + "author_name": "Nadine Ajzenberg", + "author_inst": "Department of Hematology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; University of Paris, LVTS, INSERM 114" + }, + { + "author_name": "Benjamin Terrier", + "author_inst": "Medical Intensive Care Unit, Assistance Publique-Hopitaux de Paris Cochin University Hospital, Paris, France." + }, + { + "author_name": "Fr\u00e9d\u00e9ric Pene", + "author_inst": "Department of Internal Medicine, Assistance Publique-Hopitaux de Paris, Cochin University Hospital, Paris, France." + }, + { + "author_name": "Jade Ghosn", + "author_inst": "Department of Infectious and Tropical Diseases, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Anti" + }, + { + "author_name": "Yazdan Yazdanpanah", + "author_inst": "Department of Infectious and Tropical Diseases, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Anti" + }, + { + "author_name": "Benoit Visseaux", + "author_inst": "Department of Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evo" + }, + { + "author_name": "Diane Descamps", + "author_inst": "Department of Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evo" + }, + { + "author_name": "Jean-Francois Timsit", + "author_inst": "Medical and Infectious Diseases Intensive Care Unit, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections" + }, + { + "author_name": "Renato Costa Monteiro", + "author_inst": "Immunological Dysfunction Unit, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France ; University of Paris, Center fo" + }, + { + "author_name": "Agnes Lehuen", + "author_inst": "University of Paris, Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.31.20184952", "rel_title": "Risk Factors for ICU Admission, Mechanical Ventilation and Mortality in Hospitalized Patients with COVID-19 in Hubei, China.", @@ -1213790,109 +1217247,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.09.01.278689", - "rel_title": "Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility", - "rel_date": "2020-09-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.01.278689", - "rel_abs": "A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to be defined. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an \"up\" conformation for binding to ACE2 receptor. Hamsters infected with D614 or G614 variants developed similar levels of weight loss. However, the G614 virus produced higher infectious titers in the nasal washes and trachea, but not lungs, than the D614 virus. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. For antibody neutralization, sera from D614 virus-infected hamsters consistently exhibit higher neutralization titers against G614 virus than those against D614 virus, indicating that (i) the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19 and (ii) therapeutic antibodies should be tested against the circulating G614 virus before clinical development.\n\nImportanceUnderstanding the evolution of SARS-CoV-2 during the COVID-19 pandemic is essential for disease control and prevention. A spike protein mutation D614G emerged and became dominant soon after the pandemic started. By engineering the D614G mutation into an authentic wild-type SARS-CoV-2 strain, we demonstrate the importance of this mutation to (i) enhanced viral replication on human lung epithelial cells and primary human airway tissues, (ii) improved viral fitness in the upper airway of infected hamsters, and (iii) increased susceptibility to neutralization. Together with clinical findings, our work underscores the importance of this mutation in viral spread, vaccine efficacy, and antibody therapy.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Jessica A Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Yang Liu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jianying Liu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Hongjie Xia", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Bryan A Johnson", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kumari G Lokugamage", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xianwen Zhang", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Antonio E Muruato", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jing Zou", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Camila R Fontes-Garfias", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Divya Mirchandani", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Dionna Scharton", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "John P Bilello", - "author_inst": "Gilead" - }, - { - "author_name": "Zhiqiang Ku", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Zhiqiang An", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Birte Kalveram", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Alexander N Freiberg", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Vineet D Menachery", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kenneth S Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Scott C Weaver", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.01.278366", "rel_title": "An intestinal cell type in zebrafish is the nexus for the SARS-CoV-2 receptor and the Renin-Angiotensin-Aldosterone System that contributes to COVID-19 comorbidities", @@ -1214116,6 +1217470,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.02.280180", + "rel_title": "Induction of a regulatory myeloid program in bacterial sepsis and severe COVID-19", + "rel_date": "2020-09-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.02.280180", + "rel_abs": "A recent estimate suggests that one in five deaths globally are associated with sepsis1. To date, no targeted treatment is available for this syndrome, likely due to substantial patient heterogeneity2,3 and our lack of insight into sepsis immunopathology4. These issues are highlighted by the current COVID-19 pandemic, wherein many clinical manifestations of severe SARS-CoV-2 infection parallel bacterial sepsis5-8. We previously reported an expanded CD14+ monocyte state, MS1, in patients with bacterial sepsis or non-infectious critical illness, and validated its expansion in sepsis across thousands of patients using public transcriptomic data9. Despite its marked expansion in the circulation of bacterial sepsis patients, its relevance to viral sepsis and association with disease outcomes have not been examined. In addition, the ontogeny and function of this monocyte state remain poorly characterized. Using public transcriptomic data, we show that the expression of the MS1 program is associated with sepsis mortality and is up-regulated in monocytes from patients with severe COVID-19. We found that blood plasma from bacterial sepsis or COVID-19 patients with severe disease induces emergency myelopoiesis and expression of the MS1 program, which are dependent on the cytokines IL-6 and IL-10. Finally, we demonstrate that MS1 cells are broadly immunosuppressive, similar to monocytic myeloid-derived suppressor cells (MDSCs), and have decreased responsiveness to stimulation. Our findings highlight the utility of regulatory myeloid cells in sepsis prognosis, and the role of systemic cytokines in inducing emergency myelopoiesis during severe bacterial and SARS-CoV-2 infections.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Miguel Reyes", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Michael R. Filbin", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Roby P. Bhattacharyya", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Abraham Sonny", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Arnav Mehta", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Kianna Billman", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Kyle R. Kays", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "- MGH COVID-19 Collection & Processing Team", + "author_inst": "-" + }, + { + "author_name": "Alexandra-Chloe Villani", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Moshe Sade-Feldman", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Marcia B. Goldberg", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Paul C. Blainey", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Nir Hacohen", + "author_inst": "Broad Institute of MIT and Harvard" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.08.30.20184796", "rel_title": "Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary patient samples", @@ -1215744,61 +1219165,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.26.20182303", - "rel_title": "Risk factors for SARS-CoV-2 infection, hospitalisation, and death in Catalonia, Spain: a population-based cross-sectional study", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182303", - "rel_abs": "OBJECTIVETo identify the different subpopulations that are susceptible for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and hospitalisation or death due to coronavirus disease 2019 (COVID-19) in Catalonia, Spain.\n\nDESIGNCross-sectional study.\n\nSETTINGData collected from the Catalan Health Surveillance System (CatSalut) in Catalonia, a region of Spain.\n\nPARTICIPANTSUsing data collected between 1 March and 1 June 2020, we conducted the following comparative analyses: people infected by SARS-CoV-2 (328 892) vs Catalonias entire population (7 699 568); COVID-19 cases who required hospitalisation (37 638) vs cases who did not require hospitalisation (291 254); and COVID-19 cases who died during the study period vs cases who did not die during the study period (12 287).\n\nMAIN OUTCOME MEASURESThree clinical outcomes related to COVID-19 (infection, hospitalisation, or death). We analysed sociodemographic and environment variables (such as residing in a nursing home) and the presence of previous comorbidities.\n\nRESULTSA total of 328 892 cases were considered to be infected with SARS-CoV-2 (4.27% of total population). The main risk factors for the diagnostic were: female gender (risk ratio [RR] =1.49; 95% confidence interval [95% CI] =1.48-1.50), age (4564 years old; RR=1.02; 95% CI=1.01-1.03), high comorbidity burden (GMA index) (RR=3.03; 95% CI=2.97-3.09), reside in a nursing home (RR=11.82; 95% CI=11.66-11.99), and smoking (RR=1.06; 95% CI=1.05-1.07). During the study period, there were 37 638 (11.4 %) hospitalisations due to COVID-19, and the risk factors were: male gender (RR=1.45; 95% CI=1.43-1.48), age > 65 (RR=2.38; 95% CI=2.28-2.48), very low individual income (RR=1.03; 95% CI=0.97-1.08), and high burden of comorbidities (GMA index) (RR=5.15; 95% CI=4.89-5.42). The individual comorbidities with higher burden were obesity (RR=1.23; 95% CI=1.20-1.25), chronic obstructive pulmonary disease (RR=1.19; 95% CI=1.15-1.22), heart failure (RR=1.19; 95% CI=1.16-1.22), diabetes mellitus (RR=1.07; 95% CI=1.04-1.10), and neuropsychiatric comorbidities (RR=1.06; 95% CI=1.03-1.10). A total of 12 287 deaths (3.73%) were attributed to COVID-19, and the main risk factors were: male gender (RR=1.73; 95% CI=1.67-1.81), age > 65 (RR=37.45; 95% CI=29.23-47.93), residing in a nursing home (RR=9.22; 95% CI=8.81-9.65), and high burden of comorbidities (GMA index) (RR=5.25; 95% CI=4.60-6.00). The individual comorbidities with higher burden were: heart failure (RR=1.21; 95% CI=1.16-1.22), chronic kidney disease (RR=1.17; 95% CI=1.13-1.22), and diabetes mellitus (RR=1.10; 95% CI=1.06-1.14). These results did not change significantly when we considered only PCR-positive patients.\n\nCONCLUSIONSFemale gender, age between 45 to 64 years old, high burden of comorbidities, and factors related to environment (nursing home) play a relevant role in SARS-CoV-2 infection and transmission. In addition, we found risk factors for hospitalisation and death due to COVID-19 that had not been described to date, including comorbidity burden, neuro-psychiatric disorders, and very low individual income. This study supports interventions for transmission control beyond stratify-and-shield strategies focused only on protecting those at risk of death. Future COVID-19 studies should examine the role of gender, the burden of comorbidities, and socioeconomic status in disease transmission, and should determine its relationship to workplaces, especially healthcare centres and nursing homes.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Judit Villar-Garcia", - "author_inst": "Medical Research Institute Hospital del Mar-IMIM, Barcelona, Spain" - }, - { - "author_name": "Rosa Maria Vivanco-Hidalgo", - "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya, Barcelona, Spain" - }, - { - "author_name": "Montserrat Cleries", - "author_inst": "Area de sistemes de informacio, Servei Catala de la Salut, Generalitat de Catalunya Barcelona, Spain" - }, - { - "author_name": "Elisenda Martinez", - "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya Barcelona,Spain" - }, - { - "author_name": "David Monterde", - "author_inst": "Sistemes de Informacio, Institut Catala de la Salut Barcelona,Spain" - }, - { - "author_name": "Pol Perez-Sust", - "author_inst": "Area de Sistemes de Informacio. Servei Catala de la Salut Barcelona, Spain" - }, - { - "author_name": "Luis Garcia-Eroles", - "author_inst": "Area de Sistemes de Informacio. Servei Catala de la Salut Barcelona, Spain" - }, - { - "author_name": "Carol Sais", - "author_inst": "Area de Sistemes de Informacio. Servei Catala de la Salut Barcelona, Spain" - }, - { - "author_name": "Montserrat Moharra", - "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya, Barcelona, Spain" - }, - { - "author_name": "Emili Vela", - "author_inst": "Area de Sistemes de Informacio. Servei Catala de la Salut Barcelona, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.26.20182584", "rel_title": "A multipurpose machine learning approach to predict COVID-19 negative prognosis in Sao Paulo, Brazil", @@ -1216058,6 +1219424,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.08.28.20183699", + "rel_title": "Do Lockdowns Bring about Additional Mortality Benefits or Costs? Evidence based on Death Records from 300 Million Chinese People", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20183699", + "rel_abs": "After the COVID-19 outbreak, China immediately adopted stringent lockdown policies to contain the virus. Using comprehensive death records covering around 300 million Chinese people, we estimate the impacts of city and community lockdowns on non-COVID-19 mortality outside of Wuhan. Employing a difference-in-differences method, we find that lockdowns reduced the number of non-COVID-19 deaths by 4.9% (cardiovascular deaths by 6.2%, injuries by 9.2%, and non-COVID-19 pneumonia deaths by 14.3%). The health benefits are likely driven by significant reductions in air pollution, traffic, and human interactions. A back-of-the-envelope calculation shows that more than 32,000 lives could have been saved from non-COVID-19 diseases/causes during the 40 days of the lockdown on which we focus. The results suggest that the rapid and strict virus countermeasures not only effectively controlled the spread of COVID-19 but also brought about massive unintended public health benefits. These findings can help better inform policymakers around the world about the benefits and costs of city and community lockdowns policies in dealing with the COVID-19 pandemic.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jinlei Qi", + "author_inst": "National Center for Chronic and Noncommunicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 27 Nanwei Road, Xicheng Distr" + }, + { + "author_name": "Dandan Zhang", + "author_inst": "National School of Development, Peking University, 5 Yiheyuan Road, Haidian District, 100871 Beijing, China" + }, + { + "author_name": "Xiang Zhang", + "author_inst": "National School of Development, Peking University, 5 Yiheyuan Road, Haidian District, 100871 Beijing, China" + }, + { + "author_name": "Peng Yin", + "author_inst": "National Center for Chronic and Noncommunicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 27 Nanwei Road, Xicheng Distr" + }, + { + "author_name": "Jianmei Liu", + "author_inst": "National Center for Chronic and Noncommunicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 27 Nanwei Road, Xicheng Distr" + }, + { + "author_name": "Yuhang Pan", + "author_inst": "Division of Environment and Sustainability, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China" + }, + { + "author_name": "Tanakao Takana", + "author_inst": "Division of Social Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China" + }, + { + "author_name": "Peiyu Xie", + "author_inst": "National School of Development, Peking University, 5 Yiheyuan Road, Haidian District, 100871 Beijing, China" + }, + { + "author_name": "Zhaoguang Wang", + "author_inst": "National School of Development, Peking University, 5 Yiheyuan Road, Haidian District, 100871 Beijing, China" + }, + { + "author_name": "Shuocen Liu", + "author_inst": "Peking University HSBC Business School, Peking University, University Town, Nanshan District, 518055 Shenzhen, Guangdong Province, China" + }, + { + "author_name": "George Fu Gao", + "author_inst": "Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, 102206 Beijing, China" + }, + { + "author_name": "Guojun He", + "author_inst": "Division of Social Science, Division of Environment and Sustainability, and Department of Economics, Hong Kong University of Science and Technology, Clear Water" + }, + { + "author_name": "Maigeng Zhou", + "author_inst": "National Center for Chronic and Noncommunicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 27 Nanwei Road, Xicheng Distr" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.08.26.20182758", "rel_title": "Covid-19 Social Distancing Interventions by State Mandate and their Correlation to Mortality in the United States", @@ -1217070,129 +1220503,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2020.08.28.20181883", - "rel_title": "Clinical, cerebrospinal fluid and neuroimaging findings in COVID-19 encephalopathy: a case series", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20181883", - "rel_abs": "ObjectiveTo describe the clinical, neurological, neuroimaging and cerebrospinal fluid (CSF) findings associated with encephalopathy in patients admitted to a COVID-19 tertiary reference center.\n\nMethodsWe retrospectively reviewed records of consecutive patients with COVID-19 evaluated by a consulting neurology team from March 30, 2020 through May 15, 2020.\n\nResultsFifty-five patients with confirmed SARS-CoV-2 were included, 43 of whom showed encephalopathy, and were further divided into mild, moderate and severe encephalopathy groups. Nineteen patients (44%) had undergone mechanical ventilation and received intravenous sedatives. Eleven (26%) patients were on dialysis. Laboratory markers of COVID-19 severity were very common in encephalopathy patients, but did not correlate with the severity of encephalopathy. Thirty-nine patients underwent neuroimaging studies, which showed mostly non-specific changes. One patient showed lesions possibly related to CNS demyelination. Four had suffered an acute stroke. SARS-CoV-2 was detected by RT-PCR in only one of 21 CSF samples. Two CSF samples showed elevated white blood cell count and all were negative for oligoclonal bands. In our case series the severity of encephalopathy correlated with higher probability of death during hospitalization (OR = 5.5 for each increment in the degree of encephalopathy, from absent (0) to mild (1), moderate (2) or severe (3), p<0.001).\n\nConclusionIn our consecutive series with 43 encephalopathy cases, neuroimaging and CSF analysis did not support the role of direct viral CNS invasion or CNS inflammation as the cause of encephalopathy.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Raphael Tuma", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Bruno Guedes", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Rafael Carra", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Bruno Iepsen", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Julia Rodrigues", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Antonio Edvan Camelo Filho", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Gabriel Kubota", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Maira Ferrari", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Adalberto Studart-Neto", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Mariana Oku", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Sara Terrim", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Cesar Lopes", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Carlos Eduardo Passos Neto", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Matheus Dalben", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Julia De Souza", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Jose Pedro Baima", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Tomas Da Silva", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Iago Perissinotti", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Maria da Graca Martin", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurradiologia" - }, - { - "author_name": "Marcia Goncalves", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Ida Fortini", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Jerusa Smid", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Tarso Adoni", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Leandro Lucatto", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurradiologia" - }, - { - "author_name": "Ricardo Nitrini", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Helio Gomes", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - }, - { - "author_name": "Luiz Henrique Castro", - "author_inst": "Universidade de Sao Paulo, Faculdade de Medicina, Hospital das Clinicas, Departamento de Neurologia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.08.27.20183277", "rel_title": "DeepSOCIAL: Social Distancing Monitoring and Infection Risk Assessment in COVID-19 Pandemic", @@ -1217444,6 +1220754,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.27.20183483", + "rel_title": "Repeat testing for SARS-COV-2: Persistence of viral RNA is common, and clearance is slower in older age groups", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20183483", + "rel_abs": "OBJECTIVEQueenslands Novel Coronavirus (SARS-CoV-2) suppression program has been relatively successful. Initially, it involved extensive community testing and repeat sampling of positive individuals for release from isolation. This enabled study of several characteristics, including persistence of detectable virus and how apparent viral clearance rates varied by age and sex.\n\nDESIGNWe conducted an exploratory analysis of Queensland Pathology SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) test results. Kaplan Meier analyses were used to estimate median time to apparent viral clearance, and Cox regression to explore the effects of sex and age.\n\nSETTING AND PARTICIPANTSIndividuals tested for presence of SARS-CoV-2 in the upper respiratory tract between January 19 and June 4, 2020.\n\nOUTCOME MEASURESPresence of viral RNA detected by RT-PCR.\n\nRESULTSWe analyzed 97,476 individuals. Median age was 41y (range <1-105y), and 57.2% (95% CI 57.2, 57.2) were female. In total, 958 (0.98%; 95% CI 0.92,1.05) tested positive for SARS-CoV-2. Positivity rates were lower in regional areas than cities, in females (OR 0.80, 95% CI 0.70, 0.91), and in those aged 16y and below (p<0.01, test for trend).\n\nOf the 958 positive individuals, 243 had two or more (max 17) additional tests, and 92% (95% CI 88.1, 95.2) remained positive after 10 days (max 76 days) after the initial result.\n\nMedian time to apparent viral clearance was longer in those 65y and over compared to those under 65y (29 v 43 days, HR 1.85; 95% CI 1.17, 2.90), and was unaffected by sex (HR 0.93; 95% CI 0.66, 1.30).\n\nCONCLUSIONSFemales and those 16y and under were less likely to test positive for SARS-CoV-2. Detectable RNA may persist for long periods, negating the value of repeat testing for declaring individuals free of infection. Viral clearance rates appear lower in those over 65y of age compared with younger individuals.\n\n\"The known\"\n\n- Early in the COVID-19 pandemic, 2 negative RT-PCR swabs were used to achieve negative status in infected individuals\n- There are few published data on the patterns of results seen with repeat testing in Australia.\n\n\n\"The new\"\n\n- We analysed data from a large cohort of people tested for viral RNA in Queensland\n- We found that females and those 16 y and under were less likely to test positive.\n- Viral RNA was detectable for up to 76 days, with >90% testing positive for more than 10 days.\n- Viral clearance was slower in those over the age of 65.\n\n\n\"The implications\"\n\n- There is likely to be little value in repeat RT-PCR testing to declare individuals free from infection.\n\n\nThe first Australian cases of infection with SARS-CoV-2 were reported in January 2020.1 During the initial phase the peak daily infection rate was in late March 2020 and by the end of June 2020 there had been around 8000 cases and 104 deaths.2 Initially, the majority of cases were acquired outside the country rather than by local transmission.3 The cumulative incidence rates (June 2020) of around 400/million, and mortality of 4/million, were towards the lower end of the rates that have been experienced in other high-income countries, although these are rising quickly with recent outbreaks in Victoria and New South Wales.3 Rates of infection remain relatively low in Queensland.3\n\nIn Queensland, the criteria for testing individuals for SARS-CoV-2 changed during the pandemic. Initially, to be tested in Queensland people were required to meet both epidemiological (return from a high-risk country), and clinical criteria (suggestive symptoms). With progression of the pandemic, testing criteria were modified to clinical criteria only (details provided below).\n\nThe rollout of a comprehensive testing program and the availability of data from repeated within-subject testing carried out in the initial stages of the Covid-19 pandemic provided an opportunity to conduct an exploratory study to address several questions. We investigated population testing rates and how they varied over time. We estimated the proportions of individuals who returned positive tests and how these varied with location age and sex. We also estimated apparent rates of clearance of viral RNA from the upper respiratory tract of subjects with repeated tests, and the extent to these varied with age and sex.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Paulina Stehlik", + "author_inst": "Evidence-Based Practice Professorial Unit, Gold Coast University Hospital and Health Service, Southport, Queensland, Australia; Institute for Evidence-Based Pra" + }, + { + "author_name": "Kylie Alcorn", + "author_inst": "Infectious Diseases Department, Gold Coast University Hospital and Health Service, Southport, Queensland, Australia" + }, + { + "author_name": "Anna Jones", + "author_inst": "Pathology Queensland (Gold Coast Microbiology Laboratory), Health Support Queensland, Queensland Health, Southport, Queensland, Australia" + }, + { + "author_name": "Sanmarie Schlebusch", + "author_inst": "Queensland Health Forensic and Scientific Services, Brisbane, Queensland, Australia" + }, + { + "author_name": "Andre Wattiaux", + "author_inst": "Gold Coast Public Health Unit, Gold Coast University Hospital and Health Service, Carrara, Queensland, Australia." + }, + { + "author_name": "David Henry", + "author_inst": "Evidence-Based Practice Professorial Unit, Gold Coast University Hospital and Health Service, Southport, Queensland, Australia; Institute for Evidence-Based Pra" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.27.20183004", "rel_title": "A common androgen synthesis variant is associated with COVID susceptibility", @@ -1219132,25 +1222481,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.30.274506", - "rel_title": "From Face-to-Face to Online Modality: Implications for Undergraduate Learning While the World is Temporarily Closed in the Age of COVID-19", - "rel_date": "2020-08-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.30.274506", - "rel_abs": "The second half of the Spring 2020 semester has been an unprecedented time globally due to the ongoing coronavirus disease 2019 (COVID-19). COVID-19 pandemic has forced more than one billion students out of school, has disrupted the world and led all university courses switched to online instruction social distancing actions taken to limit the spread of the virus. The aim of the present study is to evaluate the pandemic related changes for undergraduate students, to assess their perspectives related to their learning, experiences in two courses, and to discuss the far-reaching potential implications for the upcoming summer and fall semesters. An electronic survey was conducted to gather data on the student perceptions and learning characteristics of this transition from face-to-face (F2F) to online at a medium-sized university in the Southeast in the Spring 2020 semester. Nearly 88% of the participants indicated that the COVID-19 pandemic impacted their education, while 19% indicated that they prefer online over F2F learning. Furthermore, the online modality significantly increased attendance in General Biology I. Our study also showed that the usage of live conferencing and digital applications increased due to the pandemic. The current research fills the gap in the existing literature by providing the first study on the effects of the ongoing COVID-19 pandemic on undergraduate learning and experiences in the most unique dual modality of the Spring 2020 semester.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Gokhan Hacisalihoglu", - "author_inst": "Florida A&M University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2020.08.25.20181347", "rel_title": "Correction of Daily Positivity Rates for contribution of various test protocols being used in a pandemic.", @@ -1219338,6 +1222668,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2020.08.25.20182048", + "rel_title": "Twitter Interaction to Analyze Covid-19 Impact in Ghana, Africa from March to July", + "rel_date": "2020-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20182048", + "rel_abs": "Present pandemic generated by Coronavirus Covid-19 has stopped the world, from Tourism, Business, Education and more. Actually, there are reported cases in every continent from America to Europe, from Europe to Australia. Africa is one continent in process of development with a variety of languages, limitations/problems and of course, abundance of culture. The aim of this paper is to analyze the impact in one country located in the middle-west, named Ghana. The data source for the analysis is Twitter(Social Network) and the analysis is using a Text Mining approach. Besides, a composition of graphics are presented considering Google search, daily reported cases. The study is exploratory to know what topics are most frequent in Great Accra Region. The conclusions are: Twitter is useful to get data for the analysis, and the interest of user from Ghana was high at the beginning but it was decreasing from April until July, probably the people is tired or adapting themselves to the actual situation.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Josimar E. Chire Saire", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Kobby Panford-Quainoo", + "author_inst": "African Institute for Mathematical Sciences Rwanda" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.25.20181362", "rel_title": "Neighborhood-Level Public Facilities and COVID-19 Transmission: A Nationwide Geospatial Study In China", @@ -1221018,97 +1224371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.25.20181198", - "rel_title": "The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya", - "rel_date": "2020-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181198", - "rel_abs": "BackgroundThe COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region.\n\nMethodsCombining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020.\n\nFindingsIn February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 22% (0-46). As the COVID-19 restrictions to physical contact are lifted, from December 2020, the probability of a large measles outbreak increased to 31% (8-51), 35% (16-52) and 43% (31-56) assuming a 15%, 50% and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 37% (17-54), 44% (29-57) and 57% (48-65) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of restrictions on contact can be overcome by conducting an SIA with [≥] 95% coverage in under-fives.\n\nInterpretationWhile contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once physical distancing is relaxed. Implementing delayed SIAs will be critical for prevention of measles outbreaks once contact restrictions are fully lifted in Kenya.\n\nFundingThe United Kingdoms Medical Research Council and the Department for International Development", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Caroline Ngendo Mburu", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "John Ojal", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Rose Chebet", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Donald Akech", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Boniface Karia", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "James Tuju", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Antipa Sigilai", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Kaja Abbas", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Mark Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Gaby Smits", - "author_inst": "National Institute of Public Health and the Environment (RIVM), The Netherlands" - }, - { - "author_name": "Pieter G.M van Gageldonk", - "author_inst": "National Institute of Public Health and the Environment (RIVM), The Netherlands" - }, - { - "author_name": "Fiona R.M van der Klis", - "author_inst": "National Institute of Public Health and the Environment (RIVM), The Netherlands" - }, - { - "author_name": "Collins Tabu", - "author_inst": "National Vaccine and Immunisation Programme, Ministry of Health, Kenya" - }, - { - "author_name": "D James Nokes", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Re" - }, - { - "author_name": "- LSHTM CMMID COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "John Anthony Scott", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi Kenya & London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Ifedayo M. O Adetifa", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya & London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.25.20182113", "rel_title": "Post-infection depression, anxiety and PTSD: a retrospective cohort study with mild COVID-19 patients", @@ -1221428,6 +1224690,101 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.08.31.270736", + "rel_title": "ACE2 and SARS-CoV-2 Expression in the Normal and COVID-19 Pancreas", + "rel_date": "2020-08-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.31.270736", + "rel_abs": "Diabetes is associated with increased mortality from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Given literature suggesting a potential association between SARS-CoV-2 infection and diabetes induction, we examined pancreatic expression of the key molecule for SARS-CoV-2 infection of cells, angiotensin-converting enzyme-2 (ACE2). Specifically, we analyzed five public scRNAseq pancreas datasets and performed fluorescence in situ hybridization, Western blotting, and immunolocalization for ACE2 with extensive reagent validation on normal human pancreatic tissues across the lifespan, as well as those from coronavirus disease 2019 (COVID-19) patients. These in silico and ex vivo analyses demonstrated pancreatic expression of ACE2 is prominent in pancreatic ductal epithelium and the microvasculature, with rare endocrine cell expression of this molecule. Pancreata from COVID-19 patients demonstrated multiple thrombotic lesions with SARS-CoV-2 nucleocapsid protein expression primarily limited to ducts. SARS-CoV-2 infection of pancreatic endocrine cells, via ACE2, appears an unlikely central pathogenic feature of COVID-19 as it relates to diabetes.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Irina Kusmartseva", + "author_inst": "University of Florida" + }, + { + "author_name": "Wenting Wu", + "author_inst": "Indiana University" + }, + { + "author_name": "Farooq Syed", + "author_inst": "Indiana University" + }, + { + "author_name": "Verena van der Heide", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Marda Jorgensen", + "author_inst": "University of Florida" + }, + { + "author_name": "Paul Joseph", + "author_inst": "University of Florida" + }, + { + "author_name": "Xiaohan Tang", + "author_inst": "University of Florida" + }, + { + "author_name": "Eduardo Candelario-Jalil", + "author_inst": "University of Florida" + }, + { + "author_name": "Changjun Yang", + "author_inst": "University of Florida" + }, + { + "author_name": "Harry Nick", + "author_inst": "University of Florida" + }, + { + "author_name": "Jack Harbert", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Amanda L Posgai", + "author_inst": "University of Florida" + }, + { + "author_name": "Richard Lloyd", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Sirlene Cechin", + "author_inst": "University of Miami" + }, + { + "author_name": "Alberto Pugliese", + "author_inst": "University of Miami" + }, + { + "author_name": "Martha Campbell-Thompson", + "author_inst": "University of Florida" + }, + { + "author_name": "Richard S Vander Heide", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Carmella Evans-Molina", + "author_inst": "Indiana University" + }, + { + "author_name": "Dirk Homann", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mark A. Atkinson", + "author_inst": "University of Florida" + } + ], + "version": "1", + "license": "cc_no", + "type": "contradictory results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.08.31.275701", "rel_title": "A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses", @@ -1223100,37 +1226457,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.08.27.270819", - "rel_title": "Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics", - "rel_date": "2020-08-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.27.270819", - "rel_abs": "The adenosine analogue remdesivir has emerged as a frontline antiviral treatment for SARS-CoV-2, with preliminary evidence that it reduces the duration and severity of illness1. Prior clinical studies have identified adverse events1,2, and remdesivir has been shown to inhibit mitochondrial RNA polymerase in biochemical experiments7, yet little is known about the specific genetic pathways involved in cellular remdesivir metabolism and cytotoxicity. Through genome-wide CRISPR-Cas9 screening and RNA sequencing, we show that remdesivir treatment leads to a repression of mitochondrial respiratory activity, and we identify five genes whose loss significantly reduces remdesivir cytotoxicity. In particular, we show that loss of the mitochondrial nucleoside transporter SLC29A3 mitigates remdesivir toxicity without a commensurate decrease in SARS-CoV-2 antiviral potency and that the mitochondrial adenylate kinase AK2 is a remdesivir kinase required for remdesivir efficacy and toxicity. This work elucidates the cellular mechanisms of remdesivir metabolism and provides a candidate gene target to reduce remdesivir cytotoxicity.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Lin Lin", - "author_inst": "Hubrecht Institute" - }, - { - "author_name": "Grace Yeo", - "author_inst": "MIT" - }, - { - "author_name": "Callie J Donahue", - "author_inst": "Boston University" - }, - { - "author_name": "Robert A Davey", - "author_inst": "Boston University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.08.26.269118", "rel_title": "Fractal signatures of SARS-CoV2 coronavirus, the indicator matrix, the fractal dimension and the 2D directional wavelet transform: A comparative study with SARS-CoV, MERS-CoV and SARS-like coronavirus.", @@ -1223290,6 +1226616,129 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.28.267526", + "rel_title": "Plasmablast-derived antibody response to acute SARS-CoV-2 infection in humans", + "rel_date": "2020-08-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.267526", + "rel_abs": "Serological and plasmablast responses and plasmablast-derived IgG monoclonal antibodies (MAbs) have been analysed in three COVID-19 patients with different clinical severities. Potent humoral responses were detected within 3 weeks of onset of illness in all patients and the serological titre was elicited soon after or concomitantly with peripheral plasmablast response. An average of 13.7% and 13.0% of plasmablast-derived MAbs were reactive with virus spike glycoprotein or nucleocapsid, respectively. A subset of anti-spike (10 of 32) and over half of anti-nucleocapsid (19 of 35) antibodies cross-reacted with other betacoronaviruses tested and harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. Fourteen of 32 anti-spike MAbs, including five anti-RBD, three anti-non-RBD S1 and six anti-S2, neutralised wild-type SARS-CoV-2 in independent assays. Anti-RBD MAbs were further grouped into four cross-inhibiting clusters, of which six antibodies from three separate clusters blocked the binding of RBD to ACE2 and five were neutralising. All ACE2-blocking anti-RBD antibodies were isolated from two patients with prolonged fever, which is compatible with substantial ACE2-blocking response in their sera. At last, the identification of non-competing pairs of neutralising antibodies would offer potential templates for the development of prophylactic and therapeutic agents against SARS-CoV-2.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Kuan-Ying A Huang", + "author_inst": "Chang Gung Memorial Hospital" + }, + { + "author_name": "Tiong Tan", + "author_inst": "MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK" + }, + { + "author_name": "Ting-Hua Chen", + "author_inst": "Genomics Research Center, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Chung-Guei Huang", + "author_inst": "Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Laboratory Medicine, Chang Gung Memori" + }, + { + "author_name": "Ruth Harvey", + "author_inst": "Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK" + }, + { + "author_name": "Saira Hussain", + "author_inst": "Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK" + }, + { + "author_name": "Cheng-Pin Chen", + "author_inst": "Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, and National Yang-Ming University, Taipei, Taiwan" + }, + { + "author_name": "Adam Harding", + "author_inst": "Sir William Dunn School of Pathology, University of Oxford, Oxford, UK" + }, + { + "author_name": "Javier Gilbert-Jaramillo", + "author_inst": "Sir William Dunn School of Pathology, University of Oxford, Oxford, UK" + }, + { + "author_name": "Xu Liu", + "author_inst": "Sir William Dunn School of Pathology, University of Oxford, Oxford, UK" + }, + { + "author_name": "Michael Knight", + "author_inst": "Sir William Dunn School of Pathology, University of Oxford, Oxford, UK" + }, + { + "author_name": "Lisa Schimanski", + "author_inst": "MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; Centre for Translational Immun" + }, + { + "author_name": "Shin-Ru Shih", + "author_inst": "Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Laboratory Medicine, Chang Gung Memori" + }, + { + "author_name": "Yi-Chun Lin", + "author_inst": "Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, and Taipei Medical University, Taipei, Taiwan" + }, + { + "author_name": "Chien-Yu Cheng", + "author_inst": "Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, and National Yang-Ming University, Taipei, Taiwan" + }, + { + "author_name": "Shu-Hsing Cheng", + "author_inst": "Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, and Taipei Medical University, Taipei, Taiwan" + }, + { + "author_name": "Yhu-Chering Huang", + "author_inst": "Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan" + }, + { + "author_name": "Tzou-Yien Lin", + "author_inst": "Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan" + }, + { + "author_name": "Rolle Rahikainen", + "author_inst": "Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK" + }, + { + "author_name": "Mark Howarth", + "author_inst": "Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK" + }, + { + "author_name": "Jia-Tsrong Jan", + "author_inst": "Genomics Research Center, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Che Ma", + "author_inst": "Genomics Research Center, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "William S James", + "author_inst": "University of Oxford" + }, + { + "author_name": "Rodney Daniels", + "author_inst": "Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK" + }, + { + "author_name": "John McCauley", + "author_inst": "Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK" + }, + { + "author_name": "Pramila Rijal", + "author_inst": "MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; Centre for Translational Immun" + }, + { + "author_name": "Alain Townsend", + "author_inst": "MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.27.271130", "rel_title": "Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium", @@ -1224489,41 +1227938,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2020.08.19.20178376", - "rel_title": "Preventing disease after exposure to COVID-19 using hydroxychloroquine: A summary of a protocol for exploratory re-analysis of age and time-nuanced effects.", - "rel_date": "2020-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178376", - "rel_abs": "BACKGROUNDA recently published randomized trial (Boulware et al., 2020, NCT04308668) of hydroxychloroquine (HCQ) for post-exposure prophylaxis found a reduction in Covid-19 of 17%. In the context of ambitious powering to detect a 50% reduction, this non-statistically significant finding could translate to a reduction of 22,000/130,828 cases (CDC 8/12/20) among US health care workers (HCW), impacting trajectory and resource utilization models that drive decisions on lockdowns and social distancing.\n\nData found only in the appendix of Boulware et al. suggested greater differences in the effect HCQ among sub-groups. There were reductions (36%) in younger (<35 years) and increases (110%) in older (>50 years) subjects. Our preliminary analysis revealed a significant negative correlation (slope -0.211, CI -0.328-0.094, p=0.016) between treatment lag and disease reduction, reaching 49% when initiated within one day (RR 0.51, CI 0.176-1.46, p=0.249).\n\nThere were also differences in disease reduction by HCQ by type of exposure (HCW - 8% vs. household contacts - 31%; RR 0.691, CI 0.398-1.2). The definitions of exposure severity did not discriminate between the numbers or duration (> 10 minutes) of exposures. Differences between exposure types may result from younger HCW and higher risks in less trained household contacts with little access to advanced PPE. The ex-protocol use of zinc and ascorbic acid were likely confounders, as was the possibly active folate placebo.\n\nExploratory reanalysis of the raw dataset may inform an age- and stage- nuanced approach to COVID-19 using HCQ testable by prospective studies and may provide insight into the various proposed mechanisms of HCQ.\n\nOBJECTIVESTo conduct an exploratory re-analysis of the de-identified raw dataset from a randomized study of the use of HCQ for post-exposure prophylaxis of COVID-19 with view to further defining: a) The time dependent effect of HCQ, b) The age dependent effect of HCQ; c) The sub-stratification of time- and age-dependent effects by exposure type and risk level, as well as by the use of zinc and ascorbic acid. d) The design of future clinical trials to test the hypotheses generated by this study.\n\nMETHODSShould granularity of data (by age, time-lag, level and type of exposure) be greater than that originally reported, Fisher Exact test will be used to compare the incidence of COVID-19 in HCQ- and control groups, for each sub-group stratification. Since the degree of loss of data granularity due to de-identification is yet unknown, exploratory analyses involving other demographic characteristics cannot be planned. Where sufficient data granularity exists, univariate regression analyses will be conducted to examine the effect of age- and time lag on any effect of HCQ. The possibility will be explored of conducting multivariate Cox regression analyses with propensity score matching to examine observational data relating to the use of zinc and ascorbic acid.\n\nThis analysis will be expanded should a dataset from a similarly designed study (Mitja et al., 2020, NCT04304053), with directionally similar results, become available. This protocol was devised using the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) incorporating the WHO Trial Registration Data Set.\n\nStudy StatusProtocol version 1.1 (August 19 2020)\n\nProtocol registered at: OSF Registries August 19 2020\n\nRegistration doi: https://doi.org/10.17605/OSF.IO/9RPYT", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "David M Wiseman", - "author_inst": "Synechion, Inc., Dallas, TX" - }, - { - "author_name": "Pierre Kory", - "author_inst": "Aurora St. Lukes Medical Center, Milwaukee, WI" - }, - { - "author_name": "Dan Mazzucco", - "author_inst": "ZSX Medical, Philadelphia, PA" - }, - { - "author_name": "Mayur S Ramesh", - "author_inst": "Henry Ford Hospital, Detroit, MI" - }, - { - "author_name": "Marcus Zervos", - "author_inst": "Henry Ford Hospital, Detroit, MI" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.24.20170175", "rel_title": "Evidence of SARS-CoV-2 transcriptional activity in cardiomyocytes of COVID-19 patients without clinical signs of cardiac involvement", @@ -1224851,6 +1228265,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.24.20180919", + "rel_title": "Sociodemographic disparities in knowledge, practices, and ability to comply with COVID-19 public health measures in Canada", + "rel_date": "2020-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20180919", + "rel_abs": "The effectiveness of public health interventions for mitigation of the coronavirus (COVID-19) pandemic depends on individual attitudes and the level of compliance toward these measures. We surveyed a representative sample of the Canadian population about risk perceptions, attitudes, and behaviours towards the Canadian COVID-19 public health response. Our analysis demonstrates that these risk perceptions, attitudes, and behaviours varied by several demographic variables identifying a number of areas in which policies could help address issues of public adherence. Examples include targeted messaging for men and younger age groups, social supports for those who need to self-isolate but may not have the means to do so, changes in workplace policies to discourage presenteeism, and provincially co-ordinated masking and safe school reopening policies. Taken together such measures are likely to mitigate the impact of the next pandemic wave in Canada.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gabrielle Brankston", + "author_inst": "University of Guelph" + }, + { + "author_name": "Eric Merkley", + "author_inst": "University of Toronto" + }, + { + "author_name": "David N Fisman", + "author_inst": "University of Toronto" + }, + { + "author_name": "Ashleigh R Tuite", + "author_inst": "University of Toronto" + }, + { + "author_name": "Zvonimir Poljak", + "author_inst": "University of Guelph" + }, + { + "author_name": "Peter J Loewen", + "author_inst": "University of Toronto" + }, + { + "author_name": "Amy L Greer", + "author_inst": "University of Guelph" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.24.20180893", "rel_title": "The Effect of Area Deprivation on COVID-19 Risk in Louisiana", @@ -1226379,61 +1229836,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.26.267831", - "rel_title": "SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution", - "rel_date": "2020-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.267831", - "rel_abs": "Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (HCW; non-cancer controls) by deep sequencing and investigated the within-host viral quasispecies of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers (HCW) from the Brazilian Cancer Institute were collected in April-May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants (iSNVs) were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%). Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to HCW (p = 0.009). Intrahost genetic diversity in cancer patients was independent of SARS-CoV-2 Ct values, and was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Such a feature may explain, at least in part, the more adverse outcomes to which cancer/COVID-19 patients experience.\n\nAuthor SummaryCancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. In this study, phylogenetic and variation analysis of SARS-CoV-2 genomes from cancer patients and non-cancer healthcare workers at the Brazilian National Cancer Institute were characterized by deep sequencing. Viral genomes showed signatures characteristic of Brazilian viruses, consistent with the hypothesis of local, community transmission rather than virus importation from abroad. Despite most genomes in patients and healthcare workers belonging to the same lineage, intrahost variability was higher in cancer patients when compared to non-cancer counterparts. The intrahost genomic diversity analysis presented in our study highlights the relaxed evolution of SARS-CoV-2 in a vulnerable population of cancer patients. The high number of minor variations can result in the selection of immune escape variants, resistance to potential drugs, and/or increased pathogenicity. The impact of this higher intrahost variability over time warrants further investigation.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Juliana Siqueira", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Livia R. Goes", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Brunna M. Alves", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Pedro S. de Carvalho", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Claudia Cicala", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "James Arthos", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Jo\u00e3o P.B. Viola", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Andr\u00e9ia C. de Melo", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "Marcelo A. Soares", - "author_inst": "Instituto Nacional de Cancer" - }, - { - "author_name": "INCA COVID-19 Task Force (names of participants listed in the acknowledgements section number of cha", - "author_inst": "" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.22.20179754", "rel_title": "Monitoring COVID-19 transmission risks by RT-PCR tracing of droplets in hospital and living environments", @@ -1226697,6 +1230099,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.23.20179820", + "rel_title": "Allocation of COVID-19 Vaccines Under Limited Supply", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20179820", + "rel_abs": "Problem definitionThis paper considers how to allocate COVID-19 vaccines to different age groups when limited vaccines are available over time.\n\nAcademic/practical relevanceVaccine is one of the most effective interventions to contain the ongoing COVID-19 pandemic. However, the initial supply of the COVID-19 vaccine will be limited. An urgent problem for the government is to determine who to get the first dose of the future COVID-19 vaccine.\n\nMethodologyWe use epidemic data from New York City to calibrate an age-structured SAPHIRE model that captures the disease dynamics within and across various age groups. The model and data allow us to derive effective static and dynamic vaccine allocation policies minimizing the number of confirmed cases or the numbers of deaths.\n\nResultsThe optimal static policies achieve a much smaller number of confirmed cases and deaths compared to other static benchmark policies including the pro rata policy. Dynamic allocation policies, including various versions of the myopic policy, significantly improve on static policies.\n\nManagerial implicationsFor static policies, our numerical study shows that prioritizing the older groups is beneficial to reduce deaths while prioritizing younger groups is beneficial to avert infections. For dynamic policies, the older groups should be vaccinated at early days and then switch to younger groups. Our analysis provides insights on how to allocate vaccines to the various age groups, which is tightly connected to the decision-makers objective.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xin Chen", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Menglong Li", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "David Simchi-Levi", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Tiancheng Zhao", + "author_inst": "University of Illinois at Urbana-Champaign" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.23.20180125", "rel_title": "SARS-CoV-2 infections and antibody responses among health care workers in a Spanish hospital after a month of follow-up", @@ -1228029,61 +1231462,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.22.20180042", - "rel_title": "Role of interfering substances in the survival of coronaviruses on surfaces and their impact on the efficiency of hand and surface disinfection", - "rel_date": "2020-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.22.20180042", - "rel_abs": "Contaminated environmental surfaces are considered to represent a significant vector for hospital-acquired viral infections. In this study, we have evaluated the impact of interfering substances on SARS-CoV-2 surface stability and virucidal efficiency of hand sanitizers and surface disinfectant. To this end, surface stability of SARS-CoV-2 was measured on stainless steel in different experimental conditions, with or without an artificial mucus/saliva mixture and compared against that of human coronavirus HCoV-229E and feline coronavirus FCoV. The impact of the mucus/saliva mixture on the virucidal efficiency of 3 commercial alcohol hand sanitizers and 1 surface chemical disinfectant against SARS-CoV-2, HCoV-229E and FCoV was then measured. Our results indicate that mucus/saliva mixture did not demonstrate a beneficial effect on the surface survival of tested viruses, with temperature being an important parameter. In addition, we demonstrated that interfering substances may play an important role in the virucidal efficacy of hand sanitizers and disinfectants, highlighting the need for adapted testing protocols that better reflect current \"real life\" conditions of use.\n\nHighlightsO_LIContaminated environmental surfaces are a significant vector for viral infections.\nC_LIO_LIWe studied the impact of interfering substances on SARS-CoV-2 surface stability and virucidal efficiency.\nC_LIO_LIMucus/saliva did not demonstrate a beneficial effect on viral surface stability, with temperature being an important parameter.\nC_LIO_LIInterfering substances are important for virucidal surface activity of disinfectants.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Lea Szpiro", - "author_inst": "VirHealth" - }, - { - "author_name": "Andres Pizzorno", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Lauranne Durimel", - "author_inst": "VirHealth" - }, - { - "author_name": "Thomas Julien", - "author_inst": "Centre International de Recherche En Infectiologie" - }, - { - "author_name": "Aurelien Traversier", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Dounia Bouchami", - "author_inst": "VirHealth" - }, - { - "author_name": "Yana Marie", - "author_inst": "VirHealth" - }, - { - "author_name": "Manuel Rosa-Calatrava", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Olivier Terrier", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Vincent Moules", - "author_inst": "VirHealth" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.23.20177501", "rel_title": "Therapeutic Prospects for Th-17 Cell Immune Storm Syndrome and Neurological Symptoms in COVID-19: Thiamine Efficacy and Safety, In-vitro Evidence and Pharmacokinetic Profile", @@ -1228595,6 +1231973,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.18.20177592", + "rel_title": "Evaluation of nasopharyngeal swab collection techniques for nucleic acid recovery and participant experience: recommendations for COVID-19 diagnostics", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177592", + "rel_abs": "Nasopharyngeal swabs are critical to the diagnosis of respiratory infections including COVID-19, but collection techniques vary. We compared two recommended nasopharyngeal swab collection techniques in adult volunteers and found that swab rotation following nasopharyngeal contact did not recover additional nucleic acid (as measured by human DNA/RNA copy number). Rotation was also less tolerable for participants. Notably, both discomfort and nucleic acid recovery were significantly higher in Asians, consistent with nasal anatomy differences. Our results suggest that it is unnecessary to rotate the swab in place following contact with the nasopharynx, and reveal that procedural discomfort levels can differ by ethnicity.\n\nsummaryNasopharyngeal swabs are critical to COVID-19 diagnostics, but collection techniques vary. Comparison of two collection techniques revealed that swab rotation did not recover more nucleic acid and was more uncomfortable. Discomfort and biological material recovery also varied by participant ethnicity.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Natalie N Kinloch", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Aniqa Shahid", + "author_inst": "BC Centre for Excellence in HIV/AIDS" + }, + { + "author_name": "Gordon Ritchie", + "author_inst": "Division of Medical Microbiology and Virology, St Paul's Hospital" + }, + { + "author_name": "Winnie Dong", + "author_inst": "BC Centre for Excellence in HIV/AIDS" + }, + { + "author_name": "Tanya Lawson", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital" + }, + { + "author_name": "Julio SG Montaner", + "author_inst": "BC Centre for Excellence in HIV/AIDS" + }, + { + "author_name": "Marc G Romney", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital" + }, + { + "author_name": "Aleksandra Stefanovic", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital" + }, + { + "author_name": "Nancy Matic", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital" + }, + { + "author_name": "Chanson J Brumme", + "author_inst": "BC Centre for Excellence inHIV/AIDS" + }, + { + "author_name": "Christopher F Lowe", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital" + }, + { + "author_name": "Zabrina L Brumme", + "author_inst": "Faculty of Health Sciences, Simon Fraser University" + }, + { + "author_name": "Victor Leung", + "author_inst": "Division of Medical Microbiology and Virology, St. Paul's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.08.20.20178012", "rel_title": "Diagnosis of SARS-CoV-2 in children: accuracy of nasopharyngeal swab compared to nasopharyngeal aspirate.", @@ -1230002,37 +1233447,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.08.21.20166355", - "rel_title": "Platelet-to-lymphocyte ratio (PLR), a novel biomarker to predict the severity of COVID-19 patients: a systematic review and meta-analysis", - "rel_date": "2020-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20166355", - "rel_abs": "BackgroundPlatelet-to-lymphocyte ratio (PLR), a novel inflammatory marker, has been suggested to be able to predict the severity of COVID-19 patients. This systematic review aims to evaluate the association between PLR levels on admission and the severity of COVID-19 patients.\n\nMethodsA systematic literature search was done on 23 July 2020 to identify peer-reviewed studies across four different databases (Ovid MEDLINE, EMBASE, SCOPUS, and the Cochrane Library), preprints from two databases (MedRxiv and SSRN), and grey literature from two databases (WHO COVID-19 Global Research Database and Center for Disease Control and Prevention COVID-19 Research Article). Research articles comparing the PLR value on admission in adult patients with COVID-19 with varying degrees of severity were included in the analysis. The following keywords were used for the search: \"COVID-19\", \"PLR\", \"severity\", and \"mortality\". The inverse variance method was used to calculate the pooled effect standardized mean difference (SMD) along with its 95% confidence interval (CI).\n\nResultsA total of seven studies were included in the meta-analysis, six of which were conducted in China. From a total of 998 participants included, 316 (31.7%) had severe diseases; and those in the severe group were generally older and had underlying diseases compared to the non-severe group. In comparison to non-severe patients, the meta-analysis showed that severe COVID-19 patients had higher PLR levels on admission (SMD 0.68; 95%CI 0.43-0.93; I2 =58%).\n\nConclusionHigh PLR levels on admission were associated with severe COVID-19 cases. Therefore, on-admission PLR level is a novel, cost-effective, and readily available biomarker with a promising prognostic role for determining the severity of COVID-19 patients.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Daniel Martin Simadibrata", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Bashar Adi Wahyu Pandhita", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Muammar Emir Ananta", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Tamara Tango", - "author_inst": "Faculty of Medicine, Universitas Indonesia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.08.21.20177923", "rel_title": "Prevalence and outcome of Covid-19 infection in cancer patients: a national VA study", @@ -1230384,6 +1233798,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.21.20177857", + "rel_title": "Homologous and heterologous antibodies to coronavirus 229E, NL63, OC43, HKU1, SARS, MERS and SARS-CoV-2 antigens in an age stratified cross-sectional serosurvey in a large tertiary hospital in The Netherlands", + "rel_date": "2020-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20177857", + "rel_abs": "Understanding the coronavirus (CoV) antibody landscape in relation to disease and susceptibility is critical for modelling of steps in the next phase during the current covid-19 pandemic. In March 2020, during the first month of the epidemic in The Netherlands, we performed cross sectional studies at two time points amongst patients of the Erasmus Medical Centre in Rotterdam, to assess the presence of antibodies against seasonal human coronaviruses (OC43, 229E, NL63, HKU1), emerging zoonotic coronaviruses (SARS, MERS) and SARS-CoV-2 in nine different age groups. We observed minimal SARS-CoV-2 reactivity early March (0.7% of sera), increasing to 3.0%, four weeks later, suggesting probably undetected cases during this early phase of the epidemic. Antibody responses were mostly coronavirus species specific at young age, but possible cross-reactivity between human seasonal CoVs was observed with increasing age.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Brenda M. Westerhuis", + "author_inst": "Viroscience, ErasmusMC" + }, + { + "author_name": "Erwin de Bruin", + "author_inst": "Viroscience, ErasmusMC" + }, + { + "author_name": "Felicity D Chandler", + "author_inst": "Viroscience, ErasmusMC" + }, + { + "author_name": "Chris R.B. Ramakers", + "author_inst": "Clinical chemistry, ErasmusMC" + }, + { + "author_name": "Nisreen M.A. Okba", + "author_inst": "Viroscience, ErasmusMC" + }, + { + "author_name": "Wentao Li", + "author_inst": "Biomolecular Health, University of Utrecht" + }, + { + "author_name": "Herman Goossens", + "author_inst": "Laboratory of Medical Microbiology, Uninversity of Antwerp" + }, + { + "author_name": "Menno D de Jong", + "author_inst": "Department of Medical Microbiology, Academic Medical Center" + }, + { + "author_name": "Berend Jan Bosch", + "author_inst": "Biomolecular Health, Utrecht University" + }, + { + "author_name": "Bart L Haagmans", + "author_inst": "Viroscience, ErasmusMC" + }, + { + "author_name": "Pieter LA Fraaij", + "author_inst": "Viroscience, ErasmusMC" + }, + { + "author_name": "Reina S Sikkema", + "author_inst": "Viroscience, ErasmusMC" + }, + { + "author_name": "Marion P.G. Koopmans", + "author_inst": "Viroscience, ErasmusMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.21.20179200", "rel_title": "Randomized placebo-controlled trials of remdesivir in severe COVID-19 patients: A Systematic Review and Meta-analysis", @@ -1231432,45 +1234913,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.20.20178822", - "rel_title": "COVID-19 Risk Perception Among U.S. Adults: Changes from February to May 2020", - "rel_date": "2020-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178822", - "rel_abs": "The COVID-19 pandemic continues to detrimentally impact the United States. Using a survey, we collected demographic and COVID-19 risk perception, behavior, knowledge, and attitude data from 672 adults across the U.S. in May 2020. These variables were compared with the results from a survey in February 2020. Participants who were older (55+ years; M = 6.3, SD = 2.0), identified as Native American/Alaska Native (M = 6.8, SD = 1.0) or Asian (M = 6.0, SD = 2.0), and those who had contracted (M = 6.8, SD = 2.0) or knew someone who had contracted COVID-19 (M = 6.2, SD = 1.7) reported higher perceived risk. Health behaviors, such as physical distancing, have shown to impact infectious disease trajectories. As the U.S. reopens its economy, public health officials and politicians must formulate culturally appropriate and evidence-based messaging and policies, based on the publics COVID-19 risk perceptions, to encourage preventive behaviors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Amyn A Malik", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "SarahAnn M McFadden", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Jad A Elharake", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Obianuju Genevieve Aguolu", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Mehr Shafiq", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Saad B Omer", - "author_inst": "Yale Institute for Global Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.20.20178970", "rel_title": "Poor knowledge of COVID-19 and unfavourable perception of the response to the pandemic by healthcare workers at the Bafoussam Regional Hospital (West Region - Cameroon)", @@ -1231782,6 +1235224,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.19.20177188", + "rel_title": "Transmission dynamics of COVID-19 in household and community settings in the United Kingdom", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20177188", + "rel_abs": "BackgroundHouseholds appear to be the highest risk setting for transmission of COVID-19. Large household transmission studies were reported in the early stages of the pandemic in Asia with secondary attack rates ranging from 5-30% but few large scale household transmission studies have been conducted outside of Asia.\n\nMethodsA prospective case ascertained study design based on the World Health Organization FFX protocol was undertaken in the UK following the detection of the first case in late January 2020. Household contacts of cases were followed using enhanced surveillance forms to establish whether they developed symptoms of COVID-19, became confirmed cases and their outcomes. Household secondary attack rates and serial intervals were estimated. Individual and household basic reproduction numbers were also estimated. The incubation period was estimated using known point source exposures that resulted in secondary cases.\n\nResultsA total of 233 households with two or more people were included with a total of 472 contacts. The overall household SAR was 37% (95% CI 31-43%) with a mean serial interval of 4.67 days, an R0 of 1.85 and a household reproduction number of 2.33. We find lower secondary attack rates in larger households. SARs were highest when the primary case was a child. We estimate a mean incubation period of around 4.5 days.\n\nConclusionsHigh rates of household transmission of COVID-19 were found in the UK emphasising the need for preventative measures in this setting. Careful monitoring of schools reopening is needed to monitor transmission from children.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Jamie Lopez Bernal", + "author_inst": "Public Health England" + }, + { + "author_name": "Nikolaos Panagiotopoulos", + "author_inst": "Public Health England" + }, + { + "author_name": "Chloe Byers", + "author_inst": "Public Health England" + }, + { + "author_name": "Tatiana Garcia Vilaplana", + "author_inst": "Public Health England" + }, + { + "author_name": "Nicola L Boddington", + "author_inst": "Public Health England" + }, + { + "author_name": "XuSheng Zhang", + "author_inst": "Public Health England" + }, + { + "author_name": "Andre Charlett", + "author_inst": "Public Health England" + }, + { + "author_name": "Suzanne Elgohari", + "author_inst": "Public Health England" + }, + { + "author_name": "Laura Coughlan", + "author_inst": "Public Health England" + }, + { + "author_name": "Rosie Whillock", + "author_inst": "Public Health England" + }, + { + "author_name": "Sophie Logan", + "author_inst": "Public Health England" + }, + { + "author_name": "Hikaru Bolt", + "author_inst": "Public Health England" + }, + { + "author_name": "Mary Sinnathamby", + "author_inst": "Public Health England" + }, + { + "author_name": "Louise Letley", + "author_inst": "Public Health England" + }, + { + "author_name": "Pauline MacDonald", + "author_inst": "Public Health England" + }, + { + "author_name": "Roberto Vivancos", + "author_inst": "Public Health England" + }, + { + "author_name": "Obaghe Edeghere", + "author_inst": "Public Health England" + }, + { + "author_name": "Charlotte Anderson", + "author_inst": "Public Health England" + }, + { + "author_name": "Karthik Paranthaman", + "author_inst": "Public Health England" + }, + { + "author_name": "Simon Cottrell", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Jim McMenamin", + "author_inst": "Health Protection Scotland" + }, + { + "author_name": "Maria Zambon", + "author_inst": "Public Health England" + }, + { + "author_name": "Gavin Dabrera", + "author_inst": "Public Health England" + }, + { + "author_name": "Mary Ramsay", + "author_inst": "Public Health England" + }, + { + "author_name": "Vanessa Saliba", + "author_inst": "Public Health England" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.22.20176669", "rel_title": "A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work.", @@ -1232958,61 +1236515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.08.19.20177980", - "rel_title": "Prevalence and correlation of symptoms and comorbidities in COVID-19 patients: A systematic review and meta-analysis", - "rel_date": "2020-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20177980", - "rel_abs": "BackgroundThe COVID-19 affected millions of people, and the patients present a constellation of symptoms and comorbidities. We aimed to chronicle the prevalence and correlations of symptoms and comorbidities, and associated covariates among the patients.\n\nMethodsWe performed a systematic review and meta-analysis [PROSPERO registration: CRD42020182677]. Databases [PubMed, SCOPUS, EMBASE, WHO, Semantic Scholar, and COVID-19 Primer] were searched for clinical studies published in English from January 1 to April 20, 2020. The pooled prevalence of symptoms and comorbidities were identified using the random effect model, and sub-groups analysis of patients age and locations were investigated. A multivariable factor analysis was also performed to show the correlation among symptoms, comorbidities and age of the COVID-19 patients.\n\nFindingsTwenty-nine articles [China (24); Outside of China (5)], with 4,884 COVID-19 patients were included in this systematic review. The meta-analysis investigated 33 symptoms, where fever [84%], cough/dry cough [61%], and fatigue/weakness [42%] were found frequent. Out of 43 comorbidities investigated, acute respiratory distress syndrome (ARDS) [61%] was a common condition, followed by hypertension [23%] and diabetes [12%]. According to the patients age, the prevalence of symptoms like fatigue/weakness, dyspnea/shortness of breath, and anorexia were highly prevalent in older adults [[≥]50 years] than younger adults [[≤]50 years]. Diabetes, hypertension, coronary heart disease, and COPD/lung disease were more prevalent comorbidities in older adults than younger adults. The patients from outside of China had significantly higher prevalence [p< 0.005] of diarrhea, fatigue, nausea, sore throat, and dyspnea, and the prevalent comorbidities in that region were diabetes, hypertension, coronary heart disease, and ARDS. The multivariable factor analysis showed positive association between a group of symptoms and comorbidities, and with the patients age.\n\nInterpretationEpitomizing the correlation of symptoms of COVID-19 with comorbidities and patients age would help clinicians effectively manage the patients.\n\nSummary boxO_TEXTBOXO_LSTWhat is already known?C_LSTO_LIThere is scarce evidence on the prevalence of all symptoms and comorbidities in COVID-19 infected older adults and patients from outside of China.\nC_LIO_LIPreviously published review studies excluded a wide range of symptoms and comorbidities from their analysis due to limited time-frame.\nC_LIO_LIStudy on the correlation of symptoms and comorbidity with age of the COVID-19 patients are not yet to be explored.\nC_LI\n\nO_LSTWhat are the new findings?C_LSTO_LIWe investigated all the reported symptoms [33] and comorbidity [43] where fever [84%], cough/dry cough [61%], fatigue/weakness [42%] and dyspnea/shortness of breath [ symptoms, and ARDS [61%], followed by hypertension [23%] and frequent comorbidity.\nC_LIO_LIKey findings, the fatigue/weakness, dyspnea/shortness of breath and anorexia were comparatively higher in older adults than younger adults, and the patients from outside of China had a higher prevalence diarrhoea, fatigue, nausea, sore throat, dyspnea, diabetes, hypertension, coronary heart disease and ARDS.\nC_LIO_LIKey findings, the symptoms comprising fever, dyspnea/shortness of breath, nausea, vomiting, abdominal pain, dizziness, anorexia and pharyngalgia; and the comorbidities including diabetes, hypertension, coronary heart disease, COPD/lung disease and ARDS were positively correlated with the COVID-19 patients age.\nC_LI\n\nO_LSTWhat do the new findings imply?C_LSTO_LIThese findings according to patients age and geographical variations may help the health care providers and policy makers.\nC_LIO_LIThis pioneering efforts in estimating the prevalence and correlations of all frequent symptoms and comorbidities will help the clinicians and disease practitioners like WHO to implement patient-centered interventions.\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mohammad Meshbahur Rahman", - "author_inst": "Biomedical Research Foundation, Dhaka-1230, Bangladesh" - }, - { - "author_name": "Badhan Bhattacharjee", - "author_inst": "Department of Biotechnology, BRAC University, Dhaka 1212, Bangladesh" - }, - { - "author_name": "Zaki Farhana", - "author_inst": "National Institute of Preventive and Social Medicine, Mohakhali, Dhaka-1212, Bangladesh" - }, - { - "author_name": "Mohammad Hamiduzzaman", - "author_inst": "College of Medicine & Public Health, Flinders University, South Australia, Australia." - }, - { - "author_name": "Muhammad Abdul Bake Chowdhury", - "author_inst": "Department of Emergency Medicine, University of Florida College of Medicine, FL 32608, USA." - }, - { - "author_name": "Mohammad Sorowar Hossain", - "author_inst": "Biomedical Research Foundation, Dhaka-1230, Bangladesh" - }, - { - "author_name": "Mahbubul H Siddiqee", - "author_inst": "Biomedical Research Foundation, Dhaka-1230, Bangladesh." - }, - { - "author_name": "Md. Ziaul Islam", - "author_inst": "Department of Community Medicine, National Institute of Preventive and Social Medicine, Mohakhali, Dhaka-1212, Bangladesh" - }, - { - "author_name": "Enayetur Raheem", - "author_inst": "Biomedical Research Foundation, Dhaka-1230, Bangladesh" - }, - { - "author_name": "Md. Jamal Uddin", - "author_inst": "Department of Statistics (Biostatistics and Epidemiology), Shahjalal University of Science & Technology, Sylhet-3114, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.20.20176529", "rel_title": "Preventing within household transmission of COVID-19: Is self-isolation outside the home feasible and acceptable?", @@ -1233304,6 +1236806,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.19.20178087", + "rel_title": "Pandemic Control in ECON-EPI Networks", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178087", + "rel_abs": "We develop an ECON-EPI network model to evaluate policies designed to improve health and economic outcomes during a pandemic. Relative to the standard epidemiological SIR set-up, we explicitly model social contacts among individuals and allow for heterogeneity in their number and stability. In addition, we embed the network in a structural economic model describing how contacts generate economic activity. We calibrate it to the New York metro area during the 2020 COVID-19 crisis and show three main results. First, the ECON-EPI network implies patterns of infections that better match the data compared to the standard SIR. The switching during the early phase of the pandemic from unstable to stable contacts is crucial for this result. Second, the model suggests the design of smart policies that reduce infections and at the same time boost economic activity. Third, the model shows that reopening sectors characterized by numerous and unstable contacts (such as large events or schools) too early leads to fast growth of infections.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Alessandra Fogli", + "author_inst": "Federal Reserve Bank of Minneapolis" + }, + { + "author_name": "Fabrizio Perri", + "author_inst": "Federal Reserve Bank of Minneapolis" + }, + { + "author_name": "Mark Ponder", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Marina Azzimonti", + "author_inst": "Stony Brook University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.08.19.20178434", "rel_title": "Estimating healthcare resource needs for COVID-19 patients in Nigeria", @@ -1234644,117 +1238177,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.18.20176743", - "rel_title": "Breastmilk; a source of SARS-CoV-2 specific IgA antibodies", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20176743", - "rel_abs": "BackgroundSince the outbreak of COVID-19, many put their hopes in the rapid development of effective immunizations. For now patient isolation, physical distancing and good hygiene are the sole measures for prevention. Processed breast milk with antibodies against SaRS-CoV-2 may serve as additional protection. We aimed to determine the presence and neutralization capacity of antibodies against SaRS-CoV-2 in breastmilk of mothers who have recovered from COVID-19.\n\nMethodsThis prospective case control study included lactating mothers, recovered from (suspected) COVID-19 and healthy controls. Serum and breastmilk was collected. To assess the presence of antibodies in breastmilk and serum, we used multiple complementary assays, namely ELISA with the SARS-CoV-2 spike protein, SARS-CoV-2 receptor binding domain (RBD) and with the SARS-CoV-2 nucleocapsid (N) protein for IgG and bridging ELISA with the SARS-CoV-2 RBD and N protein for total Ig. To assess the effect of pasteurization breastmilk was exposed to Holder Pasteurization and High Pressure Pasteurization.\n\nResultsBreastmilk contained antibodies against SARS-CoV-2 using any of the assays in 24 out of 29 (83%) proven cases, in six out of nine (67%) suspected cases and in none of the 13 controls. In vitro neutralization of SARS-CoV-2 clinical isolate virus strain was successful in a subset of serum (13%) and milk samples (26%). Although after pasteurization of the milk SARS-CoV-2 antibodies were detected with both methods of pasteurization, virus neutralizing capacity of those antibodies was only retained with the HPP approach.\n\nConclusionBreastmilk of mothers who recovered from COVID-19 contains significant amounts of IgA against SARS-CoV-2, both before and after pasteurization.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes breastmilk of mothers who have recovered from coronavirus disease 2019 (COVID-19) contain antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)?\n\nFindingsWe provide multiple lines of evidence on the presence of a variety of antibodies against SARS-CoV-2, with no such antibodies present in the controls. These antibodies are capable of neutralizing a clinical isolate of SARS-CoV-2 in vitro. We furthermore show that high pressure pasteurization hardly affects antibody levels and efficacy.\n\nMeaningBreastmilk, obtained from mothers who have recovered from COVID-19, may serve as a safe and widely applicable preventive strategy for vulnerable high risk populations", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Britt J van Keulen", - "author_inst": "Emma Children's Hospital" - }, - { - "author_name": "Michelle Romijn", - "author_inst": "Emma Children's Hospital" - }, - { - "author_name": "Albert Bondt", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Kelly A Dingess", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Eva Kontopodi", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Karlijn van der Straten", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Maurits A den Boer", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Berend J Bosch", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Philip J.M. Brouwer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Christianne J de Groot", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Max Hoek", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Wentao Li", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Dasja Pajkrt", - "author_inst": "Emma Children's Hospital" - }, - { - "author_name": "Roger W Sanders", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Anne Schoonderwoerd", - "author_inst": "Emma Children's Hospital" - }, - { - "author_name": "Sem Tamara", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Rian A.H. Timmermans", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Gestur Vidarsson", - "author_inst": "Sanquin Research" - }, - { - "author_name": "Koert J Stittelaar", - "author_inst": "Viroclinics" - }, - { - "author_name": "Theo T Rispens", - "author_inst": "Sanquin Research" - }, - { - "author_name": "Kasper A Hettinga", - "author_inst": "Wageningen University and Research" - }, - { - "author_name": "Marit J van Gils", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Albert J.R. Heck", - "author_inst": "University of Utrecht" - }, - { - "author_name": "Johannes B van Goudoever", - "author_inst": "Emma Children's Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.18.20174623", "rel_title": "Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom", @@ -1235146,6 +1238568,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.08.17.20175158", + "rel_title": "The ImmuneRACE Study: A Prospective Multicohort Study of Immune Response Action to COVID-19 Events with the ImmuneCODE\u2122 Open Access Database", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20175158", + "rel_abs": "ObjectivesThe primary aim of this study is to increase our understanding of the adaptive immune response to the SARS-CoV-2 virus by assaying the peripheral immune repertoire for virus-associated T-cell receptors (TCRs). Secondary aims include identification and characterization of SARS-CoV-2-specific B-cell receptors (BCRs) and monoclonal antibodies (mAbs) generated by antibody-producing cells during and after acute infection.\n\nTrial designImmuneRACE is a prospective, single group, multi-cohort, exploratory study of unselected eligible participants exposed to, infected with, or recovering from SARS-CoV-2.\n\nParticipantsApproximately 1000 individuals, aged 18 to 89 years and residing in 24 different geographic areas within the United States, will be enrolled, primarily using remote telemedicine technologies. Cohorts will be based on clinical history. Cohort 1 will include participants exposed to SARS-CoV-2 within 2 weeks of study entry. Cohort 2 participants will include those clinically diagnosed or with positive laboratory confirmation of active COVID-19 disease. Cohort 3 will comprise participants previously diagnosed with COVID-19 disease who have been deemed recovered based on two consecutive negative tests, clearance by a healthcare professional, or resolution of symptoms related to COVID-19. All participants must be able to communicate with the investigator and understand and comply with the requirements of the study. Protected populations and those who may not safely participate are not eligible for this study.\n\nIntervention and comparatorBlood samples and nasopharyngeal or oropharyngeal swabs will be collected from participants. Nasopharyngeal or oropharyngeal swabs will be collected by inserting a swab into the nose or throat of the participant. Samples will be shipped frozen or transported refrigerated or at room temperature to Adaptive Biotechnologies for processing, including, but not limited to, testing for coronavirus or other respiratory illnesses, DNA extraction, and TCR analysis. The immunoSEQ assay will be conducted using DNA extracted from blood samples. An electronic questionnaire will be administered to collect information pertaining to the participants medical history, symptoms, and diagnostic tests performed for COVID-19 disease. Participants will have the option to undergo additional blood draws and questionnaires over a 2-month period. In collaboration with Microsoft, we will use machine learning and artificial intelligence approaches to construct a classifier based on TCR repertoire data designed to accurately distinguish COVID-19-positive cases from unexposed controls (from the ImmuneCODE database of TCR sequences). A rigorous statistical analysis will be performed to validate the classifier.\n\nMain outcomesThe main outcomes of this study will include a comparison of disease-specific TCR signatures in patients and controls, identification of the immunodominant antigens that elicit a T-cell response to SARS-CoV-2, risk stratification based on an individuals immune signature, and determination of immune signatures of patients exposed to SARS-CoV-2 that may allow earlier detection of infection compared to available tests.\n\nTrial registration\"ImmuneRACE - Immune Response Action to COVID-19 Events (Protocol ADAP-006, version 1.0; 5/8/2020) is registered with the US National Institutes of Health and can be accessed at ClinicalTrials.gov (NCT04494893).", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jennifer N. Dines", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Thomas J. Manley", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Emily Svejnoha", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Heidi M. Simmons", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Ruth Taniguchi", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Mark Klinger", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Lance Baldo", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Harlan Robins", + "author_inst": "Adaptive Biotechnologies" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.08.17.20176602", "rel_title": "ESTIMATING CUMULATIVE COVID-19 INFECTIONS BY A NOVEL \"PANDEMIC RATE EQUATION\"", @@ -1236306,81 +1239775,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.18.20168807", - "rel_title": "Laboratory biomarkers associated with COVID-19 severity and management.", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20168807", - "rel_abs": "The heterogeneous disease course of COVID-19 is unpredictable, ranging from mild self-limiting symptoms to cytokine storms, acute respiratory distress syndrome (ARDS), multi-organ failure and death. Identification of high-risk cases will enable appropriate intervention and escalation. This study investigates the routine laboratory tests and cytokines implicated in COVID-19 for their potential application as biomarkers of disease severity, respiratory failure and need of higher-level care.\n\nFrom analysis of 203 samples, CRP, IL-6, IL-10 and LDH were most strongly correlated with the WHO ordinal scale of illness severity, the fraction of inspired oxygen delivery, radiological evidence of ARDS and level of respiratory support (p[≤]0.001). IL-6 levels of [≥]3.27pg/ml provide a sensitivity of 0.87 and specificity of 0.64 for a requirement of ventilation, and a CRP of [≥]37mg/L of 0.91 and 0.66.\n\nReliable stratification of high-risk cases has significant implications on patient triage, resource management and potentially the initiation of novel therapies in severe patients.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Stephen Keddie", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Oliver J Ziff", - "author_inst": "University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Michael KL Chou", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Rachel L Taylor", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Amanda Heslegrave", - "author_inst": "UK Dementia Research Institute, University College London, London, UK" - }, - { - "author_name": "Edmund Garr", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Neghat Lakdawala", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Andrew Church", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Dalia Ludwig", - "author_inst": "Department of Rheumatology, University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Jessica Manson", - "author_inst": "Department of Rheumatology, University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Marie Scully", - "author_inst": "Department of Haematology, University College London Hospitals NHS Foundation Trust and Cardiometabolic Programme-NIHR UCLH/UC BRC London, UK" - }, - { - "author_name": "Eleni Nastouli", - "author_inst": "Infection control department, University College London Hospitals NHS Trust, London, UK" - }, - { - "author_name": "Miles D Chapman", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Melanie Hart", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - }, - { - "author_name": "Michael P Lunn", - "author_inst": "Neuroimmunology and CSF laboratory, University College London Hospitals NHS Trust National Hospital of Neurology and Neurosurgery, Queen Square, London, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.08.17.20177022", "rel_title": "Decontaminating N95 respirators during the Covid-19 pandemic: simple and practical approaches to increase decontamination capacity, speed, safety and ease of use.", @@ -1236648,6 +1240042,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.18.20177196", + "rel_title": "SARS-CoV-2 Serologic Assays in Control and Unknown Populations Demonstrate the Necessity of Virus Neutralization Testing.", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177196", + "rel_abs": "BackgroundTo determine how serologic antibody testing outcome links with virus neutralization of SARS-CoV-2 to ascertain immune protection status, we evaluated a unique set of individuals for SARS-CoV-2 antibody detection and viral neutralization.\n\nMethodsHerein, we compare several analytic platforms with 15 positive and 30 negative SARS-CoV-2 infected controls followed by viral neutralization assessment. We then applied these platforms in a clinically relevant population: 114 individuals with unknown histories of SARS-CoV-2 infection.\n\nResultsIn control populations, the best performing antibody detection assays were SARS-CoV-2 receptor binding domain (RBD) IgG (specificity 87%, sensitivity 100%, PPV 100%, NPV 93%), spike IgG3 (specificity 93%, sensitivity 97%, PPV 93%, NPV 97%), and nucleocapsid (NP) protein IgG (specificity 93%, sensitivity 97%, PPV 93%, NPV 97%). Neutralization of positive and negative control sera showed 100% agreement. 20 unknown individuals had detectable SARS-CoV-2 antibodies with 16 demonstrating virus neutralization. The antibody assays that best predicted virus neutralization were RBD IgG (misidentified 2), spike IgG3 (misidentified 1), and NP IgG (misidentified 2).\n\nConclusionThese data suggest that meaningful evaluation of antibody assay performance requires testing in an unknown population. Further, these results indicate coupling of virus neutralization analysis to a positive antibody test is required to categorize patients based on SARS-CoV-2 immune protection status following virus exposure or vaccine administration. One of the antibody detection platforms identified in this study followed by the pseudoneutralization or focus reduction assay would provide a practical testing strategy to assess for SARS-CoV-2 antibodies with optimal prediction of correlates to neutralizing immunity.\n\nFundingSupported by NIH grants AI148684, AI151698, AI145296, and UW funds to the Center for Innate Immunity and Immune Disease.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jennifer A Rathe", + "author_inst": "University of Washington / Seattle Children's Hopsital" + }, + { + "author_name": "Emily A Hemann", + "author_inst": "University of Washington" + }, + { + "author_name": "Julie Eggenberger", + "author_inst": "University of Washington" + }, + { + "author_name": "Zhaoqi Li", + "author_inst": "University of Washington" + }, + { + "author_name": "Megan Knoll", + "author_inst": "University of Washington" + }, + { + "author_name": "Caleb Stokes", + "author_inst": "University of Washington" + }, + { + "author_name": "Tien-Ying Hsiang", + "author_inst": "University of Washington" + }, + { + "author_name": "Jason Netland", + "author_inst": "University of Washington" + }, + { + "author_name": "Marion Pepper", + "author_inst": "University of Washington" + }, + { + "author_name": "Michael Gale Jr.", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.18.20166835", "rel_title": "SARS-CoV-2 Infections Among Children in the Biospecimens from Respiratory Virus-Exposed Kids (BRAVE Kids) Study", @@ -1238160,89 +1241609,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.19.256800", - "rel_title": "Susceptibility of raccoon dogs for experimental SARS-CoV-2 infection", - "rel_date": "2020-08-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.19.256800", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China at the end of 2019, and became pandemic. The zoonotic virus most likely originated from bats, but definite intermediate hosts have not yet been identified. Raccoon dogs (Nyctereutes procyonoides) are kept for fur production, in particular in China, and were suspected as potential intermediate host for both SARS-CoV6 and SARS-CoV2. Here we demonstrate susceptibility of raccoon dogs for SARS-CoV-2 infection after intranasal inoculation and transmission to direct contact animals. Rapid, high level virus shedding, in combination with minor clinical signs and pathohistological changes, seroconversion and absence of viral adaptation highlight the role of raccoon dogs as a potential intermediate host. The results are highly relevant for control strategies and emphasize the risk that raccoon dogs may represent a potential SARS-CoV-2 reservoir. Our results support the establishment of adequate surveillance and risk mitigation strategies for kept and wild raccoon dogs.\n\nArticle Summary LineRaccoon dogs are susceptible to and efficiently transmit SARS-CoV2 and may serve as intermediate host", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Conrad Martin Freuling", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Angele Breithaupt", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Thomas Mueller", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Julia Sehl", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Anne Balkema-Buschmann", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Melanie Rissmann", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Antonia Klein", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Claudia Wylezich", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Dirk Hoeper", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Kerstin Wernike", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Andrea Aebischer", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Donata Hoffmann", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Virginia Friedrichs", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Anca Dorhoi", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Martin Groschup", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Martin Beer", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Thomas C Mettenleiter", - "author_inst": "Friedrich-Loeffler-Institut" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.20.258772", "rel_title": "What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes", @@ -1238638,6 +1242004,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.17.20176347", + "rel_title": "The necessary cooperation between governments and public in the fight against COVID-19: why non-pharmaceutical interventions may be ineffective", + "rel_date": "2020-08-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176347", + "rel_abs": "The coronavirus disease (COVID-19) outbreak is the biggest public health challenge in the last 100 years. No successful pharmaceutical treatment is yet available, thus effective public health interventions to contain COVID-19 include social distancing, isolation and quarantine measures, however the efficiency of these containment measures varied among countries and even within states in the same country. Despite Brazil being deeply affected by coronavirus, the federal government never proposed a coordinated action to control COVID-19 and Brazilian states, which are autonomous, each imposed different containment measures. The state of Goias declared strict social distancing measures in March 13, but gradually relaxed many of its first measures due specially to public pressure. Here we use a Susceptible-Infected-Recovered (SIR) model combined with Bayesian inference and a time-dependent spreading rate to assess how past state-level interventions affected the spread of COVID-19 in Goias. The interventions succeeded in decreasing the transmission rate in the state, however, after the third intervention the rate remained positive and exponential. Thus, other stricter interventions were made necessary to avoid the growth of new cases and a collapse in the health system. Governmental interventions need to be taken seriously by the population in order for them have the proposed outcome. Our results reflect the populations disregard with the measures imposed and the need for cooperation between governments and its citizens in the fight against COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Christielly Mendonca Borges", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Marco Tulio Pacheco Coelho", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Jose Alexandre Felizola Diniz-Filho", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Thiago Fernando Rangel", + "author_inst": "Universidade Federal de Goias" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.17.20161760", "rel_title": "SARS-CoV-2 (COVID-19) infection in pregnant women: characterization of symptoms and syndromes predictive of disease and severity through real-time, remote participatory epidemiology.", @@ -1240018,37 +1243415,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.16.20035691", - "rel_title": "COVID-19 ICU and mechanical ventilation patient characteristics and outcomes - A systematic review and meta-analysis", - "rel_date": "2020-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20035691", - "rel_abs": "BackgroundInsight into COVID-19 intensive care unit (ICU) patient characteristics, rates and risks of invasive mechanical ventilation (IMV) and associated outcomes as well as any regional discrepancies is critical in this pandemic for individual case management and overall resource planning.\n\nMethods and FindingsElectronic searches were performed for reports through May 1 2020 and reports on COVID-19 ICU admissions and outcomes were included using predefined search terms. Relevant data was subsequently extracted and pooled using fixed or random effects meta-analysis depending on heterogeneity. Study quality was assessed by the NIH tool and heterogeneity was assessed by I2 and Q tests. Baseline patient characteristics, ICU and IMV outcomes were pooled and meta-analyzed. Pooled odds ratios (pOR) were calculated for clinical features against ICU, IMV mortality. Subgroup analysis was carried out based on patient regions. A total of twenty-eight studies comprising 12,437 COVID-19 ICU admissions from seven countries were meta-analyzed. Pooled ICU admission rate was 21% [95% CI 0.12-0.34] and 69% of cases needed IMV [95% CI 0.61-0.75]. ICU and IMV mortality were 28.3% [95% CI 0.25-0.32], 43% [95% CI 0.29-0.58] and ICU, IMV duration was 7.78 [95% CI 6.99-8.63] and 10.12 [95% CI 7.08-13.16] days respectively. Besides confirming the significance of comorbidities and clinical findings of COVID-19 previously reported, we found the major correlates with ICU mortality were IMV [pOR 16.46, 95% CI 4.37-61.96], acute kidney injury (AKI) [pOR 12.47, 95% CI 1.52-102.7], and acute respiratory distress syndrome (ARDS) [pOR 6.52, 95% CI 2.66-16.01]. Subgroup analyses confirm significant regional discrepancies in outcomes.\n\nConclusionsThis is the most comprehensive systematic review and meta-analysis of COVID-19 ICU and IMV cases and associated outcomes to date and the only analysis to implicate IMVs associtaion with COVID-19 ICU mortality. The significant association of AKI, ARDS and IMV with mortality has implications for ICU resource planning for AKI and ARDS as well as research into optimal ventilation strategies for patients. Regional differences in outcome implies a need to develop region specific protocols for ventilatory support as well as overall treatment.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Raymond Chang", - "author_inst": "Institute of East West Medicine" - }, - { - "author_name": "Khaled Mossad Elhusseiny", - "author_inst": "Al-Azhar University" - }, - { - "author_name": "Yu-Chang Yeh", - "author_inst": "National Taiwan University Hospital" - }, - { - "author_name": "Wei-zen Sun", - "author_inst": "National Taiwan University Hospial" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.08.16.20176073", "rel_title": "Impacts on Surgery Resident Education at a first wave COVID-19 epicenter", @@ -1240412,6 +1243778,165 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.17.238444", + "rel_title": "Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity", + "rel_date": "2020-08-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.17.238444", + "rel_abs": "The human microbiota has a close relationship with human disease and it remodels components of the glycocalyx including heparan sulfate (HS). Studies of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) spike protein receptor binding domain suggest that infection requires binding to HS and angiotensin converting enzyme 2 (ACE2) in a codependent manner. Here, we show that commensal host bacterial communities can modify HS and thereby modulate SARS-CoV-2 spike protein binding and that these communities change with host age and sex. Common human-associated commensal bacteria whose genomes encode HS-modifying enzymes were identified. The prevalence of these bacteria and the expression of key microbial glycosidases in bronchoalveolar lavage fluid (BALF) was lower in adult COVID-19 patients than in healthy controls. The presence of HS-modifying bacteria decreased with age in two large survey datasets, FINRISK 2002 and American Gut, revealing one possible mechanism for the observed increase in COVID-19 susceptibility with age. In vitro, bacterial glycosidases from unpurified culture media supernatants fully blocked SARS-CoV-2 spike binding to human H1299 protein lung adenocarcinoma cells. HS-modifying bacteria in human microbial communities may regulate viral adhesion, and loss of these commensals could predispose individuals to infection. Understanding the impact of shifts in microbial community composition and bacterial lyases on SARS-CoV-2 infection may lead to new therapeutics and diagnosis of susceptibility.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC=\"FIGDIR/small/238444v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@14ff1ecorg.highwire.dtl.DTLVardef@193d84corg.highwire.dtl.DTLVardef@15d6f9eorg.highwire.dtl.DTLVardef@14b16c6_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract. Diagram of hypothesis for bacterial mediation of SARS-CoV-2 infection through heparan sulfate (HS).It is well known that host microbes groom the mucosa where they reside. Recent investigations have shown that HS, a major component of mucosal layers, is necessary for SARS-CoV-2 infection. In this study we examine the impact of microbial modification of HS on viral attachment.\n\nC_FIG", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Cameron Martino", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Benjamin P. Kellman", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Daniel R. Sandoval", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Thomas Mandel Clausen", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Clarisse A. Marotz", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Se Jin Song", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Stephen Wandro", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Livia S. Zaramela", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Rodolfo Antonio Salido Ben\u00edtez", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Qiyun Zhu", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Erick Armingol", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Yoshiki V\u00e1zquez-Baeza", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Daniel McDonald", + "author_inst": "University of California San Diego" + }, + { + "author_name": "James T. Sorrentino", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Bryn Taylor", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Pedro Belda-Ferre", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Chenguang Liang", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Yujie Zhang", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Luca Schifanella", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Nichole R. Klatt", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Aki S. Havulinna", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Pekka Jousilahti", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Shi Huang", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Niina Haiminen", + "author_inst": "IBM Research" + }, + { + "author_name": "Laxmi Parida", + "author_inst": "IBM Research" + }, + { + "author_name": "Ho-Cheol Kim", + "author_inst": "IBM Research" + }, + { + "author_name": "Austin D. Swafford", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Karsten Zengler", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Susan Cheng", + "author_inst": "Brigham and Womens Hospital" + }, + { + "author_name": "Michael Inouye", + "author_inst": "Baker Heart & Diabetes Institute, University of Melbourne, University of Cambridge" + }, + { + "author_name": "Teemu Niiranen", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Mohit Jain", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Veikko Salomaa", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Jeffrey D. Esko", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Nathan E Lewis", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Rob Knight", + "author_inst": "University of California San Diego" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.17.254839", "rel_title": "KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response", @@ -1241728,57 +1245253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.15.20175562", - "rel_title": "Impact of COVID-19 on Primary Care Mental Health Services: A Descriptive, Cross-Sectional Timeseries of Electronic Healthcare Records", - "rel_date": "2020-08-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175562", - "rel_abs": "IntroductionThere are growing concerns about the impact of the COVID-19 pandemic on mental health. With government-imposed restrictions as well as a general burden on healthcare systems, the pandemic has the potential to disrupt the access to, and delivery of, mental healthcare. Ultimately, this could potentially lead to unmet needs of individuals requiring mental health support.\n\nMethodsElectronic healthcare records from primary care psychological therapy services (Improving Access to Psychological Therapy) in England were used to examine changes in access to mental health services and service delivery during early stages of the COVID-19 pandemic. A cross-sectional, descriptive timeseries was conducted using data from 1st January 2019 to 24th May 2020 across five NHS trusts to examine patterns in referrals to services (n = 171,823) and appointments taking place (n = 865,902).\n\nResultsThe number of patients accessing mental health services dropped by an average of 55% in the 9 weeks after lockdown was announced, reaching a maximum reduction of 74% in the initial 3 weeks after lockdown in the UK. As referrals began to increase again, there was a relatively faster increase in referrals from Black, Asian, and ethnic minority groups as well an increase in referrals from more densely populated areas. Despite a reduction in access, service providers adapted to infection control guidance by rapidly shifting to remote delivery of care.\n\nInterpretationServices were able to rapidly adapt to provide continuity of care in mental healthcare. However, patients accessing services reduced dramatically, potentially placing a future burden on service providers to treat a likely backlog of patients in addition to a possible excess of patients as the long-term consequences of the pandemic become more apparent. Despite the observational nature of the data, which should be noted, the present study can inform the planning of service provision and policy.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Clarissa M. M. Bauer-Staeb", - "author_inst": "University of Bath" - }, - { - "author_name": "Alice Davis", - "author_inst": "University of Bath; Mayden" - }, - { - "author_name": "Theresa R Smith", - "author_inst": "University of Bath" - }, - { - "author_name": "David Betts", - "author_inst": "Mayden" - }, - { - "author_name": "Wendy Wilsher", - "author_inst": "Mayden" - }, - { - "author_name": "Chris Eldridge", - "author_inst": "Mayden" - }, - { - "author_name": "Emma Griffith", - "author_inst": "University of Bath; Avon and Wiltshire Mental Health Partnership NHS Trust" - }, - { - "author_name": "Julian J Faraway", - "author_inst": "University of Bath" - }, - { - "author_name": "Katherine S Button", - "author_inst": "University of Bath" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.08.14.20170290", "rel_title": "Efficient Deep Network Architecture for COVID-19 Detection Using Computed Tomography Images", @@ -1242078,6 +1245552,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.15.20175588", + "rel_title": "A data-driven epidemiological model to explain the Covid-19 pandemic in multiple countries and help in choosing mitigation strategies", + "rel_date": "2020-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175588", + "rel_abs": "Accurate models are fundamental to understand the dynamics of the COVID-19 pandemic and to evaluate different mitigation strategies. Here, we present a multi-compartmental model that fits the epidemiological data for eleven countries, despite the reduced number of fitting parameters. This model consistently explains the data for the daily infected, recovered, and dead over the first six months of the pandemic. The good quality of the fits makes it possible to explore different scenarios and evaluate the impact of both individual and collective behaviors and government-level decisions to mitigate the epidemic. We identify robust alternatives to lockdown, such as self-protection measures, and massive testing. Furthermore, communication and risk perception are fundamental to modulate the success of different strategies. The fitting/simulation tool is publicly available for use and test of other models, allowing for comparisons between different underlying assumptions, mitigation measures, and policy recommendations.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Maria Jardim Beira", + "author_inst": "Department of Physics, Instituto Superior Tecnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal" + }, + { + "author_name": "Anant Kumar", + "author_inst": "Department of Physics, Instituto Superior Tecnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal" + }, + { + "author_name": "Lilia Perfeito", + "author_inst": "Nova School of Business and Economics, Universidade Nova de Lisboa, Rua da Holanda, 1, 2775-405, Carcavelos, Portugal" + }, + { + "author_name": "Joana Goncalves-Sa", + "author_inst": "Department of Physics, Instituto Superior Tecnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal" + }, + { + "author_name": "Pedro Jose Sebastiao", + "author_inst": "Universidade de Lisboa, Instituto Superior Tecnico" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.14.20174797", "rel_title": "COVID-19 among nursing staff: Settings and regional differences", @@ -1243398,197 +1246907,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.15.252320", - "rel_title": "A SARS-CoV-2 neutralizing antibody protects from lung pathology in a COVID-19 hamster model", - "rel_date": "2020-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.15.252320", - "rel_abs": "The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from ten COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb CV07-209 neutralized authentic SARS-CoV-2 with IC50 of 3.1 ng/ml. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 [A] revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2 neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy.", - "rel_num_authors": 44, - "rel_authors": [ - { - "author_name": "Jakob Kreye", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "S Momsen Reincke", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Hans-Christian Kornau", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Elisa Sanchez-Sendin", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Victor Max Corman", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Hejun Liu", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Meng Yuan", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Nicholas C Wu", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Xueyong Zhu", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Chang-Chun D Lee", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Jakob Trimpert", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Markus Hoeltje", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Kristina Dietert", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Laura Stoeffler", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Niels von Wardenburg", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Scott van Hoof", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Marie A Homeyer", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Julius Hoffmann", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Azza Abdelgawad", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Achim D Gruber", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Luca D Bertzbach", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Daria Vladimirova", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Lucie Y Li", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Paula Charlotte Barthel", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Karl Skriner", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Andreas C Hocke", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Stefan Hippenstiel", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Martin Witzenrath", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Norbert Suttorp", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Florian Kurth", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Christiana Franke", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Matthias Endres", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Dietmar Schmitz", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - }, - { - "author_name": "Lara Maria Jeworowski", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Anja Richter", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Marie Luisa Schmidt", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Tatjana Schwarz", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Marcel Alexander Mueller", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Daniel Wendisch", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Leif E Sander", - "author_inst": "Charite - Universitaetsmedizin Berlin, Berlin, Germany." - }, - { - "author_name": "Nikolaus Osterrieder", - "author_inst": "Freie Universitaet Berlin, Berlin, Germany." - }, - { - "author_name": "Ian A Wilson", - "author_inst": "The Scripps Research Institute, La Jolla, USA." - }, - { - "author_name": "Harald Pruess", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.15.252395", "rel_title": "Susceptibility of swine cells and domestic pigs to SARS-CoV-2", @@ -1243880,6 +1247198,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.14.20175059", + "rel_title": "An Analysis of Self-reported Longcovid Symptoms on Twitter", + "rel_date": "2020-08-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20175059", + "rel_abs": "ObjectivesA majority of patients suffering from acute COVID-19 are expected to recover symptomatically and functionally. However there are reports that some people continue to experience symptoms even beyond the stage of acute infection. This phenomenon has been called longcovid.\n\nStudy designThis study attempted to analyse symptoms reported by users on twitter self-identifying as longcovid.\n\nMethodsThe search was carried out using the twitter public streaming application programming interface using a relevant search term.\n\nResultsWe could identify 89 users with usable data in the tweets posted by them. A majority of users described multiple symptoms the most common of which were fatigue, shortness of breath, pain and brainfog/concentration difficulties. The most common course of symptoms was episodic.\n\nConclusionsGiven the public health importance of this issue, the study suggests that there is a need to better study post acute-COVID symptoms.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Shubh Mohan Singh", + "author_inst": "Postgraduate Institute of Medical Education and Research Chandigarh India" + }, + { + "author_name": "Chaitanya Reddy", + "author_inst": "Postgraduate Institute of Medical Education and Research Chandigarh India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.13.20167452", "rel_title": "Abusers indoors and coronavirus outside: an examination of public discourse about COVID-19 and family violence on Twitter using machine learning", @@ -1245376,33 +1248717,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.08.13.20174755", - "rel_title": "Dynamical balance between the transmission, intervention of COVID-19 and economic development", - "rel_date": "2020-08-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174755", - "rel_abs": "The current explosive outbreak of coronavirus (COVID-19) is posing serious threats to public health and economy around the world. To clarify the coupling mechanism between this disease and economy, a new dynamical system is established. It is theoretically proved that the basic reproduction number is a nonlinear combination of parameters regarding disease transmission, intervention and economy effect, which totally determines the stability of the disease-free and endemic equilibria. Further results indicate the existence of interaction and mutual restraint among the transmission, intervention and economy, in which strong coupling of COVID-19 and economy would trigger disease outbreak and form poverty trap, while adaptive isolation of at-risk population could effectively reduce morbidity at the cost of least economic loss. Our findings can offer new insights to improve the intervention strategies against COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Zhaowang Zhang", - "author_inst": "Guilin University of Electronic Technology" - }, - { - "author_name": "Hualiang Lin", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Guanghu Zhu", - "author_inst": "Guilin University of Electronic Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.13.249847", "rel_title": "Open Science Saves Lives: Lessons from the COVID-19 Pandemic", @@ -1245662,6 +1248976,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.13.20173161", + "rel_title": "Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20173161", + "rel_abs": "The development of vaccines against SARS-CoV-2 would be greatly facilitated by the identification of immunological correlates of protection in humans. However, to date, studies on protective immunity have only been performed in animal models and correlates of protection have not been established in humans. Here, we describe an outbreak of SARS-CoV-2 on a fishing vessel associated with a high attack rate. Predeparture serological and viral RT-PCR testing along with repeat testing after return to shore was available for 120 of the 122 persons on board over a median follow-up of 32.5 days (range 18.8 to 50.5 days). A total of 104 individuals had an RT-PCR positive viral test with Ct <35 or seroconverted during the follow-up period, yielding an attack rate on board of 85.2% (104/122 individuals). Metagenomic sequencing of 39 viral genomes suggested the outbreak originated largely from a single viral clade. Only three crewmembers tested seropositive prior to the boats departure in initial serological screening and also had neutralizing and spike-reactive antibodies in follow-up assays. None of these crewmembers with neutralizing antibody titers showed evidence of bona fide viral infection or experienced any symptoms during the viral outbreak. Therefore, the presence of neutralizing antibodies from prior infection was significantly associated with protection against re-infection (Fishers exact test, p=0.002).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Amin Addetia", + "author_inst": "University of Washington" + }, + { + "author_name": "Katharine HD Crawford", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Adam Dingens", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Haiying Zhu", + "author_inst": "University of Washington" + }, + { + "author_name": "Pavitra Roychoudhury", + "author_inst": "University of Washington" + }, + { + "author_name": "Meeili Huang", + "author_inst": "University of Washington" + }, + { + "author_name": "Keith R Jerome", + "author_inst": "University of Washington" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "FRED HUTCHINSON CANCER RESEARCH CENTER" + }, + { + "author_name": "Alexander Greninger", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.11.20171272", "rel_title": "The Status and Risk Factors of COVID-19 Related Suicides in Bangladesh", @@ -1246934,101 +1250299,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.08.11.20167353", - "rel_title": "Pharmacological inhibition of the kinin-kallikrein system in severe COVID-19 A proof-of-concept study", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20167353", - "rel_abs": "Coronavirus disease-19 (COVID-19) can develop into a severe respiratory syndrome that results in up to 40% mortality. Acute lung inflammatory edema is a major pathological finding in autopsies explaining O2 diffusion failure and hypoxemia. Only dexamethasone has been shown to reduce mortality in severe cases, further supporting a role for inflammation in disease severity. SARS-CoV-2 enters cells employing angiotensin converting enzyme 2 (ACE2) as a receptor, which is highly expressed in lung alveolar cells. ACE2 is one of the components of the cellular machinery that inactivates the potent inflammatory agent bradykinin, and SARS-CoV-2 infection could interfere with the catalytic activity of ACE2, leading to accumulation of bradykinin. In this open-label, randomized clinical trial, we tested two pharmacological inhibitors of the kinin-kallikrein system that are currently approved for the treatment of hereditary angioedema, icatibant and inhibitor of C1 esterase/kallikrein, in a group of 30 patients with severe COVID-19. Neither icatibant nor inhibitor of C1 esterase/kallikrein resulted in significant changes in disease mortality and time to clinical improvement. However, both compounds promoted significant improvement of lung computed tomography scores and increased blood eosinophils, which has been reported as an indicator of disease recovery. In this small cohort, we found evidence for a beneficial role of pharmacological inhibition of the kinin-kallikrein system in two markers that indicate improved disease recovery.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Eli Mansour", - "author_inst": "University of Campinas" - }, - { - "author_name": "Andre C Palma", - "author_inst": "University of Campinas" - }, - { - "author_name": "Raisa G Ulaf", - "author_inst": "University of Campinas" - }, - { - "author_name": "Luciana C Ribeiro", - "author_inst": "University of Campinas" - }, - { - "author_name": "Ana Flavia Bernardes", - "author_inst": "University of Campinas" - }, - { - "author_name": "Thyago A Nunes", - "author_inst": "University of Campinas" - }, - { - "author_name": "Marcus V Agrela", - "author_inst": "University of Campinas" - }, - { - "author_name": "Bruna Bombassaro", - "author_inst": "University of Campinas" - }, - { - "author_name": "Milena Monfort-Pires", - "author_inst": "University of Campinas" - }, - { - "author_name": "Rafael L Camargo", - "author_inst": "University of Campinas" - }, - { - "author_name": "Eliana P Araujo", - "author_inst": "University of Campinas" - }, - { - "author_name": "Natalia S Brunetti", - "author_inst": "University of Campinas" - }, - { - "author_name": "Alessandro S Farias", - "author_inst": "University of Campinas" - }, - { - "author_name": "Antonio L Falcao", - "author_inst": "University of Campinas" - }, - { - "author_name": "Thiago M Santos", - "author_inst": "University of Campinas" - }, - { - "author_name": "Plinio Trabasso", - "author_inst": "University of Campinas" - }, - { - "author_name": "Rachel P Dertkigil", - "author_inst": "University of Campinas" - }, - { - "author_name": "Sergio S Dertkigil", - "author_inst": "University of Campinas" - }, - { - "author_name": "Maria Luiza Moretti", - "author_inst": "University of Campinas" - }, - { - "author_name": "Licio A Velloso", - "author_inst": "University of Campinas" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.11.20171843", "rel_title": "Functional SARS-CoV-2-specific immune memory persists after mild COVID-19", @@ -1247352,6 +1250622,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.13.20173757", + "rel_title": "LAMP-BEAC: Detection of SARS-CoV-2 RNA Using RT-LAMP and Molecular Beacons", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20173757", + "rel_abs": "BackgroundRapid spread of SARS-CoV-2 has led to a global pandemic, resulting in the need for rapid assays to allow diagnosis and prevention of transmission. Reverse Transcription-Polymerase Chain Reaction (RT-PCR) provides a gold standard assay for SARS-CoV-2 RNA, but tests are expensive and supply chains are potentially fragile, motivating interest in additional assay methods. Reverse Transcription and Loop-Mediated Isothermal Amplification (RT-LAMP) provides an alternative that uses orthogonal and often less expensive reagents without the need for thermocyclers. The presence of SARS-CoV-2 RNA is typically detected using dyes to report bulk amplification of DNA; however, a common artifact is nonspecific DNA amplification, which complicates detection.\n\nResultsHere we describe the design and testing of molecular beacons, which allow sequence-specific detection of SARS-CoV-2 genomes with improved discrimination in simple reaction mixtures. To optimize beacons for RT-LAMP, multiple locked nucleic acid monomers were incorporated to elevate melting temperatures. We also show how beacons with different fluorescent labels can allow convenient multiplex detection of several amplicons in \"single pot\" reactions, including incorporation of a human RNA LAMP-BEAC assay to confirm sample integrity. Comparison of LAMP-BEAC and RT-qPCR on clinical saliva samples showed good concordance between assays. To facilitate implementation, we developed custom polymerases for LAMP-BEAC and inexpensive purification procedures, which also facilitates increasing sensitivity by increasing reaction volumes.\n\nConclusionsLAMP-BEAC thus provides an affordable and simple SARS-CoV-2 RNA assay suitable for population screening; implementation of the assay has allowed robust screening of thousands of saliva samples per week.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Scott Sherrill-Mix", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Young Hwang", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Aoife M Roche", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Abigail Glascock", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Susan R Weiss", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Yize Li", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Leila Haddad", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Peter Deraska", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Caitlin Monahan", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Andrew Kromer", + "author_inst": "University of Pennsylania" + }, + { + "author_name": "Jevon Graham-Wooten", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Louis J Taylor", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Benjamin Abella", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Arupa Ganguly", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ronald G Collman", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Gregory D Van Duyne", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Frederic D Bushman", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20173807", "rel_title": "Validation of Saliva and Self-Administered Nasal Swabs for COVID-19 Testing", @@ -1248548,41 +1251901,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.10.20171819", - "rel_title": "Investigation of pooling strategies using clinical COVID-19 samples for more efficient diagnostic testing", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171819", - "rel_abs": "When testing large numbers of clinical COVID-19 samples for diagnostic purposes, pooling samples together for processing can offer significant reductions in the materials, reagents, time, and labor needed. We have evaluated two different strategies for pooling independent nasopharyngeal swab samples prior to testing with an EUA-approved SARS-CoV-2 RT-qPCR diagnostic assay. First, in the Dilution Study, we assessed the assay's ability to detect a single positive clinical sample diluted in multiple negative samples before the viral RNA extraction stage. We observed that positive samples with Ct values at ~30 can be reliably detected in pools of up to 30 independent samples, and positive samples with Ct values at ~35 can be detected in pools of 5 samples. Second, in the Reloading Study, we assessed the efficacy of reloading QIAamp viral RNA extraction columns numerous times using a single positive sample and multiple negative samples. We determined that one RNA extraction column can be reloaded with up to 20 clinical samples (1 positive and 19 negatives) sequentially without any loss of signal in the diagnostic assay. Furthermore, we found there was no significant difference in assay readout whether the positive sample was loaded first or last in a series of 20 samples. These results demonstrate that different pooling strategies can lead to increased process efficiencies for COVID-19 clinical diagnostic testing.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Samantha H Adikari", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Emily Z Alipio Lyon", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Attelia D Hollander", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Alina Deshpande", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Elizabeth Hong-Geller", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.13.20173997", "rel_title": "Deep Learning for Automated Recognition of Covid-19 from Chest X-ray Images", @@ -1248838,6 +1252156,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.13.20167064", + "rel_title": "Predicting the Impact of the COVID-19 Pandemic for the Low- and Middle-Income Countries", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20167064", + "rel_abs": "This study predicts the maximum hospital demand and number of infections for the LMICs in the first wave of COVID-19 pandemic. The epidemic is estimated to impose health care burden excessively exceeding the current capacity of hospitals in many LMICs, especially in Honduras, Central African Republic and Colombia.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Zhiwei Ding", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Feng Sha", + "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Bingyu Li", + "author_inst": "Shenzhen University" + }, + { + "author_name": "Jing Kong", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Yi Zhang", + "author_inst": "Beijing Institute of Big Data Research" + }, + { + "author_name": "Yip Paul", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Zhouwang Yang", + "author_inst": "University of Science and Technology of China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20174078", "rel_title": "Mass screening of asymptomatic persons for SARS-CoV-2 using saliva", @@ -1250082,37 +1253443,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2020.08.14.251538", - "rel_title": "Differential methylation as a mediator of COVID-19 susceptibility", - "rel_date": "2020-08-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.14.251538", - "rel_abs": "The COVID-19 outbreak shows a huge variation in prevalence and mortality on geographical level but also within populations1. The ACE2 gene, identified as the SARS-CoV2 receptor, has been shown to facilitate the viral invasion and people with higher ACE2 expression generally are more severely affected2, 3. As there is a lot of variability in ACE2 expression between individuals we hypothesized that differential DNA methylation profiles could be (one of) the confounding factors explaining this variability. Here we show that epigenetic profiling of host tissue, especially in the ACE2 promoter region and its homologue ACE1, may be important risk factors for COVID-19. Our results propose that variable methylation can explain (part of) the differential susceptibility, symptom severity and death rate for COVID-19. Our findings are a promising starting point to further evaluate the potential of ACE1/2 methylation and other candidates as a predictor for clinical outcome upon SARS-CoV2 infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sandra Steyaert", - "author_inst": "doc.ai Inc. 636 Waverley Street, Palo Alto, CA 94301" - }, - { - "author_name": "Geert Trooskens", - "author_inst": "doc.ai Inc. 636 Waverley Street, Palo Alto, CA 94301" - }, - { - "author_name": "Joris R Delanghe", - "author_inst": "Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium" - }, - { - "author_name": "Wim Van Criekinge", - "author_inst": "Biobix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.08.13.250076", "rel_title": "In Silico Design of siRNAs Targeting Existing and Future Respiratory Viruses with VirusSi", @@ -1250436,6 +1253766,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.13.248351", + "rel_title": "Designed Variants of Recombinant ACE2-Fc that Decouple Anti-SARS-CoV-2 Activities from Unwanted Cardiovascular Effects", + "rel_date": "2020-08-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.13.248351", + "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) is the entry receptor for SARS-CoV-2, and recombinant ACE2 decoys are being evaluated as new antiviral therapies. We designed and tested an antibody-like ACE2-Fc fusion protein, which has the benefit of long pharmacological half-life and the potential to facilitate immune clearance of the virus. Out of a concern that the intrinsic catalytic activity of ACE2 may unintentionally alter the balance of its hormonal substrates and cause adverse cardiovascular effects in treatment, we performed a mutagenesis screening for inactivating the enzyme. Three mutants, R273A, H378A and E402A, completely lost their enzymatic activity for either surrogate or physiological substrates. All of them remained capable of binding SARS-CoV-2 and could suppress the transduction of a pseudotyped virus in cell culture. This study established new ACE2-Fc candidates as antiviral treatment for SARS-CoV-2 without potentially harmful side effects from ACE2s catalytic actions toward its vasoactive substrates.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Pan Liu", + "author_inst": "Northewstern University" + }, + { + "author_name": "Xinfang Xie", + "author_inst": "Northwestern University" + }, + { + "author_name": "Li Gao", + "author_inst": "Northwestern University" + }, + { + "author_name": "Jing Jin", + "author_inst": "Northwestern University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.08.14.240093", "rel_title": "Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine", @@ -1251744,117 +1255105,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.10.20170894", - "rel_title": "Deciphering the state of immune silence in fatal COVID-19 patients", - "rel_date": "2020-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20170894", - "rel_abs": "Since the beginning of the SARS-CoV-2 pandemic, COVID-19 has appeared as a unique disease with unconventional tissue and systemic immune features. While COVID-19 severe forms share clinical and laboratory aspects with various pathologies such as hemophagocytic lymphohistiocytosis, sepsis or cytokine release syndrome, their exact nature remains unknown. This is severely impeding the ability to treat patients facing severe stages of the disease. To this aim, we performed an in-depth, single-cell RNA-seq analysis of more than 150.000 immune cells isolated from matched blood samples and broncho-alveolar lavage fluids of COVID-19 patients and healthy controls, and integrated it with clinical, immunological and functional ex vivo data. We unveiled an immune signature of disease severity that correlated with the accumulation of naive lymphoid cells in the lung and an expansion and activation of myeloid cells in the periphery. Moreover, we demonstrated that myeloid-driven immune suppression is a hallmark of COVID-19 evolution and arginase 1 expression is significantly associated with monocyte immune regulatory features. Noteworthy, we found monocyte and neutro-phil immune suppression loss associated with fatal clinical outcome in severe patients. Additionally, our analysis discovered that the strongest association of the patients clinical outcome and immune phenotype is the lung T cell response. We found that patients with a robust CXCR6+ effector memory T cell response have better outcomes. This result is line with the rs11385942 COVID-19 risk allel, which is in proximity to the CXCR6 gene and suggest effector memory T cell are a primary feature in COVID-19 patients. By systemically quantifying the viral landscape in the lung of severe patients, we indeed identified Herpes-Simplex-Virus 1 (HSV-1) as a potential opportunistic virus in COVID-19 patients. Lastly, we observed an unexpectedly high SARS-CoV-2 viral load in an immuno-compromised patient, allowing us to study the SARS-CoV-2 in-vivo life cycle. The development of myeloid dysfunctions and the impairment of lymphoid arm establish a condition of immune paralysis that supports secondary bacteria and virus infection and can progress to \"immune silence\" in patients facing death.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Pierre Bost", - "author_inst": "Department of Immunology, Weizmann Institute of Science, Rehovot, Israel, Systems Biology Group, Department of Computational Biology and USR 3756, Institut Past" - }, - { - "author_name": "Francesco De Sanctis", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Stefania Cane", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Stefano Ugel", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Katia Donadello", - "author_inst": "Intensive Care Unit, Department of Surgery, Dentistry, Maternity and Infant, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Monica Castellucci", - "author_inst": "The Center for Technological Platforms, University of Verona, Verona, Italy" - }, - { - "author_name": "David Eyal", - "author_inst": "Department of Immunology, Weizmann Institute of Science, Rehovot, Israel" - }, - { - "author_name": "Alessandra Fiore", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Cristina Anselmi", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Roza Maria Barouni", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Rosalinda Trovato", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Simone Caligola", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Alessia Lamolinara", - "author_inst": "CAST- Center for Advanced Studies and Technology, University of G. D Annunzio of Chieti-Pescara, Chieti, Italy" - }, - { - "author_name": "Manuela Iezzi", - "author_inst": "CAST- Center for Advanced Studies and Technology, University of G. D Annunzio of Chieti-Pescara, Chieti, Italy" - }, - { - "author_name": "Federica Facciotti", - "author_inst": "Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy" - }, - { - "author_name": "Anna Rita Mazzariol", - "author_inst": "Microbiology Unit, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Davide Gibellini", - "author_inst": "Microbiology Unit, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Pasquale De Nardo", - "author_inst": "Division of Infectious Diseases, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Evelina Tacconelli", - "author_inst": "Division of Infectious Diseases, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Leonardo Gottin", - "author_inst": "Intensive Care Unit, Department of Surgery, Dentistry, Maternity and Infant, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Enrico Polati", - "author_inst": "Intensive Care Unit, Department of Surgery, Dentistry, Maternity and Infant, University and Hospital Trust of Verona, Verona, Italy" - }, - { - "author_name": "Benno Schwikowski", - "author_inst": "Systems Biology Group, Department of Computational Biology and USR 3756, Institut Pasteur and CNRS,Paris, France" - }, - { - "author_name": "Ido Amit", - "author_inst": "Department of Immunology, Weizmann Institute of Science, Rehovot, Israel." - }, - { - "author_name": "Vincenzo Bronte", - "author_inst": "Immunology Section, Department of Medicine, University and Hospital Trust of Verona, Verona , Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.10.20171629", "rel_title": "Risk of fomite-mediated transmission of SARS-CoV-2 in child daycares, schools, and offices: a modeling study", @@ -1252078,6 +1255328,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.12.248823", + "rel_title": "Attenuated influenza virions expressing the SARS- CoV-2 receptor-binding domain induce neutralizing antibodies in mice", + "rel_date": "2020-08-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.12.248823", + "rel_abs": "An effective vaccine is essential to controlling the spread of SARS-CoV-2 virus. Here, we describe an influenza-virus-based vaccine for SARS-CoV-2. We incorporated a membrane-anchored form of the SARS-CoV-2 Spike receptor binding domain (RBD) in place of the neuraminidase (NA) coding sequence in an influenza virus also possessing a mutation that reduces the affinity of hemagglutinin for its sialic acid receptor. The resulting {Delta}NA(RBD)-Flu virus can be generated by reverse genetics and grown to high titers in cell culture. A single-dose intranasal inoculation of mice with {Delta}NA(RBD)-Flu elicits serum neutralizing antibody titers against SAR-CoV-2 comparable to those observed in humans following natural infection ([~]1:200). Furthermore, {Delta}NA(RBD)-Flu itself causes no apparent disease in mice. It might be possible to produce a vaccine similar to {Delta}NA(RBD)-Flu at scale by leveraging existing platforms for production of influenza vaccines.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andrea N Loes", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Lauren E Gentles", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Allison J Greaney", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Katharine HD Crawford", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.13.249177", "rel_title": "The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer", @@ -1253406,45 +1256691,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.09.20149286", - "rel_title": "The effect of public health policies in the transmission of COVID-19 for South American countries", - "rel_date": "2020-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.09.20149286", - "rel_abs": "ObjectivesThe analysis of transmission dynamics is crucial to determine whether mitigation or suppression measures reduce the spread of Coronavirus disease 2019 (COVID-19). This study sought to estimate the basic (R0) and time-varying (Rt) reproduction number of COVID-19 and contrast the public health measures for ten South American countries.\n\nMethodsData was obtained from the European Centre for Disease Prevention and Control. Country-specific R0 estimates during the first two weeks of the outbreak and Rt estimates after 90 days were estimated.\n\nResultsCountries used a combination of isolation, physical distancing, quarantine, and community-wide containment measures to staunch the spread of COVID-19 at different points in time. R0 ranged from 1.52 (95% confidence interval: 1.13-1.99) in Venezuela to 3.83 (3.04-4.75) in Chile, whereas Rt after 90 days ranged from 0.71 (95% credible interval: 0.39-1.05) in Uruguay to 1.20 (1.19-1.20) in Brazil. Different R0 and Rt values may be related to the testing capacity of each country.\n\nConclusionR0 in the early phase of the outbreak varied across the South American countries. The public health measures adopted in the initial period of the pandemic appear to have reduced Rt over time in each country, albeit to different levels.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Bryan Valcarcel", - "author_inst": "Milken Institute School of Public Health" - }, - { - "author_name": "Jose L Avilez", - "author_inst": "University of Waterloo" - }, - { - "author_name": "J. Smith Torres-Roman", - "author_inst": "Universidad Cientifica del Sur" - }, - { - "author_name": "Julio A Poterico", - "author_inst": "Instituto Nacional de Salud del Nino San Borja" - }, - { - "author_name": "Janina Bazalar-Palacios", - "author_inst": "Instituto de Investigacion, Universidad Catolica Los Angeles de Chimbote" - }, - { - "author_name": "Carlo La Vecchia", - "author_inst": "Department of Clinical Sciences and Community Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.11.247395", "rel_title": "Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2", @@ -1253816,6 +1257062,173 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.12.20169359", + "rel_title": "Effect of Convalescent Plasma on Mortality among Hospitalized Patients with COVID-19: Initial Three-Month Experience", + "rel_date": "2020-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20169359", + "rel_abs": "ImportancePassive antibody transfer is a longstanding treatment strategy for infectious diseases that involve the respiratory system. In this context, human convalescent plasma has been used to treat coronavirus disease 2019 (COVID-19), but the efficacy remains uncertain.\n\nObjectiveTo explore potential signals of efficacy of COVID-19 convalescent plasma.\n\nDesignOpen-label, Expanded Access Program (EAP) for the treatment of COVID-19 patients with human convalescent plasma.\n\nSettingMulticenter, including 2,807 acute care facilities in the US and territories.\n\nParticipantsAdult participants enrolled and transfused under the purview of the US Convalescent Plasma EAP program between April 4 and July 4, 2020 who were hospitalized with (or at risk of) severe or life threatening acute COVID-19 respiratory syndrome.\n\nInterventionTransfusion of at least one unit of human COVID-19 convalescent plasma using standard transfusion guidelines at any time during hospitalization. Convalescent plasma was donated by recently-recovered COVID-19 survivors, and the antibody levels in the units collected were unknown at the time of transfusion.\n\nMain Outcomes and MeasuresSeven and thirty-day mortality.\n\nResultsThe 35,322 transfused patients had heterogeneous demographic and clinical characteristics. This cohort included a high proportion of critically-ill patients, with 52.3% in the intensive care unit (ICU) and 27.5% receiving mechanical ventilation at the time of plasma transfusion. The seven-day mortality rate was 8.7% [95% CI 8.3%-9.2%] in patients transfused within 3 days of COVID-19 diagnosis but 11.9% [11.4%-12.2%] in patients transfused 4 or more days after diagnosis (p<0.001). Similar findings were observed in 30-day mortality (21.6% vs. 26.7%, p<0.0001). Importantly, a gradient of mortality was seen in relation to IgG antibody levels in the transfused plasma. For patients who received high IgG plasma (>18.45 S/Co), seven-day mortality was 8.9% (6.8%, 11.7%); for recipients of medium IgG plasma (4.62 to 18.45 S/Co) mortality was 11.6% (10.3%, 13.1%); and for recipients of low IgG plasma (<4.62 S/Co) mortality was 13.7% (11.1%, 16.8%) (p=0.048). This unadjusted dose-response relationship with IgG was also observed in thirty-day mortality (p=0.021). The pooled relative risk of mortality among patients transfused with high antibody level plasma units was 0.65 [0.47-0.92] for 7 days and 0.77 [0.63-0.94] for 30 days compared to low antibody level plasma units.\n\nConclusions and RelevanceThe relationships between reduced mortality and both earlier time to transfusion and higher antibody levels provide signatures of efficacy for convalescent plasma in the treatment of hospitalized COVID-19 patients. This information may be informative for the treatment of COVID-19 and design of randomized clinical trials involving convalescent plasma.\n\nTrial RegistrationClinicalTrials.gov Identifier: NCT04338360\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes transfusion of human convalescent plasma reduce mortality among hospitalized COVID-19 patients?\n\nFindingsTransfusion of convalescent plasma with higher antibody levels to hospitalized COVID-19 patients significantly reduced mortality compared to transfusions with low antibody levels. Transfusions within three days of COVID-19 diagnosis yielded greater reductions in mortality.\n\nMeaningEmbedded in an Expanded Access Program providing access to COVID-19 convalescent plasma and designed to assess its safety, several signals consistent with efficacy of convalescent plasma in the treatment of hospitalized COVID-19 patients emerged.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Michael J Joyner", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Jonathon W Senefeld", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Stephen A Klassen", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "John R Mills", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Patrick W Johnson", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Elitza S Theel", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Chad C Wiggins", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Katelyn A Bruno", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Allan M Klompas", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Elizabeth R Lesser", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Katie L Kunze", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Matthew A Sexton", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Juan C Diaz Soto", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Sarah E Baker", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "John R.A. Shepherd", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Noud van Helmond", + "author_inst": "Cooper Medical School of Rowan University" + }, + { + "author_name": "Camille M van Buskirk", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Jeffrey L Winters", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "James R Stubbs", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Robert F Rea", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "David O Hodge", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Vitaly Herasevich", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Emily R Whelan", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew J Clayburn", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Kathryn F Larson", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Juan G Ripoll", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Kylie J Andersen", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Matthew R Buras", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Matthew N.P. Vogt", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Joshua J Dennis", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Riley J Regimbal", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Philippe R Bauer", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Janis E Blair", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Nigel S Paneth", + "author_inst": "Michigan State University" + }, + { + "author_name": "DeLisa Fairweather", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "R. Scott Wright", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Rickey E Carter", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Arturo Casadevall", + "author_inst": "Johns Hopkins School of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.12.247940", "rel_title": "Coronacept - a potent immunoadhesin against SARS-CoV-2", @@ -1255120,53 +1258533,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.07.20167957", - "rel_title": "Mask-associated de novo headache in healthcare workers during the Covid-19 pandemic.", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20167957", - "rel_abs": "IntroductionThe pandemic caused by the new coronavirus (COVID-19) has led to changes in the development of health care activities by health professionals. We analysed whether there is an association between the appearance of \"de novo\" headache according to the type of mask used, the related factors, as well as the impact of the headache on health professionals.\n\nMethodcross-sectional study in a tertiary hospital in Extremadura, Spain. We administered an online questionnaire to healthcare workers during the period of maximum incidence of COVID-19 in our setting.\n\nResultsn=306, 244 women (79.7%), with an average age of 43 years (range 23-65). Of the total, 129 (42.2%) were physicians, 112 (36.6%) nurses and 65 (21.2%) other health workers. 208 (79.7%) used surgical masks and 53 (20.3%) used filtering masks. Of all those surveyed, 158 (51.6%) presented \"de novo\" headache. The occurrence of headache was independently associated with the use of a filtering mask, OR 2.14 (IC95% 1.07-4.32), being a nurse OR 2.09 (IC95% 1.18-3.72) or another health worker OR 6.94 (IC95% 3.01-16.04) or having a history of asthma OR 0.29 (IC95% 0.09-0.89). Depending on the type of mask used there were differences in headache intensity. And the impact of headache in the subjects who used a filtering mask was worse in the all aspects evaluated.\n\nConclusionsThe appearance of \"de novo\" headache is associated with the use of filtering masks and is more frequent in certain health care workers, causing a greater occupational, family, personal and social impact.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jose M Ramirez-Moreno", - "author_inst": "Extremadura University. School of Medicine." - }, - { - "author_name": "David Ceberino", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Alberto Gonzalez", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Belen Rebollo", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Pablo Macias", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Roshan Hariramani", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Ana M Roa", - "author_inst": "Hospital Universitario de Badajoz" - }, - { - "author_name": "Ana B Constantino", - "author_inst": "Hospital Universitario de Badajoz" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.07.20170449", "rel_title": "Outcomes of COVID-19 related hospitalisation among people with HIV in the ISARIC WHO Clinical Characterisation Protocol UK Protocol: prospective observational study", @@ -1255518,6 +1258884,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.09.20171330", + "rel_title": "A Systematic Review of the Cardiovascular Manifestations and Outcomes in the Setting of Coronavirus-19 Disease", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.09.20171330", + "rel_abs": "The impact of coronavirus disease, 2019 (COVID-19), has been profound. Though COVID-19 primarily affects the respiratory system, it has also been associated with a wide range of cardiovascular (CV) manifestations portending extremely poor prognosis. The principal hypothesis for CV involvement is through direct myocardial infection and systemic inflammation. We conducted a systematic review of the current literature to provide a foundation for understanding the CV manifestations and outcomes of COVID-19. PubMed and EMBASE databases were electronically searched from the inception of the databases through April 27th, 2020. A second literature review was conducted to include major trials and guidelines that were published after the initial search but before submission. The inclusion criteria for studies to be eligible were case reports, case series, and observation studies reporting CV outcomes among patients with COVID-19 infection. This review of the current COVID-19 disease and CV outcomes literature revealed a myriad of CV manifestations with potential avenues for treatment and prevention. Future studies are required to understand on a more mechanistic level the effect of COVID-19 on the myocardium and thus provide avenues to improve mortality and morbidity.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Samarthkumar Thakkar", + "author_inst": "Rochester General Hospital" + }, + { + "author_name": "Shilpkumar Arora", + "author_inst": "Case Western University" + }, + { + "author_name": "Ashish Kumar", + "author_inst": "Saint John's Medical College" + }, + { + "author_name": "Rahul Jaswaney", + "author_inst": "Case Western University" + }, + { + "author_name": "Mohammed Faisaluddin", + "author_inst": "Deccan College Of Medical Science" + }, + { + "author_name": "Mohammad Ammad Ud Din", + "author_inst": "Rochester General Hospital" + }, + { + "author_name": "Mariam Shariff", + "author_inst": "St John's Medical College" + }, + { + "author_name": "Kirolos Barssoum", + "author_inst": "Rochester General Hospital" + }, + { + "author_name": "Harsh P. Patel", + "author_inst": "Louis A Weiss Memorial Hospital" + }, + { + "author_name": "Nirav Arora", + "author_inst": "Lamar University" + }, + { + "author_name": "Chinmay Jani", + "author_inst": "Mount Auburn Hospital" + }, + { + "author_name": "Sejal Savani", + "author_inst": "NYU College of Dentistry" + }, + { + "author_name": "Christopher DeSimone", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Siva Mulpuru", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Abhishek Deshmukh", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.08.10.20171496", "rel_title": "Characterisation of 22446 patients attending UK emergency departments with suspected COVID-19 infection: Observational cohort study", @@ -1256790,61 +1260231,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.10.20172106", - "rel_title": "Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20172106", - "rel_abs": "Since first reported case of the new coronavirus infection in Wuhan, China, researchers and governments have witnessed an unseen rise in the number of cases. Thanks to the rapid work of Chinese scientists, the pathogen now called SARS-CoV-2 has been identified and its whole genome has been deposited in public databases by early January 2020. The availability of the genome has allowed researchers to develop Reverse Transcription - Polymerase Chain Reaction (RT-PCR) assays, which are now the gold-standard for molecular diagnosis of the respiratory syndrome COVID19. Because of the rising number of cases and rapid spreading, the world has been facing a shortage of RT-PCR supplies, especially the ones involved in RNA extraction. This has been a major bottleneck to increase testing capacity in many countries that do not significantly manufacture these supplies (Brazil included). Additionally, RT-PCR scalability is highly dependent on equipment that usually perform testing of 96 samples at a time. In this work, we describe a cost-effective molecular NGS-based test for diagnosis of COVID19, which uses a single-step RNA extraction and presents high scalability and accuracy when compared to the gold-standard RT-PCR. A single run of the NGS-based test using the Illumina NextSeq 550 mid-end sequencing equipment is able to multiplex 1,536 patients samples, providing individual semi-qualitative results (detected, not detected). Detected results are provided with fragments per million (FPM) values, which was demonstrated to correlate with RT-PCR Cycle Threshold (CT) values. Besides, usage of the high-end Illumina Novaseq platform may yield diagnostic for up to 6,144 samples in a single run. Performance results when compared with RT-PCR show general accuracy of 96% (or 98% when only samples with CT values for gene N lower than 30 are considered). We have also developed an online platform, called VarsVID(R), a Varstation(R) feature, to help test executors to easily scale testing numbers. Sample registering, wet-lab worksheets, sample sheet for sequencing and results display are all features provided by VarsVID(R) on Varstation(R). Altogether, these results will contribute to control COVID19 pandemics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Fernanda de Mello Malta", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Deyvid Emanuel Amgarten", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Felipe Camilo Val", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Rubia Anita Ferraz Santana", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Murilo Castro Cervato", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Bruna Mascaro Cordeiro de Azevedo", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Marcela de Souza Basqueira", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Camila Oliveira dos Santos Alves", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Maria Soares Nobrega", - "author_inst": "Hospital Israelita Albert Einstein" - }, - { - "author_name": "Joao Renato Rebello Pinho", - "author_inst": "Hospital Israelita Albert Einstein" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.10.20171033", "rel_title": "Post-exertion oxygen saturation as a prognostic factor for adverse outcome in patients attending the emergency department with suspected COVID-19: Observational cohort study", @@ -1257248,6 +1260634,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.08.11.246678", + "rel_title": "Opposing activities of IFITM proteins in SARS-CoV-2 infection", + "rel_date": "2020-08-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.11.246678", + "rel_abs": "Interferon-induced transmembrane proteins (IFITMs) restrict infections by many viruses, but a subset of IFITMs enhance infections by specific coronaviruses through currently unknown mechanisms. Here we show that SARS-CoV-2 Spike-pseudotyped virus and genuine SARS-CoV-2 infections are generally restricted by expression of human IFITM1, IFITM2, and IFITM3, using both gain- and loss-of-function approaches. Mechanistically, restriction of SARS-CoV-2 occurred independently of IFITM3 S-palmitoylation sites, indicating a restrictive capacity that is distinct from reported inhibition of other viruses. In contrast, the IFITM3 amphipathic helix and its amphipathic properties were required for virus restriction. Mutation of residues within the human IFITM3 endocytosis-promoting Yxx{Phi} motif converted human IFITM3 into an enhancer of SARS-CoV-2 infection, and cell-to-cell fusion assays confirmed the ability of endocytic mutants to enhance Spike-mediated fusion with the plasma membrane. Overexpression of TMPRSS2, which reportedly increases plasma membrane fusion versus endosome fusion of SARS-CoV-2, attenuated IFITM3 restriction and converted amphipathic helix mutants into strong enhancers of infection. In sum, these data uncover new pro- and anti-viral mechanisms of IFITM3, with clear distinctions drawn between enhancement of viral infection at the plasma membrane and amphipathicity-based mechanisms used for endosomal virus restriction. Indeed, the net effect of IFITM3 on SARS-CoV-2 infections may be a result of these opposing activities, suggesting that shifts in the balance of these activities could be coopted by viruses to escape this important first line innate defense mechanism.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Guoli Shi", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Adam D Kenney", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Elena Kudryashova", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Lizhi Zhang", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Luanne Hall-Stoodley", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Richard Robinson", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Dmitri Kudryashov", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Alex A. S Compton", + "author_inst": "National Cancer Institute" + }, + { + "author_name": "Jacob S Yount", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.08.11.245704", "rel_title": "Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19", @@ -1258968,25 +1262405,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2020.08.06.20169896", - "rel_title": "Prediction of Covid-19 Infections Through December 2020 for 10 US States Using a Two Parameter Transmission Model Incorporating Outdoor Temperature and School Re-Opening Effects", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169896", - "rel_abs": "Covid-19 infection case predictions (total cases) are made for August through December 2020 for 10 US States (NY, WA, GA, IL, MN, FL, OH, MI, CA, and NC). A two-parameter model based on social distance index (SDI) and disease transmission efficiency (G) parameters is used to characterize SARS-CoV-2 disease spread. Current lack of coherent and coordinated US policy causes the US to follow a linear infection growth path with a limit cycle behavior that modulates the US between accelerating and decaying infection growth on either side of a linear growth path boundary.\n\nFour prediction cases are presented:\n\nO_LINo school re-openings; fall season temperature effect\nC_LIO_LINo school re-openings; no fall season temperature effect\nC_LIO_LISchool re-openings; fall season temperature effect\nC_LIO_LISchool re-openings; no fall season temperature effect\nC_LI\n\nFall outdoor temperatures, in contrast to the 1918 pandemic, are predicted to be beneficial for dampening SARS-CoV-2 transmission in States as they pass through \"swing season\" temperature range of 70F to 50F. Physical re-opening of schools in September are predicted to accelerate infections.\n\nStates with low current infectious case numbers (eg, NY) are predicted to be minimally impacted while States with high current infectious case numbers (eg, CA and FL) will be significantly impacted by school re-openings.\n\nUpdated infection predictions will be posted monthly (Sept, Oct, Nov, Dec) with adjustments based on actual trends in SDI and G. Assessments related to outdoor temperature impact, school re-openings, and other public gathering re-openings will be discussed in updated reports.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ty A Newell", - "author_inst": "University of Illinois" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.06.20155804", "rel_title": "Characterization of Israeli COVID-19 Outbreak Drivers and Forecasting Using a Versatile Web App", @@ -1259598,6 +1263016,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.06.20169367", + "rel_title": "Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection", + "rel_date": "2020-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169367", + "rel_abs": "Most individuals infected with SARS-CoV-2 develop neutralizing antibodies that target the viral spike protein. Here we quantify how levels of these antibodies change in the months following SARS-CoV-2 infection by examining longitudinal samples collected between ~30 and 152 days post-symptom onset from a prospective cohort of 34 recovered individuals with asymptomatic, mild, or moderate-severe disease. Neutralizing antibody titers declined an average of about four-fold from one to four months post-symptom onset. This decline in neutralizing antibody titers was accompanied by a decline in total antibodies capable of binding the viral spike or its receptor-binding domain. Importantly, our data are consistent with the expected early immune response to viral infection, where an initial peak in antibody levels is followed by a decline to a lower plateau. Additional studies of long-lived B-cells and antibody titers over longer time frames are necessary to determine the durability of immunity to SARS-CoV-2.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Katharine HD Crawford", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Adam S Dingens", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Rachel Eguia", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Caitlin R Wolf", + "author_inst": "University of Washington" + }, + { + "author_name": "Naomi Wilcox", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Jennifer K Logue", + "author_inst": "University of Washington" + }, + { + "author_name": "Kiel Shuey", + "author_inst": "University of Washington" + }, + { + "author_name": "Amanda M Casto", + "author_inst": "University of Washington" + }, + { + "author_name": "Brooke Fiala", + "author_inst": "University of Washington" + }, + { + "author_name": "Samuel Wrenn", + "author_inst": "University of Washington" + }, + { + "author_name": "Deleah Pettie", + "author_inst": "University of Washington" + }, + { + "author_name": "Neil P King", + "author_inst": "University of Washington" + }, + { + "author_name": "Helen Y Chu", + "author_inst": "University of Washington" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "FRED HUTCHINSON CANCER RESEARCH CENTER" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.03.20167833", "rel_title": "Aerosol Generation from Different Wind Instruments", @@ -1260958,29 +1264447,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.06.20169656", - "rel_title": "Obtaining prevalence estimates of COVID-19: A model to inform decision-making", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169656", - "rel_abs": "ObjectivesThe primary aim was to evaluate whether randomly sampling and testing a set number of individuals for active or past COVID-19 while adjusting for misclassification error captures a simulated prevalence. The secondary aim was to quantify the impact of misclassification error bias on publicly reported case data in Maryland.\n\nMethodsUsing a stratified random sampling approach, 50,000 individuals were selected from a simulated Maryland population to estimate the prevalence of active and past COVID-19. Data from the 2014-2018 and 2018 American Community Surveys were used. The simulated prevalence was 0.5% and 1.0% for active and past COVID-19, respectively. Bayesian models, informed by published validity estimates, were used to account for misclassification error when estimating the prevalence of active and past COVID-19.\n\nResultsFailure to account for misclassification error overestimated the simulated prevalence for active and past COVID-19. Adjustment for misclassification error decreased the point estimate for active and past COVID-19 prevalence by 55% and 29%, respectively. Adjustment for sampling method and misclassification error only captured the simulated past COVID-19 prevalence. The simulated active COVID-19 prevalence was only captured when set to 0.7% and above. Adjustment for misclassification error for publicly reported Maryland data increased the estimated average daily cases by 8%.\n\nConclusionsRandom sampling and testing of COVID-19 is needed but must be accompanied by adjustment for misclassification error to avoid over- or underestimating the prevalence. This approach bolsters disease control efforts. Implementing random testing for active COVID-19 may be best in a smaller geographic area with highly prevalent cases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ida Sahlu", - "author_inst": "MITRE Corporation" - }, - { - "author_name": "Alexander B Whittaker", - "author_inst": "MITRE Corporation" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.06.20169722", "rel_title": "SARS-CoV-2 infection fatality risk in a nationwide seroepidemiological study", @@ -1261312,6 +1264778,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.06.239574", + "rel_title": "Generation of tonsil organoids as an ex vivo model for SARS-CoV-2 infection", + "rel_date": "2020-08-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.06.239574", + "rel_abs": "Palatine tonsil (hereinafter referred to as \"tonsil\") plays role in the immune systems first line of defense against foreign pathogens. Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic since the infection was first reported in China in December 2019. The aim of this study was to establish tonsil epithelial cell-derived organoids and to examine their feasibility as an ex vivo model for SARS-CoV-2 infection. Using an optimized protocol, we achieved 3D tonsil organoid culture from human tonsil tissue that reflects the distinctive characteristics of the tonsil epithelium, such as its cellular composition, histologic properties, and molecular biological features. Notably, we verified that SARS-CoV-2 can infect tonsil organoids with a robust replication efficiency. Furthermore, treatment with remdesivir, an antiviral agent, effectively protected them from viral infection. Therefore, tonsil organoids could be available for investigation of SARS-CoV-2 infection-mediated pathology and for preclinical screening of novel antiviral drug candidates.\n\nOne-sentence SummaryThis study established tonsil epithelial cell-derived organoids and demonstrated their feasibility as an ex vivo model for SARS-CoV-2 infection.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Han Kyung Kim", + "author_inst": "CHA University School of Medicine" + }, + { + "author_name": "Hyeryeon Kim", + "author_inst": "Konkuk University School of Medicine" + }, + { + "author_name": "Myoung Kyu Lee", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Woo Hee Choi", + "author_inst": "CHA University School of Medicine" + }, + { + "author_name": "Yejin Jang", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Jin Soo Shin", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Jun-Yeol Park", + "author_inst": "CHA University School of Medicine" + }, + { + "author_name": "Kang Hyun Kim", + "author_inst": "CHA University School of Medicine" + }, + { + "author_name": "Hyun Wook Han", + "author_inst": "CHA University School of Medicine" + }, + { + "author_name": "Meehyein Kim", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Young Chang Lim", + "author_inst": "Konkuk University School of Medicine" + }, + { + "author_name": "Jongman Yoo", + "author_inst": "CHA University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.06.240796", "rel_title": "Expression of ACE2, TMPRSS2, and CTSL in human airway epithelial cells under physiological and pathological conditions: Implications for SARS-CoV2 infection", @@ -1262592,61 +1266121,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.05.20168971", - "rel_title": "Features and Functions of Systemic and Mucosal Humoral Immunity Among SARS-CoV-2 Convalescent Individuals", - "rel_date": "2020-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168971", - "rel_abs": "Understanding humoral immune responses to SARS-CoV-2 infection will play a critical role in the development of vaccines and antibody-based interventions. We report systemic and mucosal antibody responses in convalescent individuals who experienced varying disease severity. Robust antibody responses to diverse SARS-CoV-2 antigens and evidence of elevated responses to endemic CoV were observed among convalescent donors. SARS-CoV-2-specific IgA and IgG responses were often negatively correlated, particularly in mucosal samples, suggesting subject-intrinsic biases in isotype switching. Assessment of antibody-mediated effector functions revealed an inverse correlation between systemic and mucosal neutralization activity and site-dependent differences in the isotype of neutralizing antibodies. Serum neutralization correlated with systemic anti-SARS-CoV-2 IgG and IgM response magnitude, while mucosal neutralization was associated with nasal SARS-CoV-2-specific IgA. These findings begin to map how diverse Ab characteristics relate to Ab functions and outcomes of infection, informing public health assessment strategies and vaccine development efforts.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Savannah E Butler", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Andrew R Crowley", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Harini Natarajan", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Shiwei Xu", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Joshua A Weiner", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Jiwon Lee", - "author_inst": "Dartmouth College" - }, - { - "author_name": "Wendy F Wieland-Alter", - "author_inst": "Dartmouth-Hitchcock Medical Center" - }, - { - "author_name": "Ruth I Connor", - "author_inst": "Dartmouth-Hitchcock Medical Center" - }, - { - "author_name": "Peter F Wright", - "author_inst": "Dartmouth-Hitchcock Medical Center" - }, - { - "author_name": "Margaret E Ackerman", - "author_inst": "Dartmouth College" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.05.20168948", "rel_title": "Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens", @@ -1263026,6 +1266500,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.04.20168450", + "rel_title": "Social Behaviors Associated with a Positive COVID-19 Test Result", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20168450", + "rel_abs": "ObjectiveTo compare behaviors of individuals who tested positive for COVID-19 relative to non-infected individuals.\n\nMethodsWe sent COVID positive cases and age/gender matched controls a survey regarding their social behaviors via MyChart (online patient portal). We called cases if they did not complete the electronic survey within two days. Data was collected from May-June 2020. Survey responses for cases without a close contact and controls were compared using Pearson chi-square or Fishers Exact tests as appropriate.\n\nResultsA total of 339 participants completed the survey (113 cases, 226 controls); 45 (40%) cases had known contact with COVID-19. Cases were more likely to have recently traveled (4% vs. 0%, p=0.01) or to work outside the home (40% vs. 25%, p=0.02). There was no difference in the rates of attending private or public gatherings, mask/glove use, hand-washing, cleaning surfaces and cleaning mail/groceries between cases and controls.\n\nConclusionsSixty percent of cases had no known contact with COVID-19, indicating ongoing community transmission and underlining the importance of contact tracing. The greater percentage of cases who work outside the home provides further evidence for social distancing.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sidra Speaker", + "author_inst": "Cleveland Clinic Lerner College of Medicine of Case Western Reserve University" + }, + { + "author_name": "Christine Marie Doherty", + "author_inst": "Cleveland Clinic Lerner College of Medicine of Case Western Reserve University" + }, + { + "author_name": "Elizabeth R Pfoh", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Aaron Dunn", + "author_inst": "Cleveland Clinic Lerner College of Medicine of Case Western Reserve University" + }, + { + "author_name": "Bryan Hair", + "author_inst": "Cleveland Clinic Lerner College of Medicine of Case Western Reserve University" + }, + { + "author_name": "Victoria Shaker", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Lynn Daboul", + "author_inst": "Cleveland Clinic Lerner College of Medicine of Case Western Reserve University" + }, + { + "author_name": "Michael B Rothberg", + "author_inst": "Cleveland Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.04.20168468", "rel_title": "Extended lifetime of respiratory droplets in a turbulent vapour puff and its implications on airborne disease transmission", @@ -1264582,57 +1268103,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.05.237339", - "rel_title": "Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein (N protein) and its consequences", - "rel_date": "2020-08-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.05.237339", - "rel_abs": "The emerging novel coronavirus SARS-CoV-2 has created a global confusing pandemic health crisis that warrants an accurate and detailed characterization of the rapidly evolving viral genome for understanding its epidemiology, pathogenesis and containment. We explored 61,485 sequences of the Nucleocapsid (N) protein, a potent diagnostic and prophylactic target, for identifying the mutations to review their roles in RT-PCR based diagnosis and observe consequent impacts. Compared to the Wuhan reference strain, a total of 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n=30,221) globally. Of these mutations, 367 occupy primer binding sites including 3-end mismatch to primer-pair of 11 well characterized primer sets. Noteworthy, CDC (USA) recommended N2 primer set contained lower mismatch than the other primer sets. Moreover, 684 amino acid (aa) substitutions located across 317 (75.66% of total aa) unique positions including 82, 21, and 83 of those in RNA binding N-terminal domain (NTD), SR-rich region, and C-terminal dimerization domain (CTD), respectively. Moreover, 11 in-frame deletions were revealed, mostly (n =10) within the highly flexible linker region, and the rest within the NTD region. Furthermore, we predicted the possible consequences of high-frequency mutations ([≥] 20) and deletions on the tertiary structure of the N protein. Remarkably, we observed that high frequency (67.94% of mutated sequences) coevolving mutations (R203K and G204R) destabilized and decreased overall structural flexibility. Despite being proposed as the alternate target to spike protein for vaccine and therapeutics, ongoing nonsynonymous evolution of the N protein may challenge the endeavors, thus need further immunoinformatics analyses. Therefore, continuous monitoring is required for tracing the ongoing evolution of the SARS-CoV-2 N protein in prophylactic and diagnostic interventions.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "M. Shaminur Rahman", - "author_inst": "Dhaka University" - }, - { - "author_name": "M. Rafiul Islam", - "author_inst": "Dhaka University" - }, - { - "author_name": "A. S. M. Rubayet Ul Alam", - "author_inst": "Jashore University of Science and Technology" - }, - { - "author_name": "Israt Islam", - "author_inst": "Dhaka University" - }, - { - "author_name": "M. Nazmul Hoque", - "author_inst": "Dhaka university" - }, - { - "author_name": "Salma Akter", - "author_inst": "Dhaka University" - }, - { - "author_name": "Md. Mizanur Rahaman", - "author_inst": "Dhaka University" - }, - { - "author_name": "Munawar Sultana", - "author_inst": "Dhaka University" - }, - { - "author_name": "M. Anwar Hossain", - "author_inst": "Dhaka University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.08.05.237404", "rel_title": "Analysis of single nucleotide polymorphisms between 2019-nCoV genomes and its impact on codon usage", @@ -1265024,6 +1268494,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.08.05.238386", + "rel_title": "Identification of SARS-CoV-2 recombinant genomes", + "rel_date": "2020-08-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.05.238386", + "rel_abs": "Viral recombination can generate novel genotypes with unique phenotypic characteristics, including transmissibility and virulence. Although the capacity for recombination among betacoronaviruses is well documented, there is limited evidence of recombination between SARS-CoV-2 strains. By identifying the mutations that primarily determine SARS-CoV-2 clade structure, we developed a lightweight approach for detecting recombinant genomes. Among the over 537,000 genomes queried, we detect 1175 putative recombinants that contain multiple mutational markers from distinct clades. Additional phylogenetic analysis and the observed co-circulation of predicted parent clades in the geographic regions of exposure further support the feasibility of recombination in these detected cases. An analysis of these detected cases did not reveal any evidence for recombination hotspots in the SARS-CoV-2 genome. Although most recombinant genotypes were detected a limited number of times, at least two recombinants are now widely transmitted. Recombinant genomes were also found to contain substitutions of concern for elevated transmissibility and lower vaccine efficacy, including D614G, N501Y, E484K, and L452R. Adjusting for an unequal probability of detecting recombinants derived from different parent clades, and for geographic variation in clade abundance, we estimate that at most 5% of circulating viruses in the USA and UK are recombinant. While the phenotypic characterization of detected recombinants was beyond the scope of our analysis, the identification of transmitted recombinants involving substitutions of concern underscores the need to sustain efforts to monitor the emergence of new genotypes generated through recombination.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "David VanInsberghe", + "author_inst": "Emory University" + }, + { + "author_name": "Andrew S Neish", + "author_inst": "Emory University" + }, + { + "author_name": "Anice C Lowen", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Katia Koelle", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.08.05.238618", "rel_title": "Analysis of the potential impact of genomic variants in SARS-CoV-2 genomes from India on molecular diagnostic assays", @@ -1266752,137 +1270253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.31.20165126", - "rel_title": "A longitudinal survey for genome-based identification of SARS-CoV-2 in sewage water in selected lockdown areas of Lahore city, Pakistan; a potential approach for future smart lockdown strategy", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20165126", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has affected more than 15 million people and, as of 22 July 2019, caused deaths of more than 0.6 million individuals globally. With the excretion of SARS-CoV-2 in the stool of symptomatic and asymptomatic COVID-19 patients, its genome detection in the sewage water can be used as a powerful epidemiological tool to predict the number of positive cases in a population. This study was conducted to detect SARS-CoV-2 genome in sewage water during the lockdown. Sewage samples, from 28 pre-selected sites, were collected on alternate days from 13-25 July, 2020 from two selected areas [Johar Town (n = 05) and Township (n = 23)], where smart lockdown were implemented by the government authorities on 9th July, 2020. Genomic RNA was extracted and the SARS-CoV-2 was detected and quantified using commercially available kit through Real-Time PCR. Out of 28, sixteen samples were positive on day one while 19, 17, 23, 17, 05 and 09 samples were positive on day 3, 5, 7, 9, 11, and 13, respectively. Results revealed a decreased positivity rate and SARS CoV-2 genome copies in sewage towards the end of lockdown however few sampling sites did not follow a clear pattern indicating the complexities in sewage water based surveillance i.e time of sampling etc. Hourly sampling from two sites for 24 hours also revealed the impact of sampling time on detection of SARS-CoV-2 genome in sewage. Results of current study insinuate a possible role of sewage-based COVID-19 surveillance in monitoring and execution of smart lockdowns.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Tahir Yaqub", - "author_inst": "University of Veterinary and Animal Sciences" - }, - { - "author_name": "Muhammad Nawaz", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Zubair Shabbir", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Asad Ali", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Imran Altaf", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Sohail Raza", - "author_inst": "University of Veterinary and Animal Sciences, Lahore" - }, - { - "author_name": "Muhammad Abu Bakr Shabbir", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Adnan Ashraf", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Syed Zahid Aziz", - "author_inst": "Water and Sanitation Agency, Lahore-Pakistan" - }, - { - "author_name": "Sohail Qadir Cheema", - "author_inst": "Water and Sanitation Agency, Lahore-Pakistan" - }, - { - "author_name": "Muhammad Bilal Shah", - "author_inst": "Water and Sanitation Agency, Lahore-Pakistan" - }, - { - "author_name": "Sohail Hassan", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Saira Rafique", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Nageen Sardar", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Adnan Mehmood", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Waqar Aziz", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Sehar Fazal", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Nadir Khan", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Tahir Khan", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Moavia Attique", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Ali Asif", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Muhammad Anwar", - "author_inst": "University of Veterinary and Animal Sciences Lahore, Pakistan" - }, - { - "author_name": "Nabeel Ahmad Awan", - "author_inst": "Specialized Healthcare & Medical Education Department, Punjab, Pakistan" - }, - { - "author_name": "Muhammad Usman Younis", - "author_inst": "Primary and Secondary Healthcare Department, Punjab-Pakistan" - }, - { - "author_name": "Muhammad Ajmal Bhatti", - "author_inst": "Primary and Secondary Healthcare Department, Punjab-Pakistan" - }, - { - "author_name": "Zarfishan Tahir", - "author_inst": "Institute of Public Health, Lahore-Pakistan" - }, - { - "author_name": "Nadia Mukhtar", - "author_inst": "Institute of Public Health, Lahore-Pakistan" - }, - { - "author_name": "Huda Sarwar", - "author_inst": "Institute of Public Health, Lahore-Pakistan" - }, - { - "author_name": "Maaz Sohail Rana", - "author_inst": "Institute of Public Health, Lahore-Pakistan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.31.20165480", "rel_title": "Clinical course and severity outcome indicators among COVID 19 hospitalized patients in relation to comorbidities distribution Mexican cohort", @@ -1267106,6 +1270476,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.31.20166249", + "rel_title": "Reconciling epidemiological models with misclassified case-counts for SARS-CoV-2 with seroprevalence surveys: A case study in Delhi, India", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20166249", + "rel_abs": "Underreporting of COVID-19 cases and deaths is a hindrance to correctly modeling and monitoring the pandemic. This is primarily due to limited testing, lack of reporting infrastructure and a large number of asymptomatic infections. In addition, diagnostic tests (RT-PCR tests for detecting current infection) and serological antibody tests for IgG (to assess past infections) are imperfect. In particular, the diagnostic tests have a high false negative rate. Epidemiologic models with a latent compartment for unascertained infections like the Susceptible-Exposed-Infected-Removed (SEIR) models can provide predictions for unreported cases and deaths under certain assumptions. Typically, the number of unascertained cases is unobserved and thus we cannot validate these estimates for a real study except for simulation studies. Population-based seroprevalence studies can provide a rough estimate of the total number of infections and help us check epidemiologic model projections. In this paper, we develop a method to account for high false negative rates in RT-PCR in an extension to the classic SEIR model. We apply this method to Delhi, the national capital region of India, with a population of 19.8 million and a COVID-19 hotspot of the country, obtaining estimates of underreporting factor for cases at 34-53 times and that for deaths at 8-13 times. Based on a recently released serological survey for Delhi with an estimated 22.86% seroprevalence, we compute adjusted estimates of the true number of infections reported by the survey (after accounting for misclassification of the antibody test results) which is largely consistent with the model outputs, yielding an underreporting factor for cases from 30-42. Together with the model and the serosurvey, this implies approximately 96-98% cases in Delhi remained unreported and whereas only 109,140 cases were reported on July 10, the true number of infections varied somewhere between 4.4-4.6 million across different estimates. While repeated serological monitoring is resource intensive, model-based adjustments, run with the most up to date data, can provide a viable option to keep track of the unreported cases and deaths and gauge the true extent of transmission of this insidious virus.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Rupam Bhattacharyya", + "author_inst": "University of Michigan, Ann Arbor" + }, + { + "author_name": "Ritwik Bhaduri", + "author_inst": "Indian Statistical Institute, Kolkata" + }, + { + "author_name": "Ritoban Kundu", + "author_inst": "Indian Statistical Institute, Kolkata" + }, + { + "author_name": "Maxwell Salvatore", + "author_inst": "University of Michigan, Ann Arbor" + }, + { + "author_name": "Bhramar Mukherjee", + "author_inst": "University of Michigan, Ann Arbor" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.31.20165019", "rel_title": "A throughput serological Western blot system using whole virus lysate for the concomitant detection of antibodies against SARS-CoV-2 and human endemic Coronaviridae", @@ -1268294,33 +1271699,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.03.20167692", - "rel_title": "COVID-19 pandemic in Djibouti: epidemiology and the response strategy followed to contain the virus during the first two months, 17 March to 16 May 2020", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167692", - "rel_abs": "BackgroundFirst cases of COVID-19 were reported from Wuhan, China, in December 2019, and it progressed rapidly. On 30 January, WHO declared the new disease as a PHEIC, then as a Pandemic on 11 March. By mid-March, the virus spread widely; Djibouti was not spared and was hit by the pandemic with the first case detected on 17 March. Djibouti worked with WHO and other partners to develop a preparedness and response plan, and implemented a series of intervention measures. MoH together with its civilian and military partners, closely followed WHO recommended strategy based on four pillars: testing, isolating, early case management, and contact tracing. From 17 March to 16 May, Djibouti performed the highest per capita tests in Africa and isolated, treated and traced the contacts of each positive case, which allowed for a rapid control of the epidemic.\n\nMethodsCOVID-19 data included in this study was collected through MoH Djibouti during the period from 17 March to 16 May 2020.\n\nResultsA total of 1,401 confirmed cases of COVID-19 were included in the study with 4 related deaths (CFR: 0.3%) and an attack rate of 0.15%. Males represented (68.4%) of the cases, with the age group 31-45 years old (34.2%) as the most affected. Djibouti conducted 17,532 tests, and was considered as a champion for COVID-19 testing in Africa with 18.2 tests per 1000 habitant. All positive cases were isolated, treated and had their contacts traced, which led to early and proactive diagnosis of cases and in turn yielded up to 95-98% asymptomatic cases. Recoveries reached 69% of the infected cases with R0 (0.91). The virus was detected in 4 regions in the country, with the highest percentage in the capital (83%).\n\nConclusionDjibouti responded to COVID-19 pandemic following an efficient and effective strategy, using a strong collaboration between civilian and military health assets that increased the response capacities of the country. Partnership, coordination, solidarity, proactivity and commitment were the pillars to confront COVID-19 pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mohamed Elhakim", - "author_inst": "World Health Organization" - }, - { - "author_name": "Saleh Banoita Tourab", - "author_inst": "Ministry of Health Djibouti" - }, - { - "author_name": "Ahmed Zouiten", - "author_inst": "World Health Organization" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.03.20167189", "rel_title": "Evaluating Data-Driven Forecasting Methods for Predicting SARS-CoV2 Cases: Evidence From 173 Countries", @@ -1268512,6 +1271890,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.07.31.20166272", + "rel_title": "Sooner than you think: a very early affective reaction to the COVID-19 pandemic and quarantine in Argentina", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20166272", + "rel_abs": "The unique circumstances created by the COVID-19 pandemic pose serious challenges to mood stability and emotional regulation at all ages. Although many people tend to react resiliently to stress, others appear to display emotional anxiety and depression-related symptoms. In this study, we carried out a survey (N = 10,053) during the first week of the general lockdown (quarantine) in Argentina to measure early affective reactions in Argentine adults. Respondents showed substantial anxious and depressive symptoms, with 33 % and 23% of participants reporting possible depressive and anxious syndromes, respectively, with the youngest group (18 to 25 y.o.) showing the highest prevalence of symptoms. Even if prior mental health problems predisposed or aggravated the reaction, participants without prior complaints showed signs of psychological impact. Using linear regression, the most important independent variables related to depressive symptoms was the feeling of loneliness followed by daily stress. In the case of anxious states, the strongest variables were negative repetitive thinking and feeling of loneliness. Other psychological, economic, and social factors are discussed.\n\nThis study is in line with previous literature that highlight the importance of the psychological impact of pandemics, but additionally demonstrates that these reactions are present at a large scale immediately after the start of quarantine with very low infectious rates as an early anticipatory adaptive reaction leading to potential negative outcomes from adjustment disorders to major disorders. In addition, the present results provide potentially relevant information about sudden environmental impacts on affective states and specific pathways for anxiety and depression to be expressed. We end by discussing implications for public policy based on considering the most vulnerable groups.\n\nKey FindingsO_LIMore than a third of the studied sample (n = 10,053) showed substantial depressive and anxious symptoms between 5 and 7 days after the start of the national quarantine.\nC_LIO_LI33.7% of the sample scored above the PHQ-9 cutoff for possible diagnosis of a depressive disorder and 23.2% for an anxiety disorder.\nC_LIO_LI28.6% of the participants showed moderate and severe levels of depressive symptoms and 23.2% showed moderate and severe levels of anxiety.\nC_LIO_LIThe youngest participants were affected the most by the situation.\nC_LIO_LIThe most important factor related to depressive symptoms was the feeling of loneliness followed by daily stress.\nC_LIO_LIThe most important factor related to anxious states was negative repetitive thinking followed by feeling of loneliness.\nC_LIO_LIThe existence of previous mental health difficulties aggravated the reactions, but even people who had not sought out treatment previously showed signs of psychological impact.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Fernando Torrente", + "author_inst": "Institute of Neuroscience and Public Policy, INECO Foundation" + }, + { + "author_name": "Adrian Ezequiel Yoris", + "author_inst": "Institute of Cognitive and Translational Neurosciences (INECO Foundation-Favaloro University-CONICET)" + }, + { + "author_name": "Daniel Low", + "author_inst": "Program in Speech and Hearing Bioscience and Technology, Harvard Medical School & MIT" + }, + { + "author_name": "Pablo Lopez", + "author_inst": "Institute of Cognitive and Translational Neurosciences (INECO Foundation-Favaloro University-CONICET)" + }, + { + "author_name": "Pedro Bekinschtein", + "author_inst": "Institute of Cognitive and Translational Neurosciences (INECO Foundation-Favaloro University-CONICET)" + }, + { + "author_name": "Marcelo Cetkovich", + "author_inst": "Institute of Cognitive and Translational Neurosciences (INECO Foundation-Favaloro University-CONICET)" + }, + { + "author_name": "Facundo Manes", + "author_inst": "Institute of Cognitive and Translational Neurosciences (INECO Foundation-Favaloro University-CONICET)" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.08.01.20162115", "rel_title": "A Study on Survival Scenario of COVID-19 patients in India: An Application of Survival Analysis on patient demographics", @@ -1269924,45 +1273345,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.03.20167262", - "rel_title": "Altitude as a protective factor from COVID-19", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167262", - "rel_abs": "The COVID-19 pandemic had a delayed onset in South America compared to Asia (outside of China), Europe or North America. In spite of the presumed time advantage for the implementation of preventive measures to help contain its spread, the pandemic in that region followed growth rates that paralleled, and currently exceed, those observed several weeks before in Europe. Indeed, in early August 2020, many countries in South and Central America presented among the highest rates in the world of COVID-19 confirmed cases and deaths per million inhabitants. Here, we have taken an ecological approach to describe the current state of the pandemic in Peru and its dynamics. Our analysis supports a protective effect of altitude from COVID-19 incidence and mortality. Further, we provide circumstantial evidence that internal migration through a specific land route is a significant factor progressively overriding the protection from COVID-19 afforded by high altitude. Finally, we show that protection by altitude is independent of poverty indexes and is inversely correlated with the prevalence in the population of risk factors associated with severe COVID-19, including hypertension and hypercholesterolemia. We discuss long-term multisystemic adaptive traits to hypobaric hypoxia as possible mechanisms that may explain the observed protective effect of high altitude from death due to COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Timothy M Thomson", - "author_inst": "Institute for Molecular Biology, IBMB-CSIC" - }, - { - "author_name": "Fresia Casas", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Harold Andre Guerrero", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "R\u00f3mulo Figueroa-Mujica", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Francisco C Villafuerte", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Claudia Machicado", - "author_inst": "Universidad Peruana Cayetano Heredia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.03.20167403", "rel_title": "The mental health and experiences of discrimination of LGBTQ+ people during the COVID-19 pandemic: Initial findings from the Queerantine Study", @@ -1270274,6 +1273656,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.08.04.20167932", + "rel_title": "Viral cultures for COVID-19 infectivity assessment. Systematic review", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20167932", + "rel_abs": "Objectiveto review the evidence from studies comparing SARS-CoV-2 culture, the best indicator of current infection and infectiousness with the results of reverse transcriptase polymerase chain reaction (RT-PCR).\n\nMethodsWe searched LitCovid, medRxiv, Google Scholar and the WHO Covid-19 database for Covid-19 using the terms viral culture or viral replication and associated synonyms up to 10 September 2020. We carried out citation matching and included studies reporting attempts to culture or observe SARS-CoV-2 matching with cutoffs for RT-PCR positivity. One reviewer extracted data for each study and a second reviewer checked end edited the extraction and summarised the narratively by sample: fecal, respiratory, environment or mixed.\n\nWhere necessary we wrote to corresponding authors of the included or background papers for additional information. We assessed quality using a modified QUADAS 2 risk of bias tool.\n\nThis review is part of an Open Evidence Review on Transmission Dynamics of COVID-19. Summaries of the included studies and the protocol (v1) are available at: https://www.cebm.net/evidence-synthesis/transmission-dynamics-of-covid-19/. Searches are updated every 2 weeks. This is the fourth version of this review that was first published on the 4th of August and updated on the 21t of August\n\nResultsWe included 29 studies reporting culturing or observing tissue invasion by SARS-CoV in sputum, naso or oropharyngeal, urine, stool, blood and environmental samples from patients diagnosed with Covid-19. The data are suggestive of a relation between the time from collection of a specimen to test, cycle threshold and symptom severity. The quality of the studies was moderate with lack of standardised reporting.\n\nTwelve studies reported that Ct values were significantly lower and log copies higher in samples producing live virus culture. Five studies reported no growth in samples based on a Ct cut-off value. These values ranged from CT > 24 for no growth to Ct [≥] 34. Two studies report a strong relationship between Ct value and ability to recover infectious virus and that the odds of live virus culture reduced by 33% for every one unit increase in Ct. A cut-off RT-PCR Ct > 30 was associated with non-infectious samples. One study that analysed the NSP, N and E gene fragments of the PCR result reported different cut-off thresholds depending on the gene fragment analysed. The duration of RNA shedding detected by PCR was far longer compared to detection of live culture. Six out of eight studies reported RNA shedding for longer than 14 days. Yet, infectivity declines after day 8 even among cases with ongoing high viral loads. A very small proportion of people re-testing positive after hospital discharge or with high Ct are likely to be infectious.\n\nConclusionProspective routine testing of reference and culture specimens are necessary for each country involved in the pandemic to establish the usefulness and reliability of PCR for Covid-19 and its relation to patients factors. Infectivity is related to the date of onset of symptoms and cycle threshold level.\n\nA binary Yes/No approach to the interpretation RT-PCR unvalidated against viral culture will result in false positives with possible segregation of large numbers of people who are no longer infectious and hence not a threat to public health.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tom Jefferson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Elizabeth Spencer", + "author_inst": "Centre for Evidence Based Medicine, University of Oxford" + }, + { + "author_name": "Jon Brassey", + "author_inst": "Trip Database Ltd" + }, + { + "author_name": "Carl Heneghan", + "author_inst": "Centre for Evidence Based Medicine, University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.01.20166678", "rel_title": "Aprepitant as a combinant with Dexamethasone reduces the inflammation via Neurokinin 1 Receptor Antagonism in severe to critical Covid-19 patients and potentiates respiratory recovery: A novel therapeutic approach", @@ -1271825,25 +1275238,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.30.20165035", - "rel_title": "Modified SIR-model applied to covid-19, similarity solutions and projections to further development", - "rel_date": "2020-08-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165035", - "rel_abs": "The SIR-model is adapted to the covid-19 pandemic through a modification that consists in making the basic reproduction number variable. Independent of it, another reproduction number is introduced, which is defined similarly to the usual net reproduction number. Due to its simple analytic form, it enables a clear interpretation for all values. A further parameter, provisionally called acceleration parameter, is introduced and applied, which enables a more differentiated characterization of the infection number dynamics. By a variable transformation the 3 equations of the modified SIR-model can be reduced to 2. The latter are solved up to ordinary integrations. The solutions are evaluated for current situations, yielding a pretty good match with the data reported. Encouraged by this, a variety of possible future developments is examined, including linear and exponential growth of the infection numbers as well as sub- and super-exponential growth. In particular, the behavior of the two reproduction numbers and the acceleration parameter is studied, which in some cases leads to surprising results. With regard to the number of unreported infections it is shown, that from the solution for a special one solutions for others can be derived by similarity transformations.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Eckhard Rebhan", - "author_inst": "Heinrich Heine Universitaet Duesseldorf" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.02.233510", "rel_title": "Mechanism of duplex unwinding by coronavirus nsp13 helicases", @@ -1272331,6 +1275725,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.03.234559", + "rel_title": "SARS-CoV-2 ORF6 disrupts nucleocytoplasmic transport through interactions with Rae1 and Nup98", + "rel_date": "2020-08-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.03.234559", + "rel_abs": "RNA viruses that replicate in the cytoplasm often disrupt nucleocytoplasmic transport to preferentially translate their own transcripts and prevent host antiviral responses. The Sarbecovirus accessory protein ORF6 has previously been shown to be the major inhibitor of interferon production in both SARS-CoV and SARS-CoV-2. SARS-CoV-2 ORF6 was recently shown to co-purify with the host mRNA export factors Rae1 and Nup98. Here, we demonstrate SARS-CoV-2 ORF6 strongly represses protein expression of co-transfected reporter constructs and imprisons host mRNA in the nucleus, which is associated with its ability to co-purify with Rae1 and Nup98. These protein-protein interactions map to the C-terminus of ORF6 and can be abolished by a single amino acid mutation in Met58. Overexpression of Rae1 restores reporter expression in the presence of SARS-CoV-2 ORF6. We further identify an ORF6 mutant containing a 9-amino acid deletion, ORF6 {Delta}22-30, in multiple SARS-CoV-2 clinical isolates that can still downregulate the expression of a co-transfected reporter and interact with Rae1 and Nup98. SARS-CoV ORF6 also interacts with Rae1 and Nup98. However, SARS-CoV-2 ORF6 more strongly co-purifies with Rae1 and Nup98 and results in significantly reduced expression of reporter proteins compared to SARS-CoV ORF6, a potential mechanism for the delayed symptom onset and pre-symptomatic transmission uniquely associated with the SARS-CoV-2 pandemic.\n\nImportanceSARS-CoV-2, the causative agent of COVID-19, is an RNA virus with a large genome that encodes accessory proteins. While these accessory proteins are not required for growth in vitro, they can contribute to the pathogenicity of the virus. One of SARS-CoV-2s accessory proteins, ORF6, was recently shown to co-purify with two host proteins, Rae1 and Nup98, involved in mRNA nuclear export. We demonstrate SARS-CoV-2 ORF6 interaction with these proteins is associated with reduced expression of a reporter protein and accumulation of poly-A mRNA within the nucleus. SARS-CoV ORF6 also shows the same interactions with Rae1 and Nup98. However, SARS-CoV-2 ORF6 more strongly represses reporter expression and co-purifies with Rae1 and Nup98 compared to SARS-CoV ORF6. The ability of SARS-CoV-2 ORF6 to more strongly disrupt nucleocytoplasmic transport than SARS-CoV ORF6 may partially explain critical differences in clinical presentation between the two viruses.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Amin Addetia", + "author_inst": "University of Washington" + }, + { + "author_name": "Nicole A.P. Lieberman", + "author_inst": "University of Washington" + }, + { + "author_name": "Quynh Phung", + "author_inst": "University of Washington" + }, + { + "author_name": "Hong Xie", + "author_inst": "University of Washington" + }, + { + "author_name": "Pavitra Roychoudhury", + "author_inst": "University of Washington" + }, + { + "author_name": "Michelle A Loprieno", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Meeili Huang", + "author_inst": "University of Washington" + }, + { + "author_name": "Lasata Shrestha", + "author_inst": "University of Washington" + }, + { + "author_name": "Keith R. Jerome", + "author_inst": "University of WA/Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.02.233536", "rel_title": "Cross-neutralization of a SARS-CoV-2 antibody to a functionally conserved site is mediated by avidity", @@ -1273931,81 +1277380,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.30.20165068", - "rel_title": "Outpatient screening of health status and lifestyle among post-bariatric patients during the Covid-19 pandemic in Sao Paulo, Brazil.", - "rel_date": "2020-08-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165068", - "rel_abs": "Background/ObjectivesThis was an out-of-hospital screening of health status and lifestyle during the Covid-19 pandemic in post-operative bariatric patients from Sao Paulo, Brazil, prevented from face-to-face health care.\n\nSubjects/MethodsIn this cross-sectional study, 66 patients were remotely (via phone call) and in-person (by home visit) assessed for health status and lifestyle habits. Results: Mean age was 47.4 years. Patients were obese grade I (30.0%), II (22.0%), and III (30.0%), and 94.2% had above reference waist circumference values. Sixty-four percent displayed high blood pressure, whereas 24% showed CRP levels above normal range. Nineteen percent of patients reported irregular use of nutritional supplementation and 6.0% reported binge eating habits. Thirty-three exhibited symptoms of depression. Mild-to-moderate and moderate-to-severe anxiety symptoms were reported by 27.4% and 11.3% of the patients; 4.5% exhibited suicidal ideation and were referred to a specialist for healthcare. Of relevance, inactive patients (59.6%) had poorer global mental and physical health scores as compared to active peers (both p<0.05). Conclusion: This out-of-hospital screening revealed that the absence of face-to-face health care due to the Covid-19 pandemic is associated with suboptimal status of physical and mental health as well as lifestyle inadequacies among patients who have recently undergone bariatric surgery.\n\nKey pointsO_LIWe performed an out-of-hospital screening in post-operative bariatric patients prevented from face-to-face health care during the Covid-19 pandemic.\nC_LIO_LISixty-five percent displayed high blood pressure, whereas 24% showed C-reactive protein levels above normal range.\nC_LIO_LIAbout one third showed mild to severe symptoms of depression, whereas [~]40% showed mild to severe anxiety symptoms.\nC_LIO_LIInactive patients (59.6%) had poorer global mental and physical health scores as compared to active peers.\nC_LIO_LIThree patients exhibited suicidal ideation and were referred to a specialist for healthcare.\nC_LIO_LIDuring the Covid-19 pandemic, there are a considerable number of post-bariatric patients in need of direct health care.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Karla Fabiana Goessler", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Carolina Ferreira Nicoletti", - "author_inst": "Univeristy of Sao Paulo" - }, - { - "author_name": "Diego Augusto Nunes Rezende", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Sofia Mendes Sieczkowska", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Gabriel Perri Esteves", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Rafael Genario", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Gersiel Nascimento Oliveira-Junior", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Kamila Meireles", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Ana Jessica Pinto", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Michele Nakahara-Melo", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Roberto Cleva", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Marco Aurelio Santo", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "John Kirwan", - "author_inst": "Pennington Biomedical Research Center" - }, - { - "author_name": "Hamilton Roschel", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Bruno Gualano", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2020.07.30.20165282", "rel_title": "A Compartmental Epidemic Model Incorporating Probable Cases to Model COVID-19 Outbreak in Regions with Limited Testing Capacity", @@ -1274341,6 +1277715,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.29.20164590", + "rel_title": "Household transmission of SARS-CoV-2: a systematic review and meta-analysis of secondary attack rate", + "rel_date": "2020-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164590", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spread by direct, indirect, or close contact with infected people via infected respiratory droplets or saliva. Crowded indoor environments with sustained close contact and conversations are a particularly high-risk setting.\n\nMethodsWe performed a meta-analysis through July 29, 2020 of SARS-CoV-2 household secondary attack rate (SAR), disaggregating by several covariates (contact type, symptom status, adult/child contacts, contact sex, relationship to index case, index case sex, number of contacts in household, coronavirus).\n\nFindingsWe identified 40 relevant published studies that report household secondary transmission. The estimated overall household SAR was 18{middle dot}8% (95% confidence interval [CI]: 15{middle dot}4%-22{middle dot}2%), which is higher than previously observed SARs for SARS-CoV and MERS-CoV. We observed that household SARs were significantly higher from symptomatic index cases than asymptomatic index cases, to adult contacts than children contacts, to spouses than other family contacts, and in households with one contact than households with three or more contacts.\n\nInterpretationTo prevent the spread of SARS-CoV-2, people are being asked to stay at home worldwide. With suspected or confirmed infections referred to isolate at home, household transmission will continue to be a significant source of transmission.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Zachary J. Madewell", + "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" + }, + { + "author_name": "Yang Yang", + "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" + }, + { + "author_name": "Ira M. Longini Jr.", + "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" + }, + { + "author_name": "M. Elizabeth Halloran", + "author_inst": "Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Biostatistics, University of Washington, Seattle, WA" + }, + { + "author_name": "Natalie E. Dean", + "author_inst": "Department of Biostatistics, University of Florida, Gainesville, FL" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.29.20164699", "rel_title": "COVID-19 Recurrent Varies with Different Combinatorial Medical Treatments Determined by Machine Learning Approaches", @@ -1275853,65 +1279262,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.30.20164327", - "rel_title": "Self-rated smell ability enables highly specific predictors of COVID-19 status: a case control study in Israel", - "rel_date": "2020-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20164327", - "rel_abs": "BackgroundClinical diagnosis of COVID-19 poses an enormous challenge to early detection and prevention of COVID-19, which is of crucial importance for pandemic containment. Cases of COVID-19 may be hard to distinguish clinically from other acute viral diseases, resulting in an overwhelming load of laboratory screening. Sudden onset of taste and smell loss emerge as hallmark of COVID-19. The optimal ways for including these symptoms in the screening of suspected COVID-19 patients should now be established.\n\nMethodsWe performed a case-control study on patients that were PCR-tested for COVID-19 (112 positive and 112 negative participants), recruited during the first wave (March 2020 - May 2020) of COVID-19 pandemic in Israel. Patients were interviewed by phone regarding their symptoms and medical history and were asked to rate their olfactory and gustatory ability before and during their illness on a 1-10 scale. Prevalence and degrees of symptoms were calculated, and odds ratios were estimated. Symptoms-based logistic-regression classifiers were constructed and evaluated on a hold-out set.\n\nResultsChanges in smell and taste occurred in 68% (95% CI 60%-76%) and 72% (64%-80%), of positive patients, with 24 (11-53 range) and 12 (6-23) respective odds ratios. The ability to smell was decreased by 0.5{+/-}1.5 in negatives, and by 4.5{+/-}3.6 in positives, and to taste by 0.4{+/-}1.5 and 4.9{+/-}3.8, respectively (mean {+/-} SD). A penalized logistic regression classifier based on 5 symptoms (degree of smell change, muscle ache, lack of appetite, fever, and a negatively contributing sore throat), has 66% sensitivity, 97% specificity and an area under the ROC curve of 0.83 (AUC) on a hold-out set. A classifier based on degree of smell change only is almost as good, with 66% sensitivity, 97% specificity and 0.81 AUC. Under the assumption of 8% positives among those tested, the predictive positive value (PPV) of this classifier is 0.68 and negative predictive value (NPV) is 0.97.\n\nConclusionsSelf-reported quantitative olfactory changes, either alone or combined with other symptoms, provide a specific and powerful tool for clinical diagnosis of COVID-19. The applicability of this tool for prioritizing COVID-19 laboratory testing is facilitated by a simple calculator presented here.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Noam Karni", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Hadar Klein", - "author_inst": "The Institute of Biochemistry, Food and Nutrition, The Hebrew University, Rehovot, Israel" - }, - { - "author_name": "Kim Asseo", - "author_inst": "The Institute of Biochemistry, Food and Nutrition, The Hebrew University, Rehovot, Israel" - }, - { - "author_name": "Yuval Benjamini", - "author_inst": "Department of Statistics, The Hebrew University, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Sarah Israel", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Musa Nimri", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Keren Olstein", - "author_inst": "Department of Clinical Microbiology and Infectious Diseases Hadassah-Hebrew University medical center" - }, - { - "author_name": "Ran Nir-Paz", - "author_inst": "Department of Clinical Microbiology and Infectious Diseases Hadassah-Hebrew University medical center" - }, - { - "author_name": "Alon Hershko", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Mordechai Muszkat", - "author_inst": "Department of Medicine, Hadassah University Hospital, Mt. Scopus Campus, Jerusalem, Israel" - }, - { - "author_name": "Masha Y Niv", - "author_inst": "The Institute of Biochemistry, Food and Nutrition, The Hebrew University, Rehovot, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.30.20165050", "rel_title": "Quantification of the association between predisposing health conditions, demographic, and behavioural factors with hospitalisation, intensive care unit admission, and death from COVID-19: a systematic review and meta-analysis", @@ -1276091,6 +1279441,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.07.30.20165084", + "rel_title": "The relative infectiousness of asymptomatic SARS-CoV-2 infected persons compared with symptomatic individuals: A rapid scoping review.", + "rel_date": "2020-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165084", + "rel_abs": "ObjectivesThe aim of this study was to conduct a scoping review of estimates of the relative infectiousness of asymptomatic persons infected with SARS-CoV-2 compared with symptomatic individuals.\n\nDesignRapid scoping review of literature available until 8th April 2020.\n\nSettingInternational studies on the infectiousness of individuals infected with SARS-CoV-2\n\nParticipantsStudies were selected for inclusion if they defined asymptomatics as a separate cohort distinct from pre-symptomatics and if they provided a quantitative measure of the infectiousness of asymptomatics relative to symptomatics.\n\nPrimary outcome measuresThe relative number of secondary cases produced by an average primary case, the relative probability of transmitting infection upon contact, and the degree of viral shedding.\n\nResultsVery few studies reported estimates of relative infectiousness of asymptomatic compared with symptomatic individuals. Significant differences exist in the definition of infectiousness. Viral shedding studies in general show no difference in shedding levels between symptomatic and asymptomatic individuals but are likely to be impacted by insufficient statistical power. Two contact tracing studies provided estimates of 0.7 and 1.0, but differences in approach and definition preclude comparison across the two studies. Finally, two modelling studies suggest a relative infectiousness of around 0.5 but one of these was more reflective of the infectiousness of undocumented rather than asymptomatic cases. Importantly, one contact tracing study showing a very low level of infectiousness of asymptomatic was not included in the analysis at this point due difficulties interpreting the reported findings.\n\nConclusionsThe present study highlights the need for additional studies in this area as a matter of urgency. For the purpose of epidemiological modelling, we cautiously suggest that at present, asymptomatics could be considered to have a degree of infectiousness which is about 0.40-0.70 that of symptomatics. However, it must be stressed that this suggestion comes from a very low evidence base and that estimates exist that are close to zero and close to 1.\n\nARTICLE SUMMARYO_ST_ABSStrengths and limitations of this studyC_ST_ABS- Differences in the definition of infectiousness and a low number of studies estimating this parameter negate the potential to provide a pooled quantitative estimate or relative infectiousness.\n- The present study highlights the need for additional studies in this area as a matter of urgency.\n- Several of the studies reviewed are in pre-print stage and are not peer-reviewed.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "David Mc Evoy", + "author_inst": "University College Dublin" + }, + { + "author_name": "Conor G McAloon", + "author_inst": "University College Dublin" + }, + { + "author_name": "Aine B Collins", + "author_inst": "University College Dublin" + }, + { + "author_name": "Kevin Hunt", + "author_inst": "University College Dublin" + }, + { + "author_name": "Francis Butler", + "author_inst": "University College Dublin" + }, + { + "author_name": "Andrew W Byrne", + "author_inst": "DAFM" + }, + { + "author_name": "Miriam Casey", + "author_inst": "University College Dublin" + }, + { + "author_name": "Ann Barber", + "author_inst": "Wageningen University" + }, + { + "author_name": "John M Griffin", + "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis" + }, + { + "author_name": "Elizabeth A Lane", + "author_inst": "Department of Agriculture, Food and the Marine" + }, + { + "author_name": "Patrick Wall", + "author_inst": "University College Dublin" + }, + { + "author_name": "Simon J More", + "author_inst": "University College Dublin" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.30.20165118", "rel_title": "Effects of COVID-19 lockdown on heart rate variability", @@ -1277375,109 +1280788,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.07.29.20164285", - "rel_title": "Disease severity dictates SARS-CoV-2-specific neutralizing antibody responses in COVID-19", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164285", - "rel_abs": "COVID-19 patients exhibit differential disease severity after SARS-CoV-2 infection. It is currently unknown as to the correlation between the magnitude of neutralizing antibody (NAb) responses and the disease severity in COVID-19 patients. In a cohort of 59 recovered patients with disease severity including severe, moderate, mild and asymptomatic, we observed the positive correlation between serum neutralizing capacity and disease severity, in particular, the highest NAb capacity in sera from the patients with severe disease, while a lack of ability of asymptomatic patients to mount competent NAbs. Furthermore, the compositions of NAb subtypes were also different between recovered patients with severe symptoms and with mild-to-moderate symptoms. These results reveal the tremendous heterogeneity of SARS-CoV-2-specific NAb responses and their correlations to disease severity, highlighting the needs of future vaccination in COVID-19 patients recovered from asymptomatic or mild illness.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Xiangyu Chen", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Zhiwei Pan", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Shuai Yue", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Fei Yu", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Junsong Zhang", - "author_inst": "Guangdong Academy of Medical Sciences" - }, - { - "author_name": "Yang Yang", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Ren Li", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Bingfeng Liu", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Xiaofan Yang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Leiqiong Gao", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Zhirong Li", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Yao Lin", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Qizhao Huang", - "author_inst": "The General Hospital of Western Theater Command" - }, - { - "author_name": "Lifan Xu", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Jianfang Tang", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Li Hu", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Jing Zhao", - "author_inst": "Third Military Medical University" - }, - { - "author_name": "Pinghuang Liu", - "author_inst": "China Agricultural University" - }, - { - "author_name": "Guozhong Zhang", - "author_inst": "China Agricultural University" - }, - { - "author_name": "Yaokai Chen", - "author_inst": "Chongqing Public Health Medical Center" - }, - { - "author_name": "Kai Deng", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Lilin Ye", - "author_inst": "Third Military Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.29.20164293", "rel_title": "Persistent fatigue following SARS-CoV-2 infection is common and independent of severity of initial infection", @@ -1277757,6 +1281067,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.28.20163931", + "rel_title": "Disparities in Case Frequency and Mortality of Coronavirus Disease 2019 (COVID-19) Among Various States in the United States", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163931", + "rel_abs": "ObjectiveTo utilize publicly reported, state-level data to identify factors associated with the frequency of cases, tests, and mortality in the US.\n\nMaterials & MethodsRetrospective study using publicly reported data collected included the number of COVID-19 cases, tests, and mortality from March 14th through April 30th, 2020. Publicly available state-level data was collected which included: demographics comorbidities, state characteristics and environmental factors. Univariate and multivariate regression analyses were performed to identify the significantly associated factors with percent mortality, case and testing frequency. All analyses were state-level analyses and not patient-level analyses.\n\nResultsA total of 1,090,500 COVID-19 cases were reported during the study period. The calculated case and testing frequency were 3,332 and 19,193 per 1,000,000 patients. There were 63,642 deaths during this period which resulted in a mortality of 5.8%. Factors including to but not limited to population density (beta coefficient 7.5, p< 0.01), transportation volume (beta coefficient 0.1, p< 0.01), tourism index (beta coefficient -0.1, p=0.02) and older age (beta coefficient 0.2, p=0.01) are associated with case frequency and percent mortality.\n\nConclusionsThere were wide variations in testing and case frequencies of COVID-19 among different states in the US. States with higher population density had a higher case and testing rate. States with larger population of elderly and higher tourism had a higher mortality.\n\nKey MessagesThere were wide variations in testing and case frequencies of COVID-19 among different states in the US.\n\nStates with higher population density had a higher case and testing rate.\n\nStates with larger population of elderly and higher tourism had a higher mortality.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rohit S. Loomba", + "author_inst": "Advocate Children's Hospital" + }, + { + "author_name": "Gaurav Aggarwal", + "author_inst": "Jersey City Medical Center" + }, + { + "author_name": "Saurabh Aggarwal", + "author_inst": "UnityPoint Health" + }, + { + "author_name": "Saul Flores", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Enrique G. Villarreal", + "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud" + }, + { + "author_name": "Juan S. Farias", + "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud" + }, + { + "author_name": "Carl J. Lavie", + "author_inst": "Ochsner Medical Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.29.20164186", "rel_title": "Back to school: use of Dried Blood Spot for the detection of SARS-CoV-2-specific immunoglobulin G (IgG) among schoolchildren in Milan, Italy.", @@ -1278977,65 +1282330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.07.24.20160101", - "rel_title": "Red blood cells injuries and hypersegmented neutrophils in COVID-19 peripheral blood film", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20160101", - "rel_abs": "In the current investigation, peripheral blood films of 15 COVID-19 patients (44.78{+/-}16.55 years), proven by computed tomographic imaging and RT-PCR for coronavirus SARS-CoV-2, were analyzed at the moment of hospital admission. Blood tests showed raised inflammatory markers (C-reactive protein 58.2{+/-}61.2 mg/L) with normal values for hemoglobin (126.2{+/-}2.6 g/L), WBC (6.8{+/-}18.74 109/L) RBC (4.55{+/-}0.99 1012/L) platelets (262.4{+/-}141.8, 109/L) MCV (79.84{+/-}8.2 fL) MCH (28{+/-}3.31 pg) and MCHC (350.3{+/-}1.15 g/L). The results revealed the presence of hypersegmented neutrophils in 66.66%% of the patients. The percentages of neutrophils with 4 and 5 lobes were 46.25 {+/-} 4.83% and 31.5 {+/-} 14.84%, respectively. Three major red blood cells morphological alteration were observed: (1) erythrocytes in \"rouleaux\" formation represented by linear erythrocytes aggregation, (2) spherocytes with the disappearance of the usual biconcave disk, and (3) echinocytes showing spiky projections. Apparent reorganization of hemoglobin is found in the majority of the analyzed erythrocytes. Rouleaux formation is observed in 33.33% of patients and spherocytes and echinocytes are present at variable levels in the all analyzed patients. The current results revealed erythrocytes injuries in COVID-19 peripheral blood, in association with hypersegmented neutrophils, alterations that could be involved in the respiratory syndrome.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Nordine Lakhdari", - "author_inst": "Department of Hematology, University Hospital Center, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Boualem Tabet", - "author_inst": "Department of Hematology, University Hospital Center, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Lila Boudraham", - "author_inst": "Department of Internal Medicine, University Hospital Center, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Malha Laoussati", - "author_inst": "Department of Internal Medicine, University Hospital Center, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Sofiane Aissanou", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Lamia Beddou", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Sihem Bensalem", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Yuva Bellik", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Lamine Bournine", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Sofiane Fatmi", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - }, - { - "author_name": "Mokrane Iguer-Ouada", - "author_inst": "AME Laboratory, Faculty of Nature and Life Sciences, Abderrahmane Mira University 06000 Bejaia, Algeria." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.07.29.20159442", "rel_title": "Early Clinical Factors Predicting the Development of Critical Disease in Japanese Patients with COVID-19: A Single-Center Retrospective, Observational Study", @@ -1279367,6 +1282661,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.07.26.20157040", + "rel_title": "Minimizing Population Health Loss in Times of Scarce Surgical Capacity", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20157040", + "rel_abs": "BackgroundCOVID-19 has put unprecedented pressure on healthcare systems worldwide, leading to a reduction of the available healthcare capacity. Our objective was to develop a decision model that supports prioritization of care from a utilitarian perspective, which is to minimize population health loss.\n\nMethodsA cohort state-transition model was developed and applied to 43 semi-elective non-paediatric surgeries commonly performed in academic hospitals. Scenarios of delaying surgery from two weeks were compared with delaying up to one year, and no surgery at all. Model parameters were based on registries, scientific literature, and the World Health Organization global burden of disease study. For each surgery, the urgency was estimated as the average expected loss of Quality-Adjusted Life-Years (QALYs) per month.\n\nResultsGiven the best available evidence, the two most urgent surgeries were bypass surgery for Fontaine III/IV peripheral arterial disease (0.23 QALY loss/month, 95%-CI: 0.09-0.24) and transaortic valve implantation (0.15 QALY loss/month, 95%-CI: 0.09-0.24). The two least urgent surgeries were placing a shunt for dialysis (0.01, 95%-CI: 0.005-0.01) and thyroid carcinoma resection (0.01, 95%-CI: 0.01-0.02): these surgeries were associated with a limited amount of health lost on the waiting list.\n\nConclusionExpected health loss due to surgical delay can be objectively calculated with our decision model based on best available evidence, which can guide prioritization of surgeries to minimize population health loss in times of scarcity. This tool should yet be placed in the context of different ethical perspectives and combined with capacity management tools to facilitate large-scale implementation.\n\nSummary boxO_ST_ABSWhat is already known on this topicC_ST_ABSThe perspective of maximizing population health, a utilitarian ethical perspective, has been described to be most defendable in times of scarcity. To prioritize surgical patients, literature mainly discusses approaches which are intra-disciplinary (e.g. within gynecological or oncological surgery) and mostly existed of narrative reviews of the literature. Some decision tools were developed, which rely on the consensus of experts on various measures of urgency (e.g. health benefit, or time until inoperable). No approach was found which transparently weighs objective factors in order to quantify a clinically relevant measure of urgency.\n\nWhat this study addsIn contrast to previously developed approaches, our approach transparently and consistently aggregates best available objective evidence across disciplines. This novel aggregated urgency measure can be easily linked with capacity management tools. Our approach can help to minimize health losses when trying to overcome delay in surgeries in times of surgical scarcity, during the COVID-19 pandemic and beyond.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Benjamin Gravesteijn", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Eline Krijkamp", + "author_inst": "Erasmus University Medical Center Rotterdam" + }, + { + "author_name": "Jan Busschbach", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Geert Geleijnse", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Isabel Retel Helmrich", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Sophie Bruinsma", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Celine van Lint", + "author_inst": "Value Based Operation Room Triage team collaborators: Chris Bangma, Ivo Beetz, Patrick Bindels, Alexandra Brandt-Kerkhof, Danielle van Diepen, Clemens Dirven, T" + }, + { + "author_name": "Ernest van Veen", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Ewout Steyerberg", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Cornelis Verhoef", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Jan van Saase", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Hester Lingsma", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "Robert Baatenburg de Jong", + "author_inst": "Erasmus Medical Center Rotterdam" + }, + { + "author_name": "- Value Based Operation Room Triage team collaborators", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "surgery" + }, { "rel_doi": "10.1101/2020.07.27.20163212", "rel_title": "Association between Alzheimer's disease and COVID-19: A bidirectional Mendelian randomization", @@ -1280707,101 +1284072,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.26.20162248", - "rel_title": "ACE2 Expression is elevated in Airway Epithelial Cells from aged and male donors but reduced in asthma", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20162248", - "rel_abs": "RationaleCOVID-19 is complicated by acute lung injury, and death in some individuals. It is caused by SARS-CoV-2 that requires the ACE2 receptor and serine proteases to enter airway epithelial cells (AECs).\n\nObjectiveTo determine what factors are associated with ACE2 expression particularly in patients with asthma and chronic obstructive pulmonary disease (COPD).\n\nMethodsWe obtained upper and lower AECs from 145 people from two independent cohorts, aged 2-89, Newcastle (n=115), and from Perth (n= 30) Australia. The Newcastle cohort was enriched with people with asthma (n=37) and COPD (n=38). Gene expression for ACE2 and other genes potentially associated with SARS-CoV-2 cell entry were assessed by quantitative PCR, protein expression was confirmed with immunohistochemistry on endobronchial biopsies and cultured AECs.\n\nResultsIncreased gene expression of ACE2 was associated with older age (p=0.02) and male sex (p=0.03), but not pack-years smoked. When we compared gene expression between adults with asthma, COPD and healthy controls, mean ACE2 expression was lower in asthma (p=0.01). Gene expression of furin, a protease that facilitates viral endocytosis, was also lower in asthma (p=0.02), while ADAM-17, a disintegrin that cleaves ACE2 from the surface was increased (p=0.02). ACE2 protein levels were lower in endobronchial biopsies from asthma patients.\n\nConclusionsIncreased ACE2 expression occurs in older people and males. Asthma patients have reduced expression. Altered ACE2 expression in the lower airway may be an important factor in virus tropism and may in part explain susceptibility factors and why asthma patients are not over-represented in those with COVID-19 complications.\n\nImpactACE2 is the primary receptor for SARS-COV-2. We demonstrate that lower airway expression of ACE2 is increased in older adults and males. We also find that lower ACE2 expression in epithelial cells occurs in people with asthma and is associated with reduced Furin expression and increased ADAM-17 expression. This may explain at least in part the relative sparing of people with asthma from severe COVID-19 disease.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Peter Wark", - "author_inst": "University of Newcastle" - }, - { - "author_name": "Prabuddha Pathinyake", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Medicine and Public Health, University of Newcastle, Newcastle, New " - }, - { - "author_name": "Gerard Kaiko", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Kristy Nichol", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Medicine and Public Health, University of Newcastle, Newcastle, New " - }, - { - "author_name": "Ayesha Ali", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Ling Chen", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Erika Suntanto", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - }, - { - "author_name": "Luke Garrat", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - }, - { - "author_name": "Sukhwinder S Sohal", - "author_inst": "Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, " - }, - { - "author_name": "Wenying Lu", - "author_inst": "Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, " - }, - { - "author_name": "Matthew Eapen", - "author_inst": "Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, College of Health and Medicine, University of Tasmania, " - }, - { - "author_name": "Christopher Oldmeadow", - "author_inst": "Hunter Medical Research Institute, Newcastle, New South Wales, Australia" - }, - { - "author_name": "Nathan Bartlett", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Andrew Reid", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Punnam Veerati", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle" - }, - { - "author_name": "Alan Hsu", - "author_inst": "Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and School of Medicine and Public Health, University of Newcastle, Newcastle, New " - }, - { - "author_name": "Thomas Iosifides", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - }, - { - "author_name": "Stephen Stick", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - }, - { - "author_name": "Philip M Hansbro", - "author_inst": "Centre for Inflammation, Centenary Institute, and Faculty of Science, University of Technology Sydney, Sydney, New South Wales, Australia" - }, - { - "author_name": "Anthony Kicic", - "author_inst": "Telethon Kids Institute, University of Western Australia, Western Australia, Australia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.07.27.20162743", "rel_title": "How much reserve capacity is justifiable for hospital pandemic preparedness? A cost-effectiveness analysis for COVID-19 in Germany", @@ -1281077,6 +1284347,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.26.20159756", + "rel_title": "Efficacy and tolerability of bevacizumab in patients with severe Covid -19", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20159756", + "rel_abs": "On the basis of Covid-19-induced pulmonary pathological and vascular changes, we hypothesized that the anti-VEGF drug bevacizumab might be beneficial for treating Covid-19 patients. We recruited 26 patients from 2-centers (China and Italy) with confirmed severe Covid-19, with respiratory rate [≥] 30 times/min, oxygen saturation [≤] 93% with ambient air, or partial arterial oxygen pressure to fraction of inspiration O2 ratio (PaO2/FiO2) >100mmHg and [≤] 300 mmHg, and diffuse pneumonia confirmed by chest radiological imaging. This trial was conducted from Feb 15 to April 5, 2020, and followed up for 28 days. Relative to comparable control patients with severe Covid-19 admitted in the same centers, bevacizumab showed clinical efficacy by improving oxygenation and shortening oxygen-support duration. Among 26 hospitalized patients with severe Covid-19 (median age, 62 years, 20 [77%] males), bevacizumab plus standard care markedly improved the PaO2/FiO2 ratios at days 1 and 7 (elevated values, day 1, 50.5 [4.0,119.0], p<0.001; day 7, 111.0 [85.0,165.0], p<0.001). By day 28, 24 (92%) patients showed improvement in oxygen-support status, 17 (65%) patients were discharged, and none showed worsen oxygen-support status nor died. Significant reduction of lesion areas and ratios were shown in chest CT or X-ray analysis within 7 days. Of 14 patients with fever, body temperature normalized within 72 hours in 13 (93%) patients. Lymphocyte counts in peripheral blood were significantly increased and CRP levels were markedly decreased as shown in available data. Our findings suggested bevacizumab plus standard care was highly beneficial for treating patients with severe Covid-19. Clinical efficacy of bevacizumab warrants double blind, randomized, placebo-controlled trials.\n\nTRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04275414, URL: https://clinicaltrials.gov/ct2/show/NCT04275414.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Jiaojiao Pang", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Feng Xu", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Gianmarco Aondio", + "author_inst": "Hospital S.p.A. Ospedale Generale di Zona Moriggia - Pelascini, Gravedona ed Uniti (CO)" + }, + { + "author_name": "Yu Li", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Alberto Fumagalli", + "author_inst": "Hospital S.p.A. Ospedale Generale di Zona Moriggia - Pelascini, Gravedona ed Uniti (CO)" + }, + { + "author_name": "Ming Lu", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Giuseppe Valmadre", + "author_inst": "Hospital S.p.A. Ospedale Generale di Zona Moriggia - Pelascini, Gravedona ed Uniti (CO)" + }, + { + "author_name": "Jie Wei", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Yuan Bian", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Margherita Canesi", + "author_inst": "Hospital S.p.A. Ospedale Generale di Zona Moriggia - Pelascini, Gravedona ed Uniti (CO)" + }, + { + "author_name": "Giovanni Damiani", + "author_inst": "Hospital S.p.A. Ospedale Generale di Zona Moriggia - Pelascini, Gravedona ed Uniti (CO)" + }, + { + "author_name": "Yuan Zhang", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Dexin Yu", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Jun Chen", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Xiang Ji", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Wenhai Sui", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Bailu Wang", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Shuo Wu", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Attila Kovacs", + "author_inst": "Hospital S.p.A. Ospedale Generale di Zona Moriggia - Pelascini, Gravedona ed Uniti (CO)" + }, + { + "author_name": "Miriam Revera", + "author_inst": "Hospital S.p.A. Ospedale Generale di Zona Moriggia - Pelascini, Gravedona ed Uniti (CO)" + }, + { + "author_name": "Hao Wang", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Ying Zhang", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Yuguo Chen", + "author_inst": "Qilu Hospital of Shandong University" + }, + { + "author_name": "Yihai Cao", + "author_inst": "Karolinska Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.27.20162321", "rel_title": "SARS-CoV-2 antibody responses determine disease severity in COVID-19 infected individuals", @@ -1282457,89 +1285838,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.28.20162941", - "rel_title": "Sensitive detection of SARS-CoV-2 seroconversion by flow cytometry reveals the presence of nucleoprotein-reactive antibodies in Covid-19-naive individuals", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20162941", - "rel_abs": "There is an ongoing need of developing sensitive and specific methods for the determination of SARS-CoV-2 seroconversion. For this purpose, we have developed a multiplexed flow cytometric bead array (C19BA) that allows the identification of IgG and IgM antibodies against three immunogenic proteins simultaneously: the spike receptor-binding domain (RBD), the spike protein subunit 1 (S1) and the nucleoprotein (N). Using different cohorts of samples collected before and after the pandemic, we show that this assay is more sensitive than ELISAs performed in our laboratory. The combination of three viral antigens allows for the interrogation of full seroconversion. Importantly, we have detected N-reactive antibodies in COVID-19-negative individuals. Here we present an immunoassay that can be easily implemented and has superior potential to detect low antibody titers compared to current gold standard serology methods.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Leire Egia-Mendikute", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Alexandre Bosch", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Endika Prieto-Fernandez", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "So Young Lee", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Borja Jimenez-Lasheras", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Ana Garcia del Rio", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Asier Antonana-Vildosola", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Chiara Bruzzone", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Maider Bizkarguenaga", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Nieves Embade", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Ruben Gil-Redondo", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Maria Luz Martinez-Chantar", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Marcos Lopez-Hoyos", - "author_inst": "Hospital Universitario Marques de Valdecilla-IDIVAL" - }, - { - "author_name": "Nicola G A Abrescia", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Jose M. Mato", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Oscar Millet", - "author_inst": "CIC bioGUNE" - }, - { - "author_name": "Asis Palazon", - "author_inst": "CIC biogune" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.07.28.20163592", "rel_title": "Evaluation of a SARS-CoV-2 surrogate virus neutralization test for detection of antibody in human, canine, cat and hamster sera", @@ -1282767,6 +1286065,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.27.20158105", + "rel_title": "Comorbidities associated with regional variations in COVID-19 mortality revealed by population-level analysis", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20158105", + "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), has developed into a global health crisis. Understanding the risk factors for poor outcomes of COVID-19 is thus important for successful management and control of the pandemic. However, the progress and severity of the epidemic across different regions show great differentiations. We hypothesized the origination of these differences are based on location-dependent variations in underlying population-wide health factors. Disease prevalence or incidence data of states and counties of the United States were collected for a group of chronic diseases, including hypertension, diabetes, obesity, stroke, coronary heart disease, heart failure, physical inactivation, and common cancers (e.g., lung, colorectal, stomach, kidney and renal). Correlation and regression analysis identified the prevalence of heart failure as a significant positive factor for region-level COVID-19 mortality. Similarly, the incidence of gastric cancer and thyroid cancer were also identified as significant factors contributing to regional variation in COVID-19 mortality. To explore the implications of these results, we re-analyzed the RNA-seq data for stomach adenocarcinoma (STAD) and colon carcinoma (COAD) from The Cancer Genome Atlas (TCGA) project. We found that expression of genes in the immune response pathways were more severely disturbed in STAD than in COAD, implicating higher probability for STAD patients or individuals with precancerous chronic stomach diseases to develop cytokine storm once infected with COVID-19. Taken together, we conclude that location variations in particular chronic diseases and cancers contribute significantly to the regional variations in COVID-19 mortality.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hongxing Yang", + "author_inst": "Merck Holding (China), a business of Merck KGaA" + }, + { + "author_name": "Fei Zhong", + "author_inst": "MilliporeSigma, a business of KGaA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.27.20159996", "rel_title": "Predicting Onset of COVID-19 with Mobility-Augmented SEIR Model", @@ -1284203,41 +1287524,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.25.20162156", - "rel_title": "30-day mortality and morbidity in COVID-19 versus influenza: A populationbased study", - "rel_date": "2020-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20162156", - "rel_abs": "BackgroundAs of July 2020, COVID-19 has caused 500,000 deaths worldwide. However, large-scale studies of COVID-19 mortality and new-onset comorbidity compared to influenza and individuals tested negative for COVID-19 are lacking. We aimed to investigate COVID-19 30-day mortality and new-onset comorbidity compared to individuals with negative COVID-19 test results and individuals tested for influenza.\n\nMethods and findingsThis population-based cohort study utilized electronic health records covering roughly half (n=2,647,229) of Denmarks population, with nationwide linkage of microbiology test results and death records. All individuals [≥]18 years tested for COVID-19 and individuals tested for influenza were followed from November 1, 2017 to June 30, 2020. The main outcome was 30-day mortality after a test for either COVID-19 or influenza. Secondary outcomes were major comorbidity diagnoses 30-days after the test for either COVID-19 or influenza. In total, 224,639 individuals were tested for COVID-19. Among inpatients positive for COVID-19, 356 of 1657 (21%) died within 30 days, which was a 3.0 to 3.1-fold increased 30-day mortality rate, when compared to influenza and COVID-19-negative inpatients (all p<0.001). For outpatients, 128 of 6,263 (2%) COVID-19-positive patients died within 30 days, which was a 5.5 to 6.9-fold increased mortality rate compared to influenza and COVID-19-negative patients, respectively (all p<0.001). Compared to hospitalized patients with influenza, new-onset ischemic stroke, diabetes and nephropathy occurred more frequently in inpatients with COVID-19 (all p<0.05).\n\nConclusionsIn this population-based study comparing COVID-19 with influenza, COVID-19 was associated with increased rates of major systemic and vascular comorbidity and substantially higher mortality, which is likely even higher than the stated 3.0 to 5.5-fold increase owing to more extensive testing for COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Vardan Nersesjan", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Moshgan Amiri", - "author_inst": "Rigshospitalet" - }, - { - "author_name": "Hanne Krarup Christensen", - "author_inst": "Bispebjerg Hospital" - }, - { - "author_name": "Michael E. Benros", - "author_inst": "Copenhagen Research Centre for Mental Health - CORE, Mental Health Centre Copenhagen, Copenhagen University Hospital, Hellerup, Denmark" - }, - { - "author_name": "Daniel Kondziella", - "author_inst": "Rigshospitalet, Copenhagen University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.25.20162073", "rel_title": "Effectiveness and Safety of Chloroquine or Hydroxychloroquine as a mono-therapy or in combination with Azithromycin in the treatment of COVID-19 patients: Systematic Review and Meta-Analysis", @@ -1284453,6 +1287739,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.26.20161570", + "rel_title": "Magnitude, demographics and dynamics of the impact of the first phase of the Covid-19 pandemic on all-cause mortality in 17 industrialised countries", + "rel_date": "2020-07-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20161570", + "rel_abs": "The Covid-19 pandemic affects mortality directly through infection as well as through changes in the social, environmental and healthcare determinants of health1. The impacts on mortality are likely to vary across countries in magnitude, timing, and age and sex composition. Here, we applied an ensemble of 16 Bayesian probabilistic models to vital statistics data, by age group and sex, to consistently and comparably estimate the impacts of the first phase of the pandemic on all-cause mortality for 17 industrialised countries. The models accounted for factors that affect death rates including seasonality, temperature, and public holidays, as well as for medium-long-term secular trends and the dependency of death rates in each week on those in preceding week(s). From mid-February through the end of May 2020, an estimated 202,900 (95% credible interval 179,400-224,900) more people died in these 17 countries than would have had the pandemic not taken place. Nearly three quarters of these excess deaths occurred in England and Wales, Italy and Spain, where less than half of the total population of these countries live. When all-cause mortality is considered, the total number of deaths, deaths per 100,000 people, and relative increase in deaths were similar between men and women in most countries. Further, in many countries, the balance of excess deaths changed from male-dominated early in the pandemic to being equal or female-dominated later on.\n\nTaken over the entire first phase of the pandemic, there was no detectable rise in all-cause mortality in New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland and for women in Austria and Switzerland (posterior probability of an increase in deaths <90%). Women in Portugal and men in Austria experienced relatively small increases in all-cause mortality, with posterior probabilities of 90-99%. For men in Switzerland and Portugal, and both sexes in the Netherlands, France, Sweden, Belgium, Italy, Scotland, Spain and England and Wales, all-cause mortality increased as a result of the pandemic with a posterior probability >99%. After accounting for population size, England and Wales and Spain experienced the highest death toll, nearly 100 deaths per 100,000 people; they also had the largest relative (percent) increase in deaths (37% (95% credible interval 30-44) in England and Wales; 38% (31-44) in Spain). New Zealand, Bulgaria, Hungary, Norway, Denmark and Finland experienced changes in deaths that ranged from possible slight declines to increases of no more than 5%. The large impact in England and Wales stems partly from having experienced (together with Spain) the highest weekly increases in deaths, more than doubling in some weeks, and having had (together with Sweden) the longest duration when deaths exceeded levels that would be expected in the absence of the pandemic.\n\nThe heterogeneous magnitude and character of the excess deaths due to the Covid-19 pandemic reflect differences in how well countries have managed the pandemic (e.g., timing, extent and adherence to lockdowns and other social distancing measures; effectiveness of test, trace and isolate mechanisms), and the resilience and preparedness of the health and social care system (e.g., effective facility and community care pathways; minimising spread of infection within hospitals and care homes, and between them and the community).", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Vasilis Kontis", + "author_inst": "Imperial College London" + }, + { + "author_name": "James E Bennett", + "author_inst": "Imperial College London" + }, + { + "author_name": "Theo Rashid", + "author_inst": "Imperial College London" + }, + { + "author_name": "Robbie M Parks", + "author_inst": "Columbia University" + }, + { + "author_name": "Jonathan Pearson-Stuttard", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michel Guillot", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Perviz Asaria", + "author_inst": "Imperial College London" + }, + { + "author_name": "Bin Zhou", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marco Battaglini", + "author_inst": "Italian National Institute of Statistics" + }, + { + "author_name": "Gianni Corsetti", + "author_inst": "Italian National Institute of Statistics" + }, + { + "author_name": "Martin McKee", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Mariachiara Di Cesare", + "author_inst": "Middlesex University London" + }, + { + "author_name": "Colin D Mathers", + "author_inst": "Independent Researcher" + }, + { + "author_name": "Majid Ezzati", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.26.20162206", "rel_title": "The performance of Mobile Cabin Hospital in combatting COVID-19 in China", @@ -1285885,97 +1289242,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.24.20161653", - "rel_title": "COVID-19 Patients Form Memory CD8+ T Cells that Recognize a Small Set of Shared Immunodominant Epitopes in SARS-CoV-2", - "rel_date": "2020-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161653", - "rel_abs": "Development of effective strategies to detect, treat, or prevent COVID-19 requires a robust understanding of the natural immune response to SARS-CoV-2, including the cellular response mediated by T cells. We used an unbiased, genome-wide screening technology, termed T-Scan, to identify specific epitopes in SARS-CoV-2 that are recognized by the memory CD8+ T cells of 25 COVID-19 convalescent patients, focusing on epitopes presented by the six most prevalent HLA types: A*02:01, A*01:01, A*03:01, A*11:01, A*24:02, and B*07:02. For each HLA type, the patients T cells recognized 3-8 immunodominant epitopes that are broadly shared among patients. Remarkably, 94% of screened patients had T cells that recognized at least one of the three most dominant epitopes for a given HLA, and 53% of patients had T cells that recognized all three. Subsequent validation studies in 18 additional A*02:01 patients confirmed the presence of memory CD8+ T cells specific for the top six A*02:01 epitopes, and single-cell sequencing revealed that patients often have many different T cell clones targeting each epitope, but that the same T cell receptor V regions are predominantly used to recognize these epitopes, even across patients. In total, we identified 29 shared epitopes across the six HLA types studied. T cells that target most of these epitopes (27 of 29) do not cross-react with the endemic coronaviruses that cause the common cold, and the epitopes do not occur in regions with high mutational variation. Notably, only 3 of the 29 epitopes reside in the spike protein, highlighting the need to design new classes of vaccines that recapitulate natural CD8+ T cell responses to SARS-CoV-2.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Andrew P Ferretti", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Tomasz Kula", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Yifan Wang", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Dalena MV Nguyen", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Adam Weinheimer", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Garrett S Dunlap", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Qikai Xu", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Nancy Nabilsi", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Candace R Perullo", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Alexander W Cristofaro", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Holly J Whitton", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Amy Virbasius", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Kenneth J Olivier Jr.", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Lyndsey B Baiamonte", - "author_inst": "Ochsner Medical Center" - }, - { - "author_name": "Angela T Alistar", - "author_inst": "Atlantic Health System Cancer Care" - }, - { - "author_name": "Eric D Whitman", - "author_inst": "Atlantic Health System Cancer Care" - }, - { - "author_name": "Sarah A Bertino", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Shrikanta Chattopadhyay", - "author_inst": "TScan Therapeutics" - }, - { - "author_name": "Gavin MacBeath", - "author_inst": "TScan Therapeutics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.21.20153650", "rel_title": "Patient characteristics and predictors of mortality in 470 adults admitted to a district general hospital in England with Covid-19", @@ -1286327,6 +1289593,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.25.20161844", + "rel_title": "Epidemiological investigation and prevention control analysis of longitudinal distribution of COVID-19 in Henan province, China", + "rel_date": "2020-07-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20161844", + "rel_abs": "ObjectiveTo analyze the vertical distribution of six cities in Henan Province,China from January 21, 2020 to June17, 2020: Xinyang City (including Gushi County), Nanyang City (including Dengzhou City), Zhumadian City (including XincaiCounty), Zhengzhou City (including Gongyi City), Puyang City and Anyang City (including Hua County) corona virus disease 2019(COVID-19) epidemiological characteristics and local prevention and control measures.\n\nMethodsData were collected and analyzed through the COVID-19 information published on the official websites of health commissions of Henan Province and six cities.\n\nResultsAs of June 17, 2020, the cumulative incidence rate of COVID-19 in Henan province was 1.33/100,000, the cumulative cure rate was 98.27%, the cumulative mortality rate was 1.73%, the age range of diagnosed cases was 5days-85years old, and the male to female ratio was 1.09:1.The confirmed cases of COVID-19 in Henan province were mainly imported cases from Hubei, accounting for 87.74%, of which the highest number was 70.50% in Zhumadian. The contact cases and local cases increased in a fluctuating manner over time.\n\nSignificanceIn this paper, epidemiological characteristics of COVID-19 in Henan province from the outbreak to the effective control within 60 days were analyzed, and effective and distinctive prevention and control measures in various cities were summarized, so as to provide a favorable reference for the further formulation and implementation of epidemic prevention and control and a valuable theoretical basis for effectively avoiding the second outbreak.\n\nImportanceEpidemic prevention and control in China has entered the normalized this new stage, this article analyze the epidemiological characteristics of COVID - 19 in henan province, and summarizes the prefecture level and effective disease prevention and control means and measures, the normalized private provide the theoretical reference to the prevention and control work, formulate and carry out, at the same time in other countries and regions of epidemic prevention and control work can also be used for reference.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Xianguang Yang", + "author_inst": "Henan Normal University" + }, + { + "author_name": "Xuelin Chen", + "author_inst": "Henan Normal University" + }, + { + "author_name": "Cuihong Ding", + "author_inst": "Henan Normal University" + }, + { + "author_name": "Zhibo Bai", + "author_inst": "Henan Normal University" + }, + { + "author_name": "Jingyi Zhu", + "author_inst": "Henan Normal University" + }, + { + "author_name": "Gege Sun", + "author_inst": "Henan Normal University" + }, + { + "author_name": "Guoying Yu", + "author_inst": "Henan Normal University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.24.20161752", "rel_title": "SEIHCRD Model for COVID-19 spread scenarios, disease predictions and estimates the basic reproduction number, case fatality rate, hospital, and ICU beds requirement", @@ -1287695,73 +1291004,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.26.222232", - "rel_title": "An alternative binding mode of IGHV3-53 antibodies to the SARS-CoV-2 receptor binding domain", - "rel_date": "2020-07-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.26.222232", - "rel_abs": "IGHV3-53-encoded neutralizing antibodies are commonly elicited during SARS-CoV-2 infection and target the receptor-binding domain (RBD) of the spike (S) protein. Such IGHV3-53 antibodies generally have a short CDR H3 due to structural constraints in binding the RBD (mode A). However, a small subset of IGHV3-53 antibodies to the RBD contain a longer CDR H3. Crystal structures of two IGHV3-53 neutralizing antibodies here demonstrate that a longer CDR H3 can be accommodated in a different binding mode (mode B). These two classes of IGHV3-53 antibodies both target the ACE2 receptor binding site, but with very different angles of approach and molecular interactions. Overall, these findings emphasize the versatility of IGHV3-53 in this common antibody response to SARS-CoV-2, where conserved IGHV3-53 germline-encoded features can be combined with very different CDR H3 lengths and light chains for SARS-CoV-2 RBD recognition and virus neutralization.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Nicholas C. Wu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Meng Yuan", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Hejun Liu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Chang-Chun D. Lee", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Xueyong Zhu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Sandhya Bangaru", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Jonathan L. Torres", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Tom G. Caniels", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Philip J.M. Brouwer", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Marit J. van Gils", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Rogier W. Sanders", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Andrew B. Ward", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Ian A. Wilson", - "author_inst": "The Scripps Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.27.222901", "rel_title": "Evolution And Genetic Diversity Of SARSCoV-2 In Africa Using Whole Genome Sequences", @@ -1288033,6 +1291275,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.24.220715", + "rel_title": "CoVaccine HT\u2122 adjuvant potentiates robust immune responses to recombinant SARS-CoV-2 Spike S1 immunisation", + "rel_date": "2020-07-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.24.220715", + "rel_abs": "The current COVID-19 pandemic has claimed hundreds of thousands of lives and its causative agent, SARS-CoV-2, has infected millions, globally. The highly contagious nature of this respiratory virus has spurred massive global efforts to develop vaccines at record speeds. In addition to enhanced immunogen delivery, adjuvants may greatly impact protective efficacy of a SARS-CoV-2 vaccine. To investigate adjuvant suitability, we formulated protein subunit vaccines consisting of the recombinant S1 domain of SARS-CoV-2 Spike protein alone or in combination with either CoVaccine HT or Alhydrogel. CoVaccine HT induced high titres of antigen-binding IgG after a single dose, facilitated affinity maturation and class switching to a greater extent than Alhydrogel and elicited potent cell-mediated immunity as well as virus neutralising antibody titres. Data presented here suggests that adjuvantation with CoVaccine HT can rapidly induce a comprehensive and protective immune response to SARS-CoV-2.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Brien K Haun", + "author_inst": "University of Hawaii at Manoa / John A. Burns School of Medicine" + }, + { + "author_name": "Chih-Yun Lai", + "author_inst": "University of Hawaii at Manoa / John A. Burns School of Medicine" + }, + { + "author_name": "Caitlin A Williams", + "author_inst": "University of Hawaii at Manoa / John A. Burns School of Medicine" + }, + { + "author_name": "Teri Ann S Wong", + "author_inst": "University of Hawaii at Manoa / John A. Burns School of Medicine" + }, + { + "author_name": "Michael M Lieberman", + "author_inst": "University of Hawaii at Manoa / John A. Burns School of Medicine" + }, + { + "author_name": "Laurent Pessaint", + "author_inst": "BIOQUAL, Inc." + }, + { + "author_name": "Hanne A Elyard", + "author_inst": "BIOQUAL, Inc." + }, + { + "author_name": "Axel T Lehrer", + "author_inst": "University of Hawaii at Manoa / John A. Burns School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.07.25.221291", "rel_title": "North American deer mice are susceptible to SARS-CoV-2", @@ -1290209,25 +1293498,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.21.20131664", - "rel_title": "Covid19 2020 projection report: Germany, Israel, Italy and USA. Mid-July 2020", - "rel_date": "2020-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20131664", - "rel_abs": "A notion of implied susceptible population size ISPS was introduced in the context of the SIR differential equations in Epidemiology, in a companion paper. It is the potential target population size for which the solution to the SIR equations would yield the current number of new affected cases. This notion is applied to the analysis and projection of Covid19 2020, illustrated on the data of Germany, Israel, Italy and USA.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Isaac Meilijson", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.21.20125138", "rel_title": "Viral RNA level, serum antibody responses, and transmission risk in discharged COVID-19 patients with recurrent positive SARS-CoV-2 RNA test results: a population-based observational cohort study", @@ -1290567,6 +1293837,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.24.20156240", + "rel_title": "COVID-19 induces a hyperactive phenotype in circulating platelets", + "rel_date": "2020-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20156240", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19), caused by novel coronavirus SARS-CoV-2, has to date affected over 13.3 million globally. Although high rates of venous thromboembolism and evidence of COVID-19-induced endothelial dysfunction have been reported, the precise aetiology of the increased thrombotic risk associated with COVID-19 infection remains to be fully elucidated.\n\nObjectivesHere, we assessed clinical platelet parameters and circulating platelet activity in patients with severe and non-severe COVID-19.\n\nMethodsAn assessment of clinical blood parameters in patients with severe COVID-19 disease (requiring intensive care), patients with non-severe disease (not requiring intensive care), general medical in-patients without COVID-19 and healthy donors was undertaken. Platelet function and activity were also assessed by secretion and specific marker analysis.\n\nResultsWe show that routine clinical blood parameters including increased MPV and decreased platelet:neutrophil ratio are associated with disease severity in COVID-19 upon hospitalisation and intensive care unit admission. Strikingly, agonist-induced ADP release was dramatically higher in COVID-19 patients compared with non-COVID-19 hospitalized patients and circulating levels of PF4, sP-selectin and TPO were also significantly elevated in COVID-19.\n\nConclusionDistinct differences exist in routine full blood count and other clinical laboratory parameters between patients with severe and non-severe COVID-19. Moreover, we have determined that COVID-19 patients possess hyperactive circulating platelets. These data suggest that abnormal platelet reactivity may contribute to hypercoagulability in COVID-19. Further investigation of platelet function in COVID-19 may provide additional insights into the aetiology of thrombotic risk in this disease and may contribute to the optimisation of thrombosis prevention and treatment strategies.\n\nEssentialsO_LIRoutine platelet-related clinical blood parameters (MPV, PNR) are associated with disease severity in COVID-19.\nC_LIO_LIAgonist-induced ADP release is dramatically higher in COVID-19 patients compared with non-COVID-19 hospitalized patients.\nC_LIO_LICirculating levels of PF4, sP-selectin levels and TPO are significantly elevated in COVID-19.\nC_LIO_LIIdentification of a hyperactive platelet phenotype may warrant re-evaluation of current thrombotic prevention strategies in COVID-19 treatment.\nC_LI", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Shane P Comer", + "author_inst": "University College Dublin, Dublin, Ireland" + }, + { + "author_name": "Sarah Cullivan", + "author_inst": "Mater Misericordiae University Hospital, Dublin Ireland" + }, + { + "author_name": "Paulina B Szklanna", + "author_inst": "University College Dublin, Dublin, Ireland" + }, + { + "author_name": "Luisa Weiss", + "author_inst": "University College Dublin, Dublin, Ireland" + }, + { + "author_name": "Steven Cullen", + "author_inst": "Royal College of Surgeons in Ireland, Dublin, Ireland" + }, + { + "author_name": "Sarah Kelliher", + "author_inst": "Mater Misericordiae University Hospital, Dublin, Ireland" + }, + { + "author_name": "Albert Smolenski", + "author_inst": "University College Dublin, Dublin, Ireland" + }, + { + "author_name": "Niamh Moran", + "author_inst": "Royal College of Surgeons in Ireland, Dublin, Ireland" + }, + { + "author_name": "Claire Murphy", + "author_inst": "Royal College of Surgeons in Ireland, Dublin, Ireland" + }, + { + "author_name": "Haidar Altaie", + "author_inst": "SAS UK Headquarters, Buckinghamshire, United Kingdom" + }, + { + "author_name": "John Curran", + "author_inst": "SAS Institute , Dublin, Ireland" + }, + { + "author_name": "Katherine O'Reilly", + "author_inst": "Mater Misericordiae University Hospital, Dublin, Ireland" + }, + { + "author_name": "Aoife G Cotter", + "author_inst": "Mater Misericordiae University Hospital, Dublin, Ireland" + }, + { + "author_name": "Brian Marsh", + "author_inst": "Mater Misericordiae University Hospital, Dublin, Ireland" + }, + { + "author_name": "Sean Gaine", + "author_inst": "Mater Misericordiae University Hospital, Dublin, Ireland" + }, + { + "author_name": "Patrick Mallon", + "author_inst": "St Vincent's University Hospital, Dublin, Ireland" + }, + { + "author_name": "Brian McCullagh", + "author_inst": "Mater Misericordiae University Hospital, Dublin, Ireland" + }, + { + "author_name": "Fionnuala N\u00ed \u00c1inle", + "author_inst": "Mater Misericordiae University Hospital, Dublin, Ireland" + }, + { + "author_name": "Barry Kevane", + "author_inst": "Mater Misericordiae University Hospital, Dublin, Ireland" + }, + { + "author_name": "Patricia B Maguire", + "author_inst": "University College Dublin, Dublin, Ireland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.24.20149815", "rel_title": "Systematic evaluation and external validation of 22 prognostic models among hospitalised adults with COVID-19: An observational cohort study", @@ -1291723,73 +1295088,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.22.20159400", - "rel_title": "Weak association of coinfection by SARS-CoV-2 and other respiratory viruses with severe cases and death", - "rel_date": "2020-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159400", - "rel_abs": "BackgroundSARS-CoV-2 is a novel coronavirus described for the first time in China in December 2019. This virus can cause a disease that ranges in spectrum from asymptomatic to severe respiratory disease with multiorgan failure, and the most severe cases are associated with some comorbidities and patient age. However, there are patients who do not have those risk factors who still develop serious disease.\n\nMethodsIn this study, we identified the presence of other respiratory viruses in positive cases of COVID-19 in Mexico to determine if any coinfections were correlated with more severe manifestations of COVID-19. We analysed 103 confirmed cases of COVID-19 using RT-qPCR for the detection of 16 other respiratory viruses.\n\nResultsOf the cases analysed, 14 (13.6%) were cases of coinfection, and 92% of them never required hospitalization, even when comorbidities and advanced age were involved. There werent significant differences between the presence of comorbidities and the mean ages of the groups\n\nConclusionsThese results suggest that coinfection is not related to more severe COVID-19 and that, depending on the virus involved, it could even lead to a better prognosis. We believe that our findings may lay the groundwork for new studies aimed at determining the biological mechanism by which this phenomenon occurs and for proposing corresponding strategies to limit the progression to severe cases of COVID-19.\n\nCLINICAL TRIAL REGISTRATIONNot apply", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Larissa Fernandes-Matano", - "author_inst": "Divisi\u00f3n de Laboratorios de Vigilancia e Investigaci\u00f3n Epidemiol\u00f3gica. Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Irma Eloisa Monroy-Mu\u00f1oz", - "author_inst": "Laboratorio de Gen\u00f3mica, Departamento de Gen\u00e9tica y Gen\u00f3mica Humana, Instituto Nacional de Perinatolog\u00eda, Isidro Espinosa de los Reyes" - }, - { - "author_name": "Luis Antonio Uribe-Noguez", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social." - }, - { - "author_name": "Mar\u00eda de los Angeles Hern\u00e1ndez-Cueto", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Brenda Sarquiz-Mart\u00ednez", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "H\u00e9ctor Daniel Pardav\u00e9-Alejandre", - "author_inst": "Laboratorio Central de Epidemiolog\t\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Andrea Santos Coy-Arechavaleta", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Julio Elias Alvarado-Yaah", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Teresita Rojas-Mendoza", - "author_inst": "Laboratorio Central de Epidemiolog\u00eda, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Clara Esperanza Santacruz-Tinoco", - "author_inst": "Divisi\u00f3n de Laboratorios de Vigilancia e Investigaci\u00f3n Epidemiol\u00f3gica. Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Concepci\u00f3n Grajales-Mu\u00f1iz", - "author_inst": "Coordinaci\u00f3n de Control T\u00e9cnico de Insumos, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "V\u00edctor Hugo Borja-Aburto", - "author_inst": "Direcci\u00f3n de Prestaciones M\u00e9dicas, Instituto Mexicano del Seguro Social" - }, - { - "author_name": "Jos\u00e9 Esteban Mu\u00f1oz-Medina", - "author_inst": "Divisi\u00f3n de Laboratorios de Vigilancia e Investigaci\u00f3n Epidemiol\u00f3gica. Instituto Mexicano del Seguro Social" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.21.20159053", "rel_title": "Prospective Observational Study of Screening Asymptomatic Healthcare Workers for SARS-CoV-2 at a Canadian Tertiary Care Center", @@ -1292085,6 +1295383,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.07.22.20158311", + "rel_title": "Hospital Trainees Worries, Perceived Sufficiency of Information and Reported Psychological Health During The COVID-19 Pandemic", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20158311", + "rel_abs": "IntroductionThe COVID-19 pandemic has been unsurpassed in clinical severity or infectivity since the 1918 Spanish influenza pandemic and continues to impact the world. During the A/H1N1 influenza pandemic, healthcare workers presented frequent concerns regarding their ownand their families health, as well as high levels of psychological distress.\n\nObjectivesTo assess hospital trainees concerns, perceived sufficiency of information, behaviour and reported psychological health during the COVID-19 pandemic in the NHS\n\nDesignCross-sectional 39-point questionnaire study conducted in May 2020\n\nSettingA large NHS foundation trust in London\n\nParticipants204 hospital trainee doctors\n\nOutcome measuresQuantitative analysis of trainees worries and concerns while working during the COVID-19 pandemic were assessed across 8 domains: trainee demographics; concerns and worries regarding COVID-19; perceived sufficiency of information about the COVID-19 pandemic; social distancing; use of personal protective equipment (PPE) and training in PPE; COVID-19 acquisition and risk; reported psychological health; and medical education.\n\nResults91.7% looked after COVID-19 patients. 91.6% were worried about COVID-19; the most frequent concern was that of family and friends dying from COVID-19 (74.6%). 22.2% reported being infected with COVID-19. 6.8% of trainees were so concerned about COVID-19 infection that they would avoid going to work. Perceived sufficiency of information about COVID-19 was moderately high. 25.9% reported that they were able to socially distance at work compared to 94.4% able to socially distance outside work. 98.2% reported using PPE and 24.7% were confident the provided PPE protected them against infection with COVID-19. 41.9% reported that their psychological health had been affected by their work with the commonest being anxiety (56.6%), emotional distress (50.9%) and burnout (37.7%). 95.6% felt it is important to have a service that provides psychological support during this pandemic and 62.5% reported they would consider using this at work.\n\nConclusionsA significant proportion of hospital trainees are worried about the COVID-19 pandemic with high levels of reported psychological distress. Given that almost a third would not use psychological support services at work, hospital leaders and liaison psychiatry need to explore the reasons for not wanting to use services at work and highlight the provision of psychological services provided outside work such that provided by the London deaneries professional support unit (PSU). Seeking solutions to support trainee wellbeing in addition to this, such as larger offices, adequate rest facilities and alternative methods of teaching, with their input would enable empowerment of trainees and improve their health and morale while working in a pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nikoo Aziminia", + "author_inst": "Barnet Hospital, Royal Free London NHS Foundation Trust, London, United Kingdom" + }, + { + "author_name": "Aria Khani", + "author_inst": "Barnet Hospital, Royal Free London NHS Foundation Trust, London, United Kingdom" + }, + { + "author_name": "Colette Smith", + "author_inst": "Institute for Global Health, University College London, London, United Kingdom" + }, + { + "author_name": "Ameet Bakhai", + "author_inst": "Barnet Hospital, Royal Free London NHS Foundation Trust, London, United Kingdom" + }, + { + "author_name": "Clifford Lisk", + "author_inst": "Barnet Hospital, Royal Free London NHS Foundation Trust, London, United Kingdom" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.07.20.20157990", "rel_title": "Comparative Incidence and Outcomes of COVID-19 in Kidney or Kidney-Pancreas Transplant Recipients Versus Kidney or Kidney-Pancreas Waitlisted Patients: A Pilot Study", @@ -1293245,113 +1296578,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2020.07.21.20159376", - "rel_title": "Cerebral Microvascular Injury in Severe COVID-19", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20159376", - "rel_abs": "Structured AbstractO_ST_ABSImportanceC_ST_ABSCerebral microvascular lesions are common in patients with severe COVID-19. Radiologic-pathologic correlation in one case suggests a combination of microvascular hemorrhagic and ischemic lesions that may reflect an underlying hypoxic mechanism of injury, which requires validation in larger studies.\n\nObjectiveTo determine the incidence, distribution, and clinical and histopathologic correlates of microvascular lesions in patients with severe COVID-19.\n\nDesignObservational, retrospective cohort study: March to May 2020.\n\nSettingSingle academic medical center.\n\nParticipantsConsecutive patients (n=16) admitted to the intensive care unit with severe COVID-19, undergoing brain MRI for evaluation of coma or focal neurologic deficits.\n\nExposuresNot applicable.\n\nMain Outcome and MeasuresHypointense microvascular lesions identified by a prototype ultrafast high-resolution susceptibility-weighted imaging (SWI) MRI sequence, counted by two neuroradiologists and categorized by neuroanatomic location. Clinical and laboratory data (most recent measurements before brain MRI). Brain autopsy and cerebrospinal fluid PCR for SARS-CoV-2 in one patient who died from severe COVID-19.\n\nResultsEleven of 16 patients (69%) had punctate and linear SWI lesions in the subcortical and deep white matter, and eight patients (50%) had >10 SWI lesions. In 4/16 patients (25%), lesions involved the corpus callosum. Brain autopsy in one patient revealed that SWI lesions corresponded to widespread microvascular injury, characterized by perivascular and parenchymal petechial hemorrhages and microscopic ischemic lesions.\n\nConclusions and RelevanceSWI lesions are common in patients with neurological manifestations of severe COVID-19 (coma and focal neurologic deficits). The distribution of lesions is similar to that seen in patients with hypoxic respiratory failure, sepsis, and disseminated intravascular coagulation. Collectively, these radiologic and histopathologic findings suggest that patients with severe COVID-19 are at risk for multifocal microvascular hemorrhagic and ischemic lesions in the subcortical and deep white matter.\n\nKey Points SectionO_ST_ABSQuestionC_ST_ABSWhat is the prevalence and pathophysiology of cerebral microvascular injury in patients with severe COVID-19?\n\nFindingsIn this retrospective cohort study of 16 patients undergoing MRI for neurologic complications of severe COVID-19, microvascular lesions were observed in 11 patients and showed an anatomic distribution similar to that seen in patients with hypoxic respiratory failure and sepsis. In one patient who died, brain autopsy revealed widespread microvascular injury, including perivascular microhemorrhages and microscopic ischemic lesions.\n\nMeaningMicrovascular injury is common in patients with severe COVID-19. Radiologic-pathologic correlation, though limited to a single case, provides insights into possible mechanisms of injury.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "John Conklin", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Matthew P. Frosch", - "author_inst": "C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital" - }, - { - "author_name": "Shibani Mukerji", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Otto Rapalino", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Mary Maher", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Pamela W. Schaefer", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Michael H. Lev", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Ramon G. Gonzalez", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Sudeshna Das", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Samantha N. Champion", - "author_inst": "C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital" - }, - { - "author_name": "Colin Magdamo", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Pritha Sen", - "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "George Kyle Harrold", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Haitham Alabsi", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Erica Normandin", - "author_inst": "Broad Institute, Massachusetts Institute of Technology and Harvard University" - }, - { - "author_name": "Bennett Shaw", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Jacob Lemieux", - "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Pardis Sabeti", - "author_inst": "Broad Institute, Massachusetts Institute of Technology and Harvard University" - }, - { - "author_name": "John A. Branda", - "author_inst": "Department of Pathology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Emery N. Brown", - "author_inst": "Broad Institute, Massachusetts Institute of Technology and Harvard University" - }, - { - "author_name": "M. Brandon Westover", - "author_inst": "Department of Neurology, Massachusetts General Hospital" - }, - { - "author_name": "Susie Y. Huang", - "author_inst": "Department of Radiology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Brian L Edlow", - "author_inst": "Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.07.21.20159327", "rel_title": "COVID-19 Vulnerability of Transgender Women With and Without HIV Infection in the Eastern and Southern U.S.", @@ -1293719,6 +1296945,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.21.20159384", + "rel_title": "Initial Experience in Predicting the Risk of Hospitalization of 496 Outpatients with COVID-19 Using a Telemedicine Risk Assessment Tool", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20159384", + "rel_abs": "TitleInitial Experience in Validation of a Telemedicine Risk Assessment Tool for Hospitalization of Patients with COVID-19\n\nImportanceRisk assessment of patients with acute coronavirus disease 2019 (COVID-19) in a telemedicine context is not well described. In the setting of large numbers of patients, a risk assessment tool may guide resource allocation not only for patient care but also for maximum healthcare and public health benefit.\n\nObjectiveTo determine whether a risk prediction tool developed and implemented in March 2020 (\"COVID-19 Telemedicine Risk Tier Assessment\") accurately predicts subsequent hospitalizations.\n\nDesignRetrospective cohort study, enrollment from March 24 to May 26, 2020 with follow-up calls until hospitalization or clinical improvement (final call date range March 27 to June 19, 2020)\n\nSettingSingle center \"Virtual Outpatient Management Clinic\" (VOMC) assessing and managing outpatients from a large quaternary medical system in Atlanta, Georgia\n\nParticipants496 patients with COVID-19 confirmed by nasopharyngeal sampling in isolation at home at the time of diagnosis. Exclusion criteria included: (1) hospitalization prior to VOMC enrollment, (2) immediate discharge from VOMC with no follow-up calls due to resolution.\n\nExposureAcute COVID-19 illness\n\nMain Outcome and MeasuresHospitalization was the outcome. Days to hospitalization was the metric. Survival analysis using Cox regression was used to determine factors associated with hospitalization.\n\nResultsThe risk-assessment rubric assigned 496 outpatients to tiers as follows: Tier 1, 237 (47.8%); Tier 2, 185 (37.3%); Tier 3, 74 (14.9%). Subsequent hospitalizations numbered 3 (1%), 15 (7%), and 17 (23%) and for Tiers 1-3, respectively. From a Cox regression model with age [≥] 60, gender, and self-reported obesity as covariates, the adjusted hazard ratios using Tier 1 as reference were: Tier 2 HR=3.74 (95% CI, 1.06-13.27; P=0.041); Tier 3 HR=10.87 (95% CI, 3.09-38.27; P<0.001). Tier was the strongest predictor of time to hospitalization.\n\nConclusions and RelevanceA telemedicine risk assessment tool prospectively applied to an outpatient population with COVID-19 identified both low-risk (Tier 1) and high-risk (Tier 3) patients with better performance than individual risk factors alone. This approach may be appropriate for optimum allocation of resources.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "James B O'Keefe", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Elizabeth J Tong", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Thomas H Taylor Jr.", + "author_inst": "Taylor Engineering, Inc." + }, + { + "author_name": "Ghazala D Datoo O'Keefe", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "David C Tong", + "author_inst": "Emory University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.21.20159335", "rel_title": "Model-free estimation of COVID-19 transmission dynamics from a complete outbreak", @@ -1294767,29 +1298028,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.24.20161604", - "rel_title": "CCOFEE-GI Study: Colombian COVID19 First Experience in Gastroentrology. Characterization of digestive manifestations in patients diagnosed with COVID-19 at a highly complex institution in Bogota D.C., Colombia", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161604", - "rel_abs": "The current pandemic caused by SARS-CoV-2 has posed an important threat to the human health, healthcare systems, economy, and structure of societies. In Colombia, the first case was diagnosed on March 6, 2020, with exponential progressive growth, and there were >200,000 confirmed cases as of July 20, 2020, in this cross-sectional, analytical, and observational study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Latinamerica, with special emphasis on gastrointestinal symptoms. Methods: Demographic and clinical data were collected, results related to the outcomes such as hospitalization time, admission to ICU, need for orotracheal intubation, and death were also included. Statistical analyses were conducted using Stata software V.15.\n\nResultsWe included 72 patients RT-PCR positive for SARS-CoV-2 (34 women and 38 men) with age 47.5 {+/-} 17.7 years; 17 (23.6%) presented at least one of the gastrointestinal symptoms (nausea/vomiting, abdominal pain, and/or diarrhea). 13 (76.47%) presented with diarrhea, 29.41% with nausea/vomiting, and five (29.41%) with abdominal pain. Diarrhea in 18.06% of all those infected with SARS-CoV-2 at the time of consultation, which was the most common digestive symptom. No significant differences were observed in requirement for endotracheal intubation, hospitalization, ICU admission, and fatal outcome between the NGIS and GIS groups (p:0.671, 0.483, 1,000, and 1,000). Conclusion: In our study, patients with gastrointestinal symptoms had no significant differences in disease severity, admission to ICU or death compared to those who did not have such symptoms.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "ALEJANDRO CONCHA-MEJIA", - "author_inst": "FUNDACION CLINICA SHAIO" - }, - { - "author_name": "REINALDO ANDRES RINCON-SANCHEZ", - "author_inst": "FUNDACION CLINICA SHAIO" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2020.07.23.20160879", "rel_title": "Factors associated with psychological distress in health-care workers during an infectious disease outbreak: A rapid living systematic review", @@ -1294957,6 +1298195,181 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.07.24.20161471", + "rel_title": "Epidemiological and cohort study finds no association between COVID-19 and Guillain-Barre syndrome", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161471", + "rel_abs": "BackgroundReports of Guillain-Barre Syndrome (GBS) have emerged during the Coronavirus Disease 2019 (COVID-19) pandemic. This epidemiological and cohort study sought to investigate any causative association between COVID-19 infection and GBS.\n\nMethodsThe epidemiology of GBS cases reported via the UK National Immunoglobulin Database were studied from 2016-2019 and compared to cases reported during the COVID-19 pandemic. For the cohort study, members of the British Peripheral Nerve Society reported all cases of GBS during the pandemic. The clinical features, investigation findings and outcomes of COVID-19 (definite or probable) and non-COVID-19 associated GBS cases were compared.\n\nResultsThe UK GBS incidence from 2016-2019 was 1.65-1.88 per 100,000 people per year. GBS and COVID-19 incidence varied between regions and did not correlate (r = 0.06, 95% CI -0.56 to 0.63, p=0.86). GBS incidence fell between March and May 2020 compared to the same months of 2016-2019. Forty-seven GBS cases were included in the cohort study (13 definite, 12 probable COVID-19 and 22 non-COVID-19). There were no significant differences in the pattern of weakness, time to nadir, neurophysiology, CSF findings or outcome. Intubation was more frequent in the COVID-19+ve cohort (7/13, 54% vs 5/22, 23% in COVID negative) thought to be related directly to COVID-19 pulmonary involvement.\n\nConclusionsThis study finds no epidemiological or phenotypic clues of SARS-CoV-2 being causative of GBS. GBS incidence has fallen during the pandemic which may be the influence of lockdown measures reducing transmission of GBS inducing pathogens such as Campylobacter jejuni and respiratory viruses.", + "rel_num_authors": 40, + "rel_authors": [ + { + "author_name": "Stephen Keddie", + "author_inst": "1. University College London, Department of Neuromuscular Diseases London, London, UK WC1E 6BT" + }, + { + "author_name": "Julia Pakpoor", + "author_inst": "Oxford University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Christina Mousele", + "author_inst": "University College London Hospitals NHS Foundation Trust National Hospital for Neurology and Neurosurgery London, London, UK WC1N 3BG" + }, + { + "author_name": "Menelaos Pipis", + "author_inst": "University College London, Department of Neuromuscular Diseases London, London, UK WC1E 6BT" + }, + { + "author_name": "Pedro M Machado", + "author_inst": "University College London, Department of Neuromuscular Diseases London, London, UK WC1E 6BT" + }, + { + "author_name": "Mark Foster", + "author_inst": "University College London Hospitals NHS Foundation Trust National Hospital for Neurology and Neurosurgery London, London, UK WC1N 3BG" + }, + { + "author_name": "Christopher J Record", + "author_inst": "St George's University Hospitals NHS Foundation Trust London, London, UK SW17 0QT" + }, + { + "author_name": "Ryan Keh", + "author_inst": "Salford Royal NHS Foundation Trust, Manchester Centre for Clinical Neuroscience Salford, Salford, UK M6 8HD" + }, + { + "author_name": "Janev Fehmi", + "author_inst": "University of Oxford Nuffield Department of Clinical Neurosciences Oxford, Oxfordshire, UK OX3 9DU" + }, + { + "author_name": "Ross W Paterson", + "author_inst": "University College London, Queen Square Institute of Neurology National Hospital for Neurology and Neurosurgery Queen Square London, London, UK WC1N 3BG" + }, + { + "author_name": "Viraj Bharambe", + "author_inst": "Walton Centre for Neurology and Neurosurgery Liverpool, Liverpool, UK L9 7LJ" + }, + { + "author_name": "Lisa Clayton", + "author_inst": "Barts Health NHS Trust London, London, UK E1 1RD +44 208 869 2623" + }, + { + "author_name": "Claire Allen", + "author_inst": "Poole Hospital NHS Foundation Trust Poole, Poole, UK BH15 2JB" + }, + { + "author_name": "Olivia Price", + "author_inst": "Basildon and Thurrock University Hospitals NHS Foundation Trust Basildon, Essex, UK SS16 5NL" + }, + { + "author_name": "Jasmine Wall", + "author_inst": "Lancashire Teaching Hospitals NHS Foundation Trust Preston, Lancashire, UK PR2 9HT" + }, + { + "author_name": "Annamaria Kiss-csenki", + "author_inst": "Hampshire Hospitals NHS Foundation Trust Winchester, Hampshire, UK SO22 5DG" + }, + { + "author_name": "Dipa P Rathnasabapathi", + "author_inst": "University Hospital Southampton NHS Foundation Trust Southampton, Southampton, UK SO16 6YD" + }, + { + "author_name": "Ruth Geraldes", + "author_inst": "University of Oxford Nuffield Department of Clinical Neurosciences Oxford, Oxfordshire, UK OX3 9DU" + }, + { + "author_name": "Tatyana Yermakova", + "author_inst": "Leeds Teaching Hospitals NHS Trust Leeds, Leeds, UK LS1 3EX" + }, + { + "author_name": "Josh King-Robson", + "author_inst": "King's College Hospital NHS Foundation Trust London, London, UK SE5 9RS" + }, + { + "author_name": "Maya Zosmer", + "author_inst": "North Middlesex University Hospital NHS Trust London, London, UK N18 1QX" + }, + { + "author_name": "Sanjeev Rajakulendran", + "author_inst": "University College London Hospitals NHS Foundation Trust National Hospital for Neurology and Neurosurgery London, London, UK WC1N 3BG" + }, + { + "author_name": "Ross Nortley", + "author_inst": "University College London, Queen Square Institute of Neurology National Hospital for Neurology and Neurosurgery Queen Square London, London, UK WC1N 3BG" + }, + { + "author_name": "Charles Marshall", + "author_inst": "Barts Health NHS Trust London, London, UK E1 1RD +44 208 869 2623" + }, + { + "author_name": "Edward Newman", + "author_inst": "Queen Elizabeth University Hospital Glasgow, Glasgow, UK G51 4TF" + }, + { + "author_name": "Niranjanan Nirmalananthan", + "author_inst": "St George's University Hospitals NHS Foundation Trust London, London, UK SW17 0QT" + }, + { + "author_name": "Guru Kumar", + "author_inst": "Darent Valley Hospital Dartford, Kent, UK DA2 8DA" + }, + { + "author_name": "Ashwin A Pinto", + "author_inst": "University Hospital Southampton NHS Foundation Trust Southampton, Southampton, UK SO16 6YD" + }, + { + "author_name": "James Holt", + "author_inst": "Walton Centre for Neurology and Neurosurgery Liverpool, Liverpool, UK L9 7LJ" + }, + { + "author_name": "Tim Lavin", + "author_inst": "Salford Royal NHS Foundation Trust, Manchester Centre for Clinical Neuroscience Salford, Salford, UK M6 8HD" + }, + { + "author_name": "Katie Brennan", + "author_inst": "Queen Elizabeth University Hospital Glasgow, Glasgow, UK G51 4TF" + }, + { + "author_name": "Michael Zandi", + "author_inst": "University College London Hospitals NHS Foundation Trust National Hospital for Neurology and Neurosurgery London, London, UK WC1N 3BG" + }, + { + "author_name": "Dipa L Jayaseelan", + "author_inst": "University College London Hospitals NHS Foundation Trust National Hospital for Neurology and Neurosurgery London, London, UK WC1N 3BG" + }, + { + "author_name": "Jane Pritchard", + "author_inst": "Imperial College Healthcare NHS Trust, Department of Neurology London, UK W2 1NY" + }, + { + "author_name": "Robert DM Hadden", + "author_inst": "King's College Hospital NHS Foundation Trust London, London, UK SE5 9RS" + }, + { + "author_name": "Hadi Manji", + "author_inst": "University College London Hospitals NHS Foundation Trust National Hospital for Neurology and Neurosurgery London, London, UK WC1N 3BG" + }, + { + "author_name": "Hugh J Willison", + "author_inst": "Queen Elizabeth University Hospital Glasgow, Glasgow, UK G51 4TF" + }, + { + "author_name": "Simon Rinaldi", + "author_inst": "University of Oxford Nuffield Department of Clinical Neurosciences Oxford, Oxfordshire, UK OX3 9DU" + }, + { + "author_name": "Aisling S Carr", + "author_inst": "University College London Hospitals NHS Foundation Trust National Hospital for Neurology and Neurosurgery London, London, UK WC1N 3BG" + }, + { + "author_name": "Michael P Lunn", + "author_inst": "University College London, Department of Neuromuscular Diseases London, London, UK WC1E 6BT" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.07.23.20161000", "rel_title": "Time to SARS-CoV-2 Clearance Among Patients with Cancer and COVID-19", @@ -1296069,41 +1299482,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.22.20160184", - "rel_title": "Forecasting hospitalizations due to COVID-19 in South Dakota, USA.", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160184", - "rel_abs": "1Anticipating the number of hospital beds needed for patients with COVID-19 remains a challenge. Early efforts to predict hospital bed needs focused on deriving predictions from SIR models, largely at the level of countries, provinces, or states. In the United States, these models rely on data reported by state health agencies. However, predictive disease and hospitalization dynamics at the state level are complicated by geographic variation in disease parameters. In addition it is difficult to make forecasts early in a pandemic due to minimal data. However, Bayesian approaches that allow models to be specified with informed prior information from areas that have already completed a disease curve can serve as prior estimates for areas that are beginning their curve. Here, a Bayesian non-linear regression (Weibull function) was used to forecast cumulative and active COVID-19 hospitalizations for South Dakota, USA. As expected, early forecasts were dominated by prior information, which was derived from New York City. Importantly, hospitalization trends also differed within South Dakota due to early peaks in an urban area, followed by later peaks in other rural areas of the state. Combining these trends led to altered forecasts with relevant policy implications.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jeff S Wesner", - "author_inst": "University of South Dakota" - }, - { - "author_name": "Dan Van Peursem", - "author_inst": "University of South Dakota" - }, - { - "author_name": "Jose Flores", - "author_inst": "University of South Dakota" - }, - { - "author_name": "Yuhlong Lio", - "author_inst": "University of South Dakota" - }, - { - "author_name": "Chelsea Wesner", - "author_inst": "University of South Dakota" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.22.20160283", "rel_title": "Heat-based Decontamination of N95 Masks Using a Commercial Laundry Dryer", @@ -1296391,6 +1299769,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.22.20160127", + "rel_title": "COVID-19 in-hospital mortality and mode of death in a dynamic and non-restricted tertiary care model in Germany", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160127", + "rel_abs": "BackgroundReported mortality of hospitalised COVID-19 patients varies substantially, particularly in critically ill patients. So far COVID-19 in-hospital mortality and modes of death under optimised care conditions have not been systematically studied.\n\nMethodsThis retrospective observational monocenter cohort study was performed after implementation of a non-restricted, dynamic tertiary care model at the University Medical Center Freiburg, an experienced ARDS and ECMO referral center. All hospitalised patients with PCR-confirmed SARS-CoV-2 infection were included. The primary endpoint was in-hospital mortality, secondary endpoints included major complications and modes of death. A multistate analysis and a Cox regression analysis for competing risk models were performed. Modes of death were determined by two independent reviewers.\n\nResultsBetween February 25, and May 8, 213 patients were included in the analysis. The median age was 65 years, 129 patients (61%) were male. 70 patients (33%) were admitted to the intensive care unit (ICU), of which 57 patients (81%) received mechanical ventilation and 23 patients (33%) extracorporeal membrane-oxygenation (ECMO) support. According to the multistate model the probability to die within 90 days after COVID-19 onset was 24% in the whole cohort. If the levels of care at time of study entry were accounted for, the probabilities to die were 16% if the patient was initially on a regular ward, 47% if in the ICU and 57% if mechanical ventilation was required at study entry. Age [≥]65 years and male sex were predictors for in-hospital death. Predominant complications - as judged by two independent reviewers - determining modes of death were multi-organ failure, septic shock and thromboembolic and hemorrhagic complications.\n\nConclusionIn a dynamic care model COVID-19-related in-hospital mortality remained substantial. In the absence of potent antiviral agents, strategies to alleviate or prevent the identified complications should be investigated. In this context, multistate analyses enable comparison of models-of-care and treatment strategies and allow estimation and allocation of health care resources.\n\nRegistrationGerman Clinical Trials Register (identifier DRKS00021775), retrospectively registered June 10, 2020.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Siegbert Rieg", + "author_inst": "Division of Infectious Diseases, Department of Medicine II, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg" + }, + { + "author_name": "Maja von Cube", + "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of" + }, + { + "author_name": "Johannes Kalbhenn", + "author_inst": "Department of Anesthesiology and Intensive Care Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, " + }, + { + "author_name": "Stefan Utzolino", + "author_inst": "Department of General and Visceral Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany" + }, + { + "author_name": "Katharina Pernice", + "author_inst": "Department of Cardiovascular Surgery, Heart Center, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, German" + }, + { + "author_name": "Lena Bechet", + "author_inst": "Division of Infectious Diseases, Department of Medicine II, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg" + }, + { + "author_name": "Johanna Baur", + "author_inst": "Department of Medicine III (Interdisciplinary Medical Intensive Care), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 791" + }, + { + "author_name": "Corinna N Lang", + "author_inst": "Department of Medicine III (Interdisciplinary Medical Intensive Care), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 791" + }, + { + "author_name": "Dirk Wagner", + "author_inst": "Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany" + }, + { + "author_name": "Martin Wolkewitz", + "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, 79104 Freiburg, Germany" + }, + { + "author_name": "Winfried V Kern", + "author_inst": "Division of Infectious Diseases, Department of Medicine II, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg" + }, + { + "author_name": "Paul Biever", + "author_inst": "Department of Cardiology and Angiology I, Heart Center Freiburg University, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.22.20160002", "rel_title": "Remdesivir for COVID-19: match-population analysis with compassionate use of Remdesivir for severe COVID-19", @@ -1297563,53 +1301004,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.07.22.212761", - "rel_title": "SARS-CoV-2-induced humoral immunity through B cell epitope analysis and neutralizing activity in COVID-19 infected individuals in Japan", - "rel_date": "2020-07-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.22.212761", - "rel_abs": "The aim of this study is to understand adaptive immunity to SARS-CoV-2 through the analysis of B cell epitope and neutralizing activity in coronavirus disease 2019 (COVID-19) patients. We obtained serum from thirteen COVID-19 patients. Most individuals revealed neutralizing activity against SARS-CoV-2 assessed by a pseudotype virus-neutralizing assay. The antibody production against the spike glycoprotein (S protein) or receptor-binding domain (RBD) of SARS-CoV-2 was elevated, with large individual differences, as assessed by ELISA. In the analysis of the predicted the linear B cell epitopes, two regions (671-690 aa. and 1146-1164 aa.), which were located in S1 and S2 but not in the RBD, were highly reactive with the sera from patients. In the further analysis of the B cell epitope within the S protein by utilizing a B cell epitope array, a hot spot in the N-terminal domain of the S protein but not the RBD was observed in individuals with neutralizing activity. Overall, the analysis of antibody production and B cell epitopes of the S protein from patient serum may provide a novel target for the vaccine development against SARS-CoV-2.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Shota Yoshida", - "author_inst": "Osaka University Graduate School of Medicine" - }, - { - "author_name": "Chikako Ono", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Hiroki Hayashi", - "author_inst": "Osaka University Graduate School of Medicine" - }, - { - "author_name": "Satoshi Shiraishi", - "author_inst": "Juso Osaka City Hospital" - }, - { - "author_name": "Tomono Kazunori", - "author_inst": "Division of Infection Control and Prevention, Osaka University Hospital" - }, - { - "author_name": "Hisashi Arase", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Yoshiharu Matsuura", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Hironori Nakagami", - "author_inst": "Osaka University Graduate School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.23.212357", "rel_title": "Single-dose intranasal vaccination elicits systemic and mucosal immunity against SARS-CoV-2", @@ -1297929,6 +1301323,57 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2020.07.21.20158956", + "rel_title": "Impact of COVID-19 on Public Research Recruitment", + "rel_date": "2020-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20158956", + "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic created a major challenge for clinical trials recruitment as early attention was focused on matters of public health and clinical care, and research--outside of COVID-19-- essentially shut down. Rally with Partners (rally.partners.org), an Internet-based portal for clinical research volunteer recruitment, continued to support studies that continued their recruitment during this period and additionally, implemented several measures to support COVID-19 research. In this paper, we summarize our experiences and preliminary results.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yichuan Grace Hsieh", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Holly Parker", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Greg Estey", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Stephen Lorenz", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Mark Wylie", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Xiaofeng Zhang", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Joseph Lopiccolo", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Lloyd Clarke", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jeanhee Chung", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.07.21.20158923", "rel_title": "Regional variability in time-varying transmission potential of COVID-19 in South Korea", @@ -1299417,37 +1302862,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.22.215731", - "rel_title": "Elucidation of Genome Polymorphisms in Emerging SARS-CoV-2", - "rel_date": "2020-07-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.22.215731", - "rel_abs": "The COVID-19 pandemic is having a devastating effect on the healthcare system and the economy of the world. The unavailability of a specific treatment regime and a candidate vaccine yet opens up scope for new approaches and discoveries of drugs for mitigation of the sufferings of humankind due to the disease. The present isolated whole-genome sequences of SARS-CoV-2 from 11 different nations subjected to evolutionary study and genome-wide association study through in silico approaches including multiple sequence alignment, phylogenetic study through MEGA7 and have been analyzed through DNAsp respectively. These investigations recognized the nucleotide varieties and single nucleotide mutations/polymorphisms on the genomic regions as well as protein-coding regions. The resulted mutations have diversified the genomic contents of SARS-CoV-2 according to the altered nucleotides found in 11 genome sequences. India and Nepal have found to have progressively more distinct species of SARS-CoV-2 with variations in Spike protein and Nucleocapsid protein-coding sites. These genomic variations might be the explanation behind the less case fatality rate of India and Nepal dependent on the populaces. The anticipated idea of this investigation upgrades the information about genomic medication and might be useful in the planning of antibodies against SARS-CoV-2.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Manisha Ray", - "author_inst": "All India Institute of Medical Sciences, Bhubaneswar" - }, - { - "author_name": "Saurav Sarkar", - "author_inst": "All India Institute of Medical Sciences, Bhubaneswar" - }, - { - "author_name": "Surya Narayan Rath", - "author_inst": "OUAT" - }, - { - "author_name": "Mukund Namdev Sable", - "author_inst": "All India Institute of Medical Sciences, Bhubaneswar" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.07.22.215590", "rel_title": "Inadequate level of knowledge, mixed outlook and poor adherence to COVID-19 prevention guideline among Ethiopians", @@ -1299635,6 +1303049,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.19.20157305", + "rel_title": "Clinical Characteristics and Outcomes for 7,995 Patients with SARS-CoV-2 Infection", + "rel_date": "2020-07-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.19.20157305", + "rel_abs": "ObjectiveSevere acute respiratory syndrome virus (SARS-CoV-2) has infected millions of people worldwide. Our goal was to identify risk factors associated with admission and disease severity in patients with SARS-CoV-2.\n\nDesignThis was an observational, retrospective study based on real-world data for 7,995 patients with SARS-CoV-2 from a clinical data repository.\n\nSettingYale New Haven Health (YNHH) is a five-hospital academic health system serving a diverse patient population with community and teaching facilities in both urban and suburban areas.\n\nPopulationsThe study included adult patients who had SARS-CoV-2 testing at YNHH between March 1 and April 30, 2020.\n\nMain outcome and performance measuresPrimary outcomes were admission and in-hospital mortality for patients with SARS-CoV-2 infection as determined by RT-PCR testing. We also assessed features associated with the need for respiratory support.\n\nResultsOf the 28605 patients tested for SARS-CoV-2, 7995 patients (27.9%) had an infection (median age 52.3 years) and 2154 (26.9%) of these had an associated admission (median age 66.2 years). Of admitted patients, 1633 (75.8%) had a discharge disposition at the end of the study period. Of these, 192 (11.8%) required invasive mechanical ventilation and 227 (13.5%) expired. Increased age and male sex were positively associated with admission and in-hospital mortality (median age 81.9 years), while comorbidities had a much weaker association with the risk of admission or mortality. Black race (OR 1.43, 95%CI 1.14-1.78) and Hispanic ethnicity (OR 1.81, 95%CI 1.50-2.18) were identified as risk factors for admission, but, among discharged patients, age-adjusted in-hospital mortality was not significantly different among racial and ethnic groups.\n\nConclusionsThis observational study identified, among people testing positive for SARS-CoV-2 infection, older age and male sex as the most strongly associated risks for admission and in-hospital mortality in patients with SARS-CoV-2 infection. While minority racial and ethnic groups had increased burden of disease and risk of admission, age-adjusted in-hospital mortality for discharged patients was not significantly different among racial and ethnic groups. Ongoing studies will be needed to continue to evaluate these risks, particularly in the setting of evolving treatment guidelines.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Jacob McPadden", + "author_inst": "Yale University" + }, + { + "author_name": "Frederick Warner", + "author_inst": "Yale University" + }, + { + "author_name": "H. Patrick Young", + "author_inst": "Yale University" + }, + { + "author_name": "Nathan C. Hurley", + "author_inst": "Yale University" + }, + { + "author_name": "Rebecca A. Pulk", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Avinainder Singh", + "author_inst": "Yale University" + }, + { + "author_name": "Thomas JS Durant", + "author_inst": "Yale University" + }, + { + "author_name": "Guannan Gong", + "author_inst": "Yale University" + }, + { + "author_name": "Nihar Desai", + "author_inst": "Yale University" + }, + { + "author_name": "Adrian Haimovich", + "author_inst": "Yale University" + }, + { + "author_name": "Richard Andrew Taylor", + "author_inst": "Yale University" + }, + { + "author_name": "Murat Gunel", + "author_inst": "Yale University" + }, + { + "author_name": "Charles S. Dela Cruz", + "author_inst": "Yale University" + }, + { + "author_name": "Shelli F Farhadian", + "author_inst": "Yale University" + }, + { + "author_name": "Jonathan Siner", + "author_inst": "Yale University" + }, + { + "author_name": "Merceditas Villanueva", + "author_inst": "Yale University" + }, + { + "author_name": "Keith Churchwell", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Allen Hsiao", + "author_inst": "Yale University" + }, + { + "author_name": "Charles J. Torre Jr.", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Eric J. Velazquez", + "author_inst": "Yale University" + }, + { + "author_name": "Roy S. Herbst", + "author_inst": "Yale University" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University" + }, + { + "author_name": "Albert I. Ko", + "author_inst": "Yale University" + }, + { + "author_name": "Bobak J. Mortazavi", + "author_inst": "Yale University" + }, + { + "author_name": "Harlan M. Krumholz", + "author_inst": "Yale University" + }, + { + "author_name": "Wade L. Schulz", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.20.20157446", "rel_title": "The change pattern and significance of IgM and IgG in the progress of COVID-19 disease", @@ -1300731,93 +1304264,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.16.20155663", - "rel_title": "Humoral Response Dynamics Following Infection with SARS-CoV-2", - "rel_date": "2020-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155663", - "rel_abs": "IntroductionSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) specific antibodies have been shown to neutralize the virus in-vitro. Understanding antibody dynamics following SARS-CoV-2 infection is therefore crucial. Sensitive measurement of SARS-CoV-2 antibodies is also vital for large seroprevalence surveys which inform government policies and public health interventions. However, rapidly waning antibodies following SARS-CoV-2 infection could jeopardize the sensitivity of serological testing on which these surveys depend.\n\nMethodsThis prospective cohort study of SARS-CoV-2 humoral dynamics in a central London hospital analyzed 137 serial samples collected from 67 participants seropositive to SARS-CoV-2 by the Meso-Scale Discovery assay. Antibody titers were quantified to the SARS-CoV-2 nucleoprotein (N), spike (S-)protein and the receptor-binding-domain (RBD) of the S-protein. Titers were log-transformed and a multivariate log-linear model with time-since-infection and clinical variables was fitted by Bayesian methods.\n\nResultsThe mean estimated half-life of the N-antibody was 52 days (95% CI 42-65). The S- and RBD-antibody had significantly longer mean half-lives of 81 days (95% CI 61-111) and 83 days (95% CI 55-137) respectively. An ACE-2-receptor competition assay demonstrated significant correlation between the S and RBD-antibody titers and ACE2-receptor blocking in-vitro. The time-to-a-negative N-antibody test for 50% of the seropositive population was predicted to be 195 days (95% CI 163-236).\n\nDiscussionAfter SARS-CoV-2 infection, the predicted half-life of N-antibody was 52 days with 50% of seropositive participants becoming seronegative to this antibody at 195 days. Widely used serological tests that depend on the N-antibody will therefore significantly underestimate the prevalence of infection following the majority of infections.\n\nSignificance statementWe believe that our study has significant and urgent public health and translational impact. Firstly, our findings demonstrate that the half-life of the SARS-CoV-2 nucleoprotein antibody is only 52 days. This has immediate and important implications for large-scale seroprevalence surveys, government policy and mathematical modelling predictions which rely on serological tests that target this antibody. Secondly, the slower decay of the SARS-CoV-2 spike protein antibody identified in this study makes assays to the spike protein a more reliable target for serological assays in the longer term. We demonstrate a strong positive linear correlation between spike/RBD antibody and ACE-2 receptor binding in vitro. Our findings are therefore likely to reflect the time to loss of a functional antibody response in SARS-CoV-2.\n\nFundingGOSH charity, Wellcome Trust (201470/Z/16/Z and 220565/Z/20/Z). GOSH NIHR Funded Biomedical Research Centre.\n\nTrial registration numberNCT04380896.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Louis Grandjean", - "author_inst": "University College London, Institute of Child Health" - }, - { - "author_name": "Anja Saso", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Arturo Ortiz", - "author_inst": "Imperial College" - }, - { - "author_name": "Tanya Lam", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "James Hatcher", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Rosie Thistlethwaite", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Mark Harris", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Timothy Best", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Marina Johnson", - "author_inst": "University College London" - }, - { - "author_name": "Helen Wagstaffe", - "author_inst": "University College London" - }, - { - "author_name": "Elizabeth Ralph", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Annabelle Mai", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Caroline Colijn", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Judith Breuer", - "author_inst": "University College London" - }, - { - "author_name": "Matthew Buckland", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Kimberly Gilmour", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "David Goldblatt", - "author_inst": "University College London" - }, - { - "author_name": "- The Co-Stars Study Team", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.21.213777", "rel_title": "Cellular events of acute, resolving or progressive COVID-19 in SARS-CoV-2 infected non-human primates", @@ -1301169,6 +1304615,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.21.214098", + "rel_title": "Molecular mechanism of SARS-CoV-2 cell entry inhibition via TMPRSS2 by Camostat and Nafamostat mesylate", + "rel_date": "2020-07-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.21.214098", + "rel_abs": "The entry of the coronavirus SARS-CoV-2 into human cells can be inhibited by the approved drugs camostat and nafamostat. Here we elucidate the molecular mechanism of these drugs by combining experiments and simulations. In vitro assays confirm the hypothesis that both drugs act by inhibiting the human protein TMPRSS2. As no experimental structure is available, we provide a model of the TMPRSS2 equilibrium structure and its fluctuations by relaxing an initial homology structure with extensive 280 microseconds of all-atom molecular dynamics (MD) and Markov modeling. We describe the binding mode of both drugs with TMPRSS2 in a Michaelis complex (MC) state preceding the formation of a long-lived covalent inhibitory state. We find that nafamostat to has a higher MC population, which in turn leads to the more frequent formation of the covalent complex and thus higher inhibition efficacy, as confirmed in vitro and consistent with previous virus cell entry assays. Our TMPRSS2-drug structures are made public to guide the design of more potent and specific inhibitors.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tim Hempel", + "author_inst": "FU Berlin" + }, + { + "author_name": "Llu\u00eds Raich", + "author_inst": "FU Berlin" + }, + { + "author_name": "Simon Olsson", + "author_inst": "FU Berlin" + }, + { + "author_name": "Frank Noe", + "author_inst": "FU Berlin" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.07.20.212837", "rel_title": "Single cell RNA sequencing of blood antigen-presenting cells in severe Covid-19 reveals multi-process defects in antiviral immunity", @@ -1302637,93 +1306114,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.19.20152322", - "rel_title": "Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy", - "rel_date": "2020-07-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.19.20152322", - "rel_abs": "From February to April, 2020, Lombardy (Italy) was the area who worldwide registered the highest numbers of SARS-CoV-2 infection. By extensively analyzing 346 whole SARS-CoV-2 genomes, we demonstrated the simultaneous circulation in Lombardy of two major viral lineages, likely derived from multiple introductions, occurring since the second half of January. Seven single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. These two lineages, and the presence of two well defined clusters inside Lineage 1, revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Claudia Alteri", - "author_inst": "University of Milan" - }, - { - "author_name": "Valeria Cento", - "author_inst": "University of Milan" - }, - { - "author_name": "Antonio Piralla", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Valentino Costabile", - "author_inst": "University of Milan" - }, - { - "author_name": "Monica Tallarita", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Luna Colagrossi", - "author_inst": "Bambino Gesu Children's Hospital" - }, - { - "author_name": "Silvia Renica", - "author_inst": "University of Milan" - }, - { - "author_name": "Federica Giardina", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Federica Novazzi", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Stefano Gaiarsa", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - }, - { - "author_name": "Elisa Matarazzo", - "author_inst": "University of Milan" - }, - { - "author_name": "Maria Antonello", - "author_inst": "University of Milan" - }, - { - "author_name": "Chiara Vismara", - "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" - }, - { - "author_name": "Roberto Fumagalli", - "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" - }, - { - "author_name": "Oscar Massimiliano Epis", - "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" - }, - { - "author_name": "Massimo Puoti", - "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" - }, - { - "author_name": "Carlo Federico Perno", - "author_inst": "University of Milan" - }, - { - "author_name": "Fausto Baldanti", - "author_inst": "Fondazione IRCCS Policlinico San Matteo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.18.210120", "rel_title": "High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients", @@ -1302987,6 +1306377,49 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.07.19.179101", + "rel_title": "Haplotype Explorer: an infection cluster visualization tool for spatiotemporal dissection of the COVID-19 pandemic", + "rel_date": "2020-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.19.179101", + "rel_abs": "The worldwide eruption of COVID-19 that began in Wuhan, China in late 2019 reached 10 million cases by late June 2020. In order to understand the epidemiological landscape of the COVID-19 pandemic, many studies have attempted to elucidate phylogenetic relationships between collected viral genome sequences using haplotype networks. However, currently available applications for network visualization are not suited to understand the COVID-19 epidemic spatiotemporally, due to functional limitations That motivated us to develop Haplotype Explorer, an intuitive tool for visualizing and exploring haplotype networks. Haplotype Explorer enables people to dissect epidemiological consequences via interactive node filters to provide spatiotemporal perspectives on multimodal spectra of infectious diseases, including introduction, outbreak, expansion, and containment, for given regions and time spans. Here, we demonstrate the effectiveness of Haplotype Explorer by showing an example of its visualization and features. The demo using SARS-CoV-2 genome sequences is available at https://github.com/TKSjp/HaplotypeExplorer\n\nSummaryA lot of software for network visualization are available, but existing software have not been optimized to infection cluster visualization against the current worldwide invasion of COVID-19 started since 2019. To reach the spatiotemporal understanding of its epidemics, we developed Haplotype Explorer. It is superior to other applications in the point of generating HTML distribution files with metadata searches which interactively reflects GISAID IDs, locations, and collection dates. Here, we introduce the features and products of Haplotype Explorer, demonstrating the time-dependent snapshots of haplotype networks inferred from total of 4,282 SARS-CoV-2 genomes.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tetsuro Kawano-Sugaya", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Koji Yatsu", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Tsuyoshi Sekizuka", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Kentaro Itokawa", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Masanori Hashino", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Rina Tanaka", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Makoto Kuroda", + "author_inst": "National Institute of Infectious Diseases" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.07.18.210211", "rel_title": "Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication", @@ -1304075,33 +1307508,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.16.20155200", - "rel_title": "Gender and trust in government modify the association between mental health and stringency of social distancing related public health measures to reduce COVID-19: a global online survey", - "rel_date": "2020-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155200", - "rel_abs": "ObjectivesTo investigate the associations between stringency of COVID-19 social distancing policies and mental health outcomes, and the moderating effect of trust in government and gender.\n\nDesign and settingCross sectional study involving secondary analysis of publicly available data from a global online COVID-19 survey and the Oxford COVID-19 Government Response Tracker.\n\nParticipants106,497 participants from 58 countries.\n\nMain outcome measuresOutcomes were a worries index and a depression index. Predictors were stringency of policies, trust in government, and gender. Multivariable regression was conducted to determine the three-way interaction between the predictor variables for mental health outcomes, adjusting for age, income and education.\n\nResultsThe median age of participants (56.4% women) was 37 years (interquartile range 29 to 48 years). Women had higher worries and depression scores than men. 45.4% distrusted the government and 43.8% trusted the government to take care of its citizens. Among those who strongly trusted the government, an increase in the stringency of policies was associated with a significant increase in the worries index. Among men who distrusted the government, an increase in policy stringency was associated with an increase in the depression index but not the worries index. In women that strongly distrusted the government, there was an inversed U-shaped association between policy stringency and both the worries and depression indices.\n\nConclusionAs the stringency of public health measures increases, so too do depression and worries. The association is moderated by gender and trust in government. For safe and effective public health measures, governments should develop strategies to increase trust in their actions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lily O'Hara", - "author_inst": "Qatar University" - }, - { - "author_name": "Hanan F Abdul Rahim", - "author_inst": "Qatar University" - }, - { - "author_name": "Zumin Shi", - "author_inst": "Qatar University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.17.20155242", "rel_title": "Genetic inhibition of interleukin-6 receptor signaling and Covid-19", @@ -1304509,6 +1307915,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2020.07.17.20155994", + "rel_title": "Effect of corticosteroid treatment on 1376 hospitalized COVID-19 patients. A cohort study.", + "rel_date": "2020-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155994", + "rel_abs": "BackgroundSince the start of the novel coronavirus 2019 (COVID-19) pandemic, corticosteroid use has been the subject of debate. The available evidence is uncertain, and knowledge on the subject is evolving. The aim of our cohort study was to evaluate the association between corticosteroid therapy and hospital mortality, in patients hospitalized with COVID-19 after balancing for possible confounders.\n\nResultsOne thousand four hundred forty four patients were admitted to our hospital with a positive RT-PCR test for SARS-CoV-2, 559 patients (39%) were exposed to corticosteroids during hospital stay, 844 (61%) were not exposed to corticosteroids.In the cohort of patients exposed to corticosteroids, 171 (30.6%) died. In the cohort of patients not exposed to corticosteroids, 183 (21.7%) died (unadjusted p <0.001). Nonetheless, exposure to corticosteroids was not associated with in-hospital mortality after balancing with overlap weight propensity score (adjusted p = 0.25). Patients in the corticosteroids cohort had reduced risk of ICU admission (adjusted p <0.001).\n\nConclusionsTreatment with corticosteroids did not affect hospital mortality in patients with COVID-19 after balancing for confounders. A possible advantage of corticosteroid therapy was to reduce Intensive Care Unit admission, which could be useful in reducing pressure on the Intensive Care Units in times of limited resources, as during the COVID-19 pandemic.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Filippo Albani", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Federica Fusina", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Enza Granato", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Cristina Capotosto", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Claudia Ceracchi", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Riccardo Gargaruti", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Giovanni Santangelo", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Luca Schiavone", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Maria Salvatrice Taranto", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Cinzia Tosati", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Elena Vavassori", + "author_inst": "Fondazione Poliambulanza" + }, + { + "author_name": "Giuseppe Natalini", + "author_inst": "Fondazione Poliambulanza" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.16.20155796", "rel_title": "Validation of a new automated chemiluminescent anti-SARS-CoV-2 IgM and IgG antibody assay system detecting both N and S proteins in Japan", @@ -1305901,61 +1309370,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.16.206847", - "rel_title": "Longitudinal analysis of the humoral response to SARS-CoV-2 spike RBD in convalescent plasma donors", - "rel_date": "2020-07-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.16.206847", - "rel_abs": "Hema-Quebec, the blood supplier in the Province of Quebec, Canada, collects and tests convalescent plasma used in a clinical trial to determine the clinical efficacy of this product for the treatment of hospitalized COVID-19 patients. So far, we have collected 1159 plasma units from 282 COVID-19 convalescent donors. The presence of antibodies to the receptor binding domain (RBD) of SARS-CoV-2 spike protein in convalescent donors was established at the first donation. Seropositive donors were asked to donate additional plasma units every six days. Until now, 15 donors have donated at least four times and, in some cases, up to nine times. This allowed us to perform a longitudinal analysis of the persistence of SARS-CoV-2 RBD-specific antibodies in these repeat donors, with the first donation occurring 33-77 days after symptoms onset and donations up to 71-114 days after symptoms onset thereafter. In all donors, the level of antibodies remained relatively stable up to about 76 days after symptoms onset but then started to decrease more rapidly to reach, in some convalescent donors, a seronegative status within 100-110 days after symptoms onset. The decline in anti-RBD antibodies was not related to the number of donations but strongly correlated with the numbers of days after symptoms onset (r = 0.821). This suggests that de novo secretion of SARS-CoV-2 RBD antibodies by short-lived plasma cells stopped about 2-3 months after disease onset, an observation that has important implications for convalescent plasma collection and seroprevalence studies undertaken several months after the peak of infection.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jos\u00e9e Perreault", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Tony Tremblay", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Marie-Jos\u00e9e Fournier", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Mathieu Drouin", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Guillaume Beaudoin-Bussi\u00e8res", - "author_inst": "CRCHUM" - }, - { - "author_name": "J\u00e9r\u00e9mie Pr\u00e9vost", - "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Antoine Lewin", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - }, - { - "author_name": "Philippe B\u00e9gin", - "author_inst": "CHU Ste-Justine" - }, - { - "author_name": "Andr\u00e9s Finzi", - "author_inst": "Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Ren\u00e9e Bazin", - "author_inst": "H\u00e9ma-Qu\u00e9bec" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.15.204339", "rel_title": "Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria", @@ -1306287,6 +1309701,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.13.20152181", + "rel_title": "Progressive worsening of the respiratory and gut microbiome in children during the first two months of COVID-19", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152181", + "rel_abs": "Children are less susceptible to COVID-19 and manifests lower morbidity and mortality after infection, for which a multitude of mechanisms may be proposed. Whether the normal development of gut-airway microbiome is affected by COVID-19 has not been evaluated. We demonstrate that COVID-19 alters the respiratory and gut microbiome of children. Alteration of the microbiome was divergent between the respiratory tract and gut, albeit the dysbiosis was dominated by genus Pseudomonas and sustained for up to 25-58 days in different individuals. The respiratory microbiome distortion persisted in 7/8 children for at least 19-24 days after discharge from the hospital. The gut microbiota showed early dysbiosis towards later restoration in some children, but not others. Disturbed development of both gut and respiratory microbiomes, and prolonged respiratory dysbiosis in children imply possible long-term complications after clinical recovery from COVID-19, such as predisposition to an increased health risk in the post-COVID-19 era.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Rong Xu", + "author_inst": "Institut Pasteur of Shanghai, Chinese Academy of Sciences" + }, + { + "author_name": "Pengcheng Liu", + "author_inst": "Children's Hospital of Fudan University" + }, + { + "author_name": "Tao Zhang", + "author_inst": "Yunnan University" + }, + { + "author_name": "Qunfu Wu", + "author_inst": "Yunnan University" + }, + { + "author_name": "Mei Zeng", + "author_inst": "Children's Hospital of Fudan University" + }, + { + "author_name": "Yingying Ma", + "author_inst": "Shanghai Public Health Clinical Center" + }, + { + "author_name": "Xia Jin", + "author_inst": "Shanghai Public Health Clinical Center" + }, + { + "author_name": "Jin Xu", + "author_inst": "Children's Hospital of Fudan University" + }, + { + "author_name": "Zhigang Zhang", + "author_inst": "Yunnan University" + }, + { + "author_name": "Chiyu Zhang", + "author_inst": "Shanghai Public Health Clinical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.13.20151944", "rel_title": "Seroprevalence of Hospital Staff in Province with Zero COVID-19 cases", @@ -1308107,89 +1311576,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.14.20151126", - "rel_title": "SARS-CoV-2 infection induces robust, neutralizing antibody responses that are stable for at least three months", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20151126", - "rel_abs": "SARS-CoV-2 has caused a global pandemic with millions infected and numerous fatalities. Questions regarding the robustness, functionality and longevity of the antibody response to the virus remain unanswered. Here we report that the vast majority of infected individuals with mild-to-moderate COVID-19 experience robust IgG antibody responses against the viral spike protein, based on a dataset of 19,860 individuals screened at Mount Sinai Health System in New York City. We also show that titers are stable for at least a period approximating three months, and that anti-spike binding titers significantly correlate with neutralization of authentic SARS-CoV-2. Our data suggests that more than 90% of seroconverters make detectible neutralizing antibody responses and that these titers are stable for at least the near-term future.\n\nOne Sentence SummaryAntibody responses induced by natural mild-to-moderate SARS-CoV-2 infection are robust, neutralizing and are stable for at least 3 months.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ania Wajnberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Fatima Amanat", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adolfo Firpo", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Deena Altman", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Mark Bailey", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Mayce Mansour", - "author_inst": "MOUNT SINAI HOSPITAL" - }, - { - "author_name": "Meagan McMahon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Philip Meade", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Damodara Rao Mendu", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Kimberly Muellers", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Daniel Stadlbauer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Kimberly Stone", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Shirin Strohmeier", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Judith Aberg", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "David Reich", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Carlos Cordon-Cardo", - "author_inst": "Mount Sinai Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.15.20140095", "rel_title": "Preparedness, Perceived Impact and Concerns of health Care Workers in a Teaching Hospital during Coronavirus Disease 2019 (COVID-19)", @@ -1308421,6 +1311807,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.07.17.20155986", + "rel_title": "ABO polymorphism and SARS-CoV-2 infection - a meta-analysis", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155986", + "rel_abs": "At present, existing evidence about the association between SARS-CoV-2 infection and ABO blood group polymorphism is preliminary and controversial. In this meta-analysis we investigate this association and determine SARS-CoV-2 positive individuals odds of having a specific blood group compared to controls.\n\nWe performed a systematic search on MEDLINE and LitCovid databases for studies published through July 15, 2020. Seven studies met inclusion criteria for meta-analysis, including a total of 13 subgroups of populations (7503 SARS-CoV-2 positive cases and 2962160 controls).\n\nWe analysed the odds of having each blood group among SARS-CoV-2 positive patients compared with controls. Random-effects models were used to obtain the overall pooled odds ratio (OR). Subgroup and sensitivity analyses were performed in order to explore the source of heterogeneity and results consistency.\n\nThe results of our meta-analysis indicate that SARS-CoV-2 positive individuals are more likely to have blood group A (pooled OR 1.23, 95%CI: 1.09-1.40) and less likely to have blood group O (pooled OR=0.77, 95%CI: 0.67-0.88).\n\nFurther studies are needed to investigate the mechanisms at the basis of this association, which may affect the kinetics of the pandemic according to the blood group distribution within the population.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Davide Golinelli", + "author_inst": "Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum - University of Bologna." + }, + { + "author_name": "Erik Boetto", + "author_inst": "Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum - University of Bologna." + }, + { + "author_name": "Elisa Maietti", + "author_inst": "Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum - University of Bologna." + }, + { + "author_name": "Maria Pia Fantini", + "author_inst": "Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum - University of Bologna." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2020.07.16.20154088", "rel_title": "IgG antibody seroconversion and the clinical progression of COVID-19 pneumonia: A retrospective, cohort study", @@ -1310049,69 +1313466,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.17.20155929", - "rel_title": "Role of intermediate care unit admission and non-invasive respiratory support during the COVID-19 pandemic: a retrospective cohort study", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155929", - "rel_abs": "BackgroundThe COVID-19 pandemic has led to shortage of Intensive Care Unit (ICU) capacity. We developed a triage strategy including non-invasive respiratory support and admission to the intermediate care unit (IMCU). ICU admission was restricted to patients requiring invasive ventilation.\n\nObjectivesThe aim of this study is to describe the characteristics and outcomes of patients admitted to the intermediate care unit.\n\nMethodRetrospective cohort including consecutive patients admitted between March 28th and April 27th 2020. The primary outcome was the proportion of patients with severe hypoxemic respiratory failure avoiding ICU admission. Secondary outcomes included the rate of emergency intubation, 28-days mortality and predictors of ICU admission.\n\nResultsOne hundred fifty seven patients with COVID-19 associated pneumonia were admitted to the IMCU. Among the 85 patients admitted for worsening respiratory failure, 52/85 (61%) avoided ICU admission. In multivariate analysis, PaO2/FiO2 (OR 0.98; 95% CI 0.96 to 0.99) and Body Mass Index (OR 0.88; 95% CI 0.78 to 0.98) were significantly associated with ICU admission. No death or emergency intubation occurred in the intermediate care unit. Among the 72 patients transferred from the ICU, 60/72 (83%) presented neurological complications.\n\nConclusionsNon-invasive respiratory support including High-Flow Nasal Oxygen and continuous positive airway pressure prevents ICU admission for a large proportion of patients with COVID-19 hypoxemic respiratory failure. In the context of the COVID pandemic, intermediate care units may play an important role in preserving ICU capacity by avoiding ICU admission for patients with worsening respiratory failure and allowing early discharge of ICU patients.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Olivier Grosgurin", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Antonio Leidi", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Pauline Darbellay-Farhoumand", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Sebastian Carballo", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jean-luc Reny", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Dan Adler", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Bernardo Bollen Pinto", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Anne Rossel", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jacques Serratrice", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Thomas Agoritsas", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jerome Stirnemann", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Christophe Marti", - "author_inst": "Geneva University Hospitals" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.07.17.20155937", "rel_title": "Disease-associated antibody phenotypes and probabilistic seroprevalence estimates during the emergence of SARS-CoV-2", @@ -1310523,6 +1313877,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.07.17.207019", + "rel_title": "Identification of SARS-CoV-2 3CL Protease Inhibitors by a Quantitative High-throughput Screening", + "rel_date": "2020-07-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.17.207019", + "rel_abs": "The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emphasized the urgency to develop effective therapeutics. Drug repurposing screening is regarded as one of the most practical and rapid approaches for the discovery of such therapeutics. The 3C like protease (3CLpro), or main protease (Mpro) of SARS-CoV-2 is a valid drug target as it is a specific viral enzyme and plays an essential role in viral replication. We performed a quantitative high throughput screening (qHTS) of 10,755 compounds consisting of approved and investigational drugs, and bioactive compounds using a SARS-CoV-2 3CLpro assay. Twenty-three small molecule inhibitors of SARS-CoV-2 3CLpro have been identified with IC50s ranging from 0.26 to 28.85 M. Walrycin B (IC50 = 0.26 {micro}M), Hydroxocobalamin (IC50 = 3.29 {micro}M), Suramin sodium (IC50 = 6.5 {micro}M), Z-DEVD-FMK (IC50 = 6.81 {micro}M), LLL-12 (IC50 = 9.84 {micro}M), and Z-FA-FMK (IC50 = 11.39 {micro}M) are the most potent 3CLpro inhibitors. The activities of anti-SARS-CoV-2 viral infection was confirmed in 7 of 23 compounds using a SARS-CoV-2 cytopathic effect assay. The results demonstrated a set of SARS-CoV-2 3CLpro inhibitors that may have potential for further clinical evaluation as part of drug combination therapies to treating COVID-19 patients, and as starting points for chemistry optimization for new drug development.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Wei Zhu", + "author_inst": "NIH/NCATS" + }, + { + "author_name": "Miao Xu", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA" + }, + { + "author_name": "Catherine Z. Chen", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA" + }, + { + "author_name": "Hui Guo", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA" + }, + { + "author_name": "Min Shen", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA" + }, + { + "author_name": "Xin Hu", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA" + }, + { + "author_name": "Paul Shinn", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA" + }, + { + "author_name": "Carleen Klumpp-Thomas", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA" + }, + { + "author_name": "Samuel G. Michael", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA" + }, + { + "author_name": "Wei Zheng", + "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.07.08.193193", "rel_title": "Vinegar and Its Active Component Acetic Acid Inhibit SARS-CoV-2 Infection In Vitro and Ex Vivo", @@ -1311687,89 +1315096,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.15.20154765", - "rel_title": "Controlling COVID-19 via test-trace-quarantine", - "rel_date": "2020-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154765", - "rel_abs": "Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures. However, these interventions have had enormous societal and economic costs. Here we demonstrate the feasibility of an alternative control strategy, test-trace-quarantine: routine testing of primarily symptomatic individuals, tracing and testing their known contacts, and placing their contacts in quarantine. We performed this analysis using Covasim, an open-source agent-based model, which was calibrated to detailed demographic, mobility, and epidemiological data for the Seattle region from January through June 2020. With current levels of mask use and schools remaining closed, we found that high but achievable levels of testing and tracing are sufficient to maintain epidemic control even under a return to full workplace and community mobility and with low vaccine coverage. The easing of mobility restrictions in June 2020 and subsequent scale-up of testing and tracing programs through September provided real-world validation of our predictions. Although we show that test-trace-quarantine can control the epidemic in both theory and practice, its success is contingent on high testing and tracing rates, high quarantine compliance, relatively short testing and tracing delays, and moderate to high mask use. Thus, in order for test-trace-quarantine to control transmission with a return to high mobility, strong performance in all aspects of the program is required.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Cliff C Kerr", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Dina Mistry", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Robyn M Stuart", - "author_inst": "Department of Mathematical Sciences, University of Copenhagen" - }, - { - "author_name": "Katherine Rosenfeld", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Gregory R Hart", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Rafael C Nunez", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Jamie A Cohen", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Prashanth Selvaraj", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Romesh G Abeysuriya", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Michal Jastrzebski", - "author_inst": "GitHub, Inc." - }, - { - "author_name": "Lauren George", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Brittany Hagedorn", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Jasmina Panovska-Griffiths", - "author_inst": "UCL" - }, - { - "author_name": "Meaghan Fagalde", - "author_inst": "Public Health - Seattle and King County" - }, - { - "author_name": "Jeffrey Duchin", - "author_inst": "Public Health - Seattle and King County" - }, - { - "author_name": "Michael Famulare", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Daniel J Klein", - "author_inst": "Institute for Disease Modeling" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.14.20153775", "rel_title": "Direct-to-Consumer Chat-Based Remote Care Before and During the COVID-19 Outbreak", @@ -1311949,6 +1315275,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, + { + "rel_doi": "10.1101/2020.07.14.20153981", + "rel_title": "Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20153981", + "rel_abs": "BackgroundThe detection of SARS-CoV-2 by real-time polymerase chain reaction (PCR) in respiratory samples collected from persons recovered from COVID-19 does not necessarily indicate shedding of infective virions. By contrast, the isolation of SARS-CoV-2 using cell-based culture likely indicates infectivity, but there are limited data on the correlation between SARS-CoV-2 culture and PCR. Here we review our experience using SARS-CoV-2 culture to determine infectivity and safe de-isolation of COVID-19 patients.\n\nMethods195 patients with diverse severity of COVID-19 were tested (outpatients [n=178]), inpatients [n=12] and ICU [n=5]). SARS-CoV-2 PCR positive samples were cultured in Vero C1008 cells and inspected daily for cytopathic effect (CPE). SARS-CoV-2-induced CPE was confirmed by PCR of culture supernatant. Where no CPE was documented, PCR was performed on day four to confirm absence of virus replication. Cycle threshold (Ct) values of the day four PCR (Ctculture) and the PCR of the original clinical sample (Ctsample) were compared, and positive cultures were defined as a Ctsample - Ctculture value of [≥]3.\n\nFindingsOf 234 samples collected, 228 (97%) were from the upper respiratory tract. SARS-CoV-2 was only successfully isolated from samples with Ctsample values <32, including in 28/181 (15%), 19/42 (45%) and 9/11 samples (82%) collected from outpatients, inpatients and ICU patients, respectively. The mean duration from symptom onset to culture positivity was 4.5 days (range 0-18 days). SARS-CoV-2 was significantly more likely to be isolated from samples collected from inpatients (p<0.001) and ICU patients (p<0.0001) compared with outpatients, and in samples with lower Ctsample values.\n\nConclusionSARS-CoV-2 culture may be used as a surrogate marker for infectivity and inform de-isolation protocols.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Kerri Basile", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Kenneth McPhie", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Ian Carter", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Susan Alderson", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Hossinur Rahman", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Linda Donovan", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Shanil Kumar", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Tyna Tran", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Danny Ko", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Tharshini Sivaruban", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Christine Ngo", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Cheryl Toi", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Matthew V O'Sullivan", + "author_inst": "CIDMLS-ICPMR, CIDM-PH, Marie Bashir Institute for Infectious Diseases and Biosecurity" + }, + { + "author_name": "Vitali Sintchenko", + "author_inst": "CIDMLS-ICPMR, CIDM-PH, Marie Bashir Institute for Infectious Diseases and Biosecurity" + }, + { + "author_name": "Sharon C-A Chen", + "author_inst": "CIDMLS-ICPMR, CIDM-PH, Marie Bashir Institute for Infectious Diseases and Biosecurity" + }, + { + "author_name": "Susan Maddocks", + "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead NSW 2" + }, + { + "author_name": "Dominic E Dwyer", + "author_inst": "CIDMLS-ICPMR, CIDM-PH, Marie Bashir Institute for Infectious Diseases and Biosecurity" + }, + { + "author_name": "Jen Kok", + "author_inst": "CIDMLS-ICPMR, CIDM-PH" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.15.20154310", "rel_title": "Observational Study of Chlorpromazine in Hospitalized Patients with Covid-19", @@ -1313201,41 +1316614,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.13.20153049", - "rel_title": "Mechanistic Transmission Modeling of COVID-19 on the Diamond Princess Cruise Ship Demonstrates the Importance of Aerosol Transmission", - "rel_date": "2020-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20153049", - "rel_abs": "BackgroundThe current prevailing position is that coronavirus disease 2019 (COVID-19) is transmitted primarily through large respiratory droplets within close proximity (i.e., 1-2 m) of infected individuals. However, quantitative information on the relative importance of specific transmission pathways of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (i.e., droplets, aerosols, and fomites across short- and long-range distances) remains limited.\n\nMethodsTo evaluate the relative importance of multiple transmission routes for SARS-CoV-2, we leveraged detailed information available from the Diamond Princess Cruise Ship outbreak that occurred in early 2020. We developed a framework that combines stochastic Markov chain and negative exponential dose-response modeling with available empirical data on mechanisms of SARS-CoV-2 dynamics and human behaviors, which informs a modified version of the Reed-Frost epidemic model to predict daily and cumulative daily case counts on the ship. We modeled 21,600 scenarios to generate a matrix of solutions across a full range of assumptions for eight unknown or uncertain epidemic and mechanistic transmission factors, including the magnitude of droplet and aerosol emissions from infected individuals, the infectious dose for deposition of droplets and aerosols to the upper and lower respiratory tracts, and others.\n\nFindingsA total of 132 model iterations met acceptability criteria (R2 > 0.95 for modeled vs. reported cumulative daily cases and R2 > 0 for daily cases). Analyzing only these successful model iterations yields insights into the likely values for uncertain parameters and quantifies the likely contributions of each defined mode of transmission. Mean estimates of the contributions of short-range, long-range, and fomite transmission modes to infected cases aboard the ship across the entire simulation time period were 35%, 35%, and 30%, respectively. Mean estimates of the contributions of large respiratory droplets and small respiratory aerosols were 41% and 59%. Short-range transmission was the dominant mode after passenger quarantine began, albeit due primarily to aerosol transmission, not droplets.\n\nInterpretationOur results demonstrate that aerosol inhalation was likely the dominant contributor to COVID-19 transmission among passengers aboard the Diamond Princess Cruise Ship. Moreover, close-range and long-range transmission likely contributed similarly to disease progression aboard the ship, with fomite transmission playing a smaller role. The passenger quarantine also affected the importance of each mode, demonstrating the impacts of the interventions. Although cruise ships represent unique built environments with high ventilation rates and no air recirculation, these findings underscore the importance of implementing public health measures that target the control of inhalation of aerosols in addition to ongoing measures targeting control of large droplet and fomite transmission, not only aboard cruise ships but in other indoor environments as well.\n\nFundingFunding information is not available.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Parham Azimi", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Zahra Keshavarz", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Jose Guillermo Cedeno Laurent", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Brent R. Stephens", - "author_inst": "Illinois Institute of Technology" - }, - { - "author_name": "Joseph G. Allen", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.14.20153304", "rel_title": "Post lockdown COVID-19 seroprevalence and circulation at the time of delivery, France", @@ -1313551,6 +1316929,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.13.20152884", + "rel_title": "AN AFFORDABLE ANTI-SARS-COV-2 SPIKE ELISA TEST FOR EARLY DETECTION OF IgG SEROCONVERSION SUITED FOR LARGE-SCALE SURVEILLANCE STUDIES IN LOW-INCOME COUNTRIES", + "rel_date": "2020-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152884", + "rel_abs": "Accurate serological tests are essential tools to allow adequate monitoring and control of COVID-19 spread. Production of a low-cost and high-quality recombinant viral antigen can enable the development of reliable and affordable serological assays, which are urgently needed to facilitate epidemiological surveillance studies in low-income economies. Trimeric SARS-COV-2 spike (S) protein was produced in serum-free, suspension-adapted HEK293 cells. Highly purified S protein was used to develop an ELISA, named S-UFRJ test. It was standardized to work with different types of samples: (i) plasma or serum from venous blood samples; (ii) eluates from dried blood spots (DBS) obtained by collecting blood drops from a finger prick. We developed a cost-effective, scalable technology to produce S protein based on its stable expression in HEK293 cells. Using this recombinant antigen, we presented a workflow for test development in the setting of a pandemic, starting from limited amounts of samples up to reaching final validation with hundreds of samples. Test specificity was determined to be 98.6%, whereas sensitivity was 95% for samples collected 11 or more days after symptoms onset. A ROC analysis allowed optimizing the cut-off and confirming the high accuracy of the test. Endpoint titers were shown to correlate with virus neutralization assessed as PRNT90. There was excellent agreement between plasma and DBS samples, significantly simplifying sample collection, storing, and shipping. An overall cost estimate revealed that the final retail price could be in the range of one US dollar. The S-UFRJ assay developed herein meets the quality requirements of high sensitivity and specificity. The low cost and the use of mailable DBS samples allow for serological surveillance and follow-up of SARS-CoV-2 vaccination of populations regardless of geographical and socio-economic aspects. We hope the detailed guidelines for the development of an affordable and accurate anti-spike SARS-COV-2 ELISA, such as S-UFRJ described here, will stimulate governmental and non-governmental health agencies in other countries to engage in much-needed large-scale studies monitoring the spread and immunity to SARS-COV-2 infection.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Renata G. F. Alvim", + "author_inst": "COPPE, Chemical Engineering Program, Cell Culture Engineering Lab, Federal University of Rio de Janeiro - UFRJ, Brazil" + }, + { + "author_name": "Tulio M. Lima", + "author_inst": "COPPE, Chemical Engineering Program, Cell Culture Engineering Lab; School of Chemistry, EPQB Program;Federal University of Rio de Janeiro - UFRJ, Brazil" + }, + { + "author_name": "Danielle A. S. Rodrigues", + "author_inst": "Institute of Microbiology, Immunology Dept., Federal University of Rio de Janeiro - UFRJ, Brazil" + }, + { + "author_name": "Federico F. Marsili", + "author_inst": "COPPE, Chemical Engineering Program, Cell Culture Engineering Lab.; Institute of Chemistry, Biochemistry Program; Federal University of Rio de Janeiro - UFRJ, B" + }, + { + "author_name": "Vicente B.T. Bozza", + "author_inst": "Institute of Biophysics Carlos Chagas Filho, Program in Immunobiology, Federal University of Rio de Janeiro - UFRJ, Brazil" + }, + { + "author_name": "Luiza M. Higa", + "author_inst": "Biology Institute, Molecular Virology Lab., Federal University of Rio de Janeiro - UFRJ, Brazil" + }, + { + "author_name": "Fabio L. Monteiro", + "author_inst": "Biology Institute, Molecular Virology Lab., Federal University of Rio de Janeiro - UFRJ, Brazil." + }, + { + "author_name": "Daniel P. B. Abreu", + "author_inst": "COPPE, Chemical Engineering Program, Cell Culture Engineering Lab, Federal University of Rio de Janeiro - UFRJ, Brazil" + }, + { + "author_name": "Isabela C. Leitao", + "author_inst": "Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro - UFRJ, Brazil." + }, + { + "author_name": "Renato S. Carvalho", + "author_inst": "School of Pharmacy, Pharmaceutical Biotechnology Dept., Federal University of Rio de Janeiro - UFRJ, Brazil" + }, + { + "author_name": "Rafael M. Galliez", + "author_inst": "Medical School, Infectious and Parasitic Disease Dept., Federal University of Rio de Janeiro - UFRJ, Brazil." + }, + { + "author_name": "Terezinha M. P. P. Castineiras", + "author_inst": "Medical School, Infectious and Parasitic Disease Dept., Federal University of Rio de Janeiro - UFRJ, Brazil." + }, + { + "author_name": "Alberto Nobrega", + "author_inst": "Institute of Microbiology, Immunology Dept., Federal University of Rio de Janeiro - UFRJ, Brazil." + }, + { + "author_name": "Leonardo H. Travassos", + "author_inst": "Institute of Biophysics Carlos Chagas Filho, Program in Immunobiology, Federal University of Rio de Janeiro - UFRJ, Brazil." + }, + { + "author_name": "Amilcar Tanuri", + "author_inst": "Biology Institute, Molecular Virology Lab., Federal University of Rio de Janeiro - UFRJ, Brazil." + }, + { + "author_name": "Orlando C. Ferreira Jr.", + "author_inst": "Biology Institute, Molecular Virology Lab., Federal University of Rio de Janeiro - UFRJ, Brazil." + }, + { + "author_name": "Leda R. Castilho", + "author_inst": "COPPE, Chemical Engineering Program, Cell Culture Engineering Lab.; Institute of Chemistry, Biochemistry Program; Federal University of Rio de Janeiro - UFRJ, B" + }, + { + "author_name": "Andre M. Vale", + "author_inst": "Institute of Biophysics Carlos Chagas Filho, Program in Immunobiology, Federal University of Rio de Janeiro - UFRJ, Brazil." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.13.20152900", "rel_title": "Comparison of the COVID-19 infection risks by close contact and aerosol transmission", @@ -1314891,77 +1318356,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.15.204404", - "rel_title": "A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells", - "rel_date": "2020-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.204404", - "rel_abs": "SARS-CoV-2 infections pose a global threat to human health and an unprecedented research challenge. Among the most urgent tasks is obtaining a detailed understanding of the molecular interactions that facilitate viral replication or contribute to host defense mechanisms in infected cells. While SARS-CoV-2 co-opts cellular factors for viral translation and genome replication, a comprehensive map of the host cell proteome in direct contact with viral RNA has not been elucidated. Here, we use RNA antisense purification and mass spectrometry (RAP-MS) to obtain an unbiased and quantitative picture of the human proteome that directly binds the SARS-CoV-2 RNA in infected human cells. We discover known host factors required for coronavirus replication, regulators of RNA metabolism and host defense pathways, along with dozens of potential drug targets among direct SARS-CoV-2 binders. We further integrate the SARS-CoV-2 RNA interactome with proteome dynamics induced by viral infection, linking interactome proteins to the emerging biology of SARS-CoV-2 infections. Validating RAP-MS, we show that CNBP, a regulator of proinflammatory cytokines, directly engages the SARS-CoV-2 RNA. Supporting the functional relevance of identified interactors, we show that the interferon-induced protein RYDEN suppresses SARS-CoV-2 ribosomal frameshifting and demonstrate that inhibition of SARS-CoV-2-bound proteins is sufficient to manipulate viral replication. The SARS-CoV-2 RNA interactome provides an unprecedented molecular perspective on SARS-CoV-2 infections and enables the systematic dissection of host dependency factors and host defense strategies, a crucial prerequisite for designing novel therapeutic strategies.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nora Schmidt", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Caleb A Lareau", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Hasmik Keshishian", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Randy Melanson", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Matthias Zimmer", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Luisa Kirschner", - "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University Wuerzburg" - }, - { - "author_name": "Jens Ade", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Simone Werner", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Neva Caliskan", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Eric S Lander", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Joerg Vogel", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg" - }, - { - "author_name": "Steven A Carr", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Jochen Bodem", - "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University Wuerzburg" - }, - { - "author_name": "Mathias Munschauer", - "author_inst": "Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Wuerzburg, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.15.205229", "rel_title": "The S1 protein of SARS-CoV-2 crosses the blood-brain barrier: Kinetics, distribution, mechanisms, and influence of ApoE genotype, sex, and inflammation", @@ -1315153,6 +1318547,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.12.20151191", + "rel_title": "COVID-19 scenarios for the United States", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20151191", + "rel_abs": "The United States (US) has not been spared in the ongoing pandemic of novel coronavirus disease1,2. COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to cause death and disease in all 50 states, as well as significant economic damage wrought by the non-pharmaceutical interventions (NPI) adopted in attempts to control transmission3. We use a deterministic, Susceptible, Exposed, Infectious, Recovered (SEIR) compartmental framework4,5 to model possible trajectories of SARS-CoV-2 infections and the impact of NPI6 at the state level. Model performance was tested against reported deaths from 01 February to 04 July 2020. Using this SEIR model and projections of critical driving covariates (pneumonia seasonality, mobility, testing rates, and mask use per capita), we assessed some possible futures of the COVID-19 pandemic from 05 July through 31 December 2020. We explored future scenarios that included feasible assumptions about NPIs including social distancing mandates (SDMs) and levels of mask use. The range of infection, death, and hospital demand outcomes revealed by these scenarios show that action taken during the summer of 2020 will have profound public health impacts through to the year end. Encouragingly, we find that an emphasis on universal mask use may be sufficient to ameliorate the worst effects of epidemic resurgences in many states. Masks may save as many as 102,795 (55,898-183,374) lives, when compared to a plausible reference scenario in December. In addition, widespread mask use may markedly reduce the need for more socially and economically deleterious SDMs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- I IHME COVID-19 Forecasting Team", + "author_inst": "" + }, + { + "author_name": "Simon I Hay", + "author_inst": "Institute for Health Metrics and Evaluation, University of Washington" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.13.20150177", "rel_title": "Development of a severity of disease score and classification model by machine learning for hospitalized COVID-19 patients", @@ -1316505,37 +1319922,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.05.20146043", - "rel_title": "Luminore CopperTouch\u2122 surface coating effectively inactivates SARS-CoV-2, Ebola and Marburg viruses in vitro", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20146043", - "rel_abs": "We investigated the ability of Luminore CopperTouch copper and copper-nickel surfaces to inactivate filoviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For this purpose, we compared viral titers in Vero cells from viral droplets exposed to copper surfaces for 30 min. The copper and copper-nickel surfaces inactivated 99.9% of the viral titer of both Ebola and Marburg viruses. The copper surfaces also inactivated 99% of SARS-CoV-2 titers in 2 hours to close to the limit of detection. These data add Ebolavirus, Marburgvirus, and SARS-CoV-2 (COVID-19) to the list of pathogens that can be inactivated by exposure to copper ions, validating Luminore CopperTouch technology (currently the only Environmental Protection Agency-registered cold spray antimicrobial surface technology) as an efficacious, cost-friendly tool to improve infection control in hospitals, long-term care facilities, schools, hotels, buses, trains, airports, and other highly trafficked areas.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Emily Mantlo", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Slobodan Paessler", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Alexey V Seregin", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Alfred T Mitchell", - "author_inst": "Luminore CopperTouch" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.10.20150623", "rel_title": "Maternal and perinatal characteristics and outcomes of pregnancies complicated with COVID-19 in Kuwait", @@ -1316911,6 +1320297,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.11.20151472", + "rel_title": "The competing risk between in-hospital mortality and recovery: A pitfall in COVID-19 survival analysis research", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.11.20151472", + "rel_abs": "BackgroundA plethora of studies on COVID-19 investigating mortality and recovery have used the Cox Proportional Hazards (Cox PH) model without taking into account the presence of competing risks. We investigate, through extensive simulations, the bias in estimating the hazard ratio (HR) and the absolute risk reduction (ARR) of death when competing risks are ignored, and suggest an alternative method.\n\nMethodsWe simulated a fictive clinical trial on COVID-19 mimicking studies investigating interventions such as Hydroxychloroquine, Remdesivir, or convalescent plasma. The outcome is time from randomization until death. Six scenarios for the effect of treatment on death and recovery were considered. The HR and the 28-day ARR of death were estimated using the Cox PH and the Fine and Gray (FG) models. Estimates were then compared with the true values, and the magnitude of misestimation was quantified.\n\nResultsThe Cox PH model misestimated the true HR and the 28-day ARR of death in the majority of scenarios. The magnitude of misestimation increased when recovery was faster and/or chance of recovery was higher. In some scenarios, this model has shown harmful treatment effect when it was beneficial. Estimates obtained from FG model were all consistent and showed no misestimation or changes in direction.\n\nConclusionThere is a substantial risk of misleading results in COVID-19 research if recovery and death due to COVID-19 are not considered as competing risk events. We strongly recommend the use of a competing risk approach to re-analyze relevant published data that have used the Cox PH model.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Abderrahim Oulhaj", + "author_inst": "Institute of Public Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates" + }, + { + "author_name": "Luai A. Ahmed", + "author_inst": "Institute of Public Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates" + }, + { + "author_name": "Juergen Prattes", + "author_inst": "Medical University of Graz, Department of Internal Medicine; Section of Infectious Diseases and Tropical Medicine" + }, + { + "author_name": "Abubaker Suliman", + "author_inst": "Institute of Public Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates" + }, + { + "author_name": "Ahmed Alsuwaidi", + "author_inst": "Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates" + }, + { + "author_name": "Rami H. Al-Rifai", + "author_inst": "Institute of Public Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates" + }, + { + "author_name": "Harald Sourij", + "author_inst": "Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University of Graz, Austria" + }, + { + "author_name": "Ingrid Van Keilegom", + "author_inst": "ORSTAT, KU Leuven, Belgium" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.11.20150912", "rel_title": "A simplified SARS-CoV-2 detection protocol for research laboratories", @@ -1318267,25 +1321700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.13.20152637", - "rel_title": "Modelling suggests blood group incompatibility may substantially reduce SARS-CoV-2 transmission", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152637", - "rel_abs": "Several independent datasets suggest blood type A is over-represented and type O under-represented among COVID-19 patients. Here, I model a scenario in which ABO transfusion incompatibility reduces the chance of a patient transmitting the virus to an incompatible recipient. Comparison of model outputs to published data on COVID-19 prevalence indicates that if this scenario holds true, ABO incompatibility may reduce virus transmissibility by 60% or more. Paradoxically, however, targeted vaccination of either high-susceptibility type A or \"super-spreader\" type O individuals is less effective than random vaccination at blocking community spread of the virus. Instead, the key is to maintain blood type diversity amongst the remaining susceptible individuals. I stress that these results illustrate a theoretical model of ABO blood group interaction with virus transmission and require confirmation by observation.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Peter James Ellis", - "author_inst": "University of Kent" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.13.20152330", "rel_title": "Discrete simulation analysis of COVID-19 and prediction of isolation bed numbers", @@ -1318485,6 +1321899,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.13.20152587", + "rel_title": "Linear epitope landscape of SARS-CoV-2 Spike protein constructed from 1,051 COVID-19 patients", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152587", + "rel_abs": "Neutralization antibodies and vaccines for treating COVID-19 are desperately needed. For precise development of antibodies and vaccines, the key is to understand which part of SARS-CoV-2 Spike protein is highly immunogenic on a systematic way. We generate a linear epitope landscape of Spike protein by analyzing serum IgG response of 1,051 COVID-19 patients with a peptide microarray. We reveal two regions that rich of linear epitopes, i.e., CTD and a region close to the S2 cleavage site and fusion peptide. Unexpectedly, we find RBD is lack of linear epitope. Besides 3 moderate immunogenic peptides from RBD, 16 highly immunogenic peptides from other regions of Spike protein are determined. These peptides could serve as the base for precise development of antibodies and vaccines for COVID-19 on a systematic level.\n\nOne sentence summaryA linear epitope landscape of SARS-CoV-2 Spike protein is generated by analyzing serum IgG response of 1,051 COVID-19 patients.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Yang Li", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Mingliang Ma", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Qing Lei", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Feng Wang", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Ziyong Sun", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Xionglin Fan", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Sheng-ce Tao", + "author_inst": "Shanghai Jiao Tong University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.13.20152678", "rel_title": "Interest in COVID-19 vaccine trials participation among young adults in China: Willingness, reasons for hesitancy, and demographic and psychosocial determinants", @@ -1319925,33 +1323382,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.10.20150508", - "rel_title": "ICU admissions and in-hospital deaths linked to covid-19 in the Paris region are correlated with previously observed ambient temperature", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150508", - "rel_abs": "OBJECTIVETo study the effect of weather on severity indicators of coronavirus disease 2019 (covid-19).\n\nDESIGNEcological study.\n\nSETTINGParis region.\n\nPOPULATIONSeverely ill patients with covid-19.\n\nMAIN OUTCOME MEASURESDaily covid-19-related intensive care unit (ICU) admission and in-hospital deaths in the Paris region, and the daily weather characteristics of Paris midtown.\n\nRESULTSDaily ICU admissions and in-hospital deaths were strongly and negatively correlated to ambient temperatures, with a time lag. The highest Pearson correlation coefficients and statistically significant P values were found 8 days before occurrence of ICU admissions and 15 days before deaths.\n\nCONCLUSIONSThe study findings show a strong effect of previously observed ambient temperature that has an effect on severity indicators of covid-19.\n\nStrengths and limitations of this studyWe assessed the link between weather characteristics with a time lag and covid-19-related hospital severity indicators.\n\nThis is the first study, with reliable data, to find a strong negative correlation between previously observed ambient temperature with covid-19-related iCU admissions and in-hospital deaths.\n\nIt is compatible with the natural history (including hospitalisation) of covid-19 outbreak in a highly developed country.\n\nWe also report the duration after which iCU admissions and in-Hospital deaths occurs following temperature variation (respectively median of 8 and 15 days).\n\nOur analyses are mainly valid for temperate climate countries.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mehdi Mejdoubi", - "author_inst": "Centre Hospitalier de Valenciennes" - }, - { - "author_name": "Xavier Kyndt", - "author_inst": "Centre Hospitalier de Valenciennes" - }, - { - "author_name": "Mehdi Djennaoui", - "author_inst": "Centre Hospitalier de Valenciennes" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.09.20150219", "rel_title": "Estimating the time-varying reproduction number of COVID-19 with a state-space method", @@ -1320075,6 +1323505,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.09.20150227", + "rel_title": "A minimal model for household effects in epidemics", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20150227", + "rel_abs": "Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence.\n\nWe introduce a minimal model that incorporates these household effects in the framework of mean-field theory and numerical simulations. We show that the reproduction number R0 depends on the household size in a surprising way: linearly for relatively small households, and as a square root of size for larger households. We discuss the implications of the findings for the lockdown, test, tracing, and isolation policies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Greg Huber", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Mason Kamb", + "author_inst": "University of Washington" + }, + { + "author_name": "Kyle Kawagoe", + "author_inst": "University of Chicago" + }, + { + "author_name": "Lucy Li", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Boris Veytsman", + "author_inst": "Chan Zuckerberg Initiative" + }, + { + "author_name": "David Yllanes", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Dan Zigmond", + "author_inst": "Chan Zuckerberg Initiative" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.10.20150003", "rel_title": "Obesity, walking pace and risk of severe COVID-19: Analysis of UK Biobank", @@ -1321279,45 +1324752,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.10.20149013", - "rel_title": "The Age Pattern of the Male- to- Female Ratio in Mortality from COVID-19 Mirrors that of Cardiovascular Disease but not Cancer in the General Population", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20149013", - "rel_abs": "BackgroundMales are at a higher risk of dying from COVID-19. Older age and cardiovascular disease are also associated with COVID-19 mortality. We compared the male-to-female (sex) ratios in mortality by age for COVID-19 with cardiovascular mortality and cancer mortality in the general population.\n\nMethodsWe obtained data from official government sources in the US and five European countries: Italy, Spain, France, Germany, and the Netherlands. We analyzed COVID-19 deaths by sex and age in these countries and similarly analyzed their deaths from cardiovascular disease (coronary heart disease or stroke) and cancer, the two leading age-related causes of death in middle-to-high income countries.\n\nFindingsIn both the US and European countries, the sex ratio of deaths from COVID-19 exceeded one throughout adult life. The sex ratio increased up to a peak in midlife, and then declined markedly in later life. This pattern was also observed for the sex ratio of deaths from cardiovascular disease, but not cancer, in the general populations of the US and European countries.\n\nInterpretationThe sex ratios of deaths from COVID-19 and from cardiovascular disease exhibit similar patterns across the adult life course. The underlying mechanisms are poorly understood, but could stem partially from sex-related biological differences that underlie the similar pattern for cardiovascular disease. These include, we propose, comparatively longer telomeres in females, ovarian hormones, and X chromosome mosaicism.\n\nFundingThe authors received no specific funding for this work.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSMortality from COVID-19 is higher in males and older persons. We searched PubMed.gov in June 2020, with no date restrictions, for articles published in English using the search terms \"COVID-19\", \"deaths\", \"mortality\", \"sex\", \"male\", \"female\", \"age\", \"disaggregated\", \"ratio\", and \"stratified\". We identified studies in several countries that stratified COVID-19 mortality data by age or by sex, but no study examined male-to-female (sex) ratios by age at a multi-national level.\n\nAdded value of this studyTo our knowledge, this is the first study to aggregate data on COVID-19 deaths at a multi-national level, and analyze how the sex ratio in deaths varies by age, taking into account the population at risk in each sex/age stratum. We found a distinctive pattern in sex ratio of deaths by age, illuminating the nature of the sex effect on death from COVID-19. Moreover, we found a similar pattern in sex ratio of deaths by age for cardiovascular disease, which is strongly associated with increased risk of dying from COVID-19. We did not find a similar age pattern for the sex ratio in deaths by cancer.\n\nImplications of all the available evidenceThe sex ratio in deaths from COVID-19 peaks in middle age and decreases at older ages, a pattern mirrored in deaths from cardiovascular disease. This intriguing similarity warrants research about whether sex-based differences in mortality from COVID-19 and from cardiovascular disease in general are partly due to common biological causes.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ila Nimgaonkar", - "author_inst": "Rutgers Robert Wood Johnson Medical School" - }, - { - "author_name": "Linda Valeri", - "author_inst": "Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Ezra S. Susser", - "author_inst": "Mailman School of Public Health, Columbia University and New York State Psychiatric Institute" - }, - { - "author_name": "Sabiha Hussain", - "author_inst": "Rutgers Robert Wood Johnson Medical School" - }, - { - "author_name": "Jag Sunderram", - "author_inst": "Rutgers Robert Wood Johnson Medical School" - }, - { - "author_name": "Abraham Aviv", - "author_inst": "Rutgers New Jersey Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.09.20149534", "rel_title": "Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis.", @@ -1321529,6 +1324963,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.09.20149138", + "rel_title": "Negative impact of the COVID-19 pandemic on sleep quantitative parameters, quality, and circadian alignment: Implications for psychological well-being and emotional regulation", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149138", + "rel_abs": "BackgroundThe COVID-19 pandemic has spread worldwide, affecting millions of people and exposing them to home quarantine, isolation, and social distancing. While recent reports showed increased distress and depressive/anxiety state related to COVID-19 crisis, we investigated how home quarantine affected sleep parameters in healthy individuals.\n\nMethods160 healthy individuals who were in home quarantine in April 2020 for at least one month participated in this study. Participants rated and compared their quantitative sleep parameters (time to go to bed, sleep duration, getting-up time) and sleep quality factors, pre-and during home quarantine due to the COVID-19 pandemic. Furthermore, participants chronotype was determined to see if sleep parameters are differentially affected in different chronotypes.\n\nResultsThe time to fall asleep and get-up in the morning were significantly delayed in all participants, indicating a significant circadian misalignment. Sleep quality was reported to be significantly poorer in all participants and chronotypes, and included more daily disturbances (more sleep disturbances, higher daily dysfunctions due to low quality of sleep) and less perceived sleep quality (lower subjective sleep quality, longer time taken to fall asleep at night, more use of sleep medication for improving sleep quality) during home quarantine.\n\nConclusionsHome quarantine due to COVID-19 pandemic has a detrimental impact on sleep quality. Online interventions including self-help sleep programs, stress management, relaxation practices, stimulus control, sleep hygiene, and mindfulness training are available interventions in the current situation.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Mohammad Ali Salehinejad", + "author_inst": "Department of Psychology and Neurosciences, Leibniz Research Centre for Working Environment and Human Factors" + }, + { + "author_name": "Maryam Majidinezhad", + "author_inst": "Iran University of Medical Science, Tehran, Iran" + }, + { + "author_name": "Elham Ghanavati", + "author_inst": "Ruhr-University Bochum, Department of Psychology, Bochum, Germany" + }, + { + "author_name": "Sahar Kouestanian", + "author_inst": "Institute for Cognitive Science Studies, Tehran, Iran" + }, + { + "author_name": "Carmelo M. Vicario", + "author_inst": "Department of Cognitive Sciences, University of Messina, Messina, Italy" + }, + { + "author_name": "Michael A. Nitsche", + "author_inst": "Department of Psychology and Neurosciences, Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany" + }, + { + "author_name": "Vahid Nejati", + "author_inst": "Department of Psychology, Shahid Beheshti University, Tehran, Iran" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.09.20149401", "rel_title": "Bibliometric Analysis of COVID-19 in the Context of Migration Health: A Study Protocol", @@ -1323017,117 +1326494,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.08.20148999", - "rel_title": "Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2", - "rel_date": "2020-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148999", - "rel_abs": "Until vaccines and effective therapeutics become available, the practical way to transit safely out of the current lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of result, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms, and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of [~]200 coronavirus disease (CoVID-19)-suspected patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. The system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Mohammed A Rohaim", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Emily Clayton", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Irem Sahin", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Julianne Vilela", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Manar E Khalifa", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Mohammed Q Al-Natour", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Mahmoud Bayoumi", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Aurore Poirier", - "author_inst": "The University of Surrey" - }, - { - "author_name": "Manoharanehru Branavan", - "author_inst": "Brunel University London" - }, - { - "author_name": "Mukunthan Tharmakulasingam", - "author_inst": "University of Surrey," - }, - { - "author_name": "Nouman S Chaudhry", - "author_inst": "The University of Surrey" - }, - { - "author_name": "Ravinder Sodi", - "author_inst": "Department of Biochemistry, Poole & Bournemouth Hospitals NHS Trust, Longfleet Road, Poole, UK BH15 2JB" - }, - { - "author_name": "Amy Brown", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Peter Burkhart", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Wendy Hacking", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Judy Botham", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Joe Boyce", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Hayley Wilkinson", - "author_inst": "The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS, Foundation Trust, UK" - }, - { - "author_name": "Craig Williams", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Michelle Bates", - "author_inst": "The Lancaster University" - }, - { - "author_name": "Roberto La Ragione", - "author_inst": "University of Surrey" - }, - { - "author_name": "Wamadeva Balachandran", - "author_inst": "College of Engineering, Design and Physical Sciences, Brunel University London, Kingston Lane, Uxbridge, UK" - }, - { - "author_name": "Anil Fernando", - "author_inst": "The University of Surrey" - }, - { - "author_name": "Muhammad Munir", - "author_inst": "Lancaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.07.20148478", "rel_title": "Natural killer cell activation related to clinical outcome of COVID-19", @@ -1323463,6 +1326829,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.09.20149831", + "rel_title": "ALeRT-COVID: Attentive Lockdown-awaRe Transfer Learning for Predicting COVID-19 Pandemics in Different Countries", + "rel_date": "2020-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149831", + "rel_abs": "Countries across the world are in different stages of COVID-19 trajectory, among which many have implemented the lockdown measures to prevent its spread. Although the lockdown is effective in such prevention, it may put the economy into a depression. Predicting the epidemic progression with government switching the lockdown on or off is critical. We propose a transfer learning approach called ALeRT-COVID using attention-based recurrent neural network (RNN) architecture to predict the epidemic trends for different countries. A source model was trained on the pre-defined source countries and then transferred to each target country. The lockdown measure was introduced to our model as a predictor and the attention mechanism was utilized to learn the different contributions of the confirmed cases in the past days to the future trend. Results demonstrated that the transfer learning strategy is helpful especially for early-stage countries. By introducing the lockdown predictor and the attention mechanism, ALeRT-COVID showed a significant improvement on the prediction performance. We predicted the confirmed cases in one week when extending and easing lockdown separately. Results showed the lockdown measures is still necessary for a number of countries. We expect our research can help different countries to make better decisions on the lockdown measures.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yingxue Li", + "author_inst": "Ping An Healthcare Technology" + }, + { + "author_name": "Wenxiao Jia", + "author_inst": "Ping An Healthcare Technology" + }, + { + "author_name": "Junmei Wang", + "author_inst": "Ping An Healthcare Technology" + }, + { + "author_name": "Jianying Guo", + "author_inst": "Ping An Healthcare Technology" + }, + { + "author_name": "Qin Liu", + "author_inst": "Ping An Healthcare Technology" + }, + { + "author_name": "Xiang Li", + "author_inst": "Ping An Healthcare Technology" + }, + { + "author_name": "Guotong Xie", + "author_inst": "Ping An Healthcare Technology" + }, + { + "author_name": "Fei Wang", + "author_inst": "Weill Cornell Medical College" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.08.20149039", "rel_title": "A model of COVID-19 propagation based on a gamma subordinated negative binomial branching process: A tool for decision making with small populations", @@ -1324883,89 +1328296,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.07.09.196188", - "rel_title": "SARS-CoV-2 infection in the lungs of human ACE2 transgenic mice causes severe inflammation, immune cell infiltration, and compromised respiratory function", - "rel_date": "2020-07-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.196188", - "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) emerged in late 2019 and has spread worldwide resulting in the Coronavirus Disease 2019 (COVID-19) pandemic. Although animal models have been evaluated for SARS-CoV-2 infection, none have recapitulated the severe lung disease phenotypes seen in hospitalized human cases. Here, we evaluate heterozygous transgenic mice expressing the human ACE2 receptor driven by the epithelial cell cytokeratin-18 gene promoter (K18-hACE2) as a model of SARS-CoV-2 infection. Intranasal inoculation of SARS-CoV-2 in K18-hACE2 mice results in high levels of viral infection in lung tissues with additional spread to other organs. Remarkably, a decline in pulmonary function, as measured by static and dynamic tests of respiratory capacity, occurs 4 days after peak viral titer and correlates with an inflammatory response marked by infiltration into the lung of monocytes, neutrophils, and activated T cells resulting in pneumonia. Cytokine profiling and RNA sequencing analysis of SARS-CoV-2-infected lung tissues show a massively upregulated innate immune response with prominent signatures of NF-kB-dependent, type I and II interferon signaling, and leukocyte activation pathways. Thus, the K18-hACE2 model of SARS-CoV-2 infection recapitulates many features of severe COVID-19 infection in humans and can be used to define the mechanistic basis of lung disease and test immune and antiviral-based countermeasures.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Emma S Winkler", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Adam L Bailey", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Natasha M Kafai", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Sharmila Nair", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Broc T McCune", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Jinsheng Yu", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Julie M Fox", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Rita E Chen", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "James T Earnest", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Shamus P Keeler", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Jon H Ritter", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Liang-I Kang", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Sarah Dort", - "author_inst": "SCIREQ Scientific Respiratory Equipment Inc" - }, - { - "author_name": "Annette Robichaud", - "author_inst": "SCIREQ Scientific Respiratory Equipment Inc" - }, - { - "author_name": "Richard Head", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Michael J Holtzman", - "author_inst": "Washington University School of Medicine in St. Louis" - }, - { - "author_name": "Michael S Diamond", - "author_inst": "Washington University School of Medicine in St. Louis" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.09.194027", "rel_title": "Severely ill COVID-19 patients display augmented functional properties in SARS-CoV-2-reactive CD8+ T cells", @@ -1325365,6 +1328695,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.10.197095", + "rel_title": "Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology", + "rel_date": "2020-07-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.10.197095", + "rel_abs": "Humanity has seen numerous pandemics during its course of evolution. The list includes many such as measles, Ebola, SARS, MERS, etc. Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. As of 4th July 2020, COVID-19 has affected over 10 million people from 170+ countries, and 5,28,364 deaths. Genomic technologies have enabled us to understand the genomic constitution of the pathogens, their virulence, evolution, rate of mutations, etc. To date, more than 60,000 virus genomes have been deposited in the public depositories like GISAID and NCBI. While we are writing this, India is the 3rd most-affected country with COVID-19 with 0.6 million cases, and >18000 deaths. Gujarat is the fourth highest affected state with 5.44 percent death rate compared to national average of 2.8 percent.\n\nHere, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. The other significant deleterious variant found in diseased patients from Gujarat and the world is G25563T, which is located in Orf3a and has a potential role in viral pathogenesis. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Madhvi Joshi", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Apurvasinh C Puvar", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Dinesh Kumar", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Afzal Ansari", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Maharshi Pandya", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Janvi Raval", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Zarna Patel", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Pinal Trivedi", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Monika Gandhi", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Labdhi Pandya", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Komal Patel", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Nitin Savaliya", + "author_inst": "Gujarat Biotechnology Research Centre" + }, + { + "author_name": "Snehal Bagatharia", + "author_inst": "Gujarat State Biotechnology Mission" + }, + { + "author_name": "Sachin Kumar", + "author_inst": "Indian Institute of Technology Guwahati" + }, + { + "author_name": "Chaitanya Joshi", + "author_inst": "Gujarat Biotechnology Research Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.07.10.194498", "rel_title": "Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection", @@ -1327136,153 +1330541,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.08.193045", - "rel_title": "A single-dose live-attenuated YF17D-vectored SARS-CoV2 vaccine candidate", - "rel_date": "2020-07-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.08.193045", - "rel_abs": "The explosively expanding COVID-19 pandemic urges the development of safe, efficacious and fast-acting vaccines to quench the unrestrained spread of SARS-CoV-2. Several promising vaccine platforms, developed in recent years, are leveraged for a rapid emergency response to COVID-191. We employed the live-attenuated yellow fever 17D (YF17D) vaccine as a vector to express the prefusion form of the SARS-CoV-2 Spike antigen. In mice, the vaccine candidate, tentatively named YF-S0, induces high levels of SARS-CoV-2 neutralizing antibodies and a favorable Th1 cell-mediated immune response. In a stringent hamster SARS-CoV-2 challenge model2, vaccine candidate YF-S0 prevents infection with SARS-CoV-2. Moreover, a single dose confers protection from lung disease in most vaccinated animals even within 10 days. These results warrant further development of YF-S0 as a potent SARS-CoV-2 vaccine candidate.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Lorena Sanchez Felipe", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Thomas Vercruysse", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Sapna Sharma", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Ji Ma", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Viktor Lemmens", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Dominique van Looveren", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Mahadesh Prasad Arkalagud Javarappa", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Robbert Boudewijns", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Bert Malengier-Devlies", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Suzanne F. Kaptein", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Laurens Liesenborghs", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Carolien De Keyzer", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Lindsey Bervoets", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Madina Rasulova", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Laura Seldeslachts", - "author_inst": "KU Leuven" - }, - { - "author_name": "Sander Jansen", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Michael Bright Yakass", - "author_inst": "KU Leuven - Rega Institute, University of Ghana" - }, - { - "author_name": "Osbourne Quaye", - "author_inst": "University of Ghana" - }, - { - "author_name": "Li-Hsin Li", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Xin Zhang", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Sebastiaan ter Horst", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Niraj Mishra", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Lotte Coelmont", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Christopher Cawthorne", - "author_inst": "KU Leuven" - }, - { - "author_name": "Koen Van Laere", - "author_inst": "KU Leuven" - }, - { - "author_name": "Ghislain Opdenakker", - "author_inst": "KU Leuven" - }, - { - "author_name": "Greetje Van de Velde", - "author_inst": "KU Leuven" - }, - { - "author_name": "Birgit Weynand", - "author_inst": "KU Leuven" - }, - { - "author_name": "Dirk E. Teuwen", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Patrick Matthys", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Johan Neyts", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Hendrik Jan Thibaut", - "author_inst": "KU Leuven - Rega Institute" - }, - { - "author_name": "Kai Dallmeier", - "author_inst": "KU Leuven - Rega Institute for Medical Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.09.195230", "rel_title": "Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease", @@ -1327590,6 +1330848,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.06.20147470", + "rel_title": "Chloroquine for treatment of COVID-19 - a pig in a poke?", + "rel_date": "2020-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147470", + "rel_abs": "Structured abstractO_ST_ABSObjectiveC_ST_ABSChloroquine has been frequently administered for treatment of coronavirus disease 2019 but there are serious concerns about its efficacy and cardiac safety. Our objective was to investigate the pharmacokinetics and safety of chloroquine in hospitalized COVID-19 patients.\n\nDesignA prospective observational study.\n\nSettingDutch hospitals\n\nPatientsPatients admitted to the hospital for treatment of COVID-19.\n\nInterventionsPharmacokinetic sampling\n\nMeasurementsThe plasma concentrations of chloroquine and desethylchloroquine and QTc time.\n\nMain ResultsA total of 83 patients were included. The median (IQR) plasma concentration chloroquine during treatment was 1.05 mol/L (0.63 - 1.55 mol/L). None of the patients reached exposure exceeding the concentration to inhibit SARS-CoV-2 replication by 90% (IC90) of 6.9 M. Furthermore, {Delta}QTc >60 milliseconds occurred after initiation of chloroquine treatment in 34% patients and during treatment QTc [≥]500 milliseconds was observed in 46% of patients.\n\nConclusionsRecommended dose chloroquine treatment results in plasma concentrations that are unlikely to inhibit viral replication. Furthermore, the incidence of QTc prolongation was high. The preclinical promise of chloroquine as antiviral treatment in patients with COVID-19 is overshadowed by its cardiac toxicity and lack of effective exposure. It is unlikely that a positive clinical effect will be found with chloroquine for treatment of COVID-19.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Roger J.M. Bruggemann", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Dirk J.A.R. Moes", + "author_inst": "Leiden University Medical Center, Leiden, The Netherlands" + }, + { + "author_name": "Koen p van Rhee", + "author_inst": "Tergooi hospital, Hilversum, The Netherlands" + }, + { + "author_name": "Nils E van 't Veer", + "author_inst": "Amphia hospital, Breda, The Netherlands" + }, + { + "author_name": "Birgit C.P. Koch", + "author_inst": "Erasmus Medisch Centrum, Rotterdam, The Netherlands" + }, + { + "author_name": "Mara van Rossum", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Annemieke Vermeulen Windsant", + "author_inst": "Jeroen Bosch Hospital, Den Bosch, Netherlands" + }, + { + "author_name": "Monique H.E. Reijers", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Roland R.J. van Kimmenade", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Jannette Rahamat-Langedoen", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Thijs C.D. Rettig", + "author_inst": "Amphia Hospital, Breda, The Netherlands" + }, + { + "author_name": "Rutger van Raalte", + "author_inst": "Tergooi Hospital, Hilversum, The Netherlands" + }, + { + "author_name": "Judith van Paassen", + "author_inst": "Leiden University Medical Center, Leiden, The Netherlands" + }, + { + "author_name": "Florens Polderman", + "author_inst": "Jeroen Bosch Hospital, Den Bosch, The Netherlands" + }, + { + "author_name": "Paul D van der Linden", + "author_inst": "Tergooi Hospital, Hilversum, The Netherlands" + }, + { + "author_name": "Tim Frenzel", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Quirijn de Mast", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "David M Burger", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Jeroen Schouten", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Frank van de Veerdonk", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Peter Pickkers", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + }, + { + "author_name": "Rob ter Heine", + "author_inst": "Radboudumc, Nijmegen, The Netherlands" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.03.20145383", "rel_title": "SARS-CoV-2 sample-to-answer nucleic acid testing in a tertiary care emergency department: evaluation and utility", @@ -1329002,41 +1332363,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.03.179028", - "rel_title": "Genes associated with liver damage signalling pathways may impact the severity of COVID-19 symptoms in Spanish and Italian populations", - "rel_date": "2020-07-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.03.179028", - "rel_abs": "AimThe novel SARS-CoV-2 virus, which causes the COVID-19 disease, has infected more than 10 million people and caused 500K deaths worldwide. In Europe, over 2 million confirmed cases have been reported, while nearly 200K people have died from the disease. Despite strict containment measures in Spain and Italy after the first reported COVID-19 patient, these two countries have remained in the top five European nations with the highest mortality rate for over two months. We hypothesised that a genetic mechanism could partially explain the poor survival outcome observed in these two countries.\n\nMethodsAn extensive literature search to identify human candidate genes linked to SARS-CoV infection, host immune evasion and disease aggressiveness was carried out. Pathway analysis (IPA) was performed to select the most significantly associated canonical signalling pathways with the genes of interest. The genetic variants at these genes with {+/-}1Mb flanking region was extracted (GRCh37/hg19 built). Over 80 million single nucleotide polymorphisms (SNPs) were analysed in genome-wide data of 2,504 individuals (1000 genomes, phase III, https://www.internationalgenome.org/). Principal component (PC) analysis was performed, ancestry by the whole genome was inferred and subsets of the regions of interest were extracted (PLINK v1.9b, http://pngu.mgh.harvard.edu/purcell/plink/). PC1 to PC20 values from five European ancestries, including the Spanish and Italian populations, were used for PC analysis. Gene function predictions were run with our genes of interest as a query to the GeneMANIA Cytoscape plugin (https://genemania.org/).\n\nResultsA total of 437 candidate genes associated with SARS were identified, including 21 correlated with COVID-19 aggressiveness. The two most significant pathways associated with all 437 genes (Caveolar-mediated Endocytosis and MSP-RON Signalling) did not show any segregation at the population level. However, the most significant canonical pathway associated with genes linked to COVID-19 aggressiveness, the Hepatic Fibrosis and Hepatic Stellate Cell Activation, showed population-specific segregation. Both the Spanish and Italian populations clustered together from the rest of Europe. This was also observed for the Finnish population but in the opposite direction. These results suggest some of the severe COVID-19 cases reported in Spain and Italy could be partially explained by a pre-existing liver condition (especially liver cancer) and/or may lead to further COVID-19 related liver complications.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Leire Moya", - "author_inst": "Queensland University of Technology, Translational Research Institute" - }, - { - "author_name": "Samaneh Farashi", - "author_inst": "Queensland University of Technology and Translational Research Institute" - }, - { - "author_name": "Prashanth Suravajhala", - "author_inst": "Birla Institute of Scientific Research" - }, - { - "author_name": "Panchadsaram Janaththani", - "author_inst": "Queensland University of Technology and Translational Research Institute" - }, - { - "author_name": "Jyotsna Batra", - "author_inst": "Queensland University of Technology, Translational Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.07.07.186122", "rel_title": "Towards the design of multiepitope-based peptide vaccine candidate against SARS-CoV-2", @@ -1329424,6 +1332750,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.08.193672", + "rel_title": "Extracellular vesicles containing ACE2 efficiently prevent infection by SARS-CoV-2 Spike protein-containing virus", + "rel_date": "2020-07-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.08.193672", + "rel_abs": "ABSTRACTSARS-CoV-2 entry is mediated by binding of the spike protein (S) to the surface receptor ACE2 and subsequent priming by TMPRRS2 allowing membrane fusion. Here, we produced extracellular vesicles (EVs) exposing ACE2 and demonstrate that ACE2-EVs are efficient decoys for SARS-CoV-2 S protein-containing lentivirus. Reduction of infectivity positively correlates with the level of ACE2, is 500 to 1500 times more efficient than with soluble ACE2 and further enhanced by the inclusion of TMPRSS2.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Federico Cocozza", + "author_inst": "INSERM U932, Institut Curie Centre de Recherche, PSL Research University, 75005 Paris, France." + }, + { + "author_name": "Ester Piovesana", + "author_inst": "INSERM U932, Institut Curie Centre de Recherche, PSL Research University, 75005 Paris, France." + }, + { + "author_name": "Nathalie N\u00e9vo", + "author_inst": "INSERM U932, Institut Curie Centre de Recherche, PSL Research University, 75005 Paris, France." + }, + { + "author_name": "Xavier Lahaye", + "author_inst": "INSERM U932, Institut Curie Centre de Recherche, PSL Research University, 75005 Paris, France." + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Virus and Immunity Unit, Institut Pasteur and CNRS UMR 3569, 75015 Paris, France." + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Virus and Immunity Unit, Institut Pasteur and CNRS UMR 3569, 75015 Paris, France." + }, + { + "author_name": "Nicolas Manel", + "author_inst": "INSERM U932, Institut Curie Centre de Recherche, PSL Research University, 75005 Paris, France." + }, + { + "author_name": "Mercedes Tkach", + "author_inst": "INSERM U932, Institut Curie Centre de Recherche, PSL Research University, 75005 Paris, France." + }, + { + "author_name": "Clotilde Th\u00e9ry", + "author_inst": "INSERM U932, Institut Curie Centre de Recherche, PSL Research University, 75005 Paris, France." + }, + { + "author_name": "Lorena Martin-Jaular", + "author_inst": "INSERM U932, Institut Curie Centre de Recherche, PSL Research University, 75005 Paris, France." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.07.08.193144", "rel_title": "Enhanced COVID-19 data for improved prediction of survival", @@ -1330492,37 +1333873,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.07.05.20140467", - "rel_title": "Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiringmechanical ventilation.", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20140467", - "rel_abs": "Mortality due to Covid-19 is highly associated with advanced age, owing in large part to severe lower respiratory tract infection. SARS-CoV-2 utilizes the host ACE2 receptor for infection. Whether ACE2 abundance in the lung contributes to age-associated vulnerability is currently unknown. We set out to characterize the RNA and protein expression profiles of ACE2 in aging human lung in the context of phenotypic parameters likely to affect lung physiology. Examining publicly available RNA sequencing data, we discovered that mechanical ventilation is a critical variable affecting lung ACE2 levels. Therefore, we investigated ACE2 protein abundance in patients either requiring mechanical ventilation or spontaneously breathing. ACE2 distribution and expression were determined in archival lung samples by immunohistochemistry (IHC). Tissues were selected from the specimen inventory at a large teaching hospital collected between 2010-2020. Twelve samples were chosen from patients receiving mechanical ventilation for acute hypoxic respiratory failure (AHRF). Twenty samples were selected from patients not requiring ventilation. We compared samples across age, ranging from 40-83 years old in the ventilated cohort and 14-80 years old in the non-ventilated cohort. Within the alveolated parenchyma, ACE2 expression is predominantly observed in type II pneumocytes (or alveolar type II / AT2 cells) and alveolar macrophages. All 12 samples from our ventilated cohort showed histologic features of diffuse alveolar damage including reactive, proliferating AT2 cells. In these cases, ACE2 was strongly upregulated with age when normalized to lung area (p = 0.004) or cellularity (p = 0.003), associated with prominent expression in AT2 cells. In non-ventilated individuals, AT2 cell reactive changes were not observed and ACE2 expression did not change with age when normalized to lung area (p = 0.231) or cellularity (p = 0.349). Additionally, we observed prominent pulmonary endothelial ACE2 expression in 2 patients on either an angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB). In summary, ACE2 expression increases with age in the setting of alveolar damage observed in patients on mechanical ventilation, providing a potential mechanism for higher Covid-19 mortality in the elderly.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Steven A Baker", - "author_inst": "Stanford University" - }, - { - "author_name": "Shirley Kowk", - "author_inst": "Stanford University" - }, - { - "author_name": "Gerald J Berry", - "author_inst": "Stanford University" - }, - { - "author_name": "Thomas J Montine", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.07.05.20146878", "rel_title": "Effect of Systemic Inflammatory Response to SARS-CoV-2 on Lopinavir and Hydroxychloroquine Plasma Concentrations", @@ -1330770,6 +1334120,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.07.06.20147009", + "rel_title": "Impact of COVID-19 Attributable Deaths on Longevity, Premature Mortality and DALY: Estimates of USA, Italy, Sweden and Germany", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147009", + "rel_abs": "In a short span of four months, the COVID-19 pandemic has added over 0.4 million deaths worldwide, which are untimely, premature and unwarranted. The USA, Italy, Germany and Sweden are four worst affected countries, accounting to over 40% of COVID-19 deaths globally. The main objective of this study is to examine the impact of COVID-19 attributable deaths on longevity, years of potential life lost (YPLL) and disability adjusted life years (DALY) in USA, Italy, Germany and Sweden. Data from United Nation Population Projection, Statista and centre for disease control and prevention were used in the analyses. Life expectancy, YPLL and DALY were estimated under four scenarios; no COVID-19 deaths, actual number of COVID-19 death as of 22nd May, 2020 and anticipating COVID-19 death share of 6% and 10% respectively. The COVID-19 attributable deaths have lowered the life expectancy by 0.4 years each in USA and Sweden, 0.5 years in Italy and 0.1 years in Germany. The loss of YPLL was 1.5, 0.5, 0.1 and 0.5 million in USA, Italy, Germany and Sweden respectively. The DALY (per 1000 population) due to COVID-19 was 4 in USA, 6 in Italy, 1 each in Germany and Sweden. Compression in life expectancy and increase in YPLL and DALY may intensify further if death continues to soar. COVID-19 has a marked impact on mortality. Reduction in longevity premature mortality and loss of DALY is higher among elderly.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sanjay K Mohanty", + "author_inst": "International Institute for Population Sciences" + }, + { + "author_name": "Manisha Dubey", + "author_inst": "Independent Consultant, New Delhi, India" + }, + { + "author_name": "Udaya S Mishra", + "author_inst": "Centre for Development Studies, Thiruvananthapuram, Kerala, India" + }, + { + "author_name": "Umakanta Sahoo", + "author_inst": "International Institute for Population Science, Mumbai, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.05.20145888", "rel_title": "Initial characterisation of ELISA assays and the immune response of the clinically correlated SARS-CoV-2 biobank SERO-BL-COVID-19 collected during the pandemic onset in Switzerland", @@ -1331778,37 +1335159,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.07.20140996", - "rel_title": "Modelling interventions to control COVID-19 outbreaks in a refugee camp", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20140996", - "rel_abs": "Refugee camp populations are expected to be vulnerable to COVID-19 due to overcrowding, unsanitary conditions, and inadequate medical facilities. Because there has been no COVID-19 outbreak in a refugee camp to date, the potential for nonpharmaceutical interventions to slow the spread of COVID-19 in refugee camps remains untested. We used an agent-based model to simulate COVID-19 outbreaks in the Moria refugee camp, and we studied the effects of feasible interventions. Subdividing the camp (sectoring) \"flattened the curve,\" reducing peak infection by up to 70% and delaying peak infection by up to several months. The use of face masks coupled with efficient isolation of infected individuals reduced the overall incidence of infection and sometimes averted epidemics altogether. These interventions must be implemented quickly to be effective. Lockdowns had little effect on COVID-19 dynamics. Our findings provide an evidence base for camp managers planning intervention strategies against COVID-19 or future epidemics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "R Tucker Gilman", - "author_inst": "Centre for Crisis Studies and Mitigation, University of Manchester, Manchester, UK" - }, - { - "author_name": "Siyana Mahroof-Shaffi", - "author_inst": "Kitrinos Healthcare, Lesbos, Greece" - }, - { - "author_name": "Christian Harkensee", - "author_inst": "Department of Paediatrics, Queen Elizabeth Hospital Gateshead, Gateshead, UK" - }, - { - "author_name": "Andrew T Chamberlain", - "author_inst": "Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.05.20146837", "rel_title": "Change points in the spread of COVID-19 question the effectiveness of nonpharmaceutical interventions in Germany", @@ -1331976,6 +1335326,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.05.20146894", + "rel_title": "A topic analysis of traditional and social media news coverage of the early COVID-19 pandemic and implications for public health communication", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20146894", + "rel_abs": "Knowledge gaps may initially exist among scientists, medical and public health professionals during pandemics, which are fertile grounds for misinformation in news media. We characterized and compared COVID-19 coverage in newspapers, television, and social media, and discussed implications for public health communication strategies that are relevant to an initial pandemic response. We conducted a Latent Dirichlet Allocation (LDA), an unsupervised topic modelling technique, analysis of 3,271 newspaper articles, 40 cable news shows transcripts, 96,000 Twitter posts, and 1,000 Reddit posts during March 4 - 12, 2020, a period chronologically early in the timeframe of the COVID-19 pandemic. Coverage of COVID-19 clustered on topics such as epidemic, politics, and the economy, and these varied across media sources. Topics dominating news were not predominantly health-related, suggesting a limited presence of public health in news coverage in traditional and social media. Examples of misinformation were identified particularly in social media. Public health entities should utilize communication specialists to create engaging informational content to be shared on social media sites. Public health officials should be attuned to their target audience to anticipate and prevent spread of common myths likely to exist within a population. This will help control misinformation in early stages of pandemics.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Wallace Chipidza", + "author_inst": "Center for Information Systems and Technology, Claremont Graduate University" + }, + { + "author_name": "Elmira Akbaripourdibazar", + "author_inst": "Center for Information Systems and Technology, Claremont Graduate University" + }, + { + "author_name": "Tendai Gwanzura", + "author_inst": "School of Community and Global Health, Claremont Graduate University" + }, + { + "author_name": "Nicole M. Gatto", + "author_inst": "School of Community and Global Health, Claremont Graduate University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.07.20148007", "rel_title": "COVID-19 incidence trends between April and June 2020: A global analysis", @@ -1333180,41 +1336561,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.03.20145409", - "rel_title": "Split ventilation with pressure regulators for patient-specific tidal volumes", - "rel_date": "2020-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145409", - "rel_abs": "As a measure of last resort during the COVID-19 pandemic, single mechanical ventilators have been repurposed to support multiple patients. In existing split-ventilator configurations using FDA-approved tubing adaptors, each patient receives the same inspiratory pressure, requiring careful matching of patients to avoid barotrauma. Progression of disease may cause tidal volumes to diverge from desired targets, and routine interventions (eg. suctioning) in one patient may adversely affect other patients. To overcome these limitations, we demonstrate a split-ventilator configuration that enables individualized patient management by incorporating a commonly available pressure regulator used for gas appliances. We validate this method by achieving various combinations of tidal volume in each of two synthetic lungs using a standard ventilator machine in combination with two gas flow analyzers. With further safety testing and instrumentation, pressure regulators may represent a viable path to substantially augment the capacity for ventilation in resource-constrained settings.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Lakshminarayan Srinivasan", - "author_inst": "Transcend Review, Inc." - }, - { - "author_name": "Chris A Rishel", - "author_inst": "Department of Anesthesia, Stanford University School of Medicine" - }, - { - "author_name": "Barrett J. Larson", - "author_inst": "Department of Anesthesia, Stanford University School of Medicine" - }, - { - "author_name": "Juhwan Yoo", - "author_inst": "Electrical Engineer" - }, - { - "author_name": "Ned Shelton", - "author_inst": "Mechanical Engineer" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.07.03.20145912", "rel_title": "Ultraviolet A Radiation and COVID-19 Deaths: A Multi Country Study", @@ -1333406,6 +1336752,93 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.07.06.189803", + "rel_title": "Animal Model Prescreening: Pre-exposure to SARS-CoV-2 impacts responses in the NHP model", + "rel_date": "2020-07-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.06.189803", + "rel_abs": "COVID-19 presents herculean challenges to research and scientific communities for producing diagnostic and treatment solutions. Any return to normalcy requires rapid development of countermeasures, with animal models serving as a critical tool in testing vaccines and therapeutics. Animal disease status and potential COVID-19 exposure prior to study execution may severely bias efficacy testing. We developed a toolbox of immunological and molecular tests to monitor countermeasure impact on disease outcome and evaluate pre-challenge COVID-19 status. Assay application showed critical necessity for animal pre-screening. Specifically, real-time PCR results documented pre-exposure of an African Green Monkey prior to SARS-CoV-2 challenge with sequence confirmation as a community-acquired exposure. Longitudinal monitoring of nasopharyngeal swabs and serum showed pre-exposure impacted both viral disease course and resulting immunological response. This study demonstrates utility in a comprehensive pre-screening strategy for animal models, which captured the first documented case of community-acquired, non-human primate infection.\n\nOne Sentence SummaryPre-exposure to SARS-CoV-2 affects biomarker responses in animal models, highlighting a need for robust pre-screening protocols prior to medical countermeasure studies.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Keersten M Ricks", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Andrew S Herbert", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Jeffrey W Koehler", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Paul A Kuehnert", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Tamara L Clements", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Charles J Shoemaker", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Ana I Kuehne", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Susan R Coyne", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Korey L Delp", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Kristen S Akers", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "John M Dye", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Jay W Hooper", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Jeffrey M Smith", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Jeffrey R Kugelman", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Brett F Beitzel", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Kathleen M Gibson", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Sara C Johnston", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + }, + { + "author_name": "Timothy D Minogue", + "author_inst": "United States Army Medical Research Institute of Infectious Diseases" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.07.06.188953", "rel_title": "Identification of potent and safe antiviral therapeutic candidates against SARS-CoV-2", @@ -1334562,37 +1337995,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.03.20146134", - "rel_title": "Timing of PCR and Antibody Testing in Patients with COVID-19 associated dermatologic manifestations", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20146134", - "rel_abs": "A recent study from Spain noted 40 patients with chilblain-like lesions in suspected COVID-19.1 None tested PCR positive for SARS-CoV-2, but 30% had detectable antibodies. The rapid increase in chilblain/pernio-like cases during the COVID-19 pandemic is likely SARS-CoV-2-associated. The relationship between skin symptom onset and COVID-19 PCR/antibody test timing, however, remains uncharacterized.\n\nWe established an international registry for cutaneous manifestations of COVID-19.2, 3 Providers reported time between dermatologic symptom onset and positive/negative COVID-19 laboratory results, when available.\n\nFrom 8 April-30 June, 2020, 906 laboratory-confirmed or suspected COVID-19 cases with dermatologic manifestations were reported, 534 of which were chilblains/pernio.3 Among PCR-tested patients, 57%(n=208) overall and 15%(n=23) of chilblains/pernio cases were PCR-positive. Antibody positivity was 37%(n=39) overall and 19%(n=15) for chilblains/pernio.\n\nWe evaluated 163 patients with timing information on PCR and/or antibody testing (Table 1). For patients with suspected COVID-19 and any cutaneous manifestation, PCR-positive testing occurred median 6 (IQR 1-14) days after dermatologic symptoms started while PCR-negative testing occurred median 14 (IQR 7-24) days later. For patients with pernio/chilblains, PCR-positivity was noted 8 (IQR 5-14) days after symptoms and negativity median 14 (IQR 7-28) days later. Antibody testing (IgM or IgG) was positive median 30 (IQR 19-39) days after symptom onset for all dermatologic manifestations and 27 (IQR 24-33) days after chilblains/pernio onset.\n\nLike Hubiche et al, our data highlight the low frequency of SARS-CoV-2 PCR+ testing in COVID-19 patients with cutaneous manifestations. Positive predictive values for COVID-19 PCR are influenced by viral shedding kinetics, which are difficult to assess in non-respiratory presentations.4 Our data reveal that early PCR testing is more likely to be positive than later testing, even when date-of-onset is defined by cutaneous manifestations rather than systemic symptoms.\n\nMost COVID-19 antibody data are from systemically-ill patients; the kinetics of antibody production in mild-to-moderate COVID-19 infections remain unclear.5 Here, positive antibodies resulted median 30 days from disease onset, beyond the frequently used 14-21 day testing window. In outpatients with true infection, many factors influence the likelihood of a positive antibody result: antibody production, test availability, assay sensitivity, and timing of care-seeking in relation to symptom-onset. These variables influence our interpretation of individual test results and our understanding of the association between pernio and COVID-19.\n\nMore population-level testing data is necessary to optimize diagnostic test timing. Positive identification of COVID-19 in minimally-symptomatic patients, including patients with skin findings, is critical to the public health effort.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Esther E Freeman", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Devon E McMahon", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Lindy P Fox", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Marlys S Fassett", - "author_inst": "University of California San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "dermatology" - }, { "rel_doi": "10.1101/2020.07.03.20145763", "rel_title": "Oxygen and mortality in COVID-19 pneumonia: a comparative analysis of supplemental oxygen policies and health outcomes across 26 countries.", @@ -1334768,6 +1338170,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.02.20145532", + "rel_title": "Impact of anxiety associated with COVID 19 on tinnitus", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20145532", + "rel_abs": "ObjectivesTo investigate if the anxiety associated with COVID-19 is a promoting factor to tinnitus.\n\nMethodsA retrospective research design was used to compare the clinical characteristics of tinnitus between the patients in 2020 under pandemic pressure and those from the matching period in 2019. While anxiety was quantified using the Zungs Self-rating Anxiety Scale (SAS), tinnitus severity was evaluated using the Tinnitus Handicap Inventory (THI) questionnaire and the test of minimum masking level (MML). The assessments were repeated after the sound therapy plus educational counselling (STEC) and compared with EC alone therapy.\n\nResultsA large increase in anxiety was evident in 2020 in both case rate and SAS. The treatment of both methods was less effective in 2020. SAS, THI and MML were all deteriorated after the EC alone treatment in 2020, while an improvement was seen in 2019. This suggests that EC alone could not counteract the stress by COVID-19 at all, and the stress, if not managed well, can significantly increase the severity of tinnitus and associated anxiety.\n\nConclusionsBy using the EC subgroup in virtual control, we conclude that anxiety can serve as a promoting factor to tinnitus. We believe that this is the first study report that confirm the causative/promotive role of anxiety on tinnitus.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Li Xia", + "author_inst": "Sichuan Provincial People Hospital and Sichuan Academy of Medical Sciences" + }, + { + "author_name": "Jian Wang", + "author_inst": "School of Communication Science and Disorders, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada" + }, + { + "author_name": "Dong Chuan", + "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Sichuan Provincial People Hospital and Sichuan Academy of Medical Sciences, Chengdu, Sichuan, 610072, China" + }, + { + "author_name": "Jiangang Fan", + "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Sichuan Provincial People Hospital and Sichuan Academy of Medical Sciences, Chengdu, Sichuan, 610072, China" + }, + { + "author_name": "Zhengnong Chen", + "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People Hospital, 200233, Shanghai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2020.07.02.20145284", "rel_title": "Dynamics of coagulopathy in patients with different COVID-19 severity", @@ -1335868,41 +1339305,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.03.20144931", - "rel_title": "Psychiatric symptoms, risk, and protective factors among university students in quarantine during the COVID-19 pandemic in China", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20144931", - "rel_abs": "This study investigated psychiatric symptoms (depression, anxiety, and traumatic stress) during state-enforced quarantine among university students in China. We conducted a cross-sectional survey with 1,912 university students during March and April 2020. Psychiatric symptoms in the mild or higher range based on clinical cut-offs were alarmingly prevalent: 67.05% reported traumatic stress symptoms, 46.55% had depressive symptoms, and 34.73% reported anxiety symptoms. Further, 19.56% endorsed some degree of suicidal ideation. We explored factors that may contribute to poor psychological health as well as those that may function as protective factors. Risk and protective factors examined included demographic variables, two known protective factors for mental health (mindfulness, perceived social support), four COVID-specific factors (COVID-19 related efficacy, perceived COVID-19 threat, perceived COVID-19 societal stigma, COVID-19 prosocial behavior) and screen media usage. Across psychiatric symptom domains, mindfulness was associated with lower symptom severity, while COVID-19 related financial stress, perceived COVID-19 societal stigma, and perceived COVID-19 threat were associated with higher symptom severity. COVID-19 threat and COVID-19 stigma showed main and interactive effects in predicting all mental health outcomes, with their combination associated with highest symptom severity. Average screen media device usage was 6 hours and usage was positively associated with depression. Female gender and COVID-19 prosocial behavior were associated with higher anxiety, while COVID-19 self-efficacy associated with lower anxiety symptoms. Study limitations and implications for treatment and prevention of affective disorders during crisis are discussed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shufang Sun", - "author_inst": "Brown University" - }, - { - "author_name": "Simon B Goldberg", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Danhua Lin", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Shan Qiao", - "author_inst": "University of South Carolina" - }, - { - "author_name": "Don Operario", - "author_inst": "Brown University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.07.02.20144899", "rel_title": "Curve-fitting approach for COVID-19 data and its physical background", @@ -1336238,6 +1339640,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.02.20144865", + "rel_title": "Highly predictive regression model of active cases of COVID-19 in a population by screening wastewater viral load", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20144865", + "rel_abs": "The quantification of the SARS-CoV-2 load in wastewater has emerged as a useful method to monitor COVID-19 outbreaks in the community. This approach was implemented in the metropolitan area of A Coruna (NW Spain), where wastewater from the treatment plant of Bens was analyzed to track the epidemics dynamic in a population of 369,098 inhabitants. We developed statistical regression models that allowed us to estimate the number of infected people from the viral load detected in the wastewater with a reliability close to 90%. This is the first wastewater-based epidemiological model that could potentially be adapted to track the evolution of the COVID-19 epidemic anywhere in the world, monitoring both symptomatic and asymptomatic individuals. It can help to understand with a high degree of reliability the true magnitude of the epidemic in a place at any given time and can be used as an effective early warning tool for predicting outbreaks.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Juan A Vallejo", + "author_inst": "Biomedical Research Institute of A Coruna" + }, + { + "author_name": "Soraya Rumbo-Feal", + "author_inst": "Biomedical Research Institute of A Coruna" + }, + { + "author_name": "Kelly Conde-Perez", + "author_inst": "Biomedical Research Institute of A Coruna" + }, + { + "author_name": "Angel Lopez-Oriona", + "author_inst": "Research Center for Information and Communication Technologies (CITIC), University of A Coruna" + }, + { + "author_name": "Javier Tarrio", + "author_inst": "Research Center for Information and Communication Technologies (CITIC), University of A Coruna" + }, + { + "author_name": "Ruben Reif", + "author_inst": "Advanced Scientific Research Center (CICA), University of A Coruna" + }, + { + "author_name": "Susana Ladra", + "author_inst": "Research Center for Information and Communication Technologies (CITIC), University of A Coruna" + }, + { + "author_name": "Bruno K Rodino-Janeiro", + "author_inst": "University of Vienna" + }, + { + "author_name": "Mohammed Nasser", + "author_inst": "Biomedical Research Institute of A Coruna" + }, + { + "author_name": "Angeles Cid", + "author_inst": "Advanced Scientific Research Center (CICA)- University of A Coruna" + }, + { + "author_name": "Maria C Veiga", + "author_inst": "Advanced Scientific Research Center (CICA)-University of A Coruna" + }, + { + "author_name": "Anton Acevedo", + "author_inst": "Hospital University Complex of A Coruna" + }, + { + "author_name": "Carlos Lamora", + "author_inst": "Public wastewater treatment plant company EDAR Bens, S.A., A Coruna" + }, + { + "author_name": "German Bou", + "author_inst": "Biomedical Research Institute-Hospital University Complex of A Coruna" + }, + { + "author_name": "Ricardo Cao", + "author_inst": "Research Center for Information and Communication Technologies (CITIC), University of A Coruna-Technological Institute for Industrial Mathematics (ITMATI), Univ" + }, + { + "author_name": "Margarita Poza", + "author_inst": "Biomedical Research Institute-University of A Coruna" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.04.187583", "rel_title": "Gender, race and parenthood impact academic productivity during the COVID-19 pandemic: from survey to action.", @@ -1337370,77 +1340851,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.02.20143206", - "rel_title": "Navigating hospitals safely through the COVID-19 epidemic tide: predicting case load for adjusting bed capacity", - "rel_date": "2020-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20143206", - "rel_abs": "BackgroundThe pressures exerted by the pandemic of COVID-19 pose an unprecedented demand on health care services. Hospitals become rapidly overwhelmed when patients requiring life-saving support outpace available capacities. We here describe methods used by a university hospital to forecast caseloads and time to peak incidence.\n\nMethodsWe developed a set of models to forecast incidence among the hospital catchment population and describe the COVID-19 patient hospital care-path. The first forecast utilized data from antecedent allopatric epidemics and parameterized the care path model according to expert opinion (static model). Once sufficient local data were available, trends for the time dependent effective reproduction number were fitted and the care-path was parameterized using hazards for real patient admission, referrals, and discharge (dynamic model).\n\nResultsThe static model, deployed before the epidemic, exaggerated the bed occupancy (general wards 116 forecasted vs 66 observed, ICU 47 forecasted vs 34 observed) and predicted the peak too late (general ward forecast April 9, observed April 8, ICU forecast April 19, observed April 8). After April 5, the dynamic model could be run daily and precision improved with increasing availability of empirical local data.\n\nConclusionsThe models provided data-based guidance in the preparation and allocation of critical resources of a university hospital well in advance of the epidemic surge, despite overestimating the service demand. Overestimates should resolve when population contact pattern before and during restrictions can be taken into account, but for now they may provide an acceptable safety margin for preparing during times of uncertainty.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Tjibbe Donker", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Fabian B\u00fcrkin", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Martin Wolkewitz", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Christian Haverkamp", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Dominic Christoffel", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Oliver Kappert", - "author_inst": "Public Health Office, Public Health District Freiburg" - }, - { - "author_name": "Thorsten Hammer", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Hans-J\u00f6rg Busch", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Paul Biever", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Johannes Kalbhenn", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Hartmut B\u00fcrkle", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Winfried Kern", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Frederik Wenz", - "author_inst": "University Medical Center Freiburg" - }, - { - "author_name": "Hajo Grundmann", - "author_inst": "UniversityMedical Center Freiburg" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.30.20143149", "rel_title": "Orthogonal Functions for Evaluating Social Distancing Impact on CoVID-19 Spread", @@ -1337588,6 +1340998,89 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.07.03.186304", + "rel_title": "Robust and sensitive detection of SARS-CoV-2 using PCR based methods", + "rel_date": "2020-07-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.03.186304", + "rel_abs": "The World Health Organization (WHO) has declared the Coronavirus disease 2019 (COVID-19) as an international health emergency. Current diagnostic tests are based on the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method, the gold standard test that involves the amplification of viral RNA. However, the RT-qPCR assay has limitations in terms of sensitivity and quantification. In this study, we tested both qPCR and droplet digital PCR (ddPCR) to detect low amounts of viral RNA. The cycle threshold (CT) of viral RNA by RT-PCR significantly varied according to the sequence of primer and probe sets with in vitro transcript (IVT) RNA or viral RNA as templates, whereas the copy number of viral RNA by ddPCR was effectively quantified with IVT RNA, cultured viral RNA, and RNA from clinical samples. Furthermore, the clinical samples were assayed via both methods, and the sensitivity of the ddPCR was determined to be significantly higher than RT-qPCR. These findings suggest that ddPCR could be used as a highly sensitive and compatible diagnostic method for viral RNA detection.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Changwoo Park", + "author_inst": "KRISS" + }, + { + "author_name": "Jina Lee", + "author_inst": "KRISS" + }, + { + "author_name": "Zohaib Ul Hassan", + "author_inst": "KRISS" + }, + { + "author_name": "Keun Bon Ku", + "author_inst": "KRICT" + }, + { + "author_name": "Seong Jun Kim", + "author_inst": "KRICT" + }, + { + "author_name": "Hong Gi Kim", + "author_inst": "KRICT" + }, + { + "author_name": "Edmond Changkyun Park", + "author_inst": "KBSi" + }, + { + "author_name": "Gun-Soo Park", + "author_inst": "KFRI" + }, + { + "author_name": "Daeui Park", + "author_inst": "KIT" + }, + { + "author_name": "Seung-Hwa Baek", + "author_inst": "KIT" + }, + { + "author_name": "Dongju Park", + "author_inst": "KRISS" + }, + { + "author_name": "Jihye Lee", + "author_inst": "IPK" + }, + { + "author_name": "Sangeun Jeon", + "author_inst": "IPK" + }, + { + "author_name": "Seungtaek Kim", + "author_inst": "IPK" + }, + { + "author_name": "Chang-Seop Lee", + "author_inst": "JBNU" + }, + { + "author_name": "Hee Min Yoo", + "author_inst": "KRISS" + }, + { + "author_name": "Seil Kim", + "author_inst": "KRISS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.07.03.186825", "rel_title": "Map of SARS-CoV-2 spike epitopes not shielded by glycans.", @@ -1338964,29 +1342457,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.30.20143586", - "rel_title": "Does Lockdown Decrease the Protective Role of ultraviolet-B (UVB) Radiation in Reducing COVID-19 Deaths?", - "rel_date": "2020-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143586", - "rel_abs": "BackgroundNations are imposing unprecedented measures at large-scale to contain the spread of COVID-19 pandemic. Recent studies indicate that measures such as lockdowns may have slowed down the growth of COVID-19. However, in addition to substantial economic and social costs, these measures also limit the exposure to Ultraviolet-B radiation (UVB). Emerging observational evidence indicate the protective role of UVB and vitamin D in reducing the severity and mortality of COVID-19 deaths. In this observational study, we empirically outline the independent protective roles of lockdown and UVB exposure as measured by ultraviolet index (UVI), whilst also examining whether the severity of lockdown is associated with a reduction in the protective role.\n\nMethodsWe apply a log-linear fixed-effects model to a panel dataset of 162 countries over a period of 108 days (n=6049). We use the cumulative number of COVID-19 deaths as the dependent variable and isolate the mitigating influence of lockdown severity on the association between UVI and growth-rates of COVID-19 deaths from time-constant country-specific and time-varying country-specific potentially confounding factors.\n\nFindingsAfter controlling for time-constant and time-varying factors, we find that a unit increase in UVI and lockdown severity are independently associated with 17% [-1.8 percentage points] and 77% [-7.9 percentage points] decline in COVID-19 deaths growth rate, indicating their respective protective roles. However, the widely utilized and least severe lockdown (recommendation to not leave the house) already fully mitigates the protective role of UVI by 95% [1.8 percentage points] indicating its downside.\n\nInterpretationWe find that lockdown severity and UVI are independently associated with a slowdown in the daily growth rates of cumulative COVID-19 deaths. However, we find consistent evidence that increase in lockdown severity is associated with a significant reduction in the protective role of UVI in reducing COVID-19 deaths. Our results suggest that lockdowns in conjunction with adequate exposure to UVB radiation might have provided even more substantial health benefits, than lockdowns alone. For example, we estimate that there would be 21% fewer deaths on average with sufficient UVB exposure while people were recommended not to leave their house. Therefore, our study outlines the importance of considering UVB exposure, especially while implementing lockdowns and may support policy decision making in countries imposing such measures.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rahul Kalippurayil Moozhipurath", - "author_inst": "Goethe University Frankfurt am Main" - }, - { - "author_name": "Lennart Kraft", - "author_inst": "Goethe University Frankfurt am Main" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.01.20144162", "rel_title": "Mass Screening for SARS-CoV-2 Infection among Residents and Staff in Twenty-eight Long-term Care Facilities in Fulton County, Georgia", @@ -1339186,6 +1342656,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.01.20144394", + "rel_title": "Temporary Immunity and Multiple Waves of COVID-19", + "rel_date": "2020-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144394", + "rel_abs": "In this work we use mathematical modeling to describe the potential phenomena which may occur if immunity to COVID-19 lasts for a finite time instead of being permanent, i.e. if a recovered COVID-19 patient may again become susceptible to the virus after a given time interval following his/her recovery. Whether this really happens or not is unknown at the current time. If it does happen, then we find that for certain combinations of parameter values (social mobility, contact tracing, immunity threshold duration etc), the disease can keep recurring in wave after wave of outbreaks, with a periodicity approximately equal to twice the immunity threshold. Such cyclical attacks can be prevented trivially if public health interventions are strong enough to contain the disease outright. Of greater interest is the finding that should such effective interventions not prove possible, then also the second and subsequent waves can be forestalled by a consciously relaxed intervention level which finishes off the first wave before the immunity threshold is breached. Such an approach leads to higher case counts in the immediate term but significantly lower counts in the long term as well as a drastically shortened overall course of the epidemic.\n\nAs we write this, there are more than 1,00,00,000 cases (at least, detected cases) and more than 5,00,000 deaths due to COVID-19 all over the globe. The unknowns surrounding this disease outnumber the knowns by orders of magnitude. One of these unknowns is how long does immunity last i.e., once a person recovers from COVID-19 infection, how long does s/he remain insusceptible to a fresh infection. Most modeling studies assume lifetime immunity, or at least sufficiently prolonged immunity as to last until the outbreak is completely over. Among the exceptions are Giordano et. al. [1] and Bjornstad et. al. [2] who account for the possibility of re-infection - while the former find no special behaviour on account of this, the latter find an oscillatory approach towards the eventual equilibrium. In an article which appeared today, Kosinski [3] has found multiple waves of COVID-19 if the immunity threshold is finite. The question of whether COVID-19 re-infection can occur is completely open as of now. A study [4] has found that for benign coronaviruses (NOT the COVID-19 pathogen!), antibodies become significantly weaker six months after the original infection, and re-infection is common from one year onwards. Although it is currently unknown whether COVID-19 re-infections can occur, the mere possibility is sufficiently frightening as to warrant a discussion of what might happen if it is true. In this Article, we use mathematical modeling to present such a discussion. Before starting off, let us declare in the clearest possible terms that this entire Article is a what-if analysis, predicated on an assumption whose veracity is not known at the current time. The contents of this Article are therefore hypothetical - as of now they are neither factual nor counter-factual.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "B Shayak", + "author_inst": "Cornell University" + }, + { + "author_name": "Mohit Manoj Sharma", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Anoop Misra", + "author_inst": "Fortis Hospital, Delhi" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.30.20143859", "rel_title": "Role of pharmacist during the COVID-19 pandemic: a scoping review", @@ -1340618,133 +1344115,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.30.20142935", - "rel_title": "A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 within nasopharyngeal and oropharyngeal swabs at Hampshire Hospitals NHS Foundation Trust", - "rel_date": "2020-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20142935", - "rel_abs": "The COVID-19 pandemic has illustrated the importance of rapid, accurate diagnostic testing for the effective triaging and cohorting of patients and timely tracking and tracing of cases. However, a surge in diagnostic testing quickly resulted in worldwide competition for the same sample preparation and real-time RT-PCR diagnostic reagents (rRT-PCR). Consequently, Hampshire Hospitals NHS Foundation Trust, UK sought to diversify their diagnostic portfolio by exploring alternative amplification chemistries including those that permit direct testing without RNA extraction. This study describes the validation of a SARS-CoV-2 RT-LAMP assay, which is an isothermal, autocycling, strand-displacement nucleic acid amplification technique which can be performed on extracted RNA (RNA RT-LAMP) or directly from swab (Direct RT-LAMP). Analytical specificity (ASp) of this new RT-LAMP assay was 100% and analytical sensitivity (ASe) was between 1[x]101 and 1[x]102 copies when using a synthetic DNA target. The overall diagnostic sensitivity (DSe) and specificity (DSp) of RNA RT-LAMP was 97% and 99% respectively, relative to the standard of care (SoC) rRT-PCR. When a CT cut-off of 33 was employed, above which increasingly evidence suggests there is a very low risk of patients shedding infectious virus, the diagnostic sensitivity was 100%. The DSe and DSp of Direct-RT-LAMP was 67% and 97%, respectively. When setting CT cut-offs of [≤]33 and [≤]25, the DSe increased to 75% and 100%, respectively. Time from swab-to-result for a strong positive sample (CT < 25) was < 15 minutes. We propose that RNA RT-LAMP could replace rRT-PCR where there is a need for increase in throughput, whereas Direct RT-LAMP could be used as a screening tool for triaging patients into appropriate hospitals wards, at GP surgeries and in care homes, or for population screening to identify super shedders. Direct RT-LAMP could also be used during times of high prevalence to save critical extraction and rRT-PCR reagents by screening out those strong positives from diagnostic pipelines.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Veronica L Fowler", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Bryony Armson", - "author_inst": "School of Biosciences and Medicine, University of Surrey" - }, - { - "author_name": "Jose L Gonzales", - "author_inst": "Wageningen Bioveterinary Research (WBVR)" - }, - { - "author_name": "Emma L Wise", - "author_inst": "School of Biosciences and Medicine, University of Surrey" - }, - { - "author_name": "Emma L. A. Howson", - "author_inst": "The Pirbright Institute" - }, - { - "author_name": "Zoe Vincent-Mistiaen", - "author_inst": "Gibraltar Health Authority" - }, - { - "author_name": "Sarah Fouch", - "author_inst": "School of Pharmacy and Biomedical Sciences, University of Portsmouth" - }, - { - "author_name": "Connor J Maltby", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Seden Grippon", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Simon Munro", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Lisa Jones", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Tom Holmes", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Claire Tillyer", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Joanne Elwell", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Amy Sowood", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Oliver de Peyer", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Sophie Dixon", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Thomas Hatcher", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Helen Knight", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Shailen Laxman", - "author_inst": "OptiSense Limited" - }, - { - "author_name": "Charlotte Walsh", - "author_inst": "GeneSys Biotech Limited" - }, - { - "author_name": "Michael Andreou", - "author_inst": "OptiSense Limited" - }, - { - "author_name": "Nick Morant", - "author_inst": "GeneSys Biotech Limited" - }, - { - "author_name": "Duncan Clark", - "author_inst": "GeneSys Biotech Limited" - }, - { - "author_name": "Rebecca Houghton", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nathan Moore", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nicholas Cortes", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Stephen P Kidd", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.30.20143255", "rel_title": "Handyfuge-LAMP: low-cost and electricity-free centrifugation forisothermal SARS-CoV-2 detection in saliva.", @@ -1341036,6 +1344406,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.30.20138446", + "rel_title": "Impact of COVID-19 related lockdown on cognition and emotion: A pilot study", + "rel_date": "2020-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20138446", + "rel_abs": "COVID-19 pandemic has posed an unprecedented challenge in front of the world contributed mostly by social distancing and lockdown. Among several other effects this pandemic has wreaked havoc on the psychology and cognition of people across the globe. In this paper we attempted to find out the impact of lockdown and social isolation on the cognition and emotion of young healthy adults with high education (n=43) by means of a questionnaire sent through email. We found that more than 50% of the participants had some kind of emotional or cognitive (dysexecutive) symptoms, as calculated through emotional symptom index (ESI) and cognitive symptom index (CSI). The correlation between cognitive and emotional symptoms was also found to be moderately strong (0.59). Although it is a pilot study and larger samples are required to draw firm conclusion, the results argue in favor of a negative impact on the cognition and emotion of healthy educated young people caused by the COVID-19 related lockdown. It can be conjectured that, if taking an older sample with a lower education, emotional and cognitive changes would be more evident.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Durjoy Lahiri", + "author_inst": "Bangur Institute of Neurosciences, IPGME&R, Kolkata" + }, + { + "author_name": "Souvik Dubey", + "author_inst": "Bangur Institute of Neurosciences, IPGME&R, Kolkata, India" + }, + { + "author_name": "Alfredo Ardila", + "author_inst": "I.M. Sechenov First Moscow State Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.06.29.20141564", "rel_title": "A phenome-wide association study (PheWAS) of COVID-19 outcomes by race using the electronic health records data in Michigan Medicine", @@ -1342616,37 +1346013,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.29.179192", - "rel_title": "Validation and Comparison of a Modified CDC Assay with two Commercially Available Assays for the Detection of SARS-CoV-2 in Respiratory Specimen", - "rel_date": "2020-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.29.179192", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has spread rapidly around the globe since it was first identified in December of 2019 in Wuhan, China. In a race to contain the infection, researchers and healthcare officials have developed several assays to help diagnose individuals with COVID-19. To help laboratories in deciding what assay to bring into testing lines, factors such as assay availability, cost, throughput, and TAT should be considered. Here we validated a modified version of the CDC assay and used it as a reference to evaluate the performance of the NeuMoDx SARS-CoV-2 and DiaSorin Simplexa Covid-19 Direct assays. In silico analysis and clinical sample testing showed that the primesr/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. The performance of the three assays were analyzed using 161 nasopharyngeal swabs specimen tested within 24 hours or 5 days from routine testing. A 100% agreement was observed between the commercial assays and the modified CDC SARS-CoV-2 assay. A deeper look at the Ct values showed no significant difference between NeuMoDx and the modified CDC SARS-CoV-2 assay, whereas DiaSorin had lower overall Ct values than the modified CDC SARS-CoV-2 assay. NeuMoDx and DiaSorin workflows were much easier to perform. NeuMoDx has the highest throughput and shortest TAT, whereas although the modified CDC SARS-CoV-2 assay has comparable throughput to DiaSorin, it has the longest hands-on time, and highest TAT.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Amorce Lima", - "author_inst": "Tampa General Hospital" - }, - { - "author_name": "Vicki Healer", - "author_inst": "Tampa General Hospital" - }, - { - "author_name": "Elaine Vendrone", - "author_inst": "Tampa General Hospital" - }, - { - "author_name": "Suzane Silbert", - "author_inst": "Tampa General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.30.172833", "rel_title": "Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples", @@ -1343050,6 +1346416,49 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.06.29.178384", + "rel_title": "A Fast and Accessible Method for the Isolation of RNA, DNA, and Protein to Facilitate the Detection of SARS-CoV-2", + "rel_date": "2020-06-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.29.178384", + "rel_abs": "Management of the COVID-19 pandemic requires widespread SARS-CoV-2 testing. A main limitation for widespread SARS-CoV-2 testing is the global shortage of essential supplies, among these, RNA extraction kits. The need for commercial RNA extraction kits places a bottleneck on tests that detect SARS-CoV-2 genetic material, including PCR-based reference tests. Here we propose an alternative method we call PEARL (Precipitation Enhanced Analyte RetrievaL) that addresses this limitation. PEARL uses a lysis solution that disrupts cell membranes and viral envelopes while simultaneously providing conditions suitable for alcohol-based precipitation of RNA, DNA, and proteins. PEARL is a fast, low-cost, and simple method that uses common laboratory reagents and offers comparable performance to commercial RNA extraction kits. PEARL offers an alternative method to isolate host and pathogen nucleic acids and proteins to streamline the detection of DNA and RNA viruses, including SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jose Carlos Ponce-Rojas", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Michael S. Costello", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Duncan A. Proctor", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Kenneth S. Kosik", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Maxwell Z Wilson", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Carolina Arias", + "author_inst": "University of California Santa Barbara" + }, + { + "author_name": "Diego Acosta-Alvear", + "author_inst": "University of California, Santa Barbara" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.29.178707", "rel_title": "Anti-frameshifting ligand active against SARS coronavirus-2 is resistant to natural mutations of the frameshift-stimulatory pseudoknot", @@ -1344558,137 +1347967,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.24.20139386", - "rel_title": "Electrocardiographic safety of daily Hydroxychloroquine 400mg plus Azithromycin 250mg as an ambulatory treatment for COVID-19 patients in Cameroon.", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139386", - "rel_abs": "ObjectiveTo determine the early electrocardiographic changes in a cohort of ambulatory cameroonian COVID-19 patients treated with hydroxychloroquine and Azithromycin.\n\nDesignProspective study.\n\nSettingTreatment centres of the city of Yaounde, Cameroon, from May 7th to 24th 2020.\n\nParticipantsWe enrolled 51 consecutive confirmed COVID-19 on RT-PCR who having mild forms of COVID-19 and treated by hydroxychloroquine 200mg twice daily during seven days plus Azithromycin 500 mg the first day and 250 mg the remaining 4 days as per national standard.\n\nMain outcomes measuresThe primary end-point was the change in QTc interval between day 0 (D0), day 3 (D3) and day 7 (D7). Secondary endpoints were changes in all other cardiac electrical conductivity patterns and the occurrence of clinical arrhythmic events during the course of treatment.\n\nResultsThe population (29 men and 22 women) was aged 39 {+/-} 11 years (range 17 to 61 years). Mean Tisdale score was 3.35{+/-}0.48. No significant change from baseline (D0) of QTc was observed at D7 (429{+/-}27 ms at D0 versus 396{+/-}26 ms at D7; p=0.27). A reduction of heart rate was observed between the D0 and D7 (75{+/-}13 bpm versus 70{+/-}13 bpm, p = 0.02) with increased QRS duration between D0 and D7 (95{+/-}10 ms versus 102{+/-}17 ms, p = 0.004). No symptomatic arrhythmic events occurred during the treatment course.\n\nConclusionsNo life-threatening modifications of the QT interval was observed in non-severe COVID-19 patients treated ambulatory with hydroxychloroquine and azithromycin. Studies are needed in critical-ill and older patients.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Liliane Mfeukeu Kuate", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "William Ngatchou", - "author_inst": "University of Douala" - }, - { - "author_name": "Mazou Ngou Temgoua", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Charles Kouanfack", - "author_inst": "University of Dschang" - }, - { - "author_name": "Daniel Lemogoum", - "author_inst": "University of Douala" - }, - { - "author_name": "Joel Noutakdie Tochie", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Armel Zemsi", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Lauriane Fomete", - "author_inst": "ANRS" - }, - { - "author_name": "Skinner Lekelem", - "author_inst": "ANRS" - }, - { - "author_name": "Sylvain Zemsi", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Joelle Tambekou Sobngwi", - "author_inst": "RSD & London School of Economics" - }, - { - "author_name": "Thiery Ntandzi", - "author_inst": "Yaounde Central Hospital" - }, - { - "author_name": "Christian Ngongang Ouankou", - "author_inst": "University of Dschang" - }, - { - "author_name": "Yves Wasnyo", - "author_inst": "Yaounde Central Hospital" - }, - { - "author_name": "Antoinette Ntsama Assiga", - "author_inst": "Yaounde Central Hospital" - }, - { - "author_name": "Jean Rene Nkeck", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Ahmadou Musa Jingi", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Magellan Guewo", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Eric Walter Pefura Yone", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Charlotte Omgba Moussi", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Paul Owono Etoundi", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Jean Cyr Yombi", - "author_inst": "Universite Catholique de Louvain" - }, - { - "author_name": "Alain Patrick Menanga", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Samuel Kingue", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Jacqueline Ze Minkande", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Jean Claude Mbanya", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Pierre Cyrille Ongolo Zogo", - "author_inst": "University of Yaounde 1" - }, - { - "author_name": "Pierre Joseph Fouda", - "author_inst": "Yaounde Central Hospital" - }, - { - "author_name": "Eugene Sobngwi", - "author_inst": "University of Yaounde 1" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.24.20131185", "rel_title": "Sentinel Coronavirus Environmental Monitoring Can Contribute to Detecting Asymptomatic SARS-CoV-2 Virus Spreaders and Can Verify Effectiveness of Workplace COVID-19 Controls", @@ -1345092,6 +1348370,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.29.20138008", + "rel_title": "SUPERSPREADING AS A REGULAR FACTOR OF THE COVID-19 PANDEMIC", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20138008", + "rel_abs": "We consider the impact of superspreading on the course of the COVID-19 epidemic. A two-component model of the epidemic has been developed, in which all infected are divided in two groups. The groups are asymptomatic superspreaders spreading the infection and sensitive persons which can only get infection. Once infected the sensitive exhibit clear symptoms and become isolated. It is shown that the ratio of increment of the number of daily cases in the beginning of the epidemic and decrement at the end of the epidemic is equal to the ratio of the spreading rates of the infection transmission from the superspreaders to potential superspreaders and to the sensitive persons, respectively. On the basis of data from 12 countries and territories it is found that the superspreaders transmit the infection to potential superspreaders approximately 4 times more often then to the sensitive persons. Specific measures to limit the epidemical incidence are proposed. The possibility of an allergic component in the disease is discussed.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Juri Dimaschko", + "author_inst": "Fachhochschule Luebeck" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.22.20136531", "rel_title": "Efficacy and Safety of Remdesivir for COVID-19 Treatment: An Analysis of Randomized, Double-Blind, Placebo-Controlled Trials", @@ -1346468,49 +1349765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.27.20141424", - "rel_title": "Incubation Period and Reproduction Number for novel coronavirus (COVID-19) infections in India", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141424", - "rel_abs": "Novel coronavirus (COVID-19) rapidly spread from China to other parts of the world. Knowledge of incubation period and reproduction number is important in controlling any epidemic. The distribution of these parameters helps estimate the epidemic size and transmission potential of the disease. We estimated incubation period and reproduction number of COVID-19 for India utilizing data reported by Ministry of Health and Family Welfare (MoHFW), Government of India (GOI) and data in public domain. The mean incubation period seems to be larger at 6.93 (SD={+/-}5.87, 95% CI: 6.11-7.75). and 95th percentile estimate for best fit normal distribution is 17.8 days. Weibull distribution, the best fit for the reproduction number estimated pre lockdown reproduction number as 2.6 (95% CI=2.34 - 2.86) and post lockdown reduced to 1.57 (95% CI=1.3 - 1.84) implying effectiveness of the epidemic response strategies. The herd immunity is estimated between 36-61% for R0 of 1.57 and 2.6 respectively.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Seema Patrikar", - "author_inst": "Armed Forces Medical College, Pune, India" - }, - { - "author_name": "Atul Kotwal", - "author_inst": "Armed Forces Medical Services, India" - }, - { - "author_name": "Vijay Bhatti", - "author_inst": "Armed Forces Medical Services, Ministry of Defence, India" - }, - { - "author_name": "Amitav Banerjee", - "author_inst": "Dr DY Patil Medical College, Pune, India" - }, - { - "author_name": "Kunal Chatterjee", - "author_inst": "Armed Forces Medical Services, Ministry of Defence, India" - }, - { - "author_name": "Renuka Kunte", - "author_inst": "Armed Forces Medical Services, Ministry of Defence, India" - }, - { - "author_name": "Murlidhar Tambe", - "author_inst": "BJ Medical College, Pune, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.27.20141739", "rel_title": "Aligning SARS-CoV-2 Indicators via an Epidemic Model: Application to Hospital Admissions and RNA Detection in Sewage Sludge", @@ -1346758,6 +1350012,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.28.20133561", + "rel_title": "Extracorporeal Cytokine Hemadsorption in Severe COVID-19 Respiratory Failure", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.28.20133561", + "rel_abs": "Despite the extracorporeal cytokine hemadsorption device CytoSorb was granted FDA emergency approval for critically ill COVID19 patients, to our knowledge no published studies are currently available to support its use. This manuscript reports the experience of the use of CytoSorb during COVID19 pandemic in Bergamo, Italy. In our pilot study, eleven COVID19 patients requiring invasive mechanical ventilation for a rapidly progressive ARDS were treated with 24 to 48 hours of extracorporeal cytokine hemadsorption.\n\nRespiratory and laboratory parameters, including a full set of inflammatory cytokines, were evaluated at different time points. A significant but transient reduction of the hyperinflammatory status was observed, along with the amelioration of the clinical and respiratory parameters.\n\nWe believe that this manuscript will provide them with important preliminary data on the use of cytokine hemadsorption devices.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Marianna Damiani", + "author_inst": "Universita degli Studi di Milano" + }, + { + "author_name": "Lucia Gandini", + "author_inst": "Univsersita degli Studi di Milano" + }, + { + "author_name": "Francesco Landi", + "author_inst": "Hematology Units, Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergam" + }, + { + "author_name": "Fabrizio Fabretti", + "author_inst": "Intensive Care Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy" + }, + { + "author_name": "Giuseppe Gritti", + "author_inst": "Hematology Units, Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy" + }, + { + "author_name": "Ivano Riva", + "author_inst": "Intensive Care, Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.06.28.20142133", "rel_title": "Superspreading in Early Transmissions of COVID-19 in Indonesia", @@ -1347818,81 +1351111,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.06.29.174623", - "rel_title": "SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery", - "rel_date": "2020-06-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.29.174623", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic resulting from zoonotic transmission of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Severe symptoms include viral pneumonia secondary to infection and inflammation of the lower respiratory tract, in some cases causing death. We developed primary human lung epithelial infection models to understand responses of proximal and distal lung epithelium to SARS-CoV-2 infection. Differentiated air-liquid interface cultures of proximal airway epithelium and 3D organoid cultures of alveolar epithelium were readily infected by SARS-CoV-2 leading to an epithelial cell-autonomous proinflammatory response. We validated the efficacy of selected candidate COVID-19 drugs confirming that Remdesivir strongly suppressed viral infection/replication. We provide a relevant platform for studying COVID-19 pathobiology and for rapid drug screening against SARS-CoV-2 and future emergent respiratory pathogens.\n\nOne Sentence SummaryA novel infection model of the adult human lung epithelium serves as a platform for COVID-19 studies and drug discovery.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Apoorva Mulay", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Bindu Konda", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Gustavo Garcia Jr.", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Changfu Yao", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Stephen Beil", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Chandani Sen", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Arunima Purkayastha", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Jay Kolls", - "author_inst": "Tulane School of Medicine" - }, - { - "author_name": "Derek Pociask", - "author_inst": "Tulane University" - }, - { - "author_name": "Patrizia Pessina", - "author_inst": "Harvard Medical School, Boston" - }, - { - "author_name": "Carolina Garcia-de-Alba", - "author_inst": "Harvard Medical School, Boston" - }, - { - "author_name": "Carla Kim", - "author_inst": "Harvard Medical School, Boston" - }, - { - "author_name": "Brigitte Gomperts", - "author_inst": "UCLA" - }, - { - "author_name": "Vaithilingaraja Arumugaswami", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Barry Stripp", - "author_inst": "Cedars-Sinai Medical Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.06.29.177030", "rel_title": "A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species", @@ -1348136,6 +1351354,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.29.177204", + "rel_title": "Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection", + "rel_date": "2020-06-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.29.177204", + "rel_abs": "BackgroundSince December 2019, the world is experiencing an unprecedented crisis due to a novel coronavirus, SARS-CoV-2. Owing to poor understanding of pathogenicity, the virus is eluding treatment and complicating recovery. Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells.\n\nResultsOur analyses uncover 21 differentially expressed lncRNAs whose functions are broadly involved in cell survival and regulation of gene expression. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. These genes are involved in cellular signaling, metabolism, immune response and RNA homeostasis. Since lncRNAs have been known to sponge microRNAs and protect expression of upregulated genes, we also identified 9 microRNAs that are induced in viral infections; however, some lncRNAs are able to block their usual suppressive effect on overexpressed genes and consequently contribute to host defense and cell survival.\n\nConclusionsOur investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rafeed Rahman Turjya", + "author_inst": "Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh" + }, + { + "author_name": "Md. Abdullah-Al-Kamran Khan", + "author_inst": "Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh" + }, + { + "author_name": "Abul B.M.M.K. Islam", + "author_inst": "Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.06.29.177154", "rel_title": "Tissue distribution of ACE2 protein in Syrian golden hamster (Mesocricetus auratus) and its possible implications in SARS CoV-2 related studies", @@ -1349488,29 +1352733,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.06.25.20139022", - "rel_title": "Problem drinking before and during the COVID-19 crisis in US and UK adults: Evidence from two population-based longitudinal studies", - "rel_date": "2020-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20139022", - "rel_abs": "BackgroundThe impact of the COVID-19 crisis on potentially harmful alcohol consumption is unclear.\n\nAimsTo test whether the prevalence of problem drinking has changed from before to during the COVID-19 crisis in the US and UK.\n\nDesign/SettingWe examined nationally representative longitudinal data on how problem drinking has changed from pre-pandemic levels among adults in the US (N=7,327; Understanding America Study) and UK (N=12,594; UK Household Longitudinal Study).\n\nMethodsIn the US, we examined rates of consuming alcohol [≥] 4 times in the past week at baseline (March, 2020) and across four waves of follow-up (April-May, 2020). In the UK we assessed the prevalence of consuming alcohol [≥] 4 times per week and weekly heavy episodic drinking using the AUDIT-C at baseline (2017-2019) and during the COVID-19 lockdown (April, 2020). We also tested whether there were specific groups at greater risk of increased problem drinking during the pandemic.\n\nResultsAmong US adults, there was a statistically significant increase in the percentage of participants reporting drinking alcohol [≥] 4 times a week which rose significantly from 11.7% to 17.9% (53% increase, p < .001) as the COVID-19 crisis developed in the US. Among UK adults, the percentage of participants reporting drinking [≥] 4 times a week increased significantly from 14.2% to 23% (62% increase, p < .001) and heavy episodic drinking at least weekly increased significantly from 9.7% to 16.6% (71% increase, p < .001) when compared to pre-COVID-19 lockdown levels. Trends were similar across population demographics, although those aged under 50 years and higher income groups displayed the largest increases.\n\nConclusionsThe COVID-19 crisis has been associated with substantial increases in problematic drinking in both US and UK adults.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Michael Daly", - "author_inst": "Maynooth University" - }, - { - "author_name": "Eric Robinson", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "addiction medicine" - }, { "rel_doi": "10.1101/2020.06.26.20138545", "rel_title": "Prevalence of SARS-CoV-2 among workers returning to Bihar gives snapshot of COVID across India", @@ -1349698,6 +1352920,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.27.175166", + "rel_title": "Modified Vaccinia Ankara Based SARS-CoV-2 Vaccine Expressing Full-Length Spike Induces Strong Neutralizing Antibody Response", + "rel_date": "2020-06-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.27.175166", + "rel_abs": "There is a great need for the development of vaccines for preventing SARS-CoV-2 infection and mitigating the COVID-19 pandemic. Here, we developed two modified vaccinia Ankara (MVA) based vaccines which express either a membrane anchored full-length spike protein (MVA/S) stabilized in a prefusion state or the S1 region of the spike (MVA/S1) which forms trimers and is secreted. Both immunogens contained the receptor-binding domain (RBD) which is a known target of antibody-mediated neutralization. Following immunizations with MVA/S or MVA/S1, both spike protein recombinants induced strong IgG antibodies to purified full-length SARS-CoV-2 spike protein. The MVA/S induced a robust antibody response to purified RBD, S1 and S2 whereas MVA/S1 induced an antibody response to the S1 region outside of the RBD region. Both vaccines induced an antibody response in the lung and that was associated with induction of bronchus-associated lymphoid tissue. MVA/S but not MVA/S1 vaccinated mice generated robust neutralizing antibody responses against SARS-CoV-2 that strongly correlated with RBD antibody binding titers. Mechanistically, S1 binding to ACE-2 was strong but reduced following prolonged pre-incubation at room temperature suggesting confirmation changes in RBD with time. These results demonstrate MVA/S is a potential vaccine candidate against SARS-CoV-2 infection.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Nanda Kishore Routhu", + "author_inst": "Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA" + }, + { + "author_name": "Sailaja Gangadhara", + "author_inst": "Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA" + }, + { + "author_name": "Narayanaiah Cheedarla", + "author_inst": "Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA" + }, + { + "author_name": "Ayalnesh Shiferaw", + "author_inst": "Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA" + }, + { + "author_name": "Sheikh Abdul Rahman", + "author_inst": "Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA" + }, + { + "author_name": "Anusmita Sahoo", + "author_inst": "Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA" + }, + { + "author_name": "Vineet D Menachery", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Katharine Floyd", + "author_inst": "Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA" + }, + { + "author_name": "Stephanie Fischinger", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA" + }, + { + "author_name": "Caroline Atyeo", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA" + }, + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA" + }, + { + "author_name": "Rama Rao Amara", + "author_inst": "Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.06.27.174979", "rel_title": "Structures, conformations and distributions of SARS-CoV-2 spike protein trimers on intact virions", @@ -1350914,45 +1354207,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.06.24.20139634", - "rel_title": "Shut and re-open: the role of schools in the spread of COVID-19 in Europe", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139634", - "rel_abs": "We investigate the effect of school closure and subsequent reopening on the transmission of COVID-19, by considering Denmark, Norway, Sweden, and German states as case studies. By comparing the growth rates in daily hospitalisations or confirmed cases under different interventions, we provide evidence that school closures contribute to a reduction in the growth rate approximately 7 days after implementation. Limited school attendance, such as older students sitting exams or the partial return of younger year groups, does not appear to significantly affect community transmission. In countries where community transmission is generally low, such as Denmark or Norway, a large-scale reopening of schools while controlling or suppressing the epidemic appears feasible. However, school reopening can contribute to statistically significant increases in the growth rate in countries like Germany, where community transmission is relatively high. In all regions, a combination of low classroom occupancy and robust test-and-trace measures were in place. Our findings underscore the need for a cautious evaluation of reopening strategies.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Helena B Stage", - "author_inst": "Department of Mathematics, University of Manchester" - }, - { - "author_name": "Joseph Shingleton", - "author_inst": "Emergency Response Department, Public Health England" - }, - { - "author_name": "Sanmitra Ghosh", - "author_inst": "MRC Biostatistics Unit, University of Cambridge" - }, - { - "author_name": "Francesca Scarabel", - "author_inst": "Laboratory of Industrial and Applied Mathematics, Department of Mathematics and Statistics, York University" - }, - { - "author_name": "Lorenzo Pellis", - "author_inst": "The University of Manchester" - }, - { - "author_name": "Thomas Finnie", - "author_inst": "Emergency Response Department, Public Health England" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.24.20139238", "rel_title": "A Multi-Task Pipeline with Specialized Streams forClassification and Segmentation of InfectionManifestations in COVID-19 Scans", @@ -1351140,6 +1354394,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.25.20138131", + "rel_title": "The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20138131", + "rel_abs": "COVID-19, is caused by SARS-CoV-2, has been started on December/2019 in Wuhan/China and spread all over the world. We analyzed RT-PCR results of 10,000 cases from April-2 to May-30, 2020 in three neighbor cities located on the Eastern of Turkey. The final study population was 7853 cases after excluded screening tests. RT-PCR were performed to detect the SARS-CoV-2-specific RdRp (RNA-dependent-RNA-polymerase) gene fragment. The number of total positive samples out of 7853 were 487; however, the number of non-repeating positive patient was 373 (4.8%). The cough and fever were the most common symptoms in positive cases. The epidemiologic studies should be performed about the prevalence of SARS-CoV-2 infection to better understand the effect of the virus all over the world.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Murat Karamese", + "author_inst": "Kafkas University, Faculty of Medicine, Department of Medical Microbiology, Kars, Turkey." + }, + { + "author_name": "Didem Ozgur", + "author_inst": "Kafkas University, Faculty of Medicine, Department of Medical Microbiology, Kars, Turkey." + }, + { + "author_name": "Ceyda Tarhan", + "author_inst": "Igdir State Hospital, Department of Otorhinolaryngology, Igdir, Turkey" + }, + { + "author_name": "Susamber Dik Altintas", + "author_inst": "Igdir State Hospital, Department of Chest Diseases, Igdir, Turkey" + }, + { + "author_name": "Okan Caliskan", + "author_inst": "Harakani State Hospital, Department of Infectious Disease and Clinical Microbiology, Kars, Turkey," + }, + { + "author_name": "Aysegul Tuna", + "author_inst": "Harakani State Hospital, Department of Infectious Disease and Clinical Microbiology, Kars, Turkey" + }, + { + "author_name": "Saliha Kazci", + "author_inst": "Ardahan State Hospital, Department of Infectious Disease and Clinical Microbiology, Ardahan, Turkey" + }, + { + "author_name": "Mursel Karadavut", + "author_inst": "Ardahan State Hospital, Department of Internal Medicine, Ardahan, Turkey" + }, + { + "author_name": "Abdullah Gumus", + "author_inst": "Kafkas University, Faculty of Medicine, Department of Medical Microbiology, Kars, Turkey." + }, + { + "author_name": "Gozde Apaydin", + "author_inst": "Igdir State Hospital, Department of Pediatric Health and Diseases, Igdir, Turkey" + }, + { + "author_name": "Necati Mumcu", + "author_inst": "Igdir State Hospital, Department of Infectious Disease and Clinical Microbiology, Igdir, Turkey" + }, + { + "author_name": "Onur Coruh", + "author_inst": "Ardahan State Hospital, Department of Anesthesiology and Reanimation, Ardahan, Turkey" + }, + { + "author_name": "Emin Ediz Tutuncu", + "author_inst": "Kafkas University, Faculty of Medicine, Department of Infectious Disease and Clinical Microbiology, Kars," + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.24.20139626", "rel_title": "Uncertainty stress, and its impact on disease fear and prevention behaviors during the COVID-19 epidemic in China: A panel study", @@ -1352384,117 +1355705,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.06.25.172510", - "rel_title": "Nanotrap(R) particles improve detection of SARS-CoV-2 for pooled sample methods, extraction-free saliva methods, and extraction-free medium methods", - "rel_date": "2020-06-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.25.172510", - "rel_abs": "Here we present a rapid and versatile method for capturing and concentrating SARS-CoV-2 from transport medium and saliva using affinity-capture magnetic hydrogel particles. We demonstrate that the method concentrates virus prior to RNA extraction, thus significantly improving detection of the virus using a real-time RT-PCR assay across a range of viral titers, from 100 to 1,000,000 viral copies/mL; in particular, detection of virus in low viral load samples is enhanced when using the method coupled with the IDT 2019-nCoV CDC EUA Kit. This method is compatible with commercially available nucleic acid extraction kits, as well with a simple heat and detergent method. Using transport medium diagnostic remnant samples that previously had been tested for SARS-CoV-2 using either the Abbott RealTime SARS-CoV-2 EUA Test (n=14) or the Cepheid Xpert Xpress SARS-CoV-2 EUA Test (n=35), we demonstrate that our method not only correctly identifies all positive samples (n = 17) but also significantly improves detection of the virus in low viral load samples. The average improvement in cycle threshold (Ct) value as measured with the IDT 2019-nCoV CDC EUA Kit was 3.1; n = 10. Finally, to demonstrate that the method could potentially be used to enable pooled testing, we spiked infectious virus or a confirmed positive diagnostic remnant sample into 5 mL and 10 mL of negative transport medium and observed significant improvement in the detection of the virus from those larger sample volumes.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Robert A Barclay", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Ivan Akhrymuk", - "author_inst": "George Mason University" - }, - { - "author_name": "Anurag Patnaik", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Victoria Callahan", - "author_inst": "George Mason University" - }, - { - "author_name": "Caitlin Lehman", - "author_inst": "George Mason University" - }, - { - "author_name": "Patrick Andersen", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Robbie Barbero", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Stephanie Barksdale", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Ross Dunlap", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Daniel Goldfarb", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Tara Jones-Roe", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Ross Kelly", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Brianna Kim", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Shida Miao", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Amy Munns", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Denton Munns", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Samip Patel", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Erica Porter", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Rosalind Ramsey", - "author_inst": "CeresNanosciences Inc." - }, - { - "author_name": "Saswata Sahoo", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Olivia Swahn", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Jack Warsh", - "author_inst": "Ceres Nanosciences Inc." - }, - { - "author_name": "Kylene Kehn-Hall", - "author_inst": "George Mason University" - }, - { - "author_name": "Ben Lepene", - "author_inst": "Ceres Nanosciences Inc." - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.26.173872", "rel_title": "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2", @@ -1352750,6 +1355960,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.25.20140004", + "rel_title": "Covid-19 Pandemic Data Analysis and Forecasting using Machine Learning Algorithms", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20140004", + "rel_abs": "India reported its first Covid-19 case on 30th Jan 2020 and the number of cases reported heavily escalated from March, 2020. This research paper analyses COVID -19 data initially at a global level and then drills down to the scenario obtained in India. Data is gathered from multiple data sources-several authentic government websites. The need of the hour is to accurately forecast when the numbers will reach at its peak and then diminish. It will be of huge help to public welfare professionals to plan the preventive measures to be taken keeping the economic balance of the country as well. Variables such as gender, geographical location, age etc. have been represented using Python and Data Visualization techniques. Time Series Forecasting techniques including Machine Learning models like Linear Regression, Support Vector Regression, Polynomial Regression and Deep Learning Forecasting Model like LSTM(Long short-term memory) are deployed to study the probable hike in cases and in the near future. A comparative analysis is also done to understand which model fits the best for our data. Data is considered till 30th July, 2020. The results show that a statistical model named sigmoid model is outperforming other models. Also the Sigmoid model is giving an estimate of the day on which we can expect the number of active cases to reach its peak and also when the curve will start to flatten. Strength of Sigmoid model lies in providing a count of date that no other model offers and thus it is the best model to predict Covid cases counts -this is unique feature of analysis in this paper. Certain feature engineering techniques have been used to transfer data into logarithmic scale as is affords better comparison removing any data extremities or outliers. Based on the predictions of the short-term interval, our model can be tuned to forecast long time intervals.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "SOHINI Sengupta", + "author_inst": "Welingkar Institute of Management" + }, + { + "author_name": "Sareeta Mugde", + "author_inst": "Welingkar Institute of Management" + }, + { + "author_name": "Garima Sharma", + "author_inst": "Welingkar Institute of Management" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.25.20139931", "rel_title": "Evaluation on the diagnostic efficiency of different methods in detecting COVID-19.", @@ -1353786,33 +1357023,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.25.171975", - "rel_title": "Increased Expression of Chondroitin Sulfotransferases following AngII may Contribute to Pathophysiology Underlying Covid-19 Respiratory Failure: Impact may be Exacerbated by Decline in Arylsulfatase B Activity", - "rel_date": "2020-06-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.25.171975", - "rel_abs": "The precise mechanisms by which Covid-19 infection leads to hypoxia and respiratory failure have not yet been elucidated. Interactions between sulfated glycosaminoglycans (GAGs) and the SARS-CoV-2 spike glycoprotein have been identified as participating in viral adherence and infectivity. The spike glycoprotein binds to respiratory epithelium through the angiotensin converting enzyme 2 (ACE2) receptor, which endogenously interacts with Angiotensin (Ang) II to yield Angiotensin 1-7. In this report, we show that stimulation of human vascular smooth muscle cells by Ang II leads to increased mRNA expression of two chondroitin sulfotransferases (CHST11 and CHST15), which are required for synthesis of chondroitin 4-sulfate (C4S) and chondroitin 4,6-disulfate (CSE), respectively. Also, increased total sulfated GAGs, increased sulfotransferase activity, and increased expression of the proteoglycans biglycan, syndecan, perlecan, and versican followed treatment by Ang II. Candesartan, an Angiotensin II receptor blocker (Arb), largely, but incompletely, inhibited these increases, and the differences from baseline remained significant. These results suggest that another effect of Ang II also contributes to the increased expression of chondroitin sulfotransferases, total sulfated GAGs, and proteoglycans. We hypothesize that activation of ACE2 may contribute to these increases and suggest that the SARS-CoV-2 spike glycoprotein interaction with ACE2 may also increase chondroitin sulfotransferases, sulfated GAGs, and proteoglycans and thereby contribute to viral adherence to bronchioalveolar cells and to respiratory compromise in SARS-CoV-2 infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sumit Bhattacharyya", - "author_inst": "University of Illinois at Chicago and Jesse Brown VAMC" - }, - { - "author_name": "Kumar Kotlo", - "author_inst": "University of Illinois at Chicago and Jesse Brown VAMC" - }, - { - "author_name": "Joanne Kramer Tobacman", - "author_inst": "University of Illinois at Chicago and Jesse Brown VAMC" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.06.25.170936", "rel_title": "Cellular exocytosis gene (EXOC6/6B): a potential molecular link for the susceptibility and mortality of COVID-19 in diabetic patients", @@ -1353975,6 +1357185,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.25.170688", + "rel_title": "Molecular evolution of SARS-CoV-2 structural genes: evidence of positive selection in spike glycoprotein", + "rel_date": "2020-06-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.25.170688", + "rel_abs": "SARS-CoV-2 caused a global pandemic in early 2020 and has resulted in more than 8,000,000 infections as well as 430,000 deaths in the world so far. Four structural proteins, envelope (E), membrane (M), nucleocapsid (N) and spike (S) glycoprotein, play a key role in controlling the entry into human cells and virion assembly of SARS-CoV-2. However, how these genes evolve during its human to human transmission is largely unknown. In this study, we screened and analyzed roughly 3090 SARS-CoV-2 isolates from GenBank database. The distribution of the four gene alleles is determined:16 for E, 40 for M, 131 for N and 173 for S genes. Phylogenetic analysis shows that global SARS-CoV-2 isolates can be clustered into three to four major clades based on the protein sequences of these genes. Intragenic recombination event isnt detected among different alleles. However, purifying selection has conducted on the evolution of these genes. By analyzing full genomic sequences of these alleles using codon-substitution models (M8, M3 and M2a) and likelihood ratio tests (LRTs) of codeML package, it reveals that codon 614 of S glycoprotein has subjected to strong positive selection pressure and a persistent D614G mutation is identified. The definitive positive selection of D614G mutation is further confirmed by internal fixed effects likelihood (IFEL) and Evolutionary Fingerprinting methods implemented in Hyphy package. In addition, another potential positive selection site at codon 5 in the signal sequence of the S protein is also identified. The allele containing D614G mutation has undergone significant expansion during SARS-CoV-2 global pandemic, implying a better adaptability of isolates with the mutation. However, L5F allele expansion is relatively restricted. The D614G mutation is located at the subdomain 2 (SD2) of C-terminal portion (CTP) of the S1 subunit. Protein structural modeling shows that the D614G mutation may cause the disruption of salt bridge among S protein monomers increase their flexibility, and in turn promote receptor binding domain (RBD) opening, virus attachment and entry into host cells. Located at the signal sequence of S protein as it is, L5F mutation may facilitate the protein folding, assembly, and secretion of the virus. This is the first evidence of positive Darwinian selection in the spike gene of SARS-CoV-2, which contributes to a better understanding of the adaptive mechanism of this virus and help to provide insights for developing novel therapeutic approaches as well as effective vaccines by targeting on mutation sites.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Xiao-Yong Zhan", + "author_inst": "The Seventh Affiliated Hospital, Sun Yat-Sen University" + }, + { + "author_name": "Ying Zhang", + "author_inst": "The Seventh Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Xuefu Zhou", + "author_inst": "The Seventh Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Ke Huang", + "author_inst": "The Seventh Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Yichao Qian", + "author_inst": "The Seventh Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Yang Leng", + "author_inst": "The Seventh Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Leping Yan", + "author_inst": "The Seventh Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Bihui Huang", + "author_inst": "The Seventh Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Yulong He", + "author_inst": "The Seventh Affiliated Hospital, Sun Yat-Sen University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.06.25.170639", "rel_title": "The discovery of potential natural products for targeting SARS-CoV-2 spike protein by virtual screening", @@ -1355347,173 +1358608,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.23.20138289", - "rel_title": "Longitudinal immunological analyses reveal inflammatory misfiring in severe COVID-19 patients", - "rel_date": "2020-06-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138289", - "rel_abs": "Recent studies have provided insights into the pathogenesis of coronavirus disease 2019 (COVID-19)1-4. Yet, longitudinal immunological correlates of disease outcome remain unclear. Here, we serially analysed immune responses in 113 COVID-19 patients with moderate (non-ICU) and severe (ICU) disease. Immune profiling revealed an overall increase in innate cell lineages with a concomitant reduction in T cell number. We identify an association between early, elevated cytokines and worse disease outcomes. Following an early increase in cytokines, COVID-19 patients with moderate disease displayed a progressive reduction in type-1 (antiviral) and type-3 (antifungal) responses. In contrast, patients with severe disease maintained these elevated responses throughout the course of disease. Moreover, severe disease was accompanied by an increase in multiple type 2 (anti-helminths) effectors including, IL-5, IL-13, IgE and eosinophils. Unsupervised clustering analysis of plasma and peripheral blood leukocyte data identified 4 immune signatures, representing (A) growth factors, (B) type-2/3 cytokines, (C) mixed type-1/2/3 cytokines, and (D) chemokines that correlated with three distinct disease trajectories of patients. The immune profile of patients who recovered with moderate disease was enriched in tissue reparative growth factor signature (A), while the profile for those with worsened disease trajectory had elevated levels of all four signatures. Thus, we identified development of a maladapted immune response profile associated with severe COVID-19 outcome and early immune signatures that correlate with divergent disease trajectories.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Carolina Lucas", - "author_inst": "Yale University" - }, - { - "author_name": "Patrick Wong", - "author_inst": "Yale University" - }, - { - "author_name": "Jon Klein", - "author_inst": "Yale University" - }, - { - "author_name": "Tiago Castro", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Julio Silva", - "author_inst": "Yale University" - }, - { - "author_name": "Maria Sundaram", - "author_inst": "Emory University" - }, - { - "author_name": "Mallory Ellingson", - "author_inst": "Yale University" - }, - { - "author_name": "Tianyang Mao", - "author_inst": "Yale University" - }, - { - "author_name": "Jieun Oh", - "author_inst": "Yale University" - }, - { - "author_name": "Benjamin Israelow", - "author_inst": "Yale University" - }, - { - "author_name": "Maria Tokuyama", - "author_inst": "Yale University" - }, - { - "author_name": "Peiwen Lu", - "author_inst": "Yale University" - }, - { - "author_name": "Arvind Venkataraman", - "author_inst": "Yale University" - }, - { - "author_name": "Annsea Park", - "author_inst": "Yale University" - }, - { - "author_name": "Subhasis Mohanty", - "author_inst": "Yale University" - }, - { - "author_name": "Haowei Wang", - "author_inst": "Yale University" - }, - { - "author_name": "Anne Louise Wyllie", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Chantal B.F. Vogels", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Rebecca Earnest", - "author_inst": "Yale University" - }, - { - "author_name": "Sarah Lapidus", - "author_inst": "Yale University" - }, - { - "author_name": "Isabel Ott", - "author_inst": "Yale University" - }, - { - "author_name": "Adam Moore", - "author_inst": "Yale University" - }, - { - "author_name": "Catherine Muenker", - "author_inst": "Yale University" - }, - { - "author_name": "John Fournier", - "author_inst": "Yale University" - }, - { - "author_name": "Melissa Campbell", - "author_inst": "Yale University" - }, - { - "author_name": "Camila Odio", - "author_inst": "Yale University" - }, - { - "author_name": "Arnau Casanovas-Massana", - "author_inst": "Yale University" - }, - { - "author_name": "- Yale IMPACT Team", - "author_inst": "" - }, - { - "author_name": "Roy Herbst", - "author_inst": "Yale University" - }, - { - "author_name": "Albert Shaw", - "author_inst": "Yale University" - }, - { - "author_name": "Ruslan Medzhitov", - "author_inst": "Yale University" - }, - { - "author_name": "Wade L Schulz", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Nathan Grubaugh", - "author_inst": "Yale University" - }, - { - "author_name": "Charles Dela Cruz", - "author_inst": "Yale University" - }, - { - "author_name": "Shelli Farhadian", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Albert Ko", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Saad Omer", - "author_inst": "Yale University" - }, - { - "author_name": "Akiko Iwasaki", - "author_inst": "Yale University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.23.20137471", "rel_title": "Initial experience with short-course corticosteroids in a small cohort of adults with severe COVID-19 in a tertiary care hospital in India", @@ -1355741,6 +1358835,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.23.20138719", + "rel_title": "Analysis and Prediction of COVID-19 Characteristics Using a Birth-and-Death Model", + "rel_date": "2020-06-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138719", + "rel_abs": "Its spreading speed together with the risk of fatality might be the main characteristic that separates COVID-19 from other infectious diseases in our recent history. In this scenario, mathematical modeling for predicting the spread of the disease could have great value in containing the disease. Several very recent papers have contributed to this purpose. In this study we propose a birth-and-death model for predicting the number of COVID-19 active cases. It relation to the Susceptible-Infected-Recovered (SIR) model has been discussed. An explicit expression for the expected number of active cases helps us to identify a stationary point on the infection curve, where the infection ceases increasing. Parameters of the model are estimated by fitting the expressions for active and total reported cases simultaneously. We analyzed the movement of the stationary point and the basic reproduction number during the infection period up to the 20th of April 2020. These provide information about the disease progression path and therefore could be really useful in designing containment strategies.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Narayanan C Viswanath", + "author_inst": "Government Engineering College, Thrissur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.22.20137828", "rel_title": "An agent based modelling approach to study lockdown efficacy for infectious disease spreads", @@ -1356876,33 +1359989,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.21.20136580", - "rel_title": "Estimation of Undetected Symptomatic and Asymptomatic cases of COVID-19 Infection and prediction of its spread in USA", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136580", - "rel_abs": "The reported COVID-19 cases in the USA have crossed over 2 million, and a large number of infected cases are undetected whose estimation can be done if country-wide antibody testing is performed. In this work, we estimate this undetected fraction of the population by modeling and simulation approach. We propose a new epidemic model SIPHERD in which three categories of infection carriers Symptomatic, Purely Asymptomatic, and Exposed are considered with different transmission rates that are taken dependent on the lockdown conditions, and the detection rate of the infected carriers is taken dependent on the tests done per day. The model is first validated for Germany and South Korea and then applied for prediction of total number of confirmed, active and death, and daily new positive cases in the United States. Our study also demonstrates the possibility of a second wave of the infection if social distancing regulations are relaxed to a large extent. We estimate that around 12.7 million people are already infected, and in the absence of any vaccine, 17.7 million (range: 16.3-19.2) people, or 5.3% (range: 4.9-5.8) of the population will be infected by when the disease spread ends in the USA. We find the Infection to Fatality Ratio to be 0.93% (range: 0.85-1.01).", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ashutosh Mahajan", - "author_inst": "Vellore Institute of Technology, Vellore, India" - }, - { - "author_name": "Ravi Solanki", - "author_inst": "Visvesvaraya National Institute of Technology, Nagpur, India" - }, - { - "author_name": "Namitha Sivadas", - "author_inst": "Vellore Institute of Technology, Vellore, India" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.21.20136341", "rel_title": "Analysis and Prediction of the COVID-19 outbreak in Pakistan", @@ -1357062,6 +1360148,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.06.21.20136598", + "rel_title": "Chest X-ray classification using Deep learning for automated COVID-19 screening", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136598", + "rel_abs": "In todays world, we find ourselves struggling to fight one of the worst pandemics in the history of humanity known as COVID-2019 caused by a coronavirus. If we detect the virus at an early stage (before it enters the lower respiratory tract), the patient can be treated quickly. Once the virus reaches the lungs, we observe ground-glass opacity in the chest X-ray due to fibrosis in the lungs. Due to the significant differences between X-ray images of an infected and non-infected person, artificial intelligence techniques can be used to identify the presence and severity of the infection. We propose a classification model that can analyze the chest X-rays and help in the accurate diagnosis of COVID-19. Our methodology classifies the chest X-rays into 4 classes viz. normal, pneumonia, tuberculosis (TB), and COVID-19. Further, the X-rays indicating COVID-19 are classified on severity-basis into mild, medium, and severe. The deep learning model used for the classification of pneumonia, TB, and normal is VGG16 with an accuracy of 95.9 %. For the segregation of normal pneumonia and COVID-19, the DenseNet-161 was used with an accuracy of 98.9 %. ResNet-18 worked best for severity classification achieving accuracy up to 76 %. Our approach allows mass screening of the people using X-rays as a primary validation for COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ankita Shelke", + "author_inst": "K. J. Somaiya College of Engineering" + }, + { + "author_name": "Madhura Inamdar", + "author_inst": "K. J. Somaiya College of Engineering" + }, + { + "author_name": "Vruddhi Shah", + "author_inst": "K. J. Somaiya College of Engineering" + }, + { + "author_name": "Amanshu Tiwari", + "author_inst": "K. J. Somaiya College of Engineering" + }, + { + "author_name": "Aafiya Hussain", + "author_inst": "K. J. Somaiya College of Engineering" + }, + { + "author_name": "Talha Chafekar", + "author_inst": "K. J. Somaiya College of Engineering" + }, + { + "author_name": "Ninad Mehendale", + "author_inst": "K. J. Somaiya College of Engineering" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.06.21.20136549", "rel_title": "Health and Economic Costs of Early, Delayed and No Suppression of COVID-19: The Case of Australia", @@ -1358094,61 +1361223,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.23.20137992", - "rel_title": "Hydroxychloroquine serum concentrations in non-critical care patients infected with SARS CoV 2", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20137992", - "rel_abs": "Hydroxychloroquine(HCQ) has been widely used to treat SARS-CoV-2 infection however HCQ pharmacokinetics in this condition have not been studied in non-critical care patient groups. Here we report the serum concentrations of HCQ in a small cohort of patients treated with HCQ as part of the RECOVERY trial.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alasdair P MacGowan", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Fergus Hamilton", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Mark Bayliss", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Liam Read", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Marie Attwood", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Alan Noel", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Sally Grier", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Anna Morley", - "author_inst": "North BristolNHS Trust" - }, - { - "author_name": "David Arnold", - "author_inst": "North Bristol NHS Trust" - }, - { - "author_name": "Nick maskell", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.06.23.20138032", "rel_title": "Factors Associated with Mental Health Outcomes in Oman during COVID19: Frontline vs Non-frontline Healthcare Workers", @@ -1358476,6 +1361550,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.06.22.20136846", + "rel_title": "Chest CT versus RT-PCR for the Detection of COVID-19: Systematic Review and Meta-Analysis", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20136846", + "rel_abs": "ObjectivesTo compare the performance of chest computed tomography (CT) scan versus reverse transcription polymerase chain reaction (RT-PCR) in the initial diagnostic assessment of coronavirus disease 2019 (COVID-19) patients.\n\nMethodsA systematic review and meta-analysis were performed as per the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. A search of electronic information was conducted to identify studies comparing the diagnostic performance within the same patient cohort of chest CT scan versus RT-PCR in COVID-19 suspected cases. Sensitivity, specificity and accuracy were primary outcome measures. Secondary outcomes included other test performance characteristics, discrepant findings between both investigations and main chest CT findings. Random effects modelling was used for the analyses.\n\nResultsThirteen non-randomised studies enrolling 4092 patients were identified. Accuracy was statistically significantly higher for RT-PCR versus chest CT (Odds Ratio [OR] = 0.22, P = 0.001). Chest CT is also less specific than RT-PCR. Ground-glass opacities and consolidations were the most common chest CT manifestations. Importantly, early small studies tended to favour chest CT versus later larger studies.\n\nConclusionChest CT is inferior to RT-PCR for the initial detection of COVID-19 and has more false positives. It may still be useful in confirming COVID-19, however, in patients with a suspicious clinical presentation, but who have a false-negative SARS-CoV-2 RT-PCR test.\n\nHighlights- Chest computed tomography (CT) is less specific in the diagnosis of coronavirus disease 2019 (COVID-19) when compared to reverse transcription polymerase chain reaction (RT-PCR).\n- The accuracy of RT-PCR is statistically significantly higher than chest CT for COVID-19.\n- Chest CT, however, can detect false-negative and true-positive RT-PCR cases.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Mohammad Karam", + "author_inst": "School of Medicine, University of Leeds" + }, + { + "author_name": "Sulaiman Althuwaikh", + "author_inst": "School of Medicine, University of Glasgow" + }, + { + "author_name": "Mohammad Alazemi", + "author_inst": "School of Medical Sciences, University of Manchester" + }, + { + "author_name": "Ahmad Abul", + "author_inst": "School of Medicine, University of Leeds" + }, + { + "author_name": "Amrit Hayre", + "author_inst": "School of Medicine, University of Leeds" + }, + { + "author_name": "Abdulmalik Alsaif", + "author_inst": "School of Medicine, University of Leeds" + }, + { + "author_name": "Barlow Gavin", + "author_inst": "Hull University Teaching Hospitals NHS Trust" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.22.20137695", "rel_title": "Serologic cross-reactivity of SARS-CoV-2 with endemic and seasonal Betacoronaviruses", @@ -1359680,77 +1362797,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.22.165803", - "rel_title": "CD209L/L-SIGN and CD209/DC-SIGN act as receptors for SARS-CoV-2 and are differentially expressed in lung and kidney epithelial and endothelial cells", - "rel_date": "2020-06-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.22.165803", - "rel_abs": "As the COVID-19 pandemic continues to spread, investigating the processes underlying the interactions between SARS-CoV-2 and its hosts is of high importance. Here, we report the identification of CD209L/L-SIGN and the related protein CD209/DC-SIGN as receptors capable of mediating SARS-CoV-2 entry into human cells. Immunofluorescence staining of human tissues revealed prominent expression of CD209L in the lung and kidney epithelium and endothelium. Multiple biochemical assays using a purified recombinant SARS-CoV-2 spike receptor binding domain (S-RBD) or S1 encompassing both NTB and RBD and ectopically expressed CD209L and CD209 revealed that CD209L and CD209 interact with S-RBD. CD209L contains two N-glycosylation sequons, at sites N92 and N361, but we determined that only site N92 is occupied. Removal of the N-glycosylation at this site enhances the binding of S-RBD with CD209L. CD209L also interacts with ACE2, suggesting a role for heterodimerization of CD209L and ACE2 in SARS-CoV-2 entry and infection in cell types where both are present. Furthermore, we demonstrate that human endothelial cells are permissive to SARS-CoV-2 infection and interference with CD209L activity by knockdown strategy or with soluble CD209L inhibits virus entry. Our observations demonstrate that CD209L and CD209 serve as alternative receptors for SARS-CoV-2 in disease-relevant cell types, including the vascular system. This property is particularly important in tissues where ACE2 has low expression or is absent, and may have implications for antiviral drug development.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Razie Amraei", - "author_inst": "Boston University" - }, - { - "author_name": "Marc Napoleon", - "author_inst": "Boston University" - }, - { - "author_name": "Wenqing Yin", - "author_inst": "Boston University" - }, - { - "author_name": "Jacob Berrigan", - "author_inst": "Boston University" - }, - { - "author_name": "Ellen Suder", - "author_inst": "Boston University" - }, - { - "author_name": "Grace Zhao", - "author_inst": "Boston University" - }, - { - "author_name": "Judith Olejnik", - "author_inst": "Boston University" - }, - { - "author_name": "Kevin Chandler", - "author_inst": "Boston University" - }, - { - "author_name": "Chaoshuang Xia", - "author_inst": "Boston University" - }, - { - "author_name": "Suryaram Gummuluru", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Elke Muhlberger", - "author_inst": "Boston University" - }, - { - "author_name": "Vipul Chitalia", - "author_inst": "Boston University" - }, - { - "author_name": "Catherine Costello", - "author_inst": "Boston University" - }, - { - "author_name": "Nader Rahimi", - "author_inst": "Boston University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.06.22.165787", "rel_title": "Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptor", @@ -1360114,6 +1363160,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.23.166900", + "rel_title": "Biochemical evidence of furin specificity and potential for phospho-regulation at Spike protein S1/S2 cleavage site in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV", + "rel_date": "2020-06-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.23.166900", + "rel_abs": "The Spike protein of the novel coronavirus SARS-CoV2 contains an insertion 680SPRRAR{downarrow}SV687 forming a cleavage motif RxxR for furin-like enzymes at the boundary of S1/S2 subunits. Cleavage at S1/S2 is important for efficient viral entry into target cells. The insertion is absent in other CoV-s of the same clade, including SARS-CoV1 that caused the 2003 outbreak. However, an analogous insertion was present in the Spike protein of the more distant Middle East Respiratory Syndrome coronavirus MERS-CoV. We show that a crucial third arginine at the left middle position, comprising a motif RRxR is required for furin recognition in vitro, while the general motif RxxR in common with MERS-CoV is not sufficient for cleavage. Further, we describe a surprising finding that the two serines at the edges of the insert SPRRAR{downarrow}SV can be efficiently phosphorylated by proline-directed and basophilic protein kinases. Both phosphorylations switch off furins ability to cleave the site. Although phosphoregulation of secreted proteins is still poorly understood, further studies, supported by a recent report of ten in vivo phosphorylated sites in the Spike protein of SARS-CoV2, could potentially uncover important novel regulatory mechanisms for SARS-CoV2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mihkel \u00d6rd", + "author_inst": "University of Tartu" + }, + { + "author_name": "Ilona Faustova", + "author_inst": "University of Tartu" + }, + { + "author_name": "Mart Loog", + "author_inst": "University of Tartu" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.23.167254", "rel_title": "ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways", @@ -1361230,37 +1364303,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.18.20135004", - "rel_title": "The long term predictions from Imperial College CovidSim Report 9", - "rel_date": "2020-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20135004", - "rel_abs": "1We present calculations using the CovidSim code which implements the Imperial College individual-based model of the COVID epidemic. Using the parameterization assumed in March 2020, we reproduce the predictions presented to inform UK government policy in March 2020. We find that CovidSim would have given a good forecast of the subsequent data if a higher initial value of R0 had been assumed. We then investigate further the whole trajectory of the epidemic, presenting results not previously published. We find that while prompt interventions are highly effective at reducing peak ICU demand, none of the proposed mitigation strategies reduces the predicted total number of deaths below 200,000. Surprisingly, some interventions such as school closures were predicted to increase the projected total number of deaths.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Graeme J Ackland", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Ken Rice", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Benjamin M Wynne", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Victoria Martin", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.18.20132977", "rel_title": "Covid19 infection spread in Greece: Ensemble forecasting models with statistically calibrated parameters and stochastic noise", @@ -1361412,6 +1364454,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.06.18.20135145", + "rel_title": "Social response to early-stage government control measures of COVID-19 in Colombia: population survey, April 8-20 2020.", + "rel_date": "2020-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20135145", + "rel_abs": "On Monday, March 16, 2020, the government of Colombia announced actions to control COVID-19. These recommendations directly affected the entire population and included: reducing physical contact; reducing mobility and cancelling unnecessary travel; working from home; cancelling mass events; a 14 day at-home isolation period for people who arrived from international trips, or in cases in which someone in the household experienced a high temperature and sustained coughing; as well as increasing the frequency of hand washing and the use of face masks on public transport.\n\nIn order to understand the public sentiment around these recommendations, Asociacion Profamilia developed an online survey through SurveyMonkey(R). The survey was completed by 3549 adult people in Colombia (+18 years) between April 8 and April 20, 2020. In this report, we present the results of the survey:\n\nO_LI98% think that the COVID-19 pandemic is a serious problem in Colombia.\nC_LIO_LI90% are concerned that someone in their family will get COVID-19.\nC_LIO_LI88% are concerned that someone in their family may have an emergency and not receive medical care.\nC_LIO_LI46% believe they will likely get infected under the current Colombian government measures.\nC_LIO_LI92% of adults reported taking at least one of the following measures to protect themselves from the COVID-19 infection:\nO_LI85% of senior citizens (60 years and older) voluntarily isolated or complied with governments mandatory isolation measures.\nC_LIO_LI82% cut down on their mobility (avoided going out, using public transportation, and traveling).\nC_LIO_LI79% of those showing symptoms voluntarily isolated themselves and complied with government isolation measures.\nC_LIO_LI78% increased the frequency in which they use disinfectants, alcohol, and sanitizing gel, and how often they wash their hands.\nC_LIO_LI73% refrained from going out to social events and crowded places.\nC_LIO_LI70% avoided kissing and shaking hands.\nC_LIO_LI69% immediately complied with the governments mandatory preventive isolation measures.\nC_LIO_LI63% avoided using public transportation.\nC_LIO_LI46% went into self-isolation (voluntary quarantine) before the government decreed it.\nC_LIO_LI32% started working from home.\nC_LI\nC_LIO_LIThis study reveals that there are at least three groups of people in the country who are responding to the pandemic and physical distancing measures in different forms: those who resist the situation (34%), those who suffer from it (26%), and those who accept it (40%).\nO_LIIn the group of people who are resisting 40% are men; 68% are under 39 years old; 40% have savings and one out ten reported mental health problems; and 64% supported the government measures.\nC_LIO_LIIn the group of people suffering from the pandemic, 73% are women, 64% are under 29 years old, 55% have an average family income over 2 million pesos COP (roughly 417 GBP), 61% have had some chronic disease or somebody in the family; 73% reported mental problems. This group had the higher support and adherence to the government measures (68%).\nC_LIO_LIIn the group of people who are adapting to the situation, 76% are women, 43% are over 49 years old, 36% have savings, and 63% have not had chronic illnesses and 73% reported mental problems. This group had the lower support and adherence to the government measures (63%).\nC_LI\nC_LIO_LI69% complied with governments mandatory preventive isolation measures. This percentage was lower (64%) among young adults (25-29 years old).\nC_LIO_LIOverall, 83% are complying with preventive isolation and physical distancing. 77% feel that complying with isolation contributes to stopping COVID-19.\nC_LIO_LIHygiene practices such as hand washing (78%), avoiding kissing and hand-shaking (70%), as well as using face masks (69%) were perceived as more effective measures to prevent the spread of the virus compared to physical distancing measures like cancelling travelling (46%), avoiding contact with people with fever or respiratory symptoms (43%), and avoiding contact with people who have travelled in the last month (35%).\nC_LIO_LI80% live in the five cities with the highest spread of COVID-19.\nO_LI50% are responsible for the care of a family member; 16% are women heads of household.\nC_LIO_LI68% mentioned do not have savings.\nC_LIO_LI25% did not work before COVID-19.\nC_LI\nC_LIO_LIThe top three concerns among the respondents were that someone in their family may get infected with COVID-19 (79%), that someone in their family may have an emergency and not receive medical care. (74%) and the fate of the poorest and most vulnerable people (71%).\nC_LIO_LIDuring quarantine, 75% have experienced issues with their mental health: 54% felt nervous; 52% have felt tired for no reason; 46% felt restless and impatient, and 34% felt anger and rage; 20% have experienced a need for sexual and reproductive health in the last 21 days which has not been met. 17% are concerned about their childrens bad behaviour and domestic violence.\nC_LIO_LI63% get informed about COVID-19 through official websites; 52% have found false information about COVID-19 and the pandemic. 40% have experienced or witnessed jokes about the spread of COVID-19, and 25% have experienced or witnessed discrimination against health care personnel.\nC_LIO_LI38% believe that the National Governments response to control the virus was clear and consistent and 29% believe that it acted in a timely and swift manner; 46% believe that the Local Governments response was clear and consistent and 42% believe that it acted in a quick and timely manner.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Juan Carlos Rivillas Sr.", + "author_inst": "Asociacion Profamilia Colombia" + }, + { + "author_name": "Rocio Murad", + "author_inst": "Asociacion Profamilia Colombia" + }, + { + "author_name": "Danny Rivera", + "author_inst": "Asociacion Profamilia Colombia" + }, + { + "author_name": "Mariana Calderon", + "author_inst": "Asociacion Profamilia Colombia" + }, + { + "author_name": "Marcela Sanchez", + "author_inst": "Asociacion Profamilia Colombia" + }, + { + "author_name": "Lina Castano", + "author_inst": "Asociacion Profamilia Colombia" + }, + { + "author_name": "Marta Royo", + "author_inst": "Asociacion Profamilia Colombia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.06.19.20135830", "rel_title": "Hospitalized COVID-19 patients treated with Convalescent Plasma in a mid-size city in the midwest", @@ -1362927,53 +1366012,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.06.20.162933", - "rel_title": "A path towards SARS-CoV-2 attenuation: metabolic pressure on CTP synthesis rules the virus evolution", - "rel_date": "2020-06-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.20.162933", - "rel_abs": "Fighting the COVID-19 epidemic summons deep understanding of the way SARS-CoV-2 taps into its host cell metabolic resources. We describe here the singular metabolic background that creates a bottleneck constraining coronaviruses to evolve towards likely attenuation in the long term. Cytidine triphosphate (CTP) is at the crossroad of the biosynthetic processes that allow the virus to multiply. This is because CTP is in demand for three essential steps. It is a building block of the virus genome, it is required for synthesis of the cytosine-based liponucleotide precursors of the viral envelope and, finally, it is a critical building block of the host transfer RNAs synthesis. The CCA 3-end of all the transfer RNAs required to translate the RNA genome and further transcripts into the proteins used to build active virus copies is not coded in the human genome. It must be synthesized de novo from CTP and ATP. Furthermore, intermediary metabolism is built on compulsory steps of synthesis and salvage of cytosine-based metabolites via uridine triphosphate (UTP) that keep limiting CTP availability. As a consequence, accidental replication errors tend to replace cytosine by uracil in the genome, unless recombination events allow the sequence to return to its ancestral sequences. We document some of the consequences of this situation in the function of viral proteins. We also highlight and provide a raison detre to viperin, an enzyme of innate antiviral immunity, which synthesizes 3-deoxy-3',4-didehydro-CTP (ddhCTP) as an extremely efficient antiviral nucleotide.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Zhihua Ou", - "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" - }, - { - "author_name": "Christos Ouzounis", - "author_inst": "Biological Computation and Process Laboratory, Centre for Research and Technology Hellas, Chemical Process and Energy Resources Institute, Thessalonica 57001, G" - }, - { - "author_name": "Daxi Wang", - "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" - }, - { - "author_name": "Wanying Sun", - "author_inst": "BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China" - }, - { - "author_name": "Junhua Li", - "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" - }, - { - "author_name": "Weijun Chen", - "author_inst": "BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China" - }, - { - "author_name": "Philippe Marliere", - "author_inst": "TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 81 rue Reaumur, 75002, Paris, France" - }, - { - "author_name": "Antoine Danchin", - "author_inst": "Kodikos Labs, Institut Cochin, 24, rue du Faubourg Saint-Jacques Paris 75014, France" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.06.20.162826", "rel_title": "anti-IL-6 versus anti-IL-6R Blocking Antibodies to Treat Acute Ebola Infection in BALB/c Mice with Potential Implications for Treating Patients Presenting with COVID-19", @@ -1363201,6 +1366239,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.20.161323", + "rel_title": "The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera", + "rel_date": "2020-06-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.20.161323", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike (S) protein that mediates SARS-CoV-2 entry into host cells is a major target for vaccines and therapeutics. Thus, insights into its sequence variations are key to understanding the infection and antigenicity of SARS-CoV-2. A dominant mutational variant at position 614 of the S protein (aspartate to glycine, D614G mutation) was observed in the SARS-CoV-2 genome sequence obtained from the Nextstrain database. Using a pseudovirus-based assay, we identified that S-D614 and S-G614 protein pseudotyped viruses share a common receptor, human angiotensin-converting enzyme 2 (ACE2), which could be blocked by recombinant ACE2 with the fused Fc region of human IgG1. However, S-D614 and S-G614 protein demonstrated functional differences. First, S-G614 protein could be cleaved by serine protease elastase-2 more efficiently. Second, S-G614 pseudovirus infected 293T-ACE2 cells significantly more efficiently than did the S-D614 pseudovirus, especially in the presence of elastase-2. Third, an elastase inhibitor approved for clinical use blocked elastase-enhanced S-G614 pseudovirus infection. Moreover, 93% (65/70) convalescent sera from patients with COVID-19 could neutralize both S-D614 and S-G614 pseudoviruses with comparable efficiencies, but about 7% (5/70) convalescent sera showed reduced neutralizing activity against the S-G614 pseudovirus. These findings have important implications for SARS-CoV-2 transmission and immune interventions.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jie Hu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Chang Long He", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Qingzhu Gao", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Gui Ji Zhang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Xiao Xia Cao", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Quan Xin Long", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Hai Jun Deng", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Lu Yi Huang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Juan Chen", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Kai Wang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ni Tang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ai Long Huang", + "author_inst": "Chongqing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.19.160630", "rel_title": "Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny", @@ -1364545,29 +1367646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.18.20135053", - "rel_title": "Short-term Forecasting of Cumulative Confirmed Cases of Covid-19 Pandemic in Somalia", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20135053", - "rel_abs": "Somalia has recorded the first confirmed Covid-19 case and first death case on March 16, and April 08, 2020, respectively. Since its arrival, it had infected 2,603 people and took the lives of 88 people while 577 patients were recovered as of 14 June, 2020. To fight this pandemic, the government requires to make the necessary plans accordingly. To plan effectively, the government needs to answer this question: what will be the effect of Covid-19 cases in the country? To answer this question accurately and objectively, forecasting the spread of confirmed Covid-19 cases will be vital. To this regard, this paper provides real times forecasts of Covid-19 cases employing Holts linear trend model without seasonality. Provided that the data employed is accurate and the past pattern of the disease will continue in the future, this model is powerful to produce real time forecasts in the future with some degree of uncertainty. With the help of these forecasts, the government can make evidence based decisions by utilizing the scarce resource available at its disposal.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dahir Abdi Ali", - "author_inst": "SIMAD University" - }, - { - "author_name": "Habshah Midi", - "author_inst": "Universiti Putra Malaysia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.19.20135756", "rel_title": "Sensitivity of RT-PCR testing of upper respiratory tract samples for SARS-CoV-2 in hospitalised patients: a retrospective cohort study.", @@ -1364859,6 +1367937,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.06.18.20134874", + "rel_title": "Modelling for prediction of the spread and severity of COVID-19 and its association with socioeconomic factors and virus types", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134874", + "rel_abs": "We report the development of a Weibull based Long-Short-Term-Memory approach (W-LSTM) for the prediction of COVID-19 disease. The W-LSTM model developed in this study, performs better in terms of MSE, R2 and MAPE, as compared to the previously published models, including ARIMA, LSTM and their variations. Using W-LSTM model, we have predicted the beginning and end of the current cycle of COVID-19 in several countries. Performance of the model was validated as satisfactory in 82% of the 50 test countries, while asking for prediction for 10 days beyond the period of training. Accuracy of the above prediction with days beyond training was assessed in comparison with the MAPE that the model gave with cumulative global data. The model was applied to study correlation between the growth of infection and deaths, and a number of effectors that may influence the epidemic. The model identified age groups, trade with China, air traffic, country temperature and CoV-2 virus types as the likely effectors of infection and virulence leading to deaths. The predictors likely to promote or suppress the epidemic were identified. Some of the predictors had significant effect on the shape parameters of Weibull distribution. The model can function on cloud, take inputs in real time and handle large data country wise, at low costs to make predictions dynamically. Such predictions are highly valuable in guiding policy makers, administration and health. Interactive curves generated from the W-LSTM model can be seen at http://collaboration.coraltele.com/covid2/.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shreshth Tuli", + "author_inst": "IIT Delhi" + }, + { + "author_name": "Shikhar Tuli", + "author_inst": "IIT Delhi" + }, + { + "author_name": "Ruchi Verma", + "author_inst": "PBEL, Hyderabad" + }, + { + "author_name": "Rakesh Tuli", + "author_inst": "UIET, Panjab University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.18.20134825", "rel_title": "Incubation period and serial interval of Covid-19 in a chain of infections in Bahia Blanca (Argentina)", @@ -1365959,41 +1369068,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.06.17.20133595", - "rel_title": "Clozapine treatment and risk of COVID-19.", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133595", - "rel_abs": "BackgroundClozapine, an antipsychotic with unique efficacy in treatment resistant psychosis, is associated with increased susceptibility to infection, including pneumonia.\n\nAimsTo investigate associations between clozapine treatment and increased risk of COVID-19 in patients with schizophrenia-spectrum disorders who are receiving antipsychotic medications, using electronic health records data, in a geographically defined population in London.\n\nMethodUsing information from South London and Maudsley NHS Foundation Trust (SLAM) clinical records, via the Clinical Record Interactive Search system, we identified 6,309 individuals who had an ICD-10 diagnosis of schizophrenia-spectrum disorders and were taking antipsychotics at the time on the COVID-19 pandemic onset in the UK. People who were on clozapine treatment were compared with those on any other antipsychotic treatment for risk of contracting COVID-19 between 1 March and 18 May 2020. We tested associations between clozapine treatment and COVID-19 infection, adjusting for gender, age, ethnicity, BMI, smoking status, and SLAM service use.\n\nResultsOf 6,309 patients, 102 tested positive for COVID-19. Individuals who were on clozapine had increased risk of COVID-19 compared with those who were on other antipsychotic medication (unadjusted HR = 2.62 (95% CI 1.73 - 3.96), which was attenuated after adjusting for potential confounders, including clinical contact (adjusted hazard ratio HR=1.76, 95% CI 1.14 - 2.72).\n\nConclusionsThese findings provide support for the hypothesis that clozapine treatment is associated with an increased risk of COVID-19. Further research will be needed in other samples to confirm this association. Potential clinical implications are discussed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Risha Govind", - "author_inst": "King's College London" - }, - { - "author_name": "Daniela Fonesca de Freitas", - "author_inst": "King's College London" - }, - { - "author_name": "Megan R Pritchard", - "author_inst": "King's College London" - }, - { - "author_name": "Richard D Hayes", - "author_inst": "King's College London" - }, - { - "author_name": "James H MacCabe", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.06.18.20134742", "rel_title": "Racial and ethnic determinants of Covid-19 risk", @@ -1366653,6 +1369727,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.18.20133660", + "rel_title": "SARS-CoV-2-specific antibody detection for sero-epidemiology: a multiplex analysis approach accounting for accurate seroprevalence", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20133660", + "rel_abs": "BackgroundThe COVID-19 pandemic demands detailed understanding of the kinetics of antibody production induced by infection with SARS-CoV-2. We aimed to develop a high throughput multiplex assay to detect antibodies to SARS-CoV-2 to assess immunity to the virus in the general population.\n\nMethodsSpike protein subunits S1 and RBD, and Nucleoprotein were coupled to distinct microspheres. Sera collected before the emergence of SARS-CoV-2 (N=224), and of non-SARS-CoV-2 influenza-like illness (N=184), and laboratory-confirmed cases of SARS-CoV-2 infection (N=115) with various severity of COVID-19 were tested for SARS-CoV-2-specific concentrations of IgG.\n\nResultsOur assay discriminated SARS-CoV-2-induced antibodies and those induced by other viruses. The assay obtained a specificity between 95.1 and 99.0% with a sensitivity ranging from 83.6-95.7%. By merging the test results for all 3 antigens a specificity of 100% was achieved with a sensitivity of at least 90%. Hospitalized COVID-19 patients developed higher IgG concentrations and the rate of IgG production increased faster compared to non-hospitalized cases.\n\nConclusionsThe bead-based serological assay for quantitation of SARS-CoV-2-specific antibodies proved to be robust and can be conducted in many laboratories. Finally, we demonstrated that testing of antibodies against different antigens increases sensitivity and specificity compared to single antigen-specific IgG determination.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Gerco den Hartog", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Rutger M Schepp", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Marjan Kuijer", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Corine GeurtsvanKessel", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Josine van Beek", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Nynke Rots", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Marion PG Koopmans", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Fiona RM van der Klis", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Robert S van Binnendijk", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.17.20133959", "rel_title": "A downscaling approach to compare COVID-19 count data from databases aggregated at different spatial scales", @@ -1368453,81 +1371578,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.17.158105", - "rel_title": "Dog Savior: Immediate Scent-Detection of SARS-COV-2 by Trained Dogs", - "rel_date": "2020-06-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.158105", - "rel_abs": "Molecular tests for viral diagnostics are essential to confront the COVID-19 pandemic, but their production and distribution cannot satisfy the current high demand. Early identification of infected people and their contacts is the key to being able to isolate them and prevent the dissemination of the pathogen; unfortunately, most countries are unable to do this due to the lack of diagnostic tools. Dogs can identify, with a high rate of precision, unique odors of volatile organic compounds generated during an infection; as a result, dogs can diagnose infectious agents by smelling specimens and, sometimes, the body of an infected individual. We trained six dogs of three different breeds to detect SARS-CoV-2 in respiratory secretions of infected patients and evaluated their performance experimentally, comparing it against the gold standard (rRT-PCR). Here we show that viral detection takes one second per specimen. After scent-interrogating 9,200 samples, our six dogs achieved independently and as a group very high sensitivity, specificity, predictive values, accuracy, and likelihood ratio, with very narrow confidence intervals. The highest metric was the negative predictive value, indicating that with a disease prevalence of 7.6%, 99.9% of the specimens indicated as negative by the dogs did not carry the virus. These findings demonstrate that dogs could be useful to track viral infection in humans, allowing COVID-19 free people to return to work safely.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Omar Vesga", - "author_inst": "Universidad de Antioquia" - }, - { - "author_name": "Andres Felipe Valencia", - "author_inst": "GRIPE, Universidad de Antioquia, Colombia; Colina K-9, La Ceja, Antioquia, Colombia." - }, - { - "author_name": "Alejandro Mira", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia; Colina K-9, La Ceja, Antioquia, Colombia" - }, - { - "author_name": "Felipe Ossa", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia; Colina K-9, La Ceja, Antioquia, Colombia" - }, - { - "author_name": "Esteban Ocampo", - "author_inst": "Colina K-9, La Ceja, Antioquia, Colombia" - }, - { - "author_name": "Maria Agudelo Perez", - "author_inst": "Hospital Universitario San Vicente Fundacion, Medellin, Colombia; GRIPE, Universidad de Antioquia, Medellin, Colombia." - }, - { - "author_name": "karl Ciouderis", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin." - }, - { - "author_name": "Laura Perez", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin." - }, - { - "author_name": "Andres Cardona", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin." - }, - { - "author_name": "Yudy Aguilar Perez", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia." - }, - { - "author_name": "Javier Mauricio Gonzalez", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia" - }, - { - "author_name": "Juan Carlos Catano Correa", - "author_inst": "GRIPE, Universidad de Antioquia, Medellin, Colombia" - }, - { - "author_name": "Yuli Agudelo Berruecos", - "author_inst": "Hospital Universitario San Vicente Fundacion, Medellin, Colombia." - }, - { - "author_name": "Juan P. Hernandez-Ortiz", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin; Departamento de Materiales y Minerales, Universidad Nacional de Colom" - }, - { - "author_name": "Jorge E. Osorio", - "author_inst": "Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia, Sede Medellin; Department of Pathobiology, School of Veterinary Medicine, University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.17.20133678", "rel_title": "FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy", @@ -1368819,6 +1371869,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.15.20038489", + "rel_title": "On Identifying and Mitigating Bias in the Estimation of the COVID-19 Case Fatality Rate", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20038489", + "rel_abs": "The relative case fatality rates (CFRs) between groups and countries are key measures of relative risk that guide policy decisions regarding scarce medical resource allocation during the ongoing COVID-19 pandemic. In the middle of an active outbreak when surveillance data is the primary source of information, estimating these quantities involves compensating for competing biases in time series of deaths, cases, and recoveries. These include time- and severity-dependent reporting of cases as well as time lags in observed patient outcomes. In the context of COVID-19 CFR estimation, we survey such biases and their potential significance. Further, we analyze theoretically the effect of certain biases, like preferential reporting of fatal cases, on naive estimators of CFR. We provide a partially corrected estimator of these naive estimates that accounts for time lag and imperfect reporting of deaths and recoveries. We show that collection of randomized data by testing the contacts of infectious individuals regardless of the presence of symptoms would mitigate bias by limiting the covariance between diagnosis and death. Our analysis is supplemented by theoretical and numerical results and a simple and fast open-source codebase.1", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anastasios Nikolas Angelopoulos", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Reese Pathak", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Rohit Varma", + "author_inst": "Southern California Eye Institute" + }, + { + "author_name": "Michael I Jordan", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.16.20129171", "rel_title": "PERSONAL PROTECTIVE EQUIPMENT (PPE) USING IN ANTALYA 112 EMERGENCY AMBULANCE SERVICES DURING OUTBREAK", @@ -1369843,49 +1372924,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.17.20106302", - "rel_title": "Standardized Testing Demonstrates Altered Odor Detection Sensitivity and Hedonics in Asymptomatic College Students as SARS-CoV-2 Emerged Locally", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20106302", - "rel_abs": "Aerosol droplets have emerged as the primary mode of SARS-Cov-2 transmission and can be spread by infectious asymptomatic/pre-symptomatic persons rendering indicators of latent viral infection essential. Olfactory impairment is now a recognized symptom of COVID-19 and is rapidly becoming one of the most reliable indicators of the disease. We compared olfaction data from asymptomatic students, who were assessed as SARS-CoV-2 was unknowingly spreading locally, to students tested prior to the arrival of the virus. This study was naturalistic by design as testing occurred in the context of four research studies, all of which used the same inclusion/exclusion criteria and the same protocol to objectively assess odor detection, identification, and hedonics with physiological tests. Data from students (Cohort II; N=22) with probable SARS-CoV-2 exposure were compared to students tested just prior to local virus transmission (Cohort I; N=25), and a normative sample of students assessed over the previous four years (N=272). Students in Cohort II demonstrated significantly reduced odor detection sensitivity compared to students in Cohort I (t=2.60; P=.01; d=0.77; CI, 0.17, 1.36), with a distribution skewed towards reduced detection sensitivity (D=0.38; P=.005). Categorically, the exposed group was significantly more likely to have hyposmia (OR=7.74; CI, 3.1, 19.40), particularly the subgroup assessed in the final week before campus closure (OR=13.61; CI, 3.40, 35.66;). The exposed cohort also rated odors as less unpleasant (P<.001, CLES=0.77). A limitation of our study is that participants were not tested for COVID-19 as testing was unavailable in the area. Objective measures of olfaction may detect olfactory impairment in asymptomatic persons who are otherwise unaware of smell loss. The development of cost-effective, objective olfaction tests that could be self-administered regularly could aid in early detection of SARS-CoV-2 exposure, which is vital to combatting this pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Julie Walsh-Messinger", - "author_inst": "University of Dayton" - }, - { - "author_name": "Sahar Kaouk", - "author_inst": "University of Dayton" - }, - { - "author_name": "Hannah Manis", - "author_inst": "University of Dayton" - }, - { - "author_name": "Rachel Kaye", - "author_inst": "Rutgers New Jersey Medical Center" - }, - { - "author_name": "Guillermo Cecchi", - "author_inst": "Thomas J. Watson Research Center" - }, - { - "author_name": "Pablo Meyer", - "author_inst": "Thomas J. Watson Research Center" - }, - { - "author_name": "Dolores Malaspina", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.16.20133066", "rel_title": "Effect of hydroxychloroquine on SARS-CoV-2 viral load in patients with COVID-19", @@ -1370097,6 +1373135,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.17.20133884", + "rel_title": "Hydroxychloroquine and mortality risk of patients with COVID-19: a systematic review and meta-analysis of human comparative studies", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133884", + "rel_abs": "BackgroundGlobal COVID-19 deaths reached at least 400,000 fatalities. Hydroxychloroquine is an antimalarial drug that elicit immunomodulatory effects and had shown in vitro antiviral effects against SRAS-CoV-2. This drug divided opinion worldwide in the medical community but also in the press, the general public and in public health policies. The aim of this systematic review and this meta-analysis was to bring a new overview on this controversial drug and to assess whether hydroxychloroquine could reduce COVID-19 mortality risk in hospitalized patients.\n\nMethods and FindingsPubmed, Web of Science, Cochrane Library, MedRxiv and grey literature were searched until 10 June 2020. Only studies of COVID-19 patients treated with hydroxychloroquine (with or without azithromycin) compared with a comparative standard care group and with full-text articles in English were included. Studies reporting effect sizes as Odds Ratios, Hazard Ratio and Relative Risk for mortality risk and the number of deaths per groups were included. This meta-analysis was conducted following PRISMA guidelines and registered on PROSPERO (Registration number: CRD42020190801). Independent extraction has been performed by two independent reviewers. Effect sizes were pooled using a random-effects model.\n\nThe initial search leaded to 112 articles, from which 16 articles met our inclusion criteria. 15 studies were retained for association between hydroxychloroquine and COVID-19 survival including 15,081 patients (8,072 patients in the hydroxychloroquine arm and 7,009 patients in the standard care arm with respectively, 1,578 deaths and 1,423 deaths). 6 studies were retained for hydroxychloroquine with azithromycin. Hydroxychloroquine was not significantly associated with mortality risk (pooled Relative Risk RR=0.82 (95% Confidence Interval: 0.62-1.07, I2=82, Pheterogeneity<0.01, n=15)) within hospitalized patients, nor in association with azithromycin (pooled Relative Risk RR=1.33 (95% CI: 0.92-1.92, I2=75%, Pheterogeneity<0.01, n=6)), nor in the numerous subgroup analysis by study design, median age population, published studies (vs unpublished articles), level of bias risk. However, stratified analysis by continents, we found a significant decreased risk of mortality associated with hydroxychlroquine alone but not with azithromycin among European (RR= 0.62 (95%CI: 0.41-0.93, n=7)) and Asian studies (RR=0.36 (95%CI:0.18-0.73, n=1)), with heterogeneity detected across continent (Pheterogeneity between=0.003). These finding should be interpreted with caution since several included studies had a low quality of evidence with a small sample size, a lack of adjustment on potential confounders or selection and intervention biases.\n\nConclusionOur meta-analysis does not support the use of hydroxychloroquine with or without azithromycin to reduce COVID-19 mortality in hospitalized patients. It raises the question of the hydroxychloroquine use outside of clinical trial. Additional results from larger randomised controlled trials are needed", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fiolet Thibault", + "author_inst": "Paris-Saclay University, INSERM U1018 (CESP)" + }, + { + "author_name": "Anthony Guihur", + "author_inst": "Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne" + }, + { + "author_name": "Mathieu Rebeaud", + "author_inst": "Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne" + }, + { + "author_name": "Matthieu Mulot", + "author_inst": "Laboratory of Soil Biodiversity, Faculty of Science, University of Neuchatel" + }, + { + "author_name": "Yahya Mahamat-Saleh", + "author_inst": "CESP, Fac. de medecine - Univ. Paris-Sud, Fac. de medecine - UVSQ, INSERM, Universite Paris Saclay" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.17.20133918", "rel_title": "Higher risk of COVID-19 hospitalization for unemployed: an analysis of 1,298,416 health insured individuals in Germany", @@ -1371465,129 +1374538,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.16.20133157", - "rel_title": "Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease.", - "rel_date": "2020-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133157", - "rel_abs": "BackgroundRapid COVID-19 diagnosis in hospital is essential for patient management and identification of infectious patients to limit the potential for nosocomial transmission. The diagnosis of infection is complicated by 30-50% of COVID-19 hospital admissions with nose/throat swabs testing negative for SARS-CoV-2 nucleic acid, frequently after the first week of illness when SARS-CoV-2 antibody responses become detectable. We assessed the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease in the emergency department.\n\nMethodsWe developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike (S) protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and S proteins from SARS-CoV-2. We tested two lateral flow rapid fingerprick tests with bands for IgG and IgM. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid POC nucleic acid amplification (NAAT) test. Additionally, serum collected at admission was retrospectively tested by in vitro neutralisation, ELISA and the candidate POC antibody tests. We evaluated the performance of the individual and combined rapid POC diagnostic tests against a composite reference standard of neutralisation and standard laboratory based RT-PCR.\n\nResults45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Using the composite reference standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our reference standard and 63.0 (IQR 41.0-72.0) years in those without disease. The overall detection rate by rapid NAAT was 79.2% (95CI 57.8-92.9%), decreasing from 100% (95% CI 65.3-98.6%) in days 1-4 to 50.0% (95% CI 11.8-88.2) for days 9-28 post symptom onset. Correct identification of COVID-19 with combined rapid POC diagnostic tests was 100% (95CI 85.8-100%) with a false positive rate of 5.3-14.3%, driven by POC LFA antibody tests.\n\nConclusionsCombined POC tests have the potential to transform our management of COVID-19, including inflammatory manifestations later in disease where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Petra Mlcochova", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Dami Collier", - "author_inst": "UCL" - }, - { - "author_name": "Allyson V Ritchie", - "author_inst": "Diagnostics for the Real World Europe Ltd" - }, - { - "author_name": "Sonny M Assennato", - "author_inst": "DRW" - }, - { - "author_name": "Myra Hosmillo", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Neha Goel", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Bo Meng", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Krishna Chatterji", - "author_inst": "NIHR Cambridge Clinical Research Facility" - }, - { - "author_name": "Vivien Mendoza", - "author_inst": "CUH NHS Trust" - }, - { - "author_name": "Nigel Temperton", - "author_inst": "University of Kent" - }, - { - "author_name": "Leo Kiss", - "author_inst": "Medical Research Council Laboratory of Molecular Biology, Cambridge" - }, - { - "author_name": "Katarzyna A Ciazyns", - "author_inst": "Medical Research Council Laboratory of Molecular Biology, Cambridge" - }, - { - "author_name": "Xiaoli Xiong", - "author_inst": "Medical Research Council Laboratory of Molecular Biology" - }, - { - "author_name": "John AG Briggs", - "author_inst": "Medical Research Council Laboratory of Molecular Biology" - }, - { - "author_name": "James Nathan", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Federica Mescia", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Hongyi Zhang", - "author_inst": "CUH NHS Trust" - }, - { - "author_name": "Petros Barmpounakis", - "author_inst": "Athens University of Economics and Business" - }, - { - "author_name": "Nikos Demeris", - "author_inst": "Cambridge Clinical Trials Unit-Cancer Theme" - }, - { - "author_name": "Richard Skells", - "author_inst": "Cambridge Clinical Trials Unit-Cancer Theme" - }, - { - "author_name": "Paul Lyons", - "author_inst": "University of Cambridge" - }, - { - "author_name": "John Bradley", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Stephen Baker", - "author_inst": "Cambridge University" - }, - { - "author_name": "Jean Pierre Allain", - "author_inst": "Diagnostics for the Real World EU Ltd" - }, - { - "author_name": "Kenneth GC Smith", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ian Goodfellow", - "author_inst": "ig299@cam.ac.uk" - }, - { - "author_name": "Ravindra K Gupta", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.16.20133140", "rel_title": "COVID-19 outcomes, risk factors and associations by race: a comprehensive analysis using electronic health records data in Michigan Medicine", @@ -1371807,6 +1374757,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.16.20133199", + "rel_title": "Epidemiological characteristics of patients with residual SARS-Cov-2 in Linyi, China", + "rel_date": "2020-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133199", + "rel_abs": "Patients with 2019 novel Coronavirus infection are probably show positive testing results again. In order to better treat these patients and provide basis for further control measures, we analyze the epidemiological outcomes and clinical features of patients with residual Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Cov-2) in Linyi city. From January 23 to March 31 in 2020, epidemiological and clinical information of confirmed patients are collected for analysis. Stool and pharyngeal swab samples are collected for RT-PCR testing. 64 confirmed patients are included and 17 patients present re-positive testing after discharge. For these 17 patients, 70.59% are family aggregated, the interval between first time of negative testing and first time of re-positive testing is 11.82{+/-}3.42 days. There is no difference between patients with continued negative testing results and re-positive testing. After discharge, the interval between first time of negative testing and first time of re-positive testing is associated with severity of disease (p=0.013). Besides, the duration from first time to last time of re-positive testing is associated with exposure or contact history (p=0.049) and severity of disease (p=0.001). The analysis reveals epidemiological characteristics of patients with residual SARS-Cov-2 and provide basis for further control measures.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Qiang Pan", + "author_inst": "Linyi Center for Disease Control and Prevention" + }, + { + "author_name": "Feng Gao", + "author_inst": "Linyi Peoples Hospital" + }, + { + "author_name": "Rensheng Peng", + "author_inst": "Center for Disease Control and Prevention of Hedong District" + }, + { + "author_name": "Mingshan Li", + "author_inst": "Fourth affiliated hospital of China Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.15.153882", "rel_title": "COVID-19 PCR Test Performance For Samples Stored At Ambient Temperature", @@ -1373355,37 +1376336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.15.20131516", - "rel_title": "National Early Warning Scores (NEWS / NEWS2) and COVID-19 deaths in care homes: a longitudinal ecological study", - "rel_date": "2020-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131516", - "rel_abs": "ObjectivesTo investigate whether patterns of National Early Warning Scores (NEWS/NEWS2) in care homes during the COVID pandemic correspond with area-level COVID-19 death registrations from care homes.\n\nStudy designLongitudinal ecological study.\n\nSetting460 Care home units using the same software package to collect data on residents, from 46 local authority areas in England.\n\nParticipants6,464 care home residents with at least one NEWS recording.\n\nExposure measure29,656 anonymised person-level NEWS from 29/12/2019 to 20/05/2020 with component physiological measures: systolic blood pressure, respiratory rate, pulse rate, temperature, and oxygen saturation. Baseline values for each measure calculated using 80th and 20th centile scores before March 2020.\n\nOutcome measureTime series comparison with Office for National Statistics (ONS) weekly reported registered deaths of care home residents where COVID-19 was the underlying cause of death, and all other deaths (excluding COVID-19) up to 10/05/2020.\n\nResultsDeaths due to COVID-19 were registered from 23/03/2020 in the study geographical areas. Between 23/03/2020 and 10/05/2020, there were 5,753 deaths (1,532 involving COVID-19 and 4,221 other causes). The proportion of above-baseline NEWS increased from 16/03/2020 and closely followed the rise and fall in COVID-19 deaths over the study period. The proportion of above-baseline oxygen saturation, respiratory rate and temperature measurements also increased approximately two weeks before peaks in care home deaths in corresponding geographical areas.\n\nConclusionsNEWS may make a useful contribution to disease surveillance in care homes during the COVID-19 pandemic. Oxygen saturation, respiratory rate and temperature could be prioritised as they appear to signal rise in mortality almost as well as total NEWS. This study reinforces the need to collate data from care homes, to monitor and protect residents health. Further work using individual level outcome data is needed to evaluate the role of NEWS in the early detection of resident illness.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Daniel Stow", - "author_inst": "Newcastle University" - }, - { - "author_name": "Robert O Barker", - "author_inst": "Newcastle University" - }, - { - "author_name": "Fiona E Matthews", - "author_inst": "Newcastle University" - }, - { - "author_name": "Barbara Hanratty", - "author_inst": "Newcastle University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.12.20127498", "rel_title": "Reducing SARS-CoV-2 infectious spreading patterns by removing S and R compartments from SIR model equation", @@ -1373645,6 +1376595,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.06.15.20132183", + "rel_title": "Commercial Airline Protocol during Covid-19 Pandemic: An Experience of Thai Airways International", + "rel_date": "2020-06-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20132183", + "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) pandemic has affected the aviation industry. Existing protocols have relied on scientifically questionable evidence and might not lead to the optimal balance between public health safety and airlines financial viability.\n\nObjectiveTo explore the implementation feasibility of Thai Airways International protocol from the perspectives of passengers and aircrews.\n\nDesignAn online questionnaire survey of passengers and an in-depth interview with aircrews.\n\nSettingTwo randomly selected repatriation flights operated by Thai Airways International using Boeing 777 aircraft (TG476 from Sydney and TG492 from Auckland to Bangkok)\n\nParticipants377 Thai passengers and 35 aircrews.\n\nResultsThe mean age of passengers was 28.14 (95%CI 26.72 to 29.55) years old; 57.03% were female. TG492 passengers were mostly students and significantly younger than that of TG476 (p<0.0001) with comparable flying experience (p=0.1192). The average body temperature was 36.52 (95%CI 36.48 to 36.55) degrees Celsius. Passengers estimated average physical distances of 1.59 (95%CI 1.48 to 1.70), 1.41 (95%CI 1.29 to 1.53), and 1.26 (95%CI 1.12 to 1.41) meters at check-in, boarding, and in-flight, respectively. Passengers were checked for body temperature during the flight 1.97 (95%CI 1.77 to 2.18) times on average which is significantly more frequent in longer than shorter flight (p<0.0001). Passengers moved around or went to the toilet during the flight 2.00 (95%CI 1.63 to 2.37) and 2.08 (95%CI 1.73 to 2.43) times which are significantly more frequent in longer than shorter flight (p=0.0186 and 0.0049, respectively). The aircrews were satisfied with the protocol and provided several practical suggestions.\n\nConclusionThe protocol was well received by the passengers and aircrews of the repatriation flights with some suggestions for improvement.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Krit Pongpirul", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Kanitha Kaewpoungngam", + "author_inst": "Dhurakij Pundit University" + }, + { + "author_name": "Korn Chotirosniramit", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Sinnop Theprugsa", + "author_inst": "Thai Airways International Public Company Limited" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.16.20132480", "rel_title": "Towards intervention development to increase the uptake of COVID-19 vaccination among those at high risk: outlining evidence-based and theoretically informed future intervention content", @@ -1375041,141 +1378022,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.06.17.156455", - "rel_title": "Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV", - "rel_date": "2020-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.156455", - "rel_abs": "The global emergence of SARS-CoV-2 urgently requires an in-depth understanding of molecular functions of viral proteins and their interactions with the host proteome. Several individual omics studies have extended our knowledge of COVID-19 pathophysiology1-10. Integration of such datasets to obtain a holistic view of virus-host interactions and to define the pathogenic properties of SARS-CoV-2 is limited by the heterogeneity of the experimental systems. We therefore conducted a concurrent multi-omics study of SARS-CoV-2 and SARS-CoV. Using state-of-the-art proteomics, we profiled the interactome of both viruses, as well as their influence on transcriptome, proteome, ubiquitinome and phosphoproteome in a lung-derived human cell line. Projecting these data onto the global network of cellular interactions revealed crosstalk between the perturbations taking place upon SARS-CoV-2 and SARS-CoV infections at different layers and identified unique and common molecular mechanisms of these closely related coronaviruses. The TGF-{beta} pathway, known for its involvement in tissue fibrosis, was specifically dysregulated by SARS-CoV-2 ORF8 and autophagy by SARS-CoV-2 ORF3. The extensive dataset (available at https://covinet.innatelab.org) highlights many hotspots that can be targeted by existing drugs and it can guide rational design of virus- and host-directed therapies, which we exemplify by identifying kinase and MMPs inhibitors with potent antiviral effects against SARS-CoV-2.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Alexey Stukalov", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Virginie Girault", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Vincent Grass", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Ozge Karayel", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Valter Bergant", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Christian Urban", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Darya A. Haas", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Yiqi Huang", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Lila Oubraham", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Anqi Wang", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Sabri M. Hamad", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Antonio Piras", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Fynn M Hansen", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Maria Tanzer", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Igor Paron", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Luca Zinzula", - "author_inst": "Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Thomas Engleitner", - "author_inst": "Institute of Molecular Oncology and Functional Genomics and Department of Medicine II, School of Medicine, Technical University of Munich, 81675 Munich, Germany" - }, - { - "author_name": "Maria Reinecke", - "author_inst": "Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany" - }, - { - "author_name": "Teresa M. Lavacca", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Rosina Ehmann", - "author_inst": "Bundeswehr Institute of Microbiology, 80937 Munich, Germany" - }, - { - "author_name": "Roman W\u00f6lfel", - "author_inst": "Bundeswehr Institute of Microbiology, 80937 Munich, Germany" - }, - { - "author_name": "J\u00f6rg Jores", - "author_inst": "Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Bernhard K\u00fcster", - "author_inst": "Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany" - }, - { - "author_name": "Ulrike Protzer", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Roland Rad", - "author_inst": "Institute of Molecular Oncology and Functional Genomics and Department of Medicine II, School of Medicine, Technical University of Munich, 81675 Munich, Germany" - }, - { - "author_name": "John Ziebuhr", - "author_inst": "Justus Liebig University Giessen, Institute of Medical Virology, 35392 Giessen, Germany" - }, - { - "author_name": "Volker Thiel", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland & Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Pietro Scaturro", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - }, - { - "author_name": "Matthias Mann", - "author_inst": "Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, 82152, Germany" - }, - { - "author_name": "Andreas Pichlmair", - "author_inst": "Technical University of Munich, School of Medicine, Institute of Virology, 81675 Munich, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.06.17.156679", "rel_title": "Rapid assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy", @@ -1375395,6 +1378241,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.10.20126458", + "rel_title": "The Impact of COVID-19 Pandemic on Cardiology Services", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20126458", + "rel_abs": "ObjectiveCOVID-19 pandemic resulted in prioritisation of NHS resources to cope with the surge in infected patients. However, there have been no studies in the UK looking at the effect of COVID-19 work pattern on the provision of cardiology services. We aim to assess the impact of the pandemic on the cardiology services and clinical activity.\n\nMethodsWe analysed key performance indicators in cardiology services in a single centre in the UK in the intervals prior and during the lockdown to assess for reduction or changes to service provisions.\n\nResultsThere has been more than 50% drop in patients presenting to cardiology and those diagnosed with myocardial infarction. All cardiology service provisions sustained significant reductions which included outpatient clinics, investigations, procedures and cardiology community services such as heart failure and cardiac rehabilitation.\n\nConclusionAs ischaemic heart disease continues to be the leading cause of death nationally and globally, cardiology services need to prepare for a significant increase in workload in the recovery phase and develop new pathways to urgently help those adversely affected by the changes in service provisions.\n\nKey QuestionsO_LIWhat is already known about this subject?\nCOVID-19 affected the way healthcare is delivered through restructuring and prioritisation of resources. It is therefore expected that COVID-19 work pattern will have an impact on the delivery of medical and surgical services. Quantifying this effect is necessary to plan on how to deal with COVID-19 sequelae in the recovery phase.\nC_LIO_LIWhat does this study add?\nAs ischaemic heart disease continues to be the leading cause of death in the world, assessing the direct and indirect effect of COVID-19 on cardiology through COVID-19 related cardiac diseases and through the restriction of cardiology provisions is necessary to plan our services in the post COVID-19 era.\nC_LIO_LIHow might this impact on clinical practice?\nThe impact of COVID-19 will be felt beyond the direct effect of COVID-19 related cardiac diseases. The provisions of cardiac services were severely restricted due to a shift in the focus in dealing with the surge of patients with COVID-19 and patients reluctance to seek medical help during the lockdown period. There was therefore a reduction across all cardiology performance indicators from referrals to investigations, diagnoses and management of cardiology patients. It is therefore expected that there will be another surge of patients seeking cardiology care and that services need to plan to treat these patients early and urgently to prevent any long term complications.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Omar Fersia", + "author_inst": "DGRI" + }, + { + "author_name": "Sue Bryant", + "author_inst": "DGRI" + }, + { + "author_name": "Rachael Nicholson", + "author_inst": "DGRI" + }, + { + "author_name": "Karen McMeeken", + "author_inst": "DGRI" + }, + { + "author_name": "Carolyn Brown", + "author_inst": "DGRI" + }, + { + "author_name": "Brenda Donaldson", + "author_inst": "DGRI" + }, + { + "author_name": "Aaron Jardine", + "author_inst": "DGRI" + }, + { + "author_name": "Valerie Grierson", + "author_inst": "DGRI" + }, + { + "author_name": "Vanessa Whalen", + "author_inst": "DGRI" + }, + { + "author_name": "Alistair Mackay", + "author_inst": "DGRI" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.06.12.20129478", "rel_title": "An International Review of Tobacco Use and the COVID-19 Pandemic: Examining Hospitalization, Asymptomatic Cases, and Severity", @@ -1376483,29 +1379384,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.14.20130518", - "rel_title": "An Extended Laboratory Validation Study and Comparative Performance Evaluation of the Abbott ID NOW COVID-19 Assay in a Coastal California Tertiary Care Medical Center", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20130518", - "rel_abs": "The Abbott ID NOW COVID-19 assay is a rapid molecular diagnostic test particularly designed for on-site, rapid turnaround point of care (POC) testing. The utilization of rapid diagnostic tests is integral to optimizing workflow within the hospital and/or procedural-based clinics. The capability to provide both rapid disposition and correct patient classification during this COVID-19 pandemic is critically important with broad infection control implications for both patients and healthcare staff. A tightly controlled, extended laboratory validation was performed at our medical center to determine the negative test agreement of the Abbott ID NOW compared with the BD MAX analyzer, a laboratory-based, two target, molecular analyzer with a sensitive cycle threshold (Ct) positive cutoff value of [≤] 42. There was strict adoption of the procedures listed in the Abbott ID NOW Instruction for Use (IFU)1 insert delineating preferred practices for \"optimal test performance.\" Under these conditions, our institution demonstrated a significant negative percent agreement with 116 out of 117 patients correlating, which equates to a 99.1% concordance similar to a recently reported correlation study2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Stewart W. Comer", - "author_inst": "Santa Barbara Cottage Hospital" - }, - { - "author_name": "David Fisk", - "author_inst": "Santa Barbara Cottage Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.06.13.20130419", "rel_title": "Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020", @@ -1376745,6 +1379623,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.13.20130484", + "rel_title": "Double COVID-19 Confirmed Case Fatality Rate in Countries with High Elderly Female Vitamin D Deficiency Prevalence", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130484", + "rel_abs": "A number of clues point to a possible role of vitamin D in fighting COVID-19: a reduction in case growth speed with solar zenith angle, higher fatality rate in black people, lower fatality rate in populations that spend more time outdoors. Yet a direct demonstration that vitamin D deficiency is associated with COVID-19 fatalities has remained elusive. We show here in a comparison of 32 countries that countries with high prevalence of vitamin D deficiency among elderly females show a confirmed case fatality rate twice as high as those with low prevalence. We then show that this effect cannot be explained by differences in life expectancy between countries. A mechanistic role for vitamin D in the severity of COVID-19 is proposed.\n\nOne Sentence SummaryVitamin D deficiency among elderly females is associated with countrywide COVID-19 confirmed case fatality rates up to twice as high as those of countries with low vitamin D deficiency prevalence.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alex Backer", + "author_inst": "Caltech" + }, + { + "author_name": "Myron Mageswaran", + "author_inst": "Vanderbilt University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.14.20130906", "rel_title": "High temperature has no impact on the reproduction number and new cases of COVID-19 in Bushehr, Iran", @@ -1377885,33 +1380786,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.15.20131136", - "rel_title": "Modelling the Occurrence of the Novel Pandemic COVID-19 Outbreak; A Box and Jenkins Approach", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131136", - "rel_abs": "The corona virus disease 2019 (COVID-19) is a novel pandemic disease that spreads very fast and causes severe respiratory problem to its carrier and thereby results to death in some cases. In this research, we studied the trend, model Nigeria daily COVID-19 cases and forecast for the future occurrences in the country at large. We adopt the Box and Jenkins approach. The time plot showed that the cases of COVID-19 rises rapidly in recent time. KPSS test confirms the non-stationarity of the process (p < 0.05) before differencing. The test also confirmed the stationarity of the process (p > 0.05) after differencing. Various ARIMA (p,d,q) were examined with their respective AICs and Log-likelihood. ARIMA (1, 2, 1) was selected as the best model due to its least AIC (559.74) and highest log likelihood (-276.87). Both Shapiro-Wilk test and Box test performed confirm the fitness of the model (p > 0.05) for the series. Forecast for 30 days was then made for COVID-19 cases in Nigeria. Conclusively, the model obtained in this research can be used to model, monitor and forecast the daily occurrence of COVID-19 cases in Nigeria.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Nurudeen Ayobami Ajadi", - "author_inst": "Federal University of Agriculture Abeokuta" - }, - { - "author_name": "Isqeel Adesegun Ogunsola", - "author_inst": "Federal University of Agriculture Abeokuta" - }, - { - "author_name": "Saddam Adams Damisa", - "author_inst": "Ahmadu Bello University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.15.20130989", "rel_title": "Predictive accuracy of a hierarchical logistic model of cumulative SARS-CoV-2 case growth", @@ -1378171,6 +1381045,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.06.14.20130922", + "rel_title": "Clinical Characteristics and Outcomes of Venous Thromboembolism in Patients Hospitalized for COVID-19: Systematic Review and Meta-Analysis", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20130922", + "rel_abs": "ObjectiveTo investigate the clinical characteristics and outcomes of Coronavirus Disease of 2019 (COVID-19) patients complicated with venous thromboembolism (VTE)\n\nMethodWe performed a comprehensive literature search of several databases to find studies that assessed VTE in hospitalized COVID-19 patients with a primary outcome of all-cause mortality and secondary outcomes of intensive care unit (ICU) admission and mechanical ventilation. We also evaluated the clinical characteristics of VTE sufferers.\n\nResultsEight studies have been included with a total of 1237 pooled subjects. Venous thromboembolism was associated with higher mortality (RR 2.48 (1.35, 4.55), p=0.003; I2 5%, p=0.35) after we performed sensitivity analysis, ICU admission (RR 2.32 (1.53, 3.52), p<0.0001; I2 80%, p <0.0001), and mechanical ventilation need (RR 2.73 (1.56, 4.78), p=0.0004; I2 77%, p=0.001). Furthermore, it was also associated to male gender (RR 1.21 (1.08, 1.35), p=0.0007; I2 12%, p=0.34), higher white blood cells count (MD 1.24 (0.08, 2.41), 0.04; I2 0%; 0.26), D-dimer (MD 4.49 (2.74, 6.25), p<0.00001; I2 67%, p=0.009) and LDH levels (MD 70.93 (19.33, 122.54), p<0.007; I2 21%, p=0.28). In addition, after sensitivity analysis was conducted, VTE also associated with older age (MD 2.79 (0.06, 5.53), p=0.05; I2 25%, p=0.24) and higher CRP levels (MD 2.57 (0.88, 4.26); p=0.003; I2 0%, p=0.96).\n\nConclusionVenous thromboembolism in COVID-19 patients was associated with increased mortality, ICU admission, and mechanical ventilation requirement. Male gender, older age, higher levels of biomarkers, including WBC count, D-Dimer, and LDH were also being considerably risks for developing VTE in COVID-19 patients during hospitalization.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Joshua Henrina", + "author_inst": "Siloam Hospitals Kebon Jeruk" + }, + { + "author_name": "Iwan Cahyo Santosa Putra", + "author_inst": "Siloam Hospitals Kebon Jeruk" + }, + { + "author_name": "Irvan Cahyadi", + "author_inst": "Siloam Hospitals Kebon Jeruk" + }, + { + "author_name": "Hoo Felicia Hadi Gunawan", + "author_inst": "Siloam Hospitals Kebon Jeruk" + }, + { + "author_name": "Alius Cahyadi", + "author_inst": "School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia" + }, + { + "author_name": "Leonardo Paskah Suciadi", + "author_inst": "Siloam Hospitals Kebon Jeruk" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.06.14.20131318", "rel_title": "Enhanced comparisons of COVID-19 mortality across populations", @@ -1379643,41 +1382556,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.06.16.154591", - "rel_title": "Antigenic evolution on global scale reveals potential natural selection of SARS-CoV-2 by pre-existing cross-reactive T cell immunity", - "rel_date": "2020-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.154591", - "rel_abs": "The mutation pattern of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is constantly changing with the places of transmission, but the reason remains to be revealed. Here, we presented the study that comprehensively analyzed the potential selective pressure of immune system restriction, which can drive mutations in circulating SARS-CoV-2 isolates. The results showed that the most common mutation sites of SARS-CoV-2 proteins were located on the non-structural protein ORF1ab and the structural protein Spike. Further analysis revealed mutations in cross-reactive epitopes between SARS-CoV-2 and seasonal coronavirus may help SARS-CoV-2 to escape cellular immunity under the long-term and large-scale community transmission. Meanwhile, the mutations on Spike protein may enhance the ability of SARS-CoV-2 to enter the host cells and escape the recognition of B-cell immunity. This study will increase the understanding of the evolutionary direction and warn about the potential immune escape ability of SARS-CoV-2, which may provide important guidance for the potential vaccine design.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Chengdong Zhang", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Xuanxuan Jin", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Xianyang Chen", - "author_inst": "Guangzhou Medical University" - }, - { - "author_name": "Qibin Leng", - "author_inst": "Guangzhou Medical University" - }, - { - "author_name": "Tianyi Qiu", - "author_inst": "Fudan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.06.16.155267", "rel_title": "Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection.", @@ -1379981,6 +1382859,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2020.06.12.20129981", + "rel_title": "A discrete-time-evolution model to forecast progress of Covid-19 outbreak", + "rel_date": "2020-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129981", + "rel_abs": "Based on well-known infection models, we constructed a new model to forecast the propagation of the Covid-19 pandemic which yields a discrete-time evolution with one day interval. The proposed model can be easily implemented with daily updated data sets of the pandemic publicly available by many sources. It has only two adjustable parameters and is able to predict the evolution of the total number of infected people in a country for the next 14 days, if parameters do not change during this time. The model incorporates the main aspects of the disease such as the the fact that there are asymptomatic and symptomatic phases (both capable of propagating the virus), and that these phases take almost two weeks before the infected person status evolves to the next (asymptomatic becomes symptomatic or symptomatic becomes either recovered or dead). One advantage of the model is that it gives directly the number of total infected people in each day (in thousands, tens of thousands or hundred of thousands). The model was tested with data from Brazil, UK and South Korea, it predicts quite well the evolution of the disease and therefore may be a useful tool to estimate the propagation of the disease.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Evaldo M. F. Curado", + "author_inst": "Centro Brasileiro de Pesquisas Fisicas" + }, + { + "author_name": "Marco R. Curado", + "author_inst": "INCT-SC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.12.20129304", "rel_title": "Increased plasma heparanase activity in COVID-19 patients", @@ -1381441,37 +1384342,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.11.20129007", - "rel_title": "COVID-19 Deaths: Which Explanatory Variables Matter the Most?", - "rel_date": "2020-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20129007", - "rel_abs": "SO_SCPLOWUMMARYC_SCPLOWAs Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spreads around the World, many questions about the disease are being answered; however, many more remain poorly understood. Although the situation is rapidly evolving, with datasets being continually corrected or updated, it is crucial to understand what factors may be driving transmission through different populations. While studies are beginning to highlight specific parameters that may be playing a role, few have attempted to thoroughly estimate the relative importance of these disparate variables that likely include: climate, population demographics, and imposed state interventions. In this report, we compiled a database of more than 28 potentially explanatory variables for each of the 50 U.S. states through early May 2020. Using a combination of traditional statistical and modern machine learning approaches, we identified those variables that were the most statistically significant, and, those that were the most important. These variables were chosen to be fiduciaries of a range of possible drivers for COVID-19 deaths in the USA. We found that population-weighted density (PWD), some \"stay at home\" metrics, monthly temperature and precipitation, race/ethnicity, and chronic low-respiratory death rate, were all statistically significant. Of these, PWD and mobility metrics dominated. This suggests that the biggest impact on COVID-19 deaths was, at least initially, a function of where you lived, and not what you did. However, clearly, increasing social distancing has the net effect of (at least temporarily) reducing the effective PWD. Our results strongly support the idea that the loosening of \"lock-down\" orders should be tailored to the local PWD. In contrast to these variables, while still statistically significant, race/ethnicity, health, and climate effects could only account for a few percent of the variability in deaths. Where associations were anticipated but were not found, we discuss how limitations in the parameters chosen may mask a contribution that might otherwise be present.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Pete Riley", - "author_inst": "Predictive Science Inc." - }, - { - "author_name": "Allison Riley", - "author_inst": "Predictive Science Inc." - }, - { - "author_name": "James Turtle", - "author_inst": "Predictive Science Inc." - }, - { - "author_name": "Michal Ben-Nun", - "author_inst": "Predictive Science Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.12.20129114", "rel_title": "How to better communicate exponential growth of infectious diseases", @@ -1381895,6 +1384765,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.06.14.150490", + "rel_title": "The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2", + "rel_date": "2020-06-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.14.150490", + "rel_abs": "To circumvent time-consuming clinical trials, testing whether existing drugs are effective inhibitors of SARS-CoV-2, has led to the discovery of Remdesivir. We decided to follow this path and screened approved medications \"off-label\" against SARS-CoV-2. In these screenings, Fluoxetine inhibited SARS-CoV-2 at a concentration of 0.8{micro}g/ml significantly, and the EC50 was determined with 387ng/ml. Fluoxetine is a racemate consisting of both stereoisomers, while the S-form is the dominant serotonin reuptake inhibitor. We found that both isomers show similar activity on the virus. Fluoxetine treatment resulted in a decrease in viral protein expression. Furthermore, Fluoxetine inhibited neither Rabies virus, human respiratory syncytial virus replication nor the Human Herpesvirus 8 or Herpes simplex virus type 1 gene expression, indicating that it acts virus-specific. We see the role of Fluoxetine in the early treatment of SARS-CoV-2 infected patients of risk groups.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Melissa Zimniak", + "author_inst": "Julius-Maximilians-University of Wuerzburg, Institute of Virology" + }, + { + "author_name": "Luisa Kirschner", + "author_inst": "Julius-Maximilians-University of Wuerzburg, Institute of Virology" + }, + { + "author_name": "Helen Hilpert", + "author_inst": "Julius-Maximilians-University of Wuerzburg, Institute of Virology" + }, + { + "author_name": "Juergen Seibel", + "author_inst": "Julius-Maximilians-University of Wuerzburg, Institute of Organic chemistry" + }, + { + "author_name": "Jochen Bodem", + "author_inst": "Julius-Maximilians-University of Wuerzburg, Institute of Virology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.10.143545", "rel_title": "In silico multi-epitope vaccine against covid19 showing effective interaction with HLA-B*15:03", @@ -1382907,181 +1385812,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.12.148387", - "rel_title": "Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient", - "rel_date": "2020-06-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.12.148387", - "rel_abs": "The COVID-19 pandemic has had unprecedented health and economic impact, but currently there are no approved therapies. We have isolated an antibody, EY6A, from a late-stage COVID-19 patient and show it neutralises SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds tightly (KD of 2 nM) the receptor binding domain (RBD) of the viral Spike glycoprotein and a 2.6[A] crystal structure of an RBD/EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues of this epitope are key to stabilising the pre-fusion Spike. Cryo-EM analyses of the pre-fusion Spike incubated with EY6A Fab reveal a complex of the intact trimer with three Fabs bound and two further multimeric forms comprising destabilized Spike attached to Fab. EY6A binds what is probably a major neutralising epitope, making it a candidate therapeutic for COVID-19.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Daming Zhou", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen M E Duyvesteyn", - "author_inst": "University of Oxford" - }, - { - "author_name": "Cheng-Pin Chen", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Chung-Guei Huang", - "author_inst": "Chang Gung University" - }, - { - "author_name": "Ting-Hua Chen", - "author_inst": "Genomics Research Center, Academia Sinica, Taipei" - }, - { - "author_name": "Shin-Ru Shih", - "author_inst": "Chang Gung University" - }, - { - "author_name": "Yi-Chun Lin", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Chien-Yu Cheng", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Shu-Hsing Cheng", - "author_inst": "Taoyuan General Hospital" - }, - { - "author_name": "Yhu-Chering Huang", - "author_inst": "Chang Gung Memorial Hospital" - }, - { - "author_name": "Tzou-Yien Lin", - "author_inst": "Chang Gung Memorial Hospital" - }, - { - "author_name": "Che Ma", - "author_inst": "Genomics Research Center, Academia Sinica, Taipei" - }, - { - "author_name": "Jiandong Huo", - "author_inst": "University of Oxford" - }, - { - "author_name": "Loic Carrique", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tomas Malinauskas", - "author_inst": "University of Oxford" - }, - { - "author_name": "Reinis R Ruza", - "author_inst": "University of Oxford" - }, - { - "author_name": "Pranav Shah", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tiong Kit Tan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Pramila Rijal", - "author_inst": "University of Oxford" - }, - { - "author_name": "Robert F Donat", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kerry Godwin", - "author_inst": "PHE, Porton Down" - }, - { - "author_name": "Karen Buttigieg", - "author_inst": "PHE Porton Down" - }, - { - "author_name": "Julia Tree", - "author_inst": "PHE Porton Down" - }, - { - "author_name": "Julika Radecke", - "author_inst": "Diamond Light Source" - }, - { - "author_name": "Neil G Paterson", - "author_inst": "Diamond Light Source" - }, - { - "author_name": "Piyasa Supasa", - "author_inst": "University of Oxford" - }, - { - "author_name": "Juthathip Mongkolsapaya", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gavin R Screaton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Miles W Carroll", - "author_inst": "PHE Porton Down" - }, - { - "author_name": "Javier G Jaramillo", - "author_inst": "University of Oxford" - }, - { - "author_name": "MIchael Knight", - "author_inst": "University of Oxford" - }, - { - "author_name": "William S James", - "author_inst": "University of Oxford" - }, - { - "author_name": "Raymond J Owens", - "author_inst": "University of Oxford" - }, - { - "author_name": "James H Naismith", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alain Townsend", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth E Fry", - "author_inst": "University of Oxford" - }, - { - "author_name": "Yuguang Zhao", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jingshan Ren", - "author_inst": "University of Oxford" - }, - { - "author_name": "David I Stuart", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kuan-Ying A Huang", - "author_inst": "Chang Gung University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.13.149880", "rel_title": "Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach", @@ -1383333,6 +1386063,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.06.12.20129999", + "rel_title": "Analysis of SARS-CoV-2 Genomes from Southern California Reveals Community Transmission Pathways in the Early Stage of the US COVID-19 Pandemic", + "rel_date": "2020-06-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129999", + "rel_abs": "Given the higher mortality rate and widespread phenomenon of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) within the United States (US) population, understanding the mutational pattern of SARS CoV-2 has global implications for detection and therapy to prevent further escalation. Los Angeles has become an epicenter of the SARS-CoV-2 pandemic in the US. Efforts to contain the spread of SARS-CoV-2 require identifying its genetic and geographic variation and understanding the drivers of these differences. For the first time, we report genetic characterization of SARS-CoV-2 genome isolates in the Los Angeles population using targeted next generation sequencing (NGS). Samples collected at Cedars Sinai Medical Center were collected from patients with confirmed SARS-CoV-2 infection. We identified and diagnosed 192 patients by our in-house qPCR assay. In this population, the highest frequency variants were in known mutations in the 5UTR, AA193 protein, RdRp and the spike glycoprotein. SARS-CoV-2 transmission within the local community was tracked by integrating mutation data with patient postal codes with two predominant community spread clusters being identified. Notably, significant viral genomic diversity was identified. Less than 10% of the Los Angeles community samples resembled published mutational profiles of SARS-CoV-2 genomes from China, while >50% of the isolates shared closely similarities to those from New York State. Based on these findings we conclude SARS-CoV-2 was likely introduced into the Los Angeles community predominantly from New York State but also via multiple other independent transmission routes including but not limited to Washington State and China.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Wenjuan Zhang", + "author_inst": "Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Jean Paul Govindavari", + "author_inst": "Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Brian Davis", + "author_inst": "Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Stephanie C Chen", + "author_inst": "Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Jong Taek Kim", + "author_inst": "Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Jianbo Song", + "author_inst": "Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Jean Lopategui", + "author_inst": "Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Jasmine T Plummer", + "author_inst": "Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA" + }, + { + "author_name": "Eric Vail", + "author_inst": "Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.06.12.20129783", "rel_title": "Heterogeneity in risk, testing and outcome of COVID-19 across outbreak settings in the Greater Toronto Area, Canada: an observational study", @@ -1384345,33 +1387126,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.09.20123836", - "rel_title": "Point of care lung ultrasound is useful when screening for CoVid-19 in Emergency Department patients.", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20123836", - "rel_abs": "BackgroundCoVid-19 can be a life-threatening lung disease or a trivial upper respiratory infection depending on whether the alveoli are involved. Emergency department (ED) screening in symptomatic patients with normal vital signs is frequently limited to oro-nasopharyngeal swabs. We tested the null hypothesis that patients being screened for CoVid-19 in the ED with normal vital signs and without hypoxia would have a point-of-care lung ultrasound (LUS) consistent with CoVid-19 less than 2% of the time.\n\nMethodsO_ST_ABSSubjectsC_ST_ABSSubjects were identified from ED ultrasound logs.\n\nInclusion criteriaAge 14 years or older with symptoms prompting ED screening for CoVid-19.\n\nExclusion criteriaKnown congestive heart failure or other chronic lung condition likely to cause excessive B lines on LUS.\n\nInterventionStructured blinded ultrasound review and chart review\n\nAnalysisWe used a two-sided exact hypothesis test for binomial random variables. We also measured LUS diagnostic performance using computed tomography as the gold standard.\n\nResultsWe reviewed 77 charts; 49 met inclusion criteria. Vital signs were normal in 30/49 patients; 10 (33%) of these patients had LUS consistent with CoVid-19. We rejected the null hypothesis (p-value < 0.001). The treating physicians interpretation of their own point of care lung ultrasounds had a sensitivity of 100% (95% CI 75%, 100%) and specificity of 80% (95% CI 68%, 89%).\n\nConclusionLUS has a meaningful detection rate for CoVid-19 in symptomatic ED patients with normal vital signs. We recommend at least LUS be used in addition to PCR testing when screening symptomatic ED patients for CoVid-19.\n\nCapsule What is knownAuscultation and chest x-ray are insufficient to screen for lung involvement when SARS-CoV-2 infection is suspected. Point of care lung ultrasound is widely available, safer, and less resource intensive than CT imaging.\n\nWhat we foundIn symptomatic patients presenting to the ED even those with normal vital signs had point of care lung ultrasound evidence of alveolar level involvement 33%of patients. Point of care lung ultrasound was 100% sensitive and 80% specific compared to CT (reference standard) when evaluating patients for Covid-19.\n\nWhat this addsPoint of care lung ultrasound or similar imaging should performed when screening symptomatic patients in whom SARS-CoV-2 infection is suspected.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andrea Hankins", - "author_inst": "Sutter Institute for Medical Research, 2801 L Street, Sacramento, CA 95816, United States of America" - }, - { - "author_name": "Heejung Bang", - "author_inst": "Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, California, United States of America" - }, - { - "author_name": "Paul Walsh", - "author_inst": "Pediatric Emergency Medicine, Sutter Medical Center Sacramento, 2825 Capitol Avenue, Sacramento, CA 95816" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.06.08.20123786", "rel_title": "Oscillations in USA COVID-19 Incidence and Mortality Data reflect societal factors", @@ -1384639,6 +1387393,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20128058", + "rel_title": "Power Laws in Superspreading Events: Evidence from Coronavirus Outbreaks and Implications for SIR Models", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128058", + "rel_abs": "While they are rare, superspreading events (SSEs), wherein a few primary cases infect an extraordinarily large number of secondary cases, are recognized as a prominent determinant of aggregate infection rates ([R]0). Existing stochastic SIR models incorporate SSEs by fitting distributions with thin tails, or finite variance, and therefore predicting almost deterministic epidemiological outcomes in large populations. This paper documents evidence from recent coronavirus outbreaks, including SARS, MERS, and COVID-19, that SSEs follow a power law distribution with fat tails, or infinite variance. We then extend an otherwise standard SIR model with the estimated power law distributions, and show that idiosyncratic uncertainties in SSEs will lead to large aggregate uncertainties in infection dynamics, even with large populations. That is, the timing and magnitude of outbreaks will be unpredictable. While such uncertainties have social costs, we also find that they on average decrease the herd immunity thresholds and the cumulative infections because per-period infection rates have decreasing marginal effects. Our findings have implications for social distancing interventions: targeting SSEs reduces not only the average rate of infection ([R]0) but also its uncertainty. To understand this effect, and to improve inference of the average reproduction numbers under fat tails, estimating the tail distribution of SSEs is vital.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Masao Fukui", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Chishio Furukawa", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.05.20123448", "rel_title": "The effectiveness of social bubbles as part of a Covid-19 lockdown exit strategy, a modelling study", @@ -1385711,153 +1388488,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.11.20125849", - "rel_title": "Renin-angiotensin system blockers and susceptibility to COVID-19: a multinational open science cohort study", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20125849", - "rel_abs": "IntroductionAngiotensin converting enzyme inhibitors (ACEs) and angiotensin receptor blockers (ARBs) could influence infection risk of coronavirus disease (COVID-19). Observational studies to date lack pre-specification, transparency, rigorous ascertainment adjustment and international generalizability, with contradictory results.\n\nMethodsUsing electronic health records from Spain (SIDIAP) and the United States (Columbia University Irving Medical Center and Department of Veterans Affairs), we conducted a systematic cohort study with prevalent ACE, ARB, calcium channel blocker (CCB) and thiazide diuretic (THZ) users to determine relative risk of COVID-19 diagnosis and related hospitalization outcomes. The study addressed confounding through large-scale propensity score adjustment and negative control experiments.\n\nResultsFollowing over 1.1 million antihypertensive users identified between November 2019 and January 2020, we observed no significant difference in relative COVID-19 diagnosis risk comparing ACE/ARB vs CCB/THZ monotherapy (hazard ratio: 0.98; 95% CI 0.84 - 1.14), nor any difference for mono/combination use (1.01; 0.90 - 1.15). ACE alone and ARB alone similarly showed no relative risk difference when compared to CCB/THZ monotherapy or mono/combination use. Directly comparing ACE vs. ARB demonstrated a moderately lower risk with ACE, non-significant for monotherapy (0.85; 0.69 - 1.05) and marginally significant for mono/combination users (0.88; 0.79 - 0.99). We observed, however, no significant difference between drug-classes for COVID-19 hospitalization or pneumonia risk across all comparisons.\n\nConclusionThere is no clinically significant increased risk of COVID-19 diagnosis or hospitalization with ACE or ARB use. Users should not discontinue or change their treatment to avoid COVID-19.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Daniel R Morales", - "author_inst": "University of Dundee" - }, - { - "author_name": "Mitchell M Conover", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Seng Chan You", - "author_inst": "Ajou University" - }, - { - "author_name": "Nicole Pratt", - "author_inst": "University of South Australia" - }, - { - "author_name": "Kristin Kostka", - "author_inst": "IQVIA" - }, - { - "author_name": "Talita Duarte Salles", - "author_inst": "IDIAPJGol" - }, - { - "author_name": "Sergio Fernandez Bertolin", - "author_inst": "IDIAPJGol" - }, - { - "author_name": "Maria Aragon", - "author_inst": "IDIAPJGol" - }, - { - "author_name": "Scott L. DuVall", - "author_inst": "Department of Veterans Affairs" - }, - { - "author_name": "Kristine Lynch", - "author_inst": "Department of Veterans Affairs" - }, - { - "author_name": "Thomas Falconer", - "author_inst": "Columbia University" - }, - { - "author_name": "Kees van Bochove", - "author_inst": "The Hyve" - }, - { - "author_name": "Cynthia Sung", - "author_inst": "Bill & Melinda Gates Medical Research Institute" - }, - { - "author_name": "Michael E. Matheny", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Christophe G. Lambert", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Fredrik Nyberg", - "author_inst": "University of Gothenburg" - }, - { - "author_name": "Thamir M AlShammari", - "author_inst": "King Saud University" - }, - { - "author_name": "Andrew E. Williams", - "author_inst": "Tufts University" - }, - { - "author_name": "Rae Woong Park", - "author_inst": "Ajou University" - }, - { - "author_name": "James Weaver", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Anthony G. Sena", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Martijn J. Schuemie", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "Peter R. Rijnbeek", - "author_inst": "Erasmus University" - }, - { - "author_name": "Ross D. Williams", - "author_inst": "Erasmus University" - }, - { - "author_name": "Jennifer C.E Lane", - "author_inst": "University of Oxford" - }, - { - "author_name": "Albert Prats Uribe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lin Zhang", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Carlos Areia", - "author_inst": "University of Oxford" - }, - { - "author_name": "Harlan Krumholz", - "author_inst": "Yale University" - }, - { - "author_name": "Daniel Prieto Alhambra", - "author_inst": "University of Oxford" - }, - { - "author_name": "Patrick B Ryan", - "author_inst": "Janssen Research and Development" - }, - { - "author_name": "George Hripcsak", - "author_inst": "Columbia University" - }, - { - "author_name": "Marc A Suchard", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.06.10.20127613", "rel_title": "On the interplay between mobility and hospitalization capacity during the COVID-19 pandemic: The SEIRHUD model", @@ -1386089,6 +1388719,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.10.20127506", + "rel_title": "Correlation between meteorological factors and COVID-19 infection in the Belem Metropolitan Region", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127506", + "rel_abs": "Many factors can influence the spread of viruses and respiratory infections. Studies have suggested that there is a direct relationship between environmental issues and population density with cases of COVID-19. In this sense, this research aims to analyze, through correlational study and Krigagem, the relationship of meteorological and demographic variables with cases of COVID-19 in regions of subtropical climate in Brazil. The results suggest that population and demographic density (hab/km2) are risk factors for the spread of SAR-Cov-2 and an increase in the daily case record of COVID-19. The distribution of cases according to age group did not present a significant disparity between men and women. Relative humidity (RH)%, average temperature {degrees}C, minimum temperature {degrees}C, maximum temperature {degrees}C, wind speed m/s and daily precipitation (rain) mm show negative relationships with cases of COVID-19 in regions of humid equatorial climate. Analysis between associations of environmental factors, wind, temperature and HR in a region is extremely important to understand the dynamics of SARS-Cov-2 in the environment. In the northern region of Brazil, low wind speed, high temperatures and high RH are observed, environmental factors that, when associated, reduce the transmission process because it hinders the movement of the virus in the environment. In this sense, it is suggested that the transmission of SARS-CoV-2 in this region is disseminated through fluids in the air between man/man and by contact between objects/men. Therefore, strategic public policies to combat the pandemic must consider the environmental factors of the regions involved and control and/or blocking the transit of people.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Felix Lelis da Silva", + "author_inst": "Federal Institute of Education Science and Tecnology of Par" + }, + { + "author_name": "Maryjane Diniz A. Gomes", + "author_inst": "Federal Institute of Education Scienceand Tecnology of Par" + }, + { + "author_name": "Andrea Pereira Lelis da Silva", + "author_inst": "Metropolitan Regional Hospital" + }, + { + "author_name": "Samio Costa de Sousa", + "author_inst": "Federal Institute of Science and Tecnology of Par" + }, + { + "author_name": "Marcos Francisco Serafim de Souza", + "author_inst": "Federal Institute of Education Scienceand Tecnology of Par" + }, + { + "author_name": "Gabriel Lelis P. da Silva", + "author_inst": "Estacio de Sa College of Castanhal" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.10.20127472", "rel_title": "Identifying novel factors associated with COVID-19 transmission and fatality using the machine learning approach", @@ -1387241,61 +1389910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2020.06.11.20128934", - "rel_title": "SARS-CoV-2 Viral Load Predicts COVID-19 Mortality", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128934", - "rel_abs": "The need for reliable and widely available SARS-CoV-2 testing is well recognized, but it will be equally necessary to develop quantitative methods that determine viral load in order to guide patient triage and medical decision making. We are the first to report that SARS-CoV-2 viral load at the time of presentation is an independent predictor of COVID-19 mortality in a large patient cohort (n=1,145). Viral loads should be used to identify higher-risk patients that may require more aggressive care and should be included as a key biomarker in the development of predictive algorithms.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elisabet Pujadas", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Fayzan Chaudhry", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Russell McBride", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Felix Richter", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Shan Zhao", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ania Wajnberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Girish Nadkarni", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benjamin S Glicksberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jane Houldsworth", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Carlos Cordon-Cardo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.11.20128900", "rel_title": "Associations between wearing masks, washing hands, and social distancing practices, and risk of COVID-19 infection in public: a cohort-based case-control study in Thailand", @@ -1387515,6 +1390129,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.06.10.20127969", + "rel_title": "Plasma levels of soluble ACE2 are associated with sex, Metabolic Syndrome, and its biomarkers in a large cohort, pointing to a possible mechanism for increased severity in COVID-19", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127969", + "rel_abs": "We examined the associations between plasma concentrations of soluble ACE2 and biomarkers of Metabolic Syndrome in a large (N=2,051) sample of individuals who participated in a commercial wellness program and who underwent deep molecular phenotyping. sACE2 levels were significantly higher in men, compared to women, and in individuals with Metabolic Syndrome, compared to controls. sACE2 levels showed reliable associations with all individuals components of Metabolic Syndrome, including obesity, hypertension, insulin resistance, hyperlipidemia, and as well as markers of liver damage. This profile of associations was statistically significantly stronger in men, compared to women, and points to preexisting cardiometabolic conditions as possible risk factors for increased severity of symptoms in some COVID-19 patients through increased expression of ACE2 in the liver.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sergey A Kornilov", + "author_inst": "Institute for Systems Biology" + }, + { + "author_name": "Isabelle Lucas", + "author_inst": "Institute for Systems Biology, Seattle, WA" + }, + { + "author_name": "Kathleen Jade", + "author_inst": "Institute for Systems Biology, Seattle, WA" + }, + { + "author_name": "Chengzhen L Dai", + "author_inst": "Institute for Systems Biology, Seattle, WA" + }, + { + "author_name": "Jennifer C Lovejoy", + "author_inst": "Institute for Systems Biology, Seattle, WA" + }, + { + "author_name": "Andrew T Magis", + "author_inst": "Institute for Systems Biology, Seattle, WA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2020.06.11.20128371", "rel_title": "Assessing the influence of parental anxiety on childhood anxiety during the COVID-19 pandemic in the United Arab Emirates", @@ -1388599,65 +1391252,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.10.20127365", - "rel_title": "Spatial and temporal regularization to estimate COVID-19 Reproduction Number R(t): Promoting piecewise smoothness via convex optimization", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127365", - "rel_abs": "Among the different indicators that quantify the spread of an epidemic, such as the on-going COVID-19, stands first the reproduction number which measures how many people can be contaminated by an infected person. In order to permit the monitoring of the evolution of this number, a new estimation procedure is proposed here, assuming a well-accepted model for current incidence data, based on past observations. The novelty of the proposed approach is twofold: 1) the estimation of the reproduction number is achieved by convex optimization within a proximal-based inverse problem formulation, with constraints aimed at promoting piecewise smoothness; 2) the approach is developed in a multivariate setting, allowing for the simultaneous handling of multiple time series attached to different geographical regions, together with a spatial (graph-based) regularization of their evolutions in time. The effective-ness of the approach is first supported by simulations, and two main applications to real COVID-19 data are then discussed. The first one refers to the comparative evolution of the reproduction number for a number of countries, while the second one focuses on French counties and their joint analysis, leading to dynamic maps revealing the temporal co-evolution of their reproduction numbers.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "patrice abry", - "author_inst": "CNRS" - }, - { - "author_name": "nelly pustelnik", - "author_inst": "CNRS" - }, - { - "author_name": "stephane roux", - "author_inst": "ENS Lyon" - }, - { - "author_name": "pablo jensen", - "author_inst": "CNRS" - }, - { - "author_name": "Patrick Flandrin", - "author_inst": "CNRS" - }, - { - "author_name": "remi gribonval", - "author_inst": "INRIA" - }, - { - "author_name": "Charles G Lucas", - "author_inst": "ENS de Lyon" - }, - { - "author_name": "eric guichard", - "author_inst": "ENSSIB" - }, - { - "author_name": "Pierre Borgnat", - "author_inst": "CNRS" - }, - { - "author_name": "nicolas garnier", - "author_inst": "CNRS" - }, - { - "author_name": "benjamin audit", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.11.20128801", "rel_title": "Early epidemic spread, percolation and Covid-19", @@ -1388853,6 +1391447,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2020.06.11.20128686", + "rel_title": "Sensitivity of commercial Anti-SARS-CoV-2 serological assays in a high-prevalence setting", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128686", + "rel_abs": "We analysed SARS-CoV-2 specific antibody responses in 42 social and working contacts of a super-spreader from the Heinsberg area in Germany. Consistent with a high-prevalence setting 26 individuals had SARS-CoV-2 antibodies determined by in-house neutralisation testing. These results were compared with four commercial assays, suggesting limited sensitivity of the assays in such a high-prevalence setting. Although SARS-CoV-2 nucleocapsid-restricted tests showed a better sensitivity, spike-based assays had a stronger correlation with neutralisation capacity.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Lisa Mueller", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Philipp Niklas Ostermann", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Andreas Walker", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Tobias Wienemann", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Alexander Mertens", + "author_inst": "Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Ortwin Adams", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Marcel Andree", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Sandra Hauka", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Nadine Luebke", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Verena Keitel", + "author_inst": "Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Ingo Drexler", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Veronica Di Cristanziano", + "author_inst": "Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany" + }, + { + "author_name": "Derik Franz Hermsen", + "author_inst": "Institute of Clinical Chemistry and Laboratory Diagnostics, Medical Faculty, University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Rolf Kaiser", + "author_inst": "Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany" + }, + { + "author_name": "Friedrich Boege", + "author_inst": "Institute of Clinical Chemistry and Laboratory Diagnostics, Medical Faculty, University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Florian Klein", + "author_inst": "Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany" + }, + { + "author_name": "Heiner Schaal", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Joerg Timm", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + }, + { + "author_name": "Tina Senff", + "author_inst": "Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Duesseldorf, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.12.20122374", "rel_title": "Temporal clinical and laboratory response to interleukin-6 receptor blockade with Tocilizumab in 89 hospitalized patients with COVID-19 pneumonia", @@ -1390685,61 +1393370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.09.20127092", - "rel_title": "Antibody response to infectious diseases and other factors accurately predict COVID-19 infection and severity risk 10-14 years later: a retrospective UK Biobank cohort study", - "rel_date": "2020-06-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20127092", - "rel_abs": "BackgroundMany risk factors have emerged for novel 2019 coronavirus disease (COVID-19). It is relatively unknown how these factors collectively predict COVID-19 infection risk, as well as risk for a severe infection (i.e., hospitalization).\n\nMethodsAmong aged adults (69.3 {+/-} 8.6 years) in UK Biobank, COVID-19 data was downloaded for 4,510 participants with 7,539 test cases. We downloaded baseline data from 10-14 years ago, including demographics, biochemistry, body mass, and other factors, as well as antibody titers for 20 common to rare infectious diseases. Permutation-based linear discriminant analysis was used to predict COVID-19 risk and hospitalization risk. Probability and threshold metrics included receiver operating characteristic curves to derive area under the curve (AUC), specificity, sensitivity, and quadratic mean.\n\nResultsThe \"best-fit\" model for predicting COVID-19 risk achieved excellent discrimination (AUC=0.969, 95% CI=0.934-1.000). Factors included age, immune markers, lipids, and serology titers to common pathogens like human cytomegalovirus. The hospitalization \"best-fit\" model was more modest (AUC=0.803, 95% CI=0.663-0.943) and included only serology titers.\n\nConclusionsAccurate risk profiles can be created using standard self-report and biomedical data collected in public health and medical settings. It is also worthwhile to further investigate if prior host immunity predicts current host immunity to COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Auriel A Willette", - "author_inst": "Iowa State University" - }, - { - "author_name": "Sara A Willette", - "author_inst": "Iowa State University" - }, - { - "author_name": "Qian Wang", - "author_inst": "Iowa State University" - }, - { - "author_name": "Colleen Pappas", - "author_inst": "Iowa State University" - }, - { - "author_name": "Brandon S Klinedinst", - "author_inst": "Iowa State University" - }, - { - "author_name": "Scott Le", - "author_inst": "Iowa State University" - }, - { - "author_name": "Brittany Larsen", - "author_inst": "Iowa State University" - }, - { - "author_name": "Amy Pollpeter", - "author_inst": "Iowa State University" - }, - { - "author_name": "Nicole Brenner", - "author_inst": "German Cancer Research Center (DKFZ)" - }, - { - "author_name": "Tim Waterboer", - "author_inst": "German Cancer Research Center (DKFZ)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.09.20127050", "rel_title": "Plasma from recovered COVID19 subjects inhibits spike protein binding to ACE2 in a microsphere-based inhibition assay", @@ -1390919,6 +1393549,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.09.20126631", + "rel_title": "Rapid characterization of the propagation of COVID-19 in different countries", + "rel_date": "2020-06-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126631", + "rel_abs": "BACKGROUNDCOVID-19 has spread rapidly, and there are still many characteristics of this new disease to be unveiled. We propose a simple method to calculate a \"figure of merit\" FC to provide an early characterization of the disease status in country C.\n\nMETHODSWe use mathematical tools to adjust a Gaussian function to the daily increase of infected patients. Maximum value and full width half maximum of the Gaussian are characteristics of the development of the development of the pandemic in each country. These parameters are supplemented by the testing volume and the mortality rate to produce just one characterizing parameter: FC. In addition, the stability of the Gaussian fits was calculated within an entire week towards the end of the study period. Seventeen different countries were fully considered, while others are considered when discussing particular properties. Data employed is publically available.\n\nFINDINGSFitted Gaussian functions render effective information about the development of COVID-19. The number of critical days vary between 11 (South Korea) and 52 (Mexico). FC varies between 1 (Australia) and 899 (Mexico). The epidemic appears stabilized in some countries and unstable in others. Some large countries are experiencing fast development of the propagation of the disease with high FC. A correlation between low (high) values of the mortality rate (and to some extent FC) and the presence (absence) of BCG vaccination is exposed.\n\nINTERPRETATIONThe adjustment of a Gaussian to daily data of COVID-19 in each country reveals the different propagation dynamics, properly characterized by the parameters proposed here. Testing plays a clear role to control the spread of the disease. Mortality rate spans more than one order of magnitude and is somewhat related to permanent massive BCG vaccination. The figure of merit, FC, introduced here spans more than 2 orders of magnitude which makes it a useful indicator to quickly find out the status of the pandemics in each territory. Geography plays a role: low population density and isolated countries can be efficient in controlling the spread of the disease.\n\nHIGHLIGHTSO_LIAn easy-to-evaluate parameter is defined to rapidly establish the status of the evolution of COVID-19 in any given territory. 17 countries in 4 continents are chosen to apply it and compare different evolutions.\nC_LIO_LIThe parameter or figure of merit (FC) is dynamic: it combines testing, mortality rate, and characteristics of the Gaussian function that fits the new daily contagions.\nC_LIO_LIFC spans more than two orders of magnitude which makes it a very sensitive indicator to promptly detect second waves or local outbreaks.\nC_LIO_LIIt is found that countries with massive BCG vaccination present low COVID-19 mortality rates and low values for FC.\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Patricio Vargas", + "author_inst": "Universidad Tecnica Federico Santa Maria" + }, + { + "author_name": "Sebastian Allende", + "author_inst": "Universidad de Santiago de Chile" + }, + { + "author_name": "Eugenio E Vogel", + "author_inst": "Universidad de La Frontera" + }, + { + "author_name": "Sigismund Kobe", + "author_inst": "Technische Universitat Dresden" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.09.20126995", "rel_title": "Impact of COVID-19 pandemic on lung cancer treatment scheduling", @@ -1392391,61 +1395052,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.06.09.20076646", - "rel_title": "Prolonged SARS-CoV-2 Viral Shedding in Patients with COVID-19 was Associated with Delayed Initiation of Arbidol Treatment: a retrospective cohort study", - "rel_date": "2020-06-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20076646", - "rel_abs": "ObjectivesEvaluate the risk factors of prolonged SARS-CoV-2 virus shedding and the impact of arbidol treatment on SARS-CoV-2 virus shedding.\n\nMethodsData were retrospective collected from adults hospitalized with COVID-19 in Wuhan Union Hospital. We described the clinical features and SARS-CoV-2 RNA shedding of patients with COVID-19 and evaluated factors associated with prolonged virus shedding by multivariate regression analysis.\n\nResultsAmong 238 patients, the median age was 55.5 years, 57.1% were female, 92.9% (221/238) used arbidol, 58.4% (139/238) used arbidol combination with interferon. The median time from illness onset to start arbidol was 8 days (IQR, 5-14 days) and the median duration of SARS-CoV-2 virus shedding was 23 days (IQR, 17.8-30 days). SARS-CoV-2 RNA clearance was significantly delayed in patients who received arbidol >7 days after illness onset, compared with those in whom arbidol treatment was started[≤]7 days after illness onset (HR, 1.738 [95% CI, 1.339-2.257], P < .001). Multivariate regression analysis revealed that prolonged viral shedding was significantly associated with initiation arbidol more than seven days after symptom onset (OR 2.078, 95% CI [1.114-3.876], P .004), more than 7 days from onset of symptoms to first medical visitation (OR 3.321, 95% CI[1.559-7.073], P .002), illness onset before Jan.31, 2020 (OR 3.223, 95% CI[1.450-7.163], P .021). Arbidol combination with interferon was also significantly associated with shorter virus shedding (OR .402, 95% CI[.206-.787], P .008).\n\nConclusionsEarly initiation of arbidol and arbidol combination with interferon as well as consulting doctor timely after illness onset were helpful for SARS-CoV-2 clearance.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Yaya Zhou", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Xinliang He", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Jianchu Zhang", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Yu e Xue", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Mengyuan Liang", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Bohan Yang", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Wanli Ma", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Qiong Zhou", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Long Chen", - "author_inst": "Wuhan union hospital" - }, - { - "author_name": "Xiaorong Wang", - "author_inst": "Wuhan union hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.10.144196", "rel_title": "Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction", @@ -1392757,6 +1395363,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.10.144642", + "rel_title": "Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy", + "rel_date": "2020-06-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.10.144642", + "rel_abs": "SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Here, we investigated the interaction of this new coronavirus with Vero cells using high resolution scanning electron microscopy. Surface morphology, the interior of infected cells and the distribution of viral particles in both environments were observed 2 and 48 hours after infection. We showed areas of viral processing, details of vacuole contents, and viral interactions with the cell surface. Intercellular connections were also approached, and viral particles were adhered to these extensions suggesting direct cell-to-cell transmission of SARS-CoV-2.\n\nHighlightsWe used high resolution scanning electron microscopy to investigate Vero cells infected with SARS-CoV-2 at 2 and 48 hours post-infection. The central conclusions of this work include: O_LIInfected cells display polarization of their cytosol forming a restricted viroplasm-like zone dedicated to virus production and morphogenesis.\nC_LIO_LIThis is the first demonstration of SARS-CoV-2 attachment by scanning electron microscopy.\nC_LIO_LIThis is the first scanning electron microscopy images of the interior of SARS-CoV-2 infected cells and exploration of their vacuole contents.\nC_LIO_LIPerspective-viewing of bordering vesicles in close association with vacuoles.\nC_LIO_LIObservation of membrane ruffles and structures suggestive of exocytosis on the surface of infected cells.\nC_LIO_LIThe first demonstration of viral surfing in cell-to-cell communication on SARS-CoV-2 infection.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Lucio Ayres Caldas", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Fabiana Avila Carneiro", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Luiza Mendonca Higa", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Fabio Luiz Monteiro", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Gustavo Peixoto da Silva", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Luciana Jesus da Costa", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Edison Luiz Durigon", + "author_inst": "Universidade de Sao Paulo Instituto de Ciencias Biomedicas" + }, + { + "author_name": "Amilcar Tanuri", + "author_inst": "UFRJ" + }, + { + "author_name": "Wanderley de Souza", + "author_inst": "Unniversidade Federal do Rio de Janeiro" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.09.142794", "rel_title": "The utility of native MS for understanding the mechanism of action of repurposed therapeutics in COVID-19: heparin as a disruptor of the SARS-CoV-2 interaction with its host cell receptor.", @@ -1393849,41 +1396506,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.08.20125708", - "rel_title": "A web survey to assess the use efficacy of personnel protective materials among allied health care workers during COVID-19 pandemic at North-East India", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125708", - "rel_abs": "The rising pandemic is resulting in increased usage of personnel protective equipment in the hospital and community. The efficient and effective use of appropriate personal protective equipment will help assure its availability and healthcare provider safety. The purpose of this study was to assess the use efficacy of PPE among health care workers through a web based survey during the pandemic. the response rate of the survey was 66.75%. 35.2% gave a full rating on a point of 5 regarding the control measures taken by the hospital, 39% of respondents did not use the PPE, 90.6% used a surgical mask while 65.9% wore the disposable gloves and only 47.6% wore the goggles/face shield More than half the respondents did not wear the shoe-cover. 97.4% used the hand sanitizer and around 97% maintained hand hygiene practice.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Dr. Rahul P Kotian", - "author_inst": "Department of Medical Imaging, College of Allied Health Sciences, SRINIVAS UNIVERSITY" - }, - { - "author_name": "Manna Debnath", - "author_inst": "Department of Medical Imaging Technology, Charotar Institute of Paramedical Sciences, Charotar University of Science and Technology." - }, - { - "author_name": "Zosangliani", - "author_inst": "Department of Radiology, Faculty of Paramedical Sciences, Assam Downtown University, Assam, India." - }, - { - "author_name": "Brayal D'souza", - "author_inst": "Department of Health Innovation, PSPH, Manipal Academy of Higher Education, Manipal." - }, - { - "author_name": "Disha Faujdar", - "author_inst": "Department of Medical Imaging Technology, College of Allied Health Sciences, Srinivas University, Mukka." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.06.08.20125872", "rel_title": "Cognitive impairment is a common comorbidity in COVID-19 deceased patients. A hospital-based retrospective cohort study.", @@ -1394315,6 +1396937,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.09.20126045", + "rel_title": "Worries and concerns among healthcare workers during the coronavirus 2019 pandemic: a web-based cross-sectional survey", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126045", + "rel_abs": "BackgroundHealthcare workers (HCWs) treating and caring for patients with emerging infectious diseases often experience psychological distress. However, the psychological impact and behavior change of the coronavirus disease 2019 (COVID-19) pandemic among HCWs are still unknown. This study aimed to investigate the worries and concerns of HCWs regarding the COVID-19 pandemic.\n\nMethodsIn this cross-sectional survey, a web-based questionnaire was distributed among HCWs working in hospitals or clinics across Japanese medical facilities from April 20 to May 1, 2020. The questionnaire comprised items on demographics, worries and concerns, perceptions regarding the sufficiency of information, and behavioral changes pertaining to the COVID-19 pandemic.\n\nResultsA total of 4386 HCWs completed the survey; 1648 (64.7%) were aged 30-39 years, 2379 (54.2%) were male, and 782 (18.1%) were frontline HCWs, directly caring for patients with COVID-19 on a daily basis. 3500 HCWs (79.8%) indicated that they were seriously worried about the pandemic. The most frequent concern was the consequence of becoming infected on their family, work, and society (87.4%). Additionally, the majority (55.5%) had restricted social contact and almost all HCWs endorsed a shortage in personal protective equipment (median, 8/9 (interquartile range; 7-9) on a Likert scale). There was no significant difference in the degree of worry between frontline and non-frontline HCWs (8/9 (7-9) vs. 8/9 (7-9), p=0.25). Frontline HCWs, compared to non-frontline HCWs, were more likely to have the need to avoid contact with families and friends (24.8% vs. 17.8%, p<0.001) and indicated that they cannot evade their professional duty during the COVID-19 pandemic (9/9 (7-9) vs. 8/9 (6-9), p<0.001). Further, the extremely low proportion of frontline HCWs reported that they would take a leave of absence to avoid infection (1.2%).\n\nConclusionsBoth frontline and non-frontline HCWs expressed comparable concerns regarding the COVID-19 pandemic. Because HCWs, especially frontline HCWs, reported that they cannot be obliged to do avoid their duty, effective mental health protection strategies should be developed and implemented for HCWs.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yuki Sahashi", + "author_inst": "Department of Cardiology, Gifu University Graduate School of Medicine; Department of Health Data Science, Graduate School of Data Science, Yokohama City Univers" + }, + { + "author_name": "Hirohisa Endo", + "author_inst": "Department of Cardiovascular Medicine, Juntendo University Graduate School of Medicine" + }, + { + "author_name": "Tadafumi Sugimoto", + "author_inst": "Department of Clinical Laboratory, Mie University Hospital" + }, + { + "author_name": "Takeru Nabeta", + "author_inst": "Department of Cardiovascular Medicine, Kitasato University School of Medicine" + }, + { + "author_name": "Kimitaka Nishizaki", + "author_inst": "Department of Cardiology and Nephrology, Hirosaki University Graduate School of Medicine" + }, + { + "author_name": "Atsushi Kikuchi", + "author_inst": "Department of Cardiology, Osaka General Medical Center" + }, + { + "author_name": "Shingo Matsumoto", + "author_inst": "Department of Cardiovascular Medicine, Toho University Graduate School of Medicine" + }, + { + "author_name": "Hiroyuki Sato", + "author_inst": "Department of Cardiology, Teine Keijinkai Hospital" + }, + { + "author_name": "Tadahiro Goto", + "author_inst": "Department of Clinical Epidemiology and Health Economics, School of Public Health, The University of Tokyo; TXP Medical Co. Ltd." + }, + { + "author_name": "Kohei Hasegawa", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School" + }, + { + "author_name": "Yuya Matsue", + "author_inst": "Department of Cardiovascular Medicine, Juntendo University Graduate School of Medicine; Department of Cardiovascular Respiratory Sleep Medicine, Juntendo Univer" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.08.20126003", "rel_title": "Does susceptibility to novel coronavirus (COVID-19) infection differ by age?: Insights from mathematical modelling", @@ -1396150,53 +1398831,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.08.20119636", - "rel_title": "No Evidence for Reduced Hospital Admissions or Increased Deaths from Stroke or Heart Attack During COVID-19", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20119636", - "rel_abs": "Articles in the UK press have claimed that hospital admissions for heart attack and stroke have declined during the COVID-19 pandemic. However, data from the West Midlands Ambulance Service have not shown any reduction in call-outs for patients with stroke or ST-Elevation Myocardial Infarction. This study examined data from University Hospital Birmingham NHS Foundation Trust, comparing admissions from week 1 of 2016 to week 17 of 2019, with the same period in 2020, pre- and post-lockdown. The results showed that there was no evidence of a reduction in the overall mean number of admissions of patients with these conditions in the post-lockdown period.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Katharine Reeves", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Samuel I Watson", - "author_inst": "University of Warwick" - }, - { - "author_name": "Tanya Pankhurst", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "University of Leicester" - }, - { - "author_name": "Suzy Gallier", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Magdalena Skrybant", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Peter J Chilton", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Richard J Lilford", - "author_inst": "University of Birmingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.08.20122143", "rel_title": "Hydroxychloroquine inhibits trained immunity - implications for COVID-19", @@ -1396432,6 +1399066,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.06.07.20124693", + "rel_title": "Changing patterns of mortality during the COVID-19 pandemic: population-based modelling to understand palliative care implications", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20124693", + "rel_abs": "BackgroundCOVID-19 has directly and indirectly caused high mortality worldwide.\n\nAimTo explore patterns of mortality during the COVID-19 pandemic and implications for palliative care provision, planning, and research.\n\nDesignDescriptive analysis and population-based modelling of routine data.\n\nParticipants and settingAll deaths registered in England and Wales between 7th March and 15th May 2020. We described the following mortality categories by age, gender and place of death: 1) baseline deaths (deaths that would typically occur in a given period) 2) COVID-19 deaths 3) additional deaths not directly attributed to COVID-19. We estimated the proportion of COVID-19 deaths among people who would be in their last year of life in the absence of the pandemic, using simple modelling with explicit assumptions.\n\nResultsDuring the first 10 weeks of the pandemic there were 101,615 baseline deaths, 41,105 COVID-19 deaths and 14,520 additional deaths. Deaths in care homes increased by 220% compared to home and hospital deaths which increased by 77% and 90%. Hospice deaths fell by 20%. Additional deaths were among older people (86% aged [≥]75 years), and most occurred in care homes (56%) and at home (43%). We estimate that 44% (38% to 50%) of COVID-19 deaths occurred among people who would have been in their last year of life in the absence of the pandemic.\n\nConclusionsHealthcare systems must ensure availability of palliative care to support people with severe COVID-19 in community and hospital settings. Integrated models of palliative care in care homes are urgently needed.\n\nKey statementsO_ST_ABSWhat is already known about the topic?C_ST_ABSO_LIThe COVID-19 pandemic has directly and indirectly resulted in high mortality in many affected nations.\nC_LIO_LIInternationally the response has been focused on prevention and curative treatments, with little emphasis on palliative care needs of people dying during the COVID-19 pandemic.\nC_LIO_LIWe do not know how many of those dying with COVID-19 would have been in their last year of life in the absence of the pandemic, and this group may have distinct care needs.\nC_LI\n\nWhat this paper addsO_LIThe number of people dying in care homes trebled during the first 10 weeks of the COVID-19 pandemic in England and Wales; many of these deaths were additional deaths, that is associated with the COVID-19 pandemic but not directly as a result of COVID-19.\nC_LIO_LIWe estimate almost half of all COVID-19 deaths occurred among people who would have been in their last year of life in the absence of the pandemic.\nC_LI\n\nImplications for practice, theory or policyO_LIHealthcare systems must ensure availability of palliative care to support people with severe COVID-19 in community and hospital settings.\nC_LIO_LIThe need for integrated models of palliative care in care home settings is imperative and research to underpin these models is warranted.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anna E Bone", + "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London" + }, + { + "author_name": "Anne M Finucane", + "author_inst": "Marie Curie Hospice Edinburgh & University of Edinburgh" + }, + { + "author_name": "Javiera Leniz", + "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London" + }, + { + "author_name": "Irene J Higginson", + "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London" + }, + { + "author_name": "Katherine E Sleeman", + "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "palliative medicine" + }, { "rel_doi": "10.1101/2020.06.08.20125203", "rel_title": "Households at Higher Risk of Losing at Least One Individual in India: if COVID-19 is a new normal", @@ -1397784,49 +1400453,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.05.20123307", - "rel_title": "Reduced ICU demand with early CPAP and proning in COVID-19 at Bradford: a single centre cohort", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123307", - "rel_abs": "BackgroundGuidance in COVID-19 respiratory failure has favoured early intubation, with concerns over the use of CPAP. We adopted early CPAP and self-proning, and evaluated the safety and efficacy of this approach.\n\nMethodsThis retrospective observational study included all patients with a positive COVID-19 PCR, and others with high clinical suspicion. Our protocol advised early CPAP and self-proning for severe cases, aiming to prevent rather than respond to deterioration. CPAP was provided outside critical care by ward staff supported by physiotherapists and an intensive critical care outreach program. Data were analysed descriptively and compared against a large UK cohort (ISARIC).\n\nResults559 patients admitted before 1/May/20 were included. 376 were discharged alive, and 183 died. 165 patients (29.5%) received CPAP, 40 (7.2%) were admitted to critical care and 28 (5.0%) were ventilated. Hospital mortality was 32.7%, and 50% for critical care. Following CPAP, 62% of patients with S:F or P:F ratios indicating moderate or severe ARDS, who were candidates for escalation, avoided intubation. Figures for critical care admission, intubation and hospital mortality are lower than ISARIC, whilst critical care mortality is similar. Following ISARIC proportions we would have admitted 92 patients to critical care and intubated 55. Using the described protocol, we intubated 28 patients from 40 admissions, and remained within our expanded critical care capacity.\n\nConclusionBradfords protocol produced good results despite our population having high levels of co-morbidity and ethnicities associated with poor outcomes. In particular we avoided overloading critical care capacity. We advocate this approach as both effective and safe.\n\nSocial media summaryThe use of early CPAP and proning in COVID-19 was associated with lower critical care admissions, intubation, and mortality at Bradford compared to a large UK cohort (ISARIC WHO CCP-UK).", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tom Lawton", - "author_inst": "Bradford Institute of Health Research & Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Kate M Wilkinson", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Aaron Corp", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Rabeia Javid", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Laura MacNally", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Michael McCooe", - "author_inst": "Bradford Institute of Health Research & Bradford Teaching Hospitals NHS Trust" - }, - { - "author_name": "Elizabeth Newton", - "author_inst": "Bradford Teaching Hospitals NHS Trust" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.06.07.20124933", "rel_title": "Who dies from COVID-19? Post-hoc explanations of mortality prediction models using coalitional game theory, surrogate trees, and partial dependence plots", @@ -1398010,6 +1400636,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.06.08.20125518", + "rel_title": "Indian Publications on SARS-CoV-2: A Bibliometric Study of WHO COVID-19 Database", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125518", + "rel_abs": "Nowadays, the whole World is under threat of Coronavirus disease (COVID-19). The ongoing COVID-19 pandemic has resulted in many fatalities and forced scientific communities to foster their Research and Development (R & D) activities. As a result, there is an enormous growth of scholarly literature on the subject. In order to combat this novel coronavirus, the open access to scientific literature is essential. On this line, many reputed academic institutions and publication firms have made their literature on COVID-19 accessible to all. By maintaining the database of updated information on global literature on Coronavirus disease, the World Health Organization (WHO) is playing a pivotal role. The present study analyzed 89 Indian publications on SARS-CoV-2 accessible through WHO COVID-19 database. The research data was restricted for the period of 2/3/2020 to 12/5/2020. The analysis was carried out in light of the objectives of the study. The study found the considerable and constant growth of Indian publications on COVID-19 from mid-April. It is interesting to note that the prolific authors belong to either AIIMS or ICMR institutes. Majority of the COVID-19 articles were found to be collaborative publications. The study noticed that no research publications on COVID-19 have appeared from North Eastern region. Regarding the research output on COVID-19, the performance of largest states like Uttar Pradesh, Madhya Pradesh and Bihar was found to be poor. Delhi state contributed highest publications on COVID-19. The All India Institute of Medical Sciences (AIIMS), New Delhi was the most productive institution in terms of publications. It is also important to note that the central government undertakings like AIIMS and ICMR, New Delhi and its affiliated institutions shared largest proportion of publications on COVID-19. The Indian Journal of Medical Research has emerged as the productive journal contributing highest number of the publications. The highest contribution in COVID-19 research takes the form of journal articles. In terms of research area, the majority of the publications were related to Epidemiology. The study reported covid, coronavirus, India, pandemic, sars etc. as the frequently occurred keywords in the COVID-19 publications. The highly cited publications were of evidenced based studies. It is observed that the studies pertaining to virology, diagnosis and treatment, clinical features etc. have received highest citations than general studies on epidemiology or pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "N Vasantha Raju", + "author_inst": "Government First Grade College, Talakadu" + }, + { + "author_name": "S.B. Patil", + "author_inst": "Department of Library & Information Science, Shivaji University, Kolhapur, Maharashtra" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.09.20126110", "rel_title": "More than privacy: Australians' concerns and misconceptions about the COVIDSafe App: a short report", @@ -1399166,53 +1401815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.07.20124594", - "rel_title": "Early Detection of Coronavirus Cases Using Chest X-ray Images Employing Machine Learning and Deep Learning Approaches", - "rel_date": "2020-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20124594", - "rel_abs": "This study aims to propose a deep learning model to detect COVID-19 positive cases more precisely utilizing chest X-ray images. We have collected and merged all the publicly available chest X-ray datasets of COVID-19 infected patients from Kaggle and Github, and pre-processed it using random sampling approach. Then, we proposed and applied an enhanced convolutional neural network (CNN) model to this dataset and obtained a 94.03% accuracy, 95.52% AUC and 94.03% f-measure for detecting COVID-19 positive patients. We have also performed a comparative performance between our proposed CNN model with several state-of-the-art machine learning classifiers including support vector machine, random forest, k-nearest neighbor, logistic regression, gaussian naive bayes, bernoulli naive bayes, decision tree, Xgboost, multilayer perceptron, nearest centroid and perceptron as well as deep learning and pre-trained models such as deep neural network, residual neural network, visual geometry group network 16, and inception network V3 were employed, where our model yielded outperforming results compared to all other models. While evaluating the performance of our models, we have emphasized on specificity along with accuracy to identify non-COVID-19 individuals more accurately, which may potentially facilitate the early detection of COVID-19 patients for their preliminary screening, especially in under-resourced health infrastructure with insufficient PCR testing systems and testing facilities. Moreover, this model could also be applicable to the cases of other lung infections.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Md. Shahriare Satu", - "author_inst": "Noakhali Science and Technology University Faculty of Business Administration" - }, - { - "author_name": "Khair Ahammed", - "author_inst": "Noakhali Science and Technology University" - }, - { - "author_name": "Mohammad Zoynul Abedin", - "author_inst": "Dailian Maritime University" - }, - { - "author_name": "Md. Auhidur Rahaman", - "author_inst": "Noakhali Science and Technology University" - }, - { - "author_name": "Shiekh Mohammed Shariful Islam", - "author_inst": "Deakin University" - }, - { - "author_name": "AKM Azad", - "author_inst": "University of Technology Sydney" - }, - { - "author_name": "Salem A. Alyami", - "author_inst": "Department of Mathematics and Statistics, Imam Mohammad Ibn Saud Islamic University, Saudi Arabia" - }, - { - "author_name": "Mohammad Ali Moni", - "author_inst": "University of New south Wales" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.06.20124123", "rel_title": "Clinical evaluation of self-collected saliva by RT-qPCR, direct RT-qPCR, RT-LAMP, and a rapid antigen test to diagnose COVID-19", @@ -1399488,6 +1402090,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.05.20123646", + "rel_title": "A scaling approach to estimate the COVID-19 infection fatality ratio from incomplete data", + "rel_date": "2020-06-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123646", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWSARS-CoV-2 has disrupted the life of billions of people around the world since the first outbreak was officially declared in China at the beginning of 2020. Yet, important questions such as how deadly it is or its degree of spread within different countries remain unanswered. In this work, we exploit the universal growth of the mortality rate with age observed in different countries since the beginning of their respective outbreaks, combined with the results of the antibody prevalence tests in the population of Spain, to unveil both unknowns. We validate these results with an analogous antibody rate survey in the canton of Geneva, Switzerland. We also argue that the official number of deaths over 70 years old is importantly underestimated in most of the countries, and we use the comparison between the official records with the number of deaths mentioning COVID-19 in the death certificates to quantify by how much. Using this information, we estimate the fatality infection ratio (IFR) for the different age segments and the fraction of the population infected in different countries assuming a uniform exposure to the virus in all age segments. We also give estimations for the non-uniform IFR using the sero-epidemiological results of Spain, showing a very similar growth of the fatality ratio with age. Only for Spain, we estimate the probability (if infected) of being identified as a case, being hospitalized or admitted in the intensive care units as function of age. In general, we observe a nearly exponential growth of the fatality ratio with age, which anticipates large differences in total IFR in countries with different demographic distributions, with numbers that range from 1.82% in Italy, to 0.62% in China or even 0.14% in middle Africa.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Beatriz Seoane", + "author_inst": "Sorbonne University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.06.20124198", "rel_title": "Predictors of Mental Health during the early Covid-19 Pandemic in the US: role of economic concerns, health worries and social distancing", @@ -1400984,49 +1403605,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.05.20123752", - "rel_title": "Changes in non-linear and time-domain heart rate variability indices between critically ill COVID-19 and all-cause sepsis patients -a retrospective study", - "rel_date": "2020-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123752", - "rel_abs": "ObjectiveTo measure heart rate variability metrics in critically ill COVID-19 patients with comparison to all-cause critically ill sepsis patients.\n\nDesign and patientsRetrospective analysis of COVID-19 patients admitted to an ICU for at least 24h at any of Emory Healthcare ICUs between March and April 2020. The comparison group was a cohort of all-cause sepsis patients prior to COVID-19 pandemic.\n\nInterventionsnone.\n\nMeasurementsContinuous waveforms were captured from the patient monitor. The EKG was then analyzed for each patient over a 300 second (s) observational window, that was shifted by 30s in each iteration from admission till discharge. A total of 23 HRV metrics were extracted in each iteration. We use the Kruskal-Wallis and Steel-Dwass tests (p < 0.05) for statistical analysis and interpretations of HRV multiple measures.\n\nResultsA total of 141 critically-ill COVID-19 patients met inclusion criteria, who were compared to 208 patients with all-cause sepsis. Demographic parameters were similar apart from a high proportion of African-Americans in the COVID-19 cohort. Three non-linear markers, including SD1:SD2, sample entropy, approximate entropy and four linear features mode of Beat-to-Beat interval (NN), Acceleration Capacity (AC), Deceleration Capacity (DC), and pNN50, were statistical significance between more than one binary combinations of the sub-groups (comparing survivors and non-survivors in both the COVID-19 and sepsis cohorts). The three nonlinear features and AC, DC, and NN (mode) were statistically significant across all four combinations. Temporal analysis of the main markers showed low variability across the 5 days of analysis, compared with sepsis patients.\n\nConclusionsHeart rate variability is broadly implicated across patients infected with SARSCoV-2, and admitted to the ICU for critical illness. Comparing these metrics to patients with all-cause sepsis suggests a unique set of expressions that differentiate this viral phenotype. This finding could be investigated further as a potential biomarker to predict poor outcome in this patient population, and could also be a starting point to measure potential autonomic dysfunction in COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rishikesan Kamaleswaran", - "author_inst": "Emory University" - }, - { - "author_name": "Ofer Sadan", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Prem Kandiah", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Qiao Li", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "James M Blum", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Craig M Coopersmith", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Timothy G Buchman", - "author_inst": "Emory University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.06.05.20122903", "rel_title": "Impact of Governmental interventions on epidemic progression and workplace activity during the COVID-19 outbreak", @@ -1401178,6 +1403756,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.06.05.20123042", + "rel_title": "THE ERA OF CORONAVIRUS; KNOWLEDGE, ATTITUDE, PRACTICES, AND BARRIERS TO HAND HYGIENE AMONG MAKERERE UNIVERSITY STUDENTS AND KATANGA COMMUNITY RESIDENTS.", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123042", + "rel_abs": "BackgroundChina reported the Novel Coronavirus at the end of the year 2019 which was, later on, declared a Pandemic by the WHO. Proper hand hygiene was identified as one of the simplest most cost-effective Covid-19 control and prevention measures. It is therefore very important to understand the compliance of the community to hand hygiene.\n\nMethodA descriptive cross-sectional study was conducted among the undergraduate students of Makerere University and residents of Katanga slum from 17th to 22nd of March, 2020. An interviewer guided questionnaire with questions on knowledge, attitude, practice, and barriers to hand hygiene was used in data collection. The collected data was analyzed using Microsoft office excel 2016 and STATA 15 software. A 95% confidence interval was used and statistical significance was P<0.05.\n\nResultsOnly 8.4% of the participants had good knowledge of hand hygiene. 11.7% of the university students had good knowledge compared to 0.9% of the Katanga residents. 29.0% of the participants had a good attitude while 50.1% had a moderate attitude to hand hygiene. University students were 6.3 times (OR: 6.3, 95%C1: (2.1 - 18.5), P=0.001) more likely to have good knowledge while Katanga residents were 3.6 times (OR: 3.6, 95%C1: (1.5 - 8.4), P=0.003) more likely to have good attitude to hand hygiene. Only 19.6% accomplished all the seven steps of handwashing. 38.4% of the participants still greeted by handshaking and 60.1% noted lack of soap as a barrier to hand hygiene and 62.9% reported having more than three barriers to hand hygiene. Participants that had been taught handwashing were more likely to have better hand hygiene knowledge and practice.\n\nConclusionDespite a fair attitude, deficiency of knowledge coupled with many barriers such as Lack of soap hindered the Practice of proper hand hygiene. Public health involvement to promote hand hygiene must be promoted.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Julius Nuwagaba", + "author_inst": "Makerere University College of Health Sciences; School of Medicine" + }, + { + "author_name": "Dave Darsit Ashok", + "author_inst": "Makerere University College of Health Sciences; School of Medicine" + }, + { + "author_name": "Thomas Balizzakiwa", + "author_inst": "Makerere University College of Health Sciences; School of Medicine" + }, + { + "author_name": "Ibrahim Kisengula", + "author_inst": "Makerere University College of Health Sciences; School of Medicine" + }, + { + "author_name": "Edna Joyce Nagaddya", + "author_inst": "Makerere University College of Health Sciences; School of Medicine" + }, + { + "author_name": "Meddy Rutayisire", + "author_inst": "Makerere University College of Health Sciences; School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.04.20122747", "rel_title": "First environmental surveillance for the presence of SARS-CoV-2 RNA in wastewater and river water in Japan", @@ -1402294,89 +1404911,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.05.137349", - "rel_title": "Synthetic Antibodies neutralize SARS-CoV-2 infection of mammalian cells", - "rel_date": "2020-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.05.137349", - "rel_abs": "Coronaviruses (CoV) are a large family of enveloped, RNA viruses that circulate in mammals and birds. Three highly pathogenic strains have caused zoonotic infections in humans that result in severe respiratory syndromes including the Middle East Respiratory Syndrome CoV (MERS), Severe Acute Respiratory Syndrome CoV (SARS), and the ongoing Coronavirus Disease 2019 (COVID-19) pandemic. Here, we describe a panel of synthetic monoclonal antibodies, built on a human IgG framework, that bind to the spike protein of SARS-CoV-2 (the causative agent of COVID-19), compete for ACE2 binding, and potently inhibit SARS-CoV-2. All antibodies that exhibited neutralization potencies at sub-nanomolar concentrations against SARS-CoV-2/USA/WA1 in Vero E6 cells, also bound to the receptor binding domain (RBD), suggesting competition for the host receptor ACE2. These antibodies represent strong immunotherapeutic candidates for treatment of COVID-19.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Shane Miersch", - "author_inst": "University of Toronto" - }, - { - "author_name": "Mart Ustav", - "author_inst": "University of Toronto" - }, - { - "author_name": "Zhijie Li", - "author_inst": "University of Toronto" - }, - { - "author_name": "James B. Case", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Safder Ganaie", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Giulia Matusali", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Francesca Colavita", - "author_inst": "National Institute for Infectious Diseases \"L. Spallanzani\" IRCCS" - }, - { - "author_name": "Daniele Lapa", - "author_inst": "National Institute for Infectious Diseases \"L. Spallanzani\" IRCCS" - }, - { - "author_name": "Maria R. Capobianchi", - "author_inst": "National Institute for Infectious Diseases \"L. Spallanzani\" IRCCS" - }, - { - "author_name": "Giuseppe Novelli", - "author_inst": "University of Rome" - }, - { - "author_name": "Jang B. Gupta", - "author_inst": "Intonation Research Laboratories" - }, - { - "author_name": "Suresh Jain", - "author_inst": "Intonation Research Laboratories" - }, - { - "author_name": "Pier Paolo Pandolfi", - "author_inst": "University of Turin" - }, - { - "author_name": "Michael S. Diamond", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Gaya Amarasinghe", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "James M. Rini", - "author_inst": "University of Toronto" - }, - { - "author_name": "Sachdev S. Sidhu", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.06.05.136887", "rel_title": "Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens", @@ -1402604,6 +1405138,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.02.20106310", + "rel_title": "Characteristics and Outcomes of Hospitalized Young Adults with Mild to Moderate Covid-19 at a University Hospital in India", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20106310", + "rel_abs": "BackgroundStormy course has been reported among hospitalized adults with covid-19 in high- and middle-income countries. To assess clinical outcomes in consecutively hospitalized patients with mild covid-19 in India we performed a study.\n\nMethodsWe developed a case registry of successive patients admitted with suspected covid-19 infection to our hospital (n=501). Covid-19 was diagnosed using reverse transcriptase polymerase chain reaction (RT-PCR). Demographic, clinical, investigations details and outcomes were recorded. Descriptive statistics are presented.\n\nResultsCovid-19 was diagnosed in 234 (46.7%) and data compared with 267 (53.3%) negative controls. Mean age of covid-9 patients was 35.1{+/-}16.6y, 59.4% were <40y and 64% men. Symptoms were in less than 10% and comorbidities were in 4-8%. History of BCG vaccination was in 49% cases vs 10% controls. Cases compared to controls had significantly greater white cell (6.96+1.89 vs 6.12+1.69x109 cells/L) and lower lymphocyte count (1.98+0.79 vs 2.32+0.91x109 cells/L). No radiological and electrocardiographic abnormality was observed. All these were isolated or quarantined in the hospital and observed. Covid-19 patients received hydroxychloroquine and azithromycin according to prevalent guidelines. One patient needed oxygen support while hospital course was uncomplicated in the rest. All were discharged alive. Conversion to virus negative status was in 10.2{+/-}6.4 days and was significantly lower in age >40y (9.1{+/-}5.2) compared to 40-59y (11.3{+/-}6.1) and [≥]60y (16.4{+/-}13.3) (p=0.001).\n\nConclusionsThis hospital-based registry shows that mildly symptomatic or asymptomatic young covid-19 patients have excellent prognosis.\n\nO_LSTWhat is already known on this subject?C_LSTO_LIHigh rates of morbidity and mortality following hospitalization for covid-19 has been reported from most developed countries.\nC_LIO_LIIn most developing countries covid-19 patients with mild disease are also hospitalized due to lack of home isolation. Clinical outcome of such patients has not been well studied.\nC_LI\n\nO_LSTWhat this study adds?C_LSTO_LIWe performed a clinical registry of successive young patients with mild covid-19 hospitalized with minimal symptoms and comorbidities.\nC_LIO_LINone of the patients developed complications and all were discharged alive.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Arvind Kumar Sharma", + "author_inst": "RUHS College of Medical Sciences, Rajasthan University of Health Sciences, Jaipur 302033 India" + }, + { + "author_name": "Asrar Ahmed", + "author_inst": "RUHS College of Medical Sciences, Rajasthan University of Medical Sciences, Jaipur 302033 India" + }, + { + "author_name": "Vaseem Naheed Baig", + "author_inst": "RUHS College of Medical Sciences, Rajasthan University of Health Sciences, Jaipur 302033 India" + }, + { + "author_name": "Prahalad Dhakad", + "author_inst": "RUHS College of Medical Sciences, Rajasthan University of Health Sciences, Jaipur 302033 India" + }, + { + "author_name": "Gaurav Dalela", + "author_inst": "RUHS College of Medical Sciences, Rajasthan University of Health Sciences, Jaipur 302033 India" + }, + { + "author_name": "Sudhanshu Kacker", + "author_inst": "RUHS College of Medical Sciences, Rajasthan University of Health Sciences, Jaipur 302033 India" + }, + { + "author_name": "Vasim Raja Panwar", + "author_inst": "Rajasthan Dental College, Bagru, Jaipur 302026 India" + }, + { + "author_name": "Raja Babu Panwar", + "author_inst": "Rajasthan University of Health Sciences, Jaipur 302033 India" + }, + { + "author_name": "Rajeev Gupta", + "author_inst": "Eternal Heart Care Centre & Research Institute, Jaipur 302017 India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.03.20067793", "rel_title": "Augmenting contact matrices with time-use data for fine-grained intervention modelling of disease dynamics: A modelling analysis", @@ -1404116,33 +1406701,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.06.02.20116855", - "rel_title": "The attitudes, perceptions and experiences of medical school applicants following the closure of schools and cancellation of public examinations in 2020 due to the COVID-19 pandemic", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20116855", - "rel_abs": "ObjectiveTo describe medical applicants experiences of education and their views on changes to medical school admissions, including the awarding of calculated grades, following the 2020 closure of schools and universities, and the cancellation of public examinations in the United Kingdom due to the COVID-19/coronavirus pandemic. To understand how applicants from diverse social backgrounds might differ in these regards.\n\nDesignCross-sectional questionnaire study forming part of the longitudinal United Kingdom Medical Applicant Cohort Study (UKMACS).\n\nSettingUnited Kingdom medical school admissions.\n\nParticipants2887 participants (68% female; 64% with at least one degree-educated parent; 63% with at least one parent in the highest socioeconomic group) completed an online questionnaire between 8th and 22nd April 2020. To be invited to complete the questionnaire, participants had to have registered to take the University Clinical Admissions Test (UCAT) in 2019 and to have agreed to be invited to take part in the study, or they needed to have completed one or more previous UKMACS questionnaires. They also need to have been seriously considering applying to study medicine in the UK for entry in 2020 between May and October 2019, and be resident in the UK or Islands/Crown Dependencies.\n\nMain outcome measuresViews on calculated grades, views on potential changes to medical school admissions and teaching in 2020 and 2021, reported experiences of education following the closure of educational institutions in March 2020.\n\nResultsRespondents had concerns about the calculated grades that will replace A-level examinations, especially female applicants and applicants from Black Asian and Minority Ethnic (BAME) backgrounds who felt teachers would find it difficult to grade and rank students accurately, as well as those from non-selective state schools and those living in deprived areas who had some concerns about the grade standardisation process. Calculated grades were not considered fair enough by a majority to use in the acceptance or rejection of medical offer-holders, but several measures - including interview and aptitude test scores - were considered fair enough to use in combination. Respondents from non-selective state (public) schools reported less use of and less access to educational resources compared to their counterparts at private/selective schools. In particular they reported less online teaching in real time, and reported spending less time studying during the lockdown.\n\nConclusionsThe coronavirus pandemic will have significant and long term impacts on the selection, education and performance of our future medical workforce. It is important that the views and experiences of medical applicants from diverse backgrounds are taken into consideration in decisions affecting their futures and the future of the profession.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Katherine Woolf", - "author_inst": "University College London" - }, - { - "author_name": "Dave Harrison", - "author_inst": "University College London" - }, - { - "author_name": "I.C. McManus", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.06.02.20120642", "rel_title": "Estimating excess visual loss in people with neovascular age-related macular degeneration during the COVID-19 pandemic", @@ -1404342,6 +1406900,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.03.20119867", + "rel_title": "The psychological effects of COVID-19 on frontline healthcare workers and how they are coping: a web-based, cross-sectional study from Pakistan", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20119867", + "rel_abs": "BackgroundHigh level stress is expected when crises starts affecting peoples lives and communities which is witnessed in the past epidemics. Infectious diseases outbreaks like the ongoing COVID19 pandemic have negative impact on healthcare workers (HCWs) mental health, which needs to be investigated. Therefore, we aimed to assess the psychological impact of COVID-19 on frontline HCWs and their coping strategies.\n\nMethodsA web-based, cross-sectional study was conducted among HCWs of the Punjab province of Pakistan. The generalized anxiety scale (GAD-7), patient health questionnaire (PHQ-9) and Brief-COPE were used to assess anxiety, depression and coping strategies.\n\nResultsThe mean age of respondents (N = 398) was 28.67 {+/-} 4.15 years, with majority of medical doctors (52%). The prevalence of anxiety and depression were 21.4% and 21.9%, respectively. There was no significant difference of anxiety and depression scores among doctors, nurses and pharmacists. Females had significantly higher anxiety (p = 0.003) and depression (p = 0.001) scores than males. Moreover, HCWs performing duties in COVID-19 ICU had significantly higher anxiety score than those from isolation wards (p = 0.020) and other departments (p = 0.014). Depression, not anxiety, score were higher among those who did not receive the infection prevention training. Most frequently adopted coping strategy was religious coping (5.98 {+/-} 1.73) followed by acceptance (5.59 {+/-} 1.55) and coping planning (4.91 {+/-} 1.85).\n\nConclusionA considerable proportion of HCWs are having generalized anxiety and depression during the ongoing COVID-19 pandemic. Our findings call for interventions to mitigate mental health risks in HCWs.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Muhammad Salman", + "author_inst": "The University of Lahore" + }, + { + "author_name": "Muhammad Hussnain Raza", + "author_inst": "Faisalabad Institute of Cardiology" + }, + { + "author_name": "Zia Ul Mustafa", + "author_inst": "District Headquarter Hospital Pakpattan" + }, + { + "author_name": "Tahir Mehmood Khan", + "author_inst": "University of Veterinary and Animal Sciences" + }, + { + "author_name": "Noman Asif", + "author_inst": "University of the Punjab" + }, + { + "author_name": "Humera Tahir", + "author_inst": "Lahore Medical and Dental College" + }, + { + "author_name": "Naureen Shehzadi", + "author_inst": "University of the Punjab" + }, + { + "author_name": "Khalid Hussain", + "author_inst": "University of the Punjab" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.02.20117739", "rel_title": "iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2", @@ -1405558,69 +1408163,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.03.20121392", - "rel_title": "Modulation of COVID-19 Epidemiology by UV-B and -A Photons from the Sun", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121392", - "rel_abs": "Solar UV-C photons do not reach Earths surface, but are known to be endowed with germicidal properties that are also effective on viruses. The effect of softer UV-B and UV-A photons, which copiously reach the Earths surface, on viruses are instead little studied, particularly on single-stranded RNA viruses.\n\nHere we combine our measurements of the action spectrum of Covid-19 in response to UV light, Solar irradiation measurements on Earth during the SARS-CoV-2 pandemics, worldwide recorded Covid-19 mortality data and our \"Solar-Pump\" diffusive model of epidemics to show that (a) UV-B/A photons have a powerful virucidal effect on the single-stranded RNA virus Covid-19 and that (b) the Solar radiation that reaches temperate regions of the Earth at noon during summers, is sufficient to inactivate 63% of virions in open-space concentrations (1.5x103 TCID50/mL, higher than typical aerosol) in less than 2 minutes.\n\nWe conclude that the characteristic seasonality imprint displayed world-wide by the SARS-Cov-2 mortality time-series throughout the diffusion of the outbreak (with temperate regions showing clear seasonal trends and equatorial regions suffering, on average, a systematically lower mortality), might have been efficiently set by the different intensity of UV-B/A Solar radiation hitting different Earths locations at different times of the year.\n\nOur results suggest that Solar UV-B/A play an important role in planning strategies of confinement of the epidemics, which should be worked out and set up during spring/summer months and fully implemented during low-solar-irradiation periods.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Fabrizio Nicastro", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Giorgia Sironi", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Elio Antonello", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Andrea Bianco", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Mara Biasin", - "author_inst": "Department of Biomedical and Clinical Sciences L. Sacco, University of Milano, Milano, Italy" - }, - { - "author_name": "John R Brucato", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Ilaria Ermolli", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Giovanni Pareschi", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Marta Salvati", - "author_inst": "ARPA Lombardia" - }, - { - "author_name": "Paolo Tozzi", - "author_inst": "INAF - Italian National Institute for Astrophysics" - }, - { - "author_name": "Daria Trabattoni", - "author_inst": "Department of Biomedical and Clinical Sciences L. Sacco, University of Milano, Milano, Italy" - }, - { - "author_name": "Mario Clerici", - "author_inst": "Department of Pathophysiology and Transplantation, University of Milano and Don C. Gnocchi Foundation, IRCCS, Milano, Italy" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.03.20121442", "rel_title": "Reduction in preterm births during the COVID-19 lockdown in Ireland: a natural experiment allowing analysis of data from the prior two decades.", @@ -1406068,6 +1408610,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.06.04.20122069", + "rel_title": "Mechanical ventilation utilization in COVID-19: A systematic review and meta-analysis", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122069", + "rel_abs": "BackgroundIn December 2019, SARS-CoV-2 caused a global pandemic with a viral infection called COVID-19. The disease usually causes respiratory symptoms but in a small proportion of patients can lead to a pneumonitis, Adult Respiratory Distress Syndrome and death. Invasive Mechanical Ventilation (IMV) is considered a life-saving treatment for COVID-19 patients and a huge demand for IMV devices was reported globally. This review aims to provide insight on the initial IMV practises for COVID-19 patients in the initial phase of the pandemic.\n\nMethodsElectronic databases (Embase and MEDLINE) were searched for applicable articles using relevant keywords. The references of included articles were hand searched. Articles that reported the use of IMV in adult COVID-19 patients were included in the review. The NIH quality assessment tool for cohort and cross-sectional studies was used to appraise studies.\n\nResults106 abstracts were identified from the databases search, of which 16 were included. 5 studies were included in the meta-analysis. In total, 9988 patients were included across all studies. The overall cases of COVID-19 requiring IMV ranged from 2-77%. Increased age and pre-existing comorbidities increased the likelihood of IMV requirement. The reported mortality rate in patients receiving IMV ranged between 50-100%. On average, IMV was required and initiated between 10-10.5 days from symptoms onset. When invasively ventilated, COVID-19 patients required IMV for a median of 10-17 days across studies. Little information was provided on ventilatory protocols or management strategies and were inconclusive.\n\nConclusionIn these initial reporting studies for the first month of the pandemic, patients receiving IMV were older and had more pre-existing co-morbidities than those who did not require IMV. The mortality rate was high in COVID-19 patients who received IMV. Studies are needed to evaluate protocols and modalities of IMV to improve outcomes and identify the populations most likely to benefit from IMV.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mohammed A Almeshari", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Nowaf Y Alobaidi", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Mansour Al Asmri", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Eyas Alhuthail", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Ziyad Alshehri", + "author_inst": "Taibah University" + }, + { + "author_name": "Farhan Alenezi", + "author_inst": "King Saud bin Abdulaziz University for Health Sciences" + }, + { + "author_name": "Elizabeth Sapey", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Dhruv Parekh", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.06.05.20113738", "rel_title": "Tocilizumab is associated with reduction of the risk of ICU admission and mortality in patients with SARS-CoV-2 infection", @@ -1407611,61 +1410200,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.04.20122044", - "rel_title": "ACE2 levels are altered in comorbidities linked to severe outcome in COVID-19", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122044", - "rel_abs": "AimsSeverity of outcome in COVID-19 is disproportionately higher among the obese, males, smokers, those suffering from hypertension, kidney disease, coronary heart disease (CHD) and/or type 2 diabetes (T2D). We examined if serum levels of ACE2, the cellular entry point for the coronavirus SARS-CoV-2, were altered in these high-risk groups.\n\nMethodsAssociations of serum ACE2 levels to hypertension, T2D, obesity, CHD, smokers and males in a single center population-based study of 5457 Icelanders from the Age, Gene/Environment Susceptibility Reykjavik Study (AGES-RS) of the elderly (mean age 75{+/-}6 years).\n\nResultsSmokers, males, and individuals with T2D or obesity have altered serum levels of ACE2 that may influence productive infection of SARS-CoV-2 in these high-risk groups.\n\nConclusionACE2 levels are upregulated in some patient groups with comorbidities linked to COVID-19 and as such may have an emerging role as outcome in COVID-19. a circulating biomarker for severity of severity of outcome in COVID-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSSeverity of outcome in COVID-19 is disproportionately higher among the obese, males, smokers, those suffering from hypertension, kidney disease, coronary heart disease (CHD) and/or type 2 diabetes (T2D). Thus, we asked if the coronavirus SARS-CoV-2 receptor ACE2 was altered in the sera from these high-risk groups?\n\nFindingsIn a single center population-based study of 5457 Icelanders, the Age, Gene/Environment Susceptibility Reykjavik Study (AGES-RS), we find that ACE2 levels are significantly elevated in serum from smokers, obese and diabetic individuals, while reduced in males.\n\nMeaningThese results demonstrate that individuals with comorbidities associated with infection of SARS-CoV-2 in these individuals. severe outcome in COVID-19 have altered serum levels of ACE2 that may influence productive", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Valur Emilsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Elias F Gudmundsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Thor Aspelund", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Brynjolfur G Jonsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Alexander Gudjonsson", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Lenore J Launer", - "author_inst": "Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Bethesda, MD 20892-9205, USA" - }, - { - "author_name": "John R Lamb", - "author_inst": "GNF Novartis, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA" - }, - { - "author_name": "Valborg Gudmundsdottir", - "author_inst": "Icelandic Heart Association" - }, - { - "author_name": "Lori L Jennings", - "author_inst": "Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge, MA 02139, USA" - }, - { - "author_name": "Vilmundur Gudnason", - "author_inst": "Icelandic Heart Association" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.06.04.20122176", "rel_title": "What variables can better predict the number of infections and deaths worldwide by SARS-CoV-2? Variation through time", @@ -1407833,6 +1410367,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.04.20122267", + "rel_title": "Anemia and iron metabolism in COVID-19: A systematic review and meta-analysis", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122267", + "rel_abs": "Iron metabolism and anemia may play an important role in multiple organ dysfunction syndrome in Coronavirus disease 2019 (COVID-19). If confirmed, this has important implications for the more than 1.62 billion people estimated to have anemia globally. We conducted a systematic review and meta-analysis to evaluate biomarkers of anemia and iron metabolism (hemoglobin, ferritin, transferrin, soluble transferrin receptor, hepcidin, haptoglobin, unsaturated iron-binding capacity, erythropoietin, free erythrocyte protoporphyrine, and prevalence of anemia) in patients diagnosed with COVID-19, and explore their prognostic value. Six bibliographic databases were searched up to May 5th 2020. We included 56 unique studies, with data from 14,044 COVID-19 patients (59 years median age). Pooled mean hemoglobin and ferritin levels in COVID-19 patients across all ages were 130.41 g/L (95% Confidence Interval (CI), 128.42; 132.39) and 673.91 ng/mL (95% CI, 420.98; 926.84), respectively. Hemoglobin levels decreased with advancing age and increasing percentage of comorbid and critically ill patients, while levels of ferritin increased with increasing male proportion and mean hemoglobin levels. Compared to moderate cases, severe cases had lower pooled mean hemoglobin [weighted mean difference (WMD), -4.21 (95% CI -6.63; -1.78)] and higher ferritin [WMD, -730.55 ng/mL (95% CI 413.24; 1047.85)]. A significant difference in mean ferritin level of 1027.23 ng/mL (95% CI 819.53; 1234.94) was found between survivors and non-survivors, but not in hemoglobin levels. No studies provided information on anemia or other biomarkers of interest. Future studies should explore the impact of iron metabolism and anemia and in the pathophysiology, prognosis, and treatment of COVID-19.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Petek Eylul Taneri", + "author_inst": "Bahcesehir University Faculty of Medicine" + }, + { + "author_name": "Sergio Alejandro Gomez-Ochoa", + "author_inst": "Cardiovascular Foundation of Colombia" + }, + { + "author_name": "Erand Llanaj", + "author_inst": "University of Debrecen Public Health Research Institute" + }, + { + "author_name": "Peter Francis Raguindin", + "author_inst": "University of Bern Institute of Social and Preventive Medicine" + }, + { + "author_name": "Lydia Z. Rojas", + "author_inst": "Cardiovascular Foundation of Colombia" + }, + { + "author_name": "Beatrice Minder Wyssmann", + "author_inst": "University Library of Bern Public Health & Primary Care Library" + }, + { + "author_name": "Doris Kopp-Heim", + "author_inst": "University Library of Bern Public Health & Primary Care Library" + }, + { + "author_name": "Wolf E. Hautz", + "author_inst": "Bern University Hospital Department of Emergency Medicine" + }, + { + "author_name": "Michele F. Eisenga", + "author_inst": "University of Groningen Department of Internal Medicine" + }, + { + "author_name": "Oscar H. Franco", + "author_inst": "University of Bern Institute of Social and Preventive Medicine" + }, + { + "author_name": "Marija Glisic", + "author_inst": "University of Bern Institute of Social and Preventive Medicine" + }, + { + "author_name": "Taulant Muka", + "author_inst": "University of Bern Institute of Social and Preventive Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.04.20122580", "rel_title": "Covid-19: analysis of a modified SEIR model, a comparison of different intervention strategies and projections for India", @@ -1409141,73 +1411738,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.02.20120808", - "rel_title": "The Relationship Between COVID-19 Infection and Risk Perception, Knowledge, Attitude As Well As Four Non-pharmaceutical Interventions (NPIs) During the Late Period Of The COVID-19 Epidemic In China An Online Cross-sectional Survey of 8158 Adults", - "rel_date": "2020-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120808", - "rel_abs": "BackgroundSo far, there has been no published population study on the relationship between COVID-19 infection and publics risk perception, information source, knowledge, attitude and four non-pharmaceutical interventions(NPI: hand washing, proper coughing habits, social distancing and mask wearing) during the COVID-19 outbreak in China.\n\nMethodsAn online survey of 8158 Chinese adults between 22 February to 5 March 2020 was conducted. Bivariate associations between categorical variables were examined using Fisher exact test. We also explored the determinants of four NPIs as well as their association with COVID-19 infection using logistic regression.\n\nResultsOf 8158 adults included, 57 (0.73%) were infected with COVID-19. The overwhelming majority of respondents showed a positive attitude (99.2%), positive risk perception (99.9%) and high knowledge levels that were among the strongest predictors of four highly adopted NPIs (hand washing:96.8%; proper coughing: 93.1%; social distancing:87.1%; mask wearing:97.9%). There was an increased risk of COVID-19 infection for those who not washing hands (2.28% vs 0.65%; RR=3.53: 95%CI: 1.53-8.15; P<0.009); not practicing proper coughing (1.79% vs 0.73%; RR=2.44: 95%CI: 1.15-5.15;P=0.026); not practicing social distancing (1.52% vs 0.58%; RR=2.63:95%CI:1.48 - 4.67; P=0.002); and not wearing a mask (7.41% vs 0.6%; RR=12.38:95%CI:5.81-26.36; P<0.001). For those who did practice all other three NPIs, wearing mask was associated with significantly reduced risk of infection compared to those who did not wear a mask (0.6% vs 16.7%; p=0.035). Similarly, for those who did not practice all or part of the other three NPIs, wearing mask was also associated with significantly reduced risk of infection. In a penalised logistic regression model including all four NPIs, wearing a mask was the only significant predictor of COVID-19 infection among four NPIs (OR=7.20; 95%CI:2.24-23.11; p<0.001).\n\nConclusionsWe found high levels of risk perception, positive attitude, desirable knowledge as well as a high level of adopting four NPIs. The relevant knowledge, risk perception and attitude were strong predictors of adapting the four NPIs. Mask wearing, among four personal NPIs, was the most effective protective measure against COVID-19 infection with added preventive effect among those who practised all or part of the other three NPIs.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Hong Xu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Yong Gan", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Daikun Zheng", - "author_inst": "Chongqing Three Gorges Medical College, Chongqing, China" - }, - { - "author_name": "Bo Wu", - "author_inst": "Wanzhou District Center for Disease Control and Prevention, Chongqing, China" - }, - { - "author_name": "Xian Zhu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Chang Xu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Chenglu Liu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Zhou Tao", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Yaoyue Hu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Min Chen", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Mingjiang Li", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Zuxun Lu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" - }, - { - "author_name": "Jack Chen", - "author_inst": "University of New South Wales" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.06.02.20120014", "rel_title": "Viral load dynamics in transmissible symptomatic patients with COVID-19", @@ -1409607,6 +1412137,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.03.20120881", + "rel_title": "A prediction model based on machine learning for diagnosing the early COVID-19 patients", + "rel_date": "2020-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20120881", + "rel_abs": "With the dramatically fast spread of COVID-9, real-time reverse transcription polymerase chain reaction (RT-PCR) test has become the gold standard method for confirmation of COVID-19 infection. However, RT-PCR tests are complicated in operation andIt usually takes 5-6 hours or even longer to get the result. Additionally, due to the low virus loads in early COVID-19 patients, RT-PCR tests display false negative results in a number of cases. Analyzing complex medical datasets based on machine learning provides health care workers excellent opportunities for developing a simple and efficient COVID-19 diagnostic system. This paper aims at extracting risk factors from clinical data of early COVID-19 infected patients and utilizing four types of traditional machine learning approaches including logistic regression(LR), support vector machine(SVM), decision tree(DT), random forest(RF) and a deep learning-based method for diagnosis of early COVID-19. The results show that the LR predictive model presents a higher specificity rate of 0.95, an area under the receiver operating curve (AUC) of 0.971 and an improved sensitivity rate of 0.82, which makes it optimal for the screening of early COVID-19 infection. We also perform the verification for generality of the best model (LR predictive model) among Zhejiang population, and analyze the contribution of the factors to the predictive models. Our manuscript describes and highlights the ability of machine learning methods for improving the accuracy and timeliness of early COVID-19 infection diagnosis. The higher AUC of our LR-base predictive model makes it a more conducive method for assisting COVID-19 diagnosis. The optimal model has been encapsulated as a mobile application (APP) and implemented in some hospitals in Zhejiang Province.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sun Nan Nan", + "author_inst": "Hangzhou Wowjoy Information Technology Co., Ltd, Hangzhou, China" + }, + { + "author_name": "Yang Ya", + "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Cen" + }, + { + "author_name": "Tang Ling Ling", + "author_inst": "Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China" + }, + { + "author_name": "Dai Yi Ning", + "author_inst": "Department of Infectious Diseases,Zhejiang Provincial People's Hospital, Hangzhou, China" + }, + { + "author_name": "Gao Hai Nv", + "author_inst": "Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China" + }, + { + "author_name": "Pan Hong Ying", + "author_inst": "Department of Infectious Diseases, Zhejiang Provincial People's Hospital, Hangzhou, China" + }, + { + "author_name": "Ju Bin", + "author_inst": "Hangzhou Wowjoy Information Technology Co., Ltd, Hangzhou, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.03.20121004", "rel_title": "Exposure to cough aerosols and development of pulmonary COVID-19", @@ -1410543,25 +1413116,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.31.20118760", - "rel_title": "Model Based Covid-19 Case Studies in the UK, the USA and India", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118760", - "rel_abs": "Time dependent spread of Covid-19 among the population of the UK, the USA and India is analyzed using a recently developed mathematical model [1-3]. Results of model predictions of case growth in these countries during the next six weeks are also presented. The model is applicable to case studies and near term predictions for other countries and regions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Santanu Basu", - "author_inst": "Sparkle Optics Corporation" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.31.20118455", "rel_title": "Hospital readmissions of discharged patients with COVID-19", @@ -1410853,6 +1413407,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.30.20117556", + "rel_title": "SIR-PID: A Proportional-Integral-Derivative Controller for COVID-19 Outbreak Containment", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117556", + "rel_abs": "Ongoing social restrictions, as distancing and lockdown, adopted by many countries for contrasting the COVID-19 epidemic spread, try to find a trade-off between induced economic crisis, healthcare system collapse and costs in terms of human lives. Applying and removing restrictions on a system with uncontrollable inertia, as represented by an epidemic outbreak, may create critical instabilities, overshoots and strong oscillations of infected people around the desirable set-point, defined as the maximum number of hospitalizations acceptable by a given healthcare system. A good understanding of the system reaction to a change of the input control variable can be reasonably achieved using a proportional-integral-derivative controller, widely used in technological applications. In this paper we make use of this basic control theory for understanding the reaction of COVID-19 propagation to social restrictions and for exploiting a very known technology to reduce the epidemic damages through the correct tuning of the containment policy.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Nicola Rossi", + "author_inst": "Istituto Nazionale di Fisica Nucleare" + }, + { + "author_name": "Aldo Ianni", + "author_inst": "Istituto Nazionale di Fisica Nucleare" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.31.20118745", "rel_title": "COVID-19 trend in Bangladesh: deviation from epidemiological model and critical analysis of the possible factors", @@ -1411869,49 +1414446,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.30.20117283", - "rel_title": "Spreading of COVID-19 in Brazil: Impacts and uncertainties in social distancing strategies", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117283", - "rel_abs": "Brazils continental dimension poses a challenge to the control of the spread of COVID-19. Due to the country specific scenario of high social and demographic heterogeneity, combined with limited testing capacity, lack of reliable data, under-reporting of cases, and restricted testing policy, the focus of this study is twofold: (i) to develop a generalized SEIRD model that implicitly takes into account the quarantine measures, and (ii) to estimate the response of the COVID-19 spread dynamics to perturbations/uncertainties. By investigating the projections of cumulative numbers of confirmed and death cases, as well as the effective reproduction number, we show that the model parameter related to social distancing measures is one of the most influential along all stages of the disease spread and the most influential after the infection peak. Due to such importance in the outcomes, different relaxation strategies of social distancing measures are investigated in order to determine which strategies are viable and less hazardous to the population. The results highlight the need of keeping social distancing policies to control the disease spread. Specifically, the considered scenario of abrupt social distancing relaxation implemented after the occurrence of the peak of positively diagnosed cases can prolong the epidemic, with a significant increase of the projected numbers of confirmed and death cases. An even worse scenario could occur if the quarantine relaxation policy is implemented before evidence of the epidemiological control, indicating the importance of the proper choice of when to start relaxing social distancing measures.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Diego Tavares Volpatto", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Anna Claudia Mello Resende", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Lucas Anjos", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Joao Vitor Oliveira Silva", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Claudia Mazza Dias", - "author_inst": "Universidade Federal Rural do Rio de Janeiro" - }, - { - "author_name": "Regina Cerqueira Almeida", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Sandra Mara Cardoso Malta", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.28.122671", "rel_title": "Optimized pseudotyping conditions for the SARS-COV2 Spike glycoprotein", @@ -1412099,6 +1414633,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.06.01.20119123", + "rel_title": "Testing for tracing or testing just for treating? A comparative analysis between strategies to face COVID-19 pandemic.", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119123", + "rel_abs": "There is some consensus in Europe and Asia about high testing rates being crucial to controlling COVID-19 pandemics. There are though misconceptions on what means an effective high testing rate. This paper demonstrates that the rate of tests per detected case (Tests/Case) is the critical variable, correlating negatively with the number of deaths. The higher the Tests/Case rate, the lower the death rate, as this predictor is causally related to contact tracing and isolation of the vectors of the disease. Doubling Tests/Case typically divides by about three the number of deaths. On the other hand, the per capita testing rate is a poor predictor for the performance of policies to fight the pandemics. The number of tests per 1,000 inhabitants (Tests/1,000) tends to correlate positively with the number of deaths. In some cases, high levels of Tests/1,000 just mean an epidemic that ran out of control, with an explosion of cases that demands high testing rates just to confirm the diagnosis of the seriously sick. This study also demonstrates that an early tracing strategy, with a high level of Tests/Case, reduces combined costs of testing and hospitalization dramatically. Therefore, the common claim that tracing strategies are unaffordable by poorer countries is incorrect. On the contrary, it is the most adequate, both from the economic and humanitarian points of view.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ricardo Knudsen", + "author_inst": "Independent consultant" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.05.30.20117929", "rel_title": "Therapeutic Anticoagulation Is Associated with Decreased Mortality in Mechanically Ventilated COVID-19 Patients", @@ -1413095,33 +1415648,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.01.20119172", - "rel_title": "SCALE19: A scalable and cost-efficient method for testing Covid-19 based on hierarchical group testing", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119172", - "rel_abs": "Containment of Covid-19 requires an extensive testing of the affected population. Some propose global testing to effectively contain Covid-19. Current tests for Covid-19 are administered individually. These tests for Covid-19 are expensive and are limited due to the lack of resources and time. We propose a simple and efficient group testing method for Covid-19. We propose a group testing method where test subjects are grouped and tested. Depending on the result of the group test, subsequent sub groups are formed and tested recursively based on a quartery search algorithm. We designed and built an evaluation model that simulates test subject population, infected test subjects according to available Covid-19 statistics, and the group testing processes in SCALE19. We considered several population models including USA and the world. Our results show that we can significantly reduce the required number of tests up to 89% without sacrificing the accuracy of the individual test of the entire population. For USA, up to 280 million tests can be reduced from the total US population of 331 million and it would be equivalent saving of $28 billion assuming a cost of $100 per test. For the world, 6.96 billion tests can be reduced from the total population of 7.8 billion and it would be equivalent to saving $696 billion. We propose SCALE19 can significantly reduce the total required number of tests compared to individual tests of the entire population. We believe SCALE19 is efficient and simple to be deployed in containment of Covid-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jeremie S Kim", - "author_inst": "Carnegie Mellon University" - }, - { - "author_name": "Justine S Kim", - "author_inst": "UPMC" - }, - { - "author_name": "Hyong Kim", - "author_inst": "Carnegie Mellon Unviersity" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.25.20112623", "rel_title": "Serological surveys in Reunion Island of the first hospitalized patients revealed that long-lived immunoglobulin G antibodies specific against SARS-CoV2 virus are rapidly vanishing in severe cases", @@ -1413369,6 +1415895,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.28.20110767", + "rel_title": "The prevalence of antibodies to SARS-CoV-2 in asymptomatic healthcare workers with intensive exposure to COVID-19", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20110767", + "rel_abs": "The prevalence of asymptomatic SARS-CoV-2 infection in healthcare workers with intensive exposure to COVID-19 is unclear. In this study, we investigated the seroprevalence of SARS-CoV-2 in 797 asymptomatic healthcare workers with intensive exposure to COVID-19 patients in Wuhan, China. Positive IgG was detected from 35 asymptomatic healthcare workers, and the prevalence of antibodies to SARS-CoV-2 in asymptomatic healthcare workers was 4.39% (35/797). None of them developed COVID-19 until May 15. 33 of them have performed at least one chest CT scan showing no viral pneumonia features, and 16 have finished at least one-time SARS-CoV-2 RNA detection with negative results. When contacting with the patients, 15 of them dressed with full personal protective equipment (PPE), and 16 worn N95 mask and gown. To the best of our knowledge, this is the first investigation reported that the seroprevalence of SARS-CoV-2 was 4.39% in asymptomatic healthcare workers with applied PPE in a high epidemic area, which may provide useful information of estimating asymptomatic infection rate in general population.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Shue Xiong", + "author_inst": "Union Hospital, Tongji Medical College, HUST" + }, + { + "author_name": "Chunxia Guo", + "author_inst": "Union Hospital, Tongji Medical College, HUST" + }, + { + "author_name": "Ulf Dittmer", + "author_inst": "University Hospital of Essen, University of Duisburg-Essen" + }, + { + "author_name": "Xin Zheng", + "author_inst": "Union Hospital, Tongji Medical College, HUST" + }, + { + "author_name": "Baoju Wang", + "author_inst": "Union Hospital, Tongji Medical College , HUST" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.27.20110601", "rel_title": "CIGB-258 immunomodulatory peptide: a novel promising treatment for critical and severe COVID-19 patients", @@ -1414781,25 +1417342,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.26.20113399", - "rel_title": "COVID-19 Trend and Forecast in India: A Joinpoint Regression Analysis", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113399", - "rel_abs": "This paper analyses the trend in daily reported confirmed cases of COVID-19 in India using joinpoint regression analysis. The analysis reveals that there has been little impact of the nation-wide lockdown and subsequent extension on the progress of the COVID-19 pandemic in the country and there is no empirical evidence to suggest that relaxations under the third and the fourth phase of the lockdown have resulted in a spike in the reported confirmed cases. The analysis also suggests that if the current trend continues, in the immediate future, then the daily reported confirmed cases of COVID-19 in the country is likely to increase to 21 thousand by 15 June 2020 whereas the total number of confirmed cases of COVID-19 will increase to around 422 thousand. The analysis calls for a population-wide testing approach to check the increase in the reported confirmed cases of COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Aalok Ranjan Chaurasia", - "author_inst": "MLC Foundation" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.27.20114512", "rel_title": "Diagnostic accuracy of a host response point-of-care test for identifying COVID-19", @@ -1415103,6 +1417645,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.02.20119875", + "rel_title": "Rapid and accurate detection of novel coronavirus SARS-CoV-2 using CRISPR-Cas3", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20119875", + "rel_abs": "Novel coronavirus SARS-CoV-2 outbreaks have rapidly spread to multiple countries, highlighting the urgent necessity for fast, sensitive, and specific diagnostic tools for virus surveillance. Here, the previously unknown collateral single-stranded DNA cleavage we observed with type I CRISPR-Cas3 highlights its potential for development as a Cas3-mediated rapid (within 40 min), low-cost, instrument-free detection method for SARS-CoV-2. This Cas3-based assay is comparable with Cas12- and real-time reverse-transcriptase PCR-based assays in its speed and sensitivity, but offers greater specificity for single-base-pair discrimination while negating the need for highly trained operators. These findings support the use of CRISPR diagnostics for point-of-care testing in patients with suspected SARS-CoV-2 infections.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kazuto Yoshimi", + "author_inst": "Institute of Medical Science, University of Tokyo" + }, + { + "author_name": "Kohei Takeshita", + "author_inst": "RIKEN SPring-8 Center" + }, + { + "author_name": "Seiya Yamayoshi", + "author_inst": "Institute of Medical Science, University of Tokyo" + }, + { + "author_name": "Satomi Shibumura", + "author_inst": "C4U Corporation" + }, + { + "author_name": "Yuko Yamauchi", + "author_inst": "Institute of Medical Science, University of Tokyo" + }, + { + "author_name": "Masaki Yamamoto", + "author_inst": "RIKEN SPring-8 Center" + }, + { + "author_name": "Hiroshi Yotsuyanagi", + "author_inst": "Institute of Medical Science, University of Tokyo" + }, + { + "author_name": "Yoshihiro Kawaoka", + "author_inst": "Institute of Medical Science, University of Tokyo" + }, + { + "author_name": "Tomoji Mashimo", + "author_inst": "Institute of Medical Science, the University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.31.20112979", "rel_title": "An open resource for T cell phenotype changes in COVID-19 identifies IL-10-producing regulatory T cells as characteristic of severe cases", @@ -1416903,29 +1419496,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20115063", - "rel_title": "The Risk of Lifting COVID-19 Confinement in Mexico", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115063", - "rel_abs": "The novel coronavirus SARS-CoV-2 has paralysed our societies, leading to self isolation and quarantine for several days. As the 10th most populated country in the world, Mexico is on a major threat by COVID-19 due to the limitations of intensive care capacities, and a total of about 1.5 hospital beds for every 1000 citizens. In this paper, we projected different scenarios to evaluate sharp or gradual quarantine lifting strategies, however, even in the hypothetical scenario that Mexico would continue with full confinement, hospitals would be reaching the maximum capacity of hospital bed occupancy. Mexican government is planning to relax the strict social distancing regulations on 1 June 2020, however, epidemic rebound risks are latent.\n\nOur results suggest that lifting social confinement needs to be gradually sparse while maintaining a decentralized region strategy among the Mexican states. To substantially lower the number of infections, predictions highlight that the elderly should remain in social confinement (approximately 11.3% of the population); the confined working class (roughly 27% of the population) must gradually return in at least four parts in consecutive months; and to the last the return of students to schools (about 21.7%). As the epidemic progresses, de-confinement strategies need to be continuously re-adjusting with the new pandemic data. Assuming the most optimistic scenario by our predictions, the smallest number of new COVID-19 cases, Mexico would require at least a 3 fold increase in hospital capacities dedicated for COVID-19. Furthermore, to observe the real dimension of the epidemic, Mexico would need to increase to at least 18 samples per 1000 people, currently is only 0.6 per 1000.\n\nAll mathematical models, including ours, are only a possibility of many of the future, however, the different scenarios that were developed here highlight that a gradual decentralized region de-confinement with a significant increase in healthcare capacities is paramount to avoid a high death toll in Mexico.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Cristy Leonor Azanza Ricardo", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Esteban Abelardo Hernandez Vargas", - "author_inst": "Frankfurt Institute for Advanced Studies" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.28.20116046", "rel_title": "Immunochromatographic assays for COVID-19 epidemiological screening: our experience", @@ -1417221,6 +1419791,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.28.20116194", + "rel_title": "Estimated Sp02/Fio2 ratio to predict mortality in patients with suspected COVID-19 in the Emergency Department: a prospective cohort study", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20116194", + "rel_abs": "BackgroundThis study examined whether the presence and severity of Type 1 Respiratory Failure (T1RF), as measured by the ratio of pulse oximetry to estimated fraction of inspired oxygen (SpO2/eFiO2 ratio), is a predictor of in-hospital mortality in patients presenting to the ED with suspected COVID-19 infection.\n\nMethodsWe undertook a prospective observational cohort study of patients admitted to hospital with suspected COVID-19 in a single ED in England. We used univariate and multiple logistic regression to examine whether the presence and severity of T1RF in the ED was independently associated with inhospital mortality.\n\nResults180 patients with suspected COVID-19 infection met the inclusion criteria for this study, of which 39 (22%) died. Severity of T1RF was associated with increased mortality with odds ratios (OR) and 95% confidence intervals of 1.58 (0.49 - 5.14), 3.60 (1.23 - 10.6) and 18.5 (5.65 - 60.8) for mild, moderate and severe T1RF, respectively. After adjusting for age, gender, pre-existing cardiovascular disease, neutrophil-lymphocyte ration (NLR) and estimated glomerular filtration rate (eGFR), the association remained, with ORs of 0.63 (0.13 - 3.03), 3.95 (0.94 - 16.6) and 45.8 (7.25 - 290). The results were consistent across a number of sensitivity analyses.\n\nConclusionsSeverity of T1RF in the ED is an important prognostic factor of mortality in patients admitted with suspected COVID-19 infection. Current prediction models frequently do not include this factor and should be applied with caution. Further large scale research on predictors of mortality in COVID-19 infection should include SpO2/eFiO2 ratios or a similar measure of respiratory dysfunction.\n\nKEY MESSAGESO_ST_ABSWhat is already known on this topicC_ST_ABSA number of studies have identified potential variables to predict mortality in patients with COVID-19 but have mainly focused on laboratory measures. The primary pathophysiology and cause of death seems to be lung injury leading to an acute respiratory distress syndrome (ARDS) like illness, clinically presenting as type 1 respiratory failure (T1RF). Despite this, only a very small number of studies have included measurements of respiratory dysfunction as predictor of mortality.\n\nWhat this study addsTo our knowledge, this is the first study to examine the association between T1RF as measured by the ratio of pulse oximetry (SpO2) and estimated fraction of inspired oxygen (FiO2) and mortality in patients admitted with suspected COVID-19. The presence and severity of T1RF are strongly associated with mortality. At the same time, other factors previously shown to be associated with mortality are potentially less important than currently assumed, once adjusted for the severity of T1RF.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Johannes von Vopelius-Feldt", + "author_inst": "North Bristol NHS Trust, Emergency Department" + }, + { + "author_name": "Daniel Watson", + "author_inst": "North Bristol NHS Trust, Emergency Department" + }, + { + "author_name": "Carla Swanson-Low", + "author_inst": "North Bristol NHS Trust, Emergency Department" + }, + { + "author_name": "James Cameron", + "author_inst": "North Bristol NHS Trust, Emergency Department" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.05.28.20115394", "rel_title": "Rapid Epidemiological Analysis of Comorbidities andTreatments as risk factors for COVID-19 in Scotland(REACT-SCOT): a population-based case-control study", @@ -1418565,37 +1421166,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.05.31.20118802", - "rel_title": "The Association Between Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers and the Number of Covid-19 Confirmed Cases and Deaths in the United States: Geospatial Study", - "rel_date": "2020-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118802", - "rel_abs": "BackgroundThe novel coronavirus SARS-Cov2 uses the angiotensin-converting enzyme 2 (ACE2) receptor as an entry point to the cell. Cardiovascular disease (CVD) is a risk factor for the novel coronavirus disease (Covid-19) with poor outcomes. We hypothesized that the rate of ACE inhibitor (ACEI) and angiotensin receptor blocker (ARB) use is associated with the rate of Covid-19 confirmed cases and deaths.\n\nMethodsWe conducted a geospatial study using publicly available county-level data. The Medicare ACEI and ARB prescription rate was exposure. The Covid-19 confirmed case and death rates were outcomes. Spatial autoregression models were adjusted for the percentage of Black residents, children, residents with at least some college degree, median household income, air quality index, CVD hospitalization rate in Medicare beneficiaries, and CVD death rate in a total county population.\n\nFindingsAfter adjustment for confounders, the ACEI use rate did not associate with Covid-19 confirmed case rate (direct county-own effect +0.11 %; 95%CI -0.31 to 0.53; P=0.600, and indirect spillover effect -0.53 %; 95%CI -3.89 to 2.84; P=0.760). The ARB use rate was associated with increased Covid-19 confirmed case rate (direct county-owned effect +0.12 %; 95%CI 0.05-0.19; P=0.002, and indirect spillover effect -0.33 %; 95%CI -2.11 to 1.44; P=0.714). Sensitivity analysis indicated an absence of significant reverse causality bias for analyses with Covid-19 confirmed case rate, but not death rate outcome.\n\nInterpretationOur results highlight the safety of ACEI use for patients with clinical indications for ACEI use. However, an increase in ARB use by 1% was associated with a 0.12 % increase in Covid-19 confirmed cases. The use of ARB, due to known ACE2 upregulation, may facilitate SARS-CoV-2 entry into target cells and increase infectivity. Cluster-randomized controlled trial is warranted to answer the question of whether the replacement of ARB by ACEI may reduce the Covid-19 confirmed case rate.\n\nFundingLGT was supported in part by the National Institute of Health (HL118277).", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kyle Johnson", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Maedeh Khayyat-Kholghi", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Blake Johnson", - "author_inst": "Flexport, San Francisco, CA" - }, - { - "author_name": "Larisa G Tereshchenko", - "author_inst": "Oregon Health & Science University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.05.31.20118695", "rel_title": "ON THE UNCERTAINTY ABOUT HERD IMMUNITY LEVELS REQUIRED TO STOP COVID-19 EPIDEMICS", @@ -1418779,6 +1421349,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.05.26.20102889", + "rel_title": "Evaluation of COVID 19 infection in 279 cancer patients treated during a 90-day period in 2020 pandemic", + "rel_date": "2020-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20102889", + "rel_abs": "BackgroundThe aim of this study was investigation of COVID-19 disease and its outcome in cancer patients who needed treatment, in a 90-day period.\n\nMethodsCancer patient who required treatment, were evaluated for potential COVID-19 infection in a 90-day period, starting from beginning of this epidemic in Iran, January, to April 19, 2020. For treatment of solid tumor patients, if they did not have symptoms related to COVID-19, just chest X-ray was requested. If they showed COVID-19 related symptoms, High Resolution CT scan of lungs was requested. For hematology cancer patients, PCR test for COVID-19 infection was requested as well. Protection measures were considered for personnel of oncology wards.\n\nResultsIn this study, 279 patients were followed up in this 90-day period. No COVID-19 infection was observed in 92 cases of breast cancer, 72 cases of colon cancer, 14 cases of gastric cancer and 12 cases of pancreaticobiliary cancer.However, in 11 cases of lung cancer, 5 cases brain tumors and 12 cases ovarian cancer; 3 case of COVID-19 were observed. In the hematology cancers group, which included 14 cases of Hodgkin Lymphoma, 23 cases of lymphoproliferative disorder, 12 cases of acute leukemia and 12 cases of multiple myeloma; three of COVID-19 were observed.\n\nConclusionPatients with cancer who need treatment can be treated by taking some measures. These measures include observing individual and collective protection principles in patients and health-care personnel, increasing patients awareness particularly about self-care behavior, performing a COVID-19 test, and taking a chest X ray, before the treatment starts", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mozaffar Aznab", + "author_inst": "Kermanshsh University of Medical science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2020.05.30.20099143", "rel_title": "SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature", @@ -1419898,73 +1422487,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20115527", - "rel_title": "Analyzing Covid-19 Data using SIRD Models", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115527", - "rel_abs": "The goal of this analysis is to estimate the effects of the diverse government intervention measures implemented to mitigate the spread of the Covid-19 epidemic. We use a process model based on a compartmental epidemiological framework Susceptible-Infected-Recovered-Dead (SIRD). Analysis of case data with such a mechanism-based model has advantages over purely phenomenological approaches because the parameters of the SIRD model can be calibrated using prior knowledge. This approach can be used to investigate how governmental interventions have affected the Covid-19-related transmission and mortality rate during the epidemic.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Abhijit Chakraborty", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "Jiaying Chen", - "author_inst": "Section for Science of Complex Systems, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090, Vienna, Austria" - }, - { - "author_name": "Amelie Desvars-Larrive", - "author_inst": "University of Veterinary Medicine Vienna" - }, - { - "author_name": "Peter Klimek", - "author_inst": "Section for Science of Complex Systems, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090, Vienna, Austria" - }, - { - "author_name": "Erwin Flores Tames", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "David Garcia", - "author_inst": "Section for Science of Complex Systems, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090, Vienna, Austria" - }, - { - "author_name": "Leonhard Horstmeyer", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "Michaela Kaleta", - "author_inst": "Section for Science of Complex Systems, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090, Vienna, Austria" - }, - { - "author_name": "Jana Lasser", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "Jenny Reddish", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - }, - { - "author_name": "Beate Pinior", - "author_inst": "Unit of Veterinary Public Health and Epidemiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, 12" - }, - { - "author_name": "Johannes Wachs", - "author_inst": "Vienna University of Economics and Business, Institute for Information Business. Welthandelsplatz 1, Vienna 1020, Austria" - }, - { - "author_name": "Peter Turchin", - "author_inst": "Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.29.124610", "rel_title": "COVID-3D: An online resource to explore the structural distribution of genetic variation in SARS-CoV-2 and its implication on therapeutic development", @@ -1420224,6 +1422746,53 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.05.30.20117614", + "rel_title": "Assessing the quality, readability and reliability of online information on COVID-19: aninfoveillance observational study", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117614", + "rel_abs": "ObjectiveThis study aimed to assess the quality, reliability and readability of internet-based information on COVID-19 available on Brazil most used search engines.\n\nMethodsA total of 68 websites were selected through Google, Bing, and Yahoo. The websites content quality and reliability were evaluated using the DISCERN questionnaire, the Journal of American Medical Association (JAMA) benchmark criteria, and the presence of the Health on Net (HON) certification. Readability was assessed by the Flesch Reading Ease adapted to Brazilian Portuguese (FRE-BP).\n\nResultsThe web contents were considered moderate to low quality according to DISCERN and JAMA mean scores. Most of the sample presented very difficult reading levels and only 7.4% displayed HON certification. Websites of Governmental and health-related authorship nature showed lower JAMA mean scores and quality and readability measures did not correlate to the webpages content type.\n\nConclusionCOVID-19 related contents available online were considered of low to moderate quality and not accessible.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Paulo Cardoso Lins Filho", + "author_inst": "Federal University of Pernambuco - Brazil" + }, + { + "author_name": "Thuanny Silva de Macedo", + "author_inst": "Federal University of Pernambuco - Brazil" + }, + { + "author_name": "Andressa Kelly Alves Ferreira", + "author_inst": "Federal University of Pernambuco - Brazil" + }, + { + "author_name": "Maria Cecilia Freire de Melo", + "author_inst": "Federal University of Pernambuco - Brazil" + }, + { + "author_name": "Millena Mirella Silva de Araujo", + "author_inst": "Federal University of Pernambuco - Brazil" + }, + { + "author_name": "Jaciel Leandro de Melo Freitas", + "author_inst": "Federal University of Pernambuco - Brazil" + }, + { + "author_name": "Thaise Urbano Caldas", + "author_inst": "State University of Pernambuco - Brazil" + }, + { + "author_name": "Arnaldo de Franca Caldas Jr.", + "author_inst": "Federal University of Pernambuco and State University of Pernambuco - Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2020.05.28.20115816", "rel_title": "Predicting social distancing index during COVID-19 outbreak through online search engines trends", @@ -1421724,61 +1424293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.28.20115964", - "rel_title": "Measuring COVID-19 and Influenza in the Real World via Person-Generated Health Data", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115964", - "rel_abs": "BackgroundSince the beginning of the COVID-19 pandemic, data from smartphones and connected sensors have been used to better understand presentation and management outside the clinic walls. However, reports on the validity of such data are still sparse, especially when it comes to symptom progression and relevance of wearable sensors.\n\nObjectiveTo understand the relevance of Person-Generated Health Data (PGHD) as a means for early detection, monitoring, and management of COVID-19 in everyday life. This type of data include quantifying prevalence and progression of symptoms from self-reports as well as changes in activity and physiological parameters continuously measured from wearable sensors, and contextualizing findings for COVID-19 patients with those from cohorts of flu patients.\n\nDesign, Setting, and ParticipantsRetrospective digital cohort study of individuals with a self-reported positive SARS-CoV-2 or influenza test followed over the period 2019-12-02 to 2020-04-27. Three cohorts were derived: Patients who self-reported being diagnosed with flu prior to the SARS-CoV-2 pandemic (N=6270, of which 1226 also contributed sensor PGHD); Patients who reported being diagnosed with flu during the SARS-CoV-2 pandemic (N=426, of which 85 also shared sensor PGHD); and patients who reported being diagnosed with COVID-19 (N=230, of which sensor PGHD was available for 41). The cohorts were derived from a large-scale digital participatory surveillance study designed to track Influenza-like Illness (ILI) incidence and burden over time.\n\nExposuresSelf-reported demographic data, comorbidities, and symptoms experienced during a diagnosed ILI episode, including SARS-CoV-2. Physiological and behavioral parameters measured daily from commercial wearable sensors, including Resting Heart Rate (RHR), total step count, and nightly sleep hours.\n\nMain Outcomes and MeasuresWe investigated the percentage of individuals experiencing symptoms of a given type (e.g. shortness of breath) across demographic groups and over time. We examined illness duration, and care seeking behavior, and how RHR, step count, and nightly sleep hours deviated from expected behavior on healthy days over the course of the infection episode.\n\nResultsSelf-reported symptoms of COVID-19 present differently from flu. COVID-19 cases tended to last longer than flu (median of 12 vs. 9 days), are uniquely characterized by chest pain/pressure, shortness of breath, and anosmia. The fraction of elevated RHR measurements collected daily from commercial wearable devices rise significantly in the 2 days surrounding ILI symptoms onset, but does not appear to do so in a way specific to COVID-19. Steps lost due to COVID-19 persists for longer than for flu.\n\nConclusion and RelevancePGHD can be a valid source of longitudinal real world data to detect and monitor COVID-19-related symptoms and behaviors at population scale. PGHD may provide continuous, near real-time feedback to intervention effectiveness that otherwise requires waiting for symptoms to develop into contacts with the healthcare system. It has also the potential to increase pre-test probability of other downstream diagnostics. To effectively leverage PGHD for participatory surveillance it is crucial to invest in the creation of trusted, long-term communication channels with individuals through which data can be efficiently collected, consented, and contextualized, while protecting the privacy of individuals and ultimately facilitating the transition in and out of care.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Nikki Marinsek", - "author_inst": "Evidation Health" - }, - { - "author_name": "Allison Shapiro", - "author_inst": "Evidation Health" - }, - { - "author_name": "Ieuan Clay", - "author_inst": "Evidation Health" - }, - { - "author_name": "Ben Bradshaw", - "author_inst": "Evidation Health" - }, - { - "author_name": "Ernesto Ramirez", - "author_inst": "Evidation Health" - }, - { - "author_name": "Jae Min", - "author_inst": "Evidation Health" - }, - { - "author_name": "Andrew Trister", - "author_inst": "Bill and Melinda Gates Foundation" - }, - { - "author_name": "Yuedong Wang", - "author_inst": "Department of Statistics and Applied Probability, University of California, Santa Barbara" - }, - { - "author_name": "Tim Althoff", - "author_inst": "University of Washington" - }, - { - "author_name": "Luca Foschini", - "author_inst": "Evidation Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.28.20115980", "rel_title": "Restarting after COVID-19: A Data-driven Evaluation of Opening Scenarios", @@ -1421946,6 +1424460,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.27.119255", + "rel_title": "Head-to-head comparison of four antigen-based rapid detection tests for the diagnosis of SARS-CoV-2 in respiratory samples", + "rel_date": "2020-05-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.27.119255", + "rel_abs": "In the context of the Covid-19 pandemic, the development and validation of rapid and easy-to-perform diagnostic methods are of high priority. We compared the performance of four rapid antigen detection tests for SARS-CoV-2 in respiratory samples. Immunochromatographic SARS-CoV-2 assays from RapiGEN, Liming bio, Savant, and Bioeasy were evaluated using universal transport medium containing naso-oropharyngeal swabs from suspected Covid-19 cases. The diagnostic accuracy was determined in comparison to SARS-CoV-2 RT-PCR. A total of 111 samples were included; 80 were RT-PCR positive. Median patients age was 40 years, 55% were female, and 88% presented within the first week after symptom onset. The evaluation of the Liming bio assay was discontinued due to insufficient performance. The overall sensitivity values of RapiGEN, Liming bio, and Bioeasy tests were 62.0% (CI95% 51.0-71.9), 16.7% (CI95% 10.0-26.5), and 85.0% (CI95% 75.6-91.2), respectively, with specificities of 100%. Sensitivity was significantly higher in samples with high viral loads (RapiGEN, 84.9%; Bioeasy, 100%). The study highlighted the significant heterogeneity of test performance among evaluated assays, which might have been influenced by the use of a non-validated sample material. The high sensitivity of some tests demonstrated that rapid antigen detection has the potential to serve as an alternative diagnostic method, especially in patients presenting with high viral loads in early phases of infection. This is particularly important in situations with limited access to RT-PCR or prolonged turnaround time. Further comparative evaluations are necessary to select products with high performance among the growing market of diagnostic tests for SARS-CoV-2.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Thomas Weitzel", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Paulette Legarraga", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Mirentxu Iruretagoyena", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Gabriel Pizarro", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Valeska Vollrath", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Rafael Araos", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Jose M. Munita", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Lorena Porte", + "author_inst": "Cl\u00ednica Alemana, Universidad del Desarrollo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.29.20117259", "rel_title": "Social Distancing Interventions in the United States: An Exploratory Investigation of Determinants and Impacts", @@ -1423030,29 +1425591,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.27.20114868", - "rel_title": "A reductive analysis of a compartmental model for COVID-19: data assimilation andforecasting for the United Kingdom", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114868", - "rel_abs": "We introduce a deterministic model that partitions the total population into the susceptible, infected, quarantined, and those traced after exposure, the recovered and the deceased. We hypothesize accessible population for transmission of the disease to be a small fraction of the total population, for instance when interventions are in force. This hypothesis, together with the structure of the set of coupled nonlinear ordinary differential equations for the populations, allows us to decouple the equations into just two equations. This further reduces to a logistic type of equation for the total infected population. The equation can be solved analytically and therefore allows for a clear interpretation of the growth and inhibiting factors in terms of the parameters in the full model. The validity of the accessible population hypothesis and the efficacy of the reduced logistic model is demonstrated by the ease of fitting the United Kingdom data for the cumulative infected and daily new infected cases. The model can also be used to forecast further progression of the disease. In an effort to find optimized parameter values compatible with the United Kingdom coronavirus data, we first determine the relative importance of the various transition rates participating in the original model. Using this we show that the original model equations provide a very good fit with the United Kingdom data for the cumulative number of infections and the daily new cases. The fact that the model calculated daily new cases exhibits a turning point, suggests the beginning of a slow-down in the spread of infections. However, since the rate of slowing down beyond the turning point is small, the cumulative number of infections is likely to saturate to about 3.52 x 105 around late July, provided the lock-down conditions continue to prevail. Noting that the fit obtained from the reduced logistic equation is comparable to that with the full model equations, the underlying causes for the limited forecasting ability of the reduced logistic equation are elucidated. The model and the procedure adopted here are expected to be useful in fitting the data for other countries and in forecasting the progression of the disease.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Garani Ananthakrishna", - "author_inst": "Materials Research Centre, Indian Institute of Science, Bengaluru 560012, India" - }, - { - "author_name": "Jagadish Kumar", - "author_inst": "Utkal University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.27.20111955", "rel_title": "Age separation dramatically reduces COVID-19 mortality rate in a computational model of a large population", @@ -1423200,6 +1425738,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.27.20115113", + "rel_title": "COVID-19 Lockdown in a Kenyan Informal Settlement: Impacts on Household Energy and Food Security", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20115113", + "rel_abs": "A COVID-19 lockdown may impact household fuel use and food security for [~]700 million sub-Saharan Africans who rely on polluting fuels (e.g. wood, kerosene) for household energy and typically work in the informal economy. In an informal settlement in Nairobi, surveys administered before (n=474) and after (n=194) a mandatory COVID-19-related community lockdown documented socioeconomic/household energy impacts. During lockdown, 95% of participants indicated income decline or cessation and 88% reported being food insecure. Three quarters of participants cooked less frequently and half altered their diet. One quarter (27%) of households primarily using liquefied petroleum gas (LPG) for cooking before lockdown switched to kerosene (14%) or wood (13%). These results indicate the livelihoods of urban Kenyan families were deleteriously affected by COVID-19 lockdown, with a likely rise in household air pollution from community-level increases in polluting fuel use. To safeguard public health, policies should prioritize enhancing clean fuel and food access among the urban poor.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Matthew Shupler", + "author_inst": "University of Liverpool" + }, + { + "author_name": "James Mwitari", + "author_inst": "Amref International University" + }, + { + "author_name": "Arthur Gohole", + "author_inst": "Amref International University" + }, + { + "author_name": "Rachel Anderson de Cuevas", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Elisa Puzzolo", + "author_inst": "University of Liverpool, Global LPG Partnership" + }, + { + "author_name": "Iva Cukic", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Emily Nix", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Daniel Pope", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.27.20115204", "rel_title": "Non-communicable diseases and inequalities increase risk of death among COVID-19 patients in Mexico", @@ -1424240,29 +1426825,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.05.25.20112797", - "rel_title": "Variation in Covid-19 Cases Across New York City", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112797", - "rel_abs": "The number of confirmed COVID-19 cases, relative to population size, has varied greatly throughout the United States and even within the same city. In different zip codes in New York City, the epicentre of the epidemic, the number of cases per 100,000 residents has ranged from 437 to 4227, a 1:10 ratio. To guide policy decisions regarding containment and reopening of the economy, schools and other institutions, it is vital to identify the factors that drive this large variation.\n\nThis paper reports on a statistical study of incidence variation by zip code across New York City. Among many socio-economic and demographic measures considered, the average household size emerges as the single most important explanatory variable: an increase in average household size by one member increases the zip code incidence rate, in our final model specification, by at least 876 cases, 23% of the range of incidence rates, at a 95% confidence level.\n\nThe percentage of the population above the age of 65, the percentage below the poverty line, and their interaction term are also strongly positively associated with zip code incidence rates, In terms of ethnic/racial characteristics, the percentages of African Americans, Hispanics and Asians within the population, are significantly associated, but the magnitude of the impact is considerably smaller. (The proportion of Asians within a zip code has a negative association.)\n\nThese significant associations may be explained by comorbidities, known to be more (less) prevalent among the black and Hispanic (Asian) population segments. In turn, the increased prevalence of these comorbidities among the black and Hispanic population, is, in large part, the result of poorer dietary habits and more limited access to healthcare, themselves driven by lower incomes\n\nContrary to popular belief, population density, per se, does not have a significantly positive impact. Indeed, population density and zip code incidence rate are negatively correlated, with a -33% correlation coefficient.\n\nOur model specification is based on a well-established epidemiologic model that explains the effects of household sizes on R0, the basic reproductive number of an epidemic.\n\nOur findings support implemented and proposed policies to quarantine pre-acute and post-acute patients, as well as nursing home admission policies", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Awi Federgruen", - "author_inst": "Columbia University" - }, - { - "author_name": "Sherin R Naha", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.05.27.20114652", "rel_title": "A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding", @@ -1424514,6 +1427076,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.27.20114736", + "rel_title": "Combining PCR and CT testing for COVID", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114736", + "rel_abs": "We analyze the effect of using a screening CT-scan for evaluation of potential COVID-19 infections in order to isolate and perform contact tracing based upon a viral pneumonia diagnosis. RT-PCR is then used for continued isolation based upon a COVID diagnosis. Both the low false negative rates and rapid results of CT-scans lead to dramatically reduced transmission. The reduction in cases after 60 days with widespread use of CT-scan screening compared to PCR by itself is as high as 50x, and the reduction of effective reproduction rate R(t) is 0.20. Our results imply that much more rapid extinction of COVID is possible by combining social distancing with CT-scans and contact tracing.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Chen Shen", + "author_inst": "New England Complex Systems Institute" + }, + { + "author_name": "Ron Mark", + "author_inst": "Mark Medical Care PLLC" + }, + { + "author_name": "Nolan J. Kagetsu", + "author_inst": "Mt. Sinai Hospital" + }, + { + "author_name": "Anton S. Becker", + "author_inst": "New England Complex Systems Institute" + }, + { + "author_name": "Yaneer Bar-Yam", + "author_inst": "New England Complex Systems Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.28.120162", "rel_title": "Plasmin cascade mediates thrombolytic events in SARS-CoV-2 infection via complement and platelet-activating systems", @@ -1425542,37 +1428139,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.05.27.20111542", - "rel_title": "Ambient air pollutants, meteorological factors and their interactions affect confirmed cases of COVID-19 in 120 Chinese cities", - "rel_date": "2020-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20111542", - "rel_abs": "Emerging evidences have confirmed effects of meteorological factors on novel coronavirus disease 2019 (COVID-19). However, few studies verify the impact of air pollutants on this pandemic. This study aims to explore the association of ambient air pollutants, meteorological factors and their interactions effect confirmed case counts of COVID-19 in 120 Chinese cities. Here, we collected total confirmed cases of COVID-19 by combining with meteorological factors and air pollutants data from 15th January 2020 to 18th March 2020 in 120 Chinese cities. Spearman correlation analysis was employed to estimate the association between two variables; univariate and multivariate negative binomial regression analysis were applied to explore the effect of air pollutants and meteorological parameters on the COVID-19 confirmed cases. Positive associations were found between the confirmed cases of COVID-19 and carbon monoxide (CO), aerodynamic particulate matter with aerodynamic diameter [≤]2.5 m (PM2.5), relative humidity (RH) and air pressure (AP). And negative association was found for sulfur dioxide (SO2). In addition, multivariate negative binomial regression analysis suggested that confirmed cases of COVID-19 was positively correlated with ozone (O3) in lag 0 day while it was negatively associated with wind velocity (WV) in lag 14 days, and the pollutants-meteorological factors interactions also associate with COVID-19. In conclusions, air pollutants and meteorological factors and their interactions all associate with COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jianli Zhou", - "author_inst": "Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern" - }, - { - "author_name": "Linyuan Qin", - "author_inst": "Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, 541001, P. R. China." - }, - { - "author_name": "Nan Liu", - "author_inst": "Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern" - }, - { - "author_name": "Xiaojing Meng", - "author_inst": "Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.26.20113886", "rel_title": "COVID-19 (SARS-CoV-2) Ventilator Resource Management Using a Network Optimization Model and Predictive System Demand", @@ -1425828,6 +1428394,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.26.20113811", + "rel_title": "Diabetes is associated with increased risk for in-hospital mortality in patients with COVID-19: a systematic review and meta-analysis comprising 18,506 patients", + "rel_date": "2020-05-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113811", + "rel_abs": "BackgroundInfectious diseases are more frequent and can be associated with worse outcomes in patients with diabetes. Our aim was to systematically review and synthesize with a meta-analysis the available observational studies reporting the effect of diabetes in mortality among hospitalized patients with COVID-19.\n\nMethodsMedline, Embase, Google Scholar, and medRxiv databases were reviewed. A random-effect model meta-analysis was used and I-square was utilized to assess the heterogeneity. In-hospital mortality was defined as the endpoint. Sensitivity, subgroup, and meta-regression analyses were performed.\n\nResults18,506 patients were included in this meta-analysis (3,713 diabetics and 14,793 non-diabetics). Patients with diabetes were associated with a higher risk of death compared to patients without diabetes (OR: 1.65; 95% CI: 1.35-1.96; I2 77.4%). The heterogeneity was high. A study level meta-regression analysis was performed for all the important covariates and no significant interactions were found between the covariates and the outcome of mortality.\n\nConclusionThis meta-analysis shows that that the likelihood of death is 65% higher in diabetic hospitalized patients with COVID-19 compared to non-diabetics. Further studies are needed to assess whether this association is independent or not, as well as to investigate to role of glucose control prior or during the disease.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Leonidas Palaiodimos", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Natalia Chamorro-Pareja", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Dimitrios Karamanis", + "author_inst": "University of Piraeus" + }, + { + "author_name": "Weijia Li", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Phaedon D Zavras", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Priyanka Mathias", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Damianos G Kokkinidis", + "author_inst": "Albert Einstein College of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2020.05.26.20114074", "rel_title": "On the true numbers of COVID-19 infections: behind the available data", @@ -1427000,49 +1429609,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.25.20112805", - "rel_title": "The association of UV with rates of COVID-19 transmission and deaths in Mexico: the possible mediating role of vitamin D.", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112805", - "rel_abs": "The first COVID-19 case in Mexico was confirmed on 26 February 2020 and by May 3 the number of registered cases had risen to 30,927. However the rate of transmission varied greatly from city to city. We used data on temperature, humidity and ultraviolet radiation (UV) from 45 cities all over the country to explore whether there was an association between these variables and rates of transmission and rates of accumulation of COVID-19 ascribed deaths. The advantage of an in-country study of this kind is that many of the variables that can confound international studies are held constant (e.g. public health policies, methods of reporting, cultural, behavioural and genetic factors). Although the official statistics undoubtedly greatly underestimate the situation in Mexico due to lack of testing, they are underestimated in all cities so this should not introduce bias across the sample. We found that temperature and humidity had no discernible association with transmission rates but that UV during the transmission period was negatively correlated with rates of transmission, suggesting a sterilizing effect. UV in the January preceding the epidemic had a slightly higher association with transmission rates than UV during the transmission period itself. We also found negative associations of UV in the transmission period and in January with rate of cumulative deaths, but at lower levels of statistical significance. We conclude that in addition to a sterilizing effect during the transmission period, UV may have a physiological effect in reducing transmission and deaths due to COVID-19, most likely through the medium of vitamin D production in the body. This follows the growing body of medical evidence that vitamin D deficiency is associated with severity of COVID-19. However, we also found a negative correlation between altitude and rates of COVID-19 transmission, distinct and independent of the UV effect, which may indicate that other physiological processes are also present. In a multiple regression, altitude and UV together accounted for 18% of the variation in transmission rates between cities.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Margaret Skutsch", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Carlos Dobler", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Matthew B.B. McCall", - "author_inst": "Radboud UMC, Nijmegen. the Netherlands" - }, - { - "author_name": "Adrian Ghilardi", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Miguel A. Salinas-Melgoza", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Naciona lAutonoma de Mexico" - }, - { - "author_name": "Michael K. McCall", - "author_inst": "Centro de Investigaciones en Geografia Ambiental, Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Gabriela Fenner-Sanchez", - "author_inst": "CESMECA-UNICACH, Geobrujas-comunidad de geografas y Grupo Estepa UNAL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.26.20112680", "rel_title": "Fast initial Covid-19 response means greater caution may be needed later", @@ -1427238,6 +1429804,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.25.20112185", + "rel_title": "Increased risk for COVID-19 among Migrants from Latin-America, Caribbean, and Sub-Saharan Africa living in Spain", + "rel_date": "2020-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112185", + "rel_abs": "Little is known regarding the relevance of racial / ethnic background on the risk of COVID-IO infection, particularly in Europe. We evaluated the risk for COVID-19 among migrants from different areas of the world within a context of universal free access to medical care. We conducted a population-based cohort analysis of the cumulative incidence of PCR-confirmed COVID-19 among adult residents at Alcorcon (Spain) in the first wave of the disease. The crude cumulative incidence among migrants (n=20419) was higher than among Spaniards (n=131599): 8.81 and 6.51 and per 1000 inhabitants respectively (p<0.001) but differed by world region of origin. By negative binomial regression, adjusted for age and sex, relative risks (RR) for COVID-19 were not significantly different from Spaniards for individuals from Europe, Asia or Northern Africa. In contrast, there was a marked increased risk for Sub-Saharan Africa (RR 3.66, 95% confidence interval (Cl) 42-9.41, p=0.007), Caribbean (RR6.35, 95% Cl 3.83-10.55, p<0.001) and Latin-America (RR6.92, 95% Cl 4.49-10.67, p <0.001). Migrants from these areas of the world may deserve a closer attention both for clinical and epidemiological reasons.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Carlos Guijarro", + "author_inst": "HOSPITAL UNIVERSITARIO FUNDACION ALCORCON. UNIVERSIDAD REY JUAN CARLOS" + }, + { + "author_name": "Elia Perez-Fernandez", + "author_inst": "HOSPITAL UNIVERSITARIO FUNDACION ALCORCON" + }, + { + "author_name": "Beatriz Gonzalez-Pineiro", + "author_inst": "HOSPITAL UNIVERSITARIO FUNDACION ALCORCON" + }, + { + "author_name": "Victoria Melendez", + "author_inst": "AYUNTAMIENTO DE ALCORCON" + }, + { + "author_name": "Maria Jose Goyanes", + "author_inst": "HOSPITAL UNIVERSITARIO FUNDACION ALCOCON" + }, + { + "author_name": "M Esther Renilla", + "author_inst": "HOSPITAL UNIVERSITARIO FUNDACION ALCORCON" + }, + { + "author_name": "Maria Luisa Casas", + "author_inst": "HOSPITAL UNIVERSTIARIO FUNDACION ALCORCON" + }, + { + "author_name": "Isabel Sastre", + "author_inst": "HOSPITAL UNIVERSITARIO FUNDACION ALCORCON" + }, + { + "author_name": "Maria Velasco", + "author_inst": "HOSPITAL UNIVERSITARIO FUNDACION ALCORCON" + }, + { + "author_name": "- Alcorcon COVID Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.26.20112565", "rel_title": "Saliva as a Candidate for COVID-19 Diagnostic Testing: A Meta-Analysis", @@ -1428690,25 +1431311,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.05.26.20113316", - "rel_title": "Scrutinising the COVID-19 data on 590.000 cases. A retrospective, population-based descriptive study for data quality surveillance and a review at 4.540.000 cases.", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113316", - "rel_abs": "BackgroundReports on the detected positive patients with COVID-19 are as per today the best estimation of a country spread of the pandemic. In order to evaluate the early indicators for true lethality and recovery time, the data where the model is built must be quality checked. Each country sets different procedures and criteria for fatality count due to COVID-19 and the health system is stressed by having insufficient testing, untracked patients and premature discharge. In this paper the dynamics behind such data quality issues are discussed throughout the disease course to support better modeling and decision-making processes in a stressed healthcare system.\n\nMethodsBased on data compiled and relayed by the Johns Hopkins University, tracking COVID-19 over 590.000 patients (march 27th, 2020), the data is clustered and compared with discrete regression. Regression parameters are restricted by a time interval of 1 day and must be meaningful for the diagnostic (i.e. a fatality cannot occur before the patient displays symptoms). Cumulative infection curves are taken and built. Infection baseline is based on the country official declaration. Infection synthetic curves are built from the Fatality count and the Recovered patient count. The adjusted parameters are {tau}=time to fatality (days), {delta}=time to discharge of recovered patients (days) and {varphi}=case fatality rate (CFR in per unit, P.U.). Therefore, the discharge rate (recovery rate) is forced to be (1-{varphi}).\n\nUsing forward or backward formulas have no other influence than the time reference. In both circumstances, time from Onset and Symptoms are neglected and shall be added if such dates are to be plot. There is a gap of two weeks since exposure to Hospital Admission to detection and the earlier the diagnose is done, the better the outcome.\n\nCumulative figures are used to smoothen the deviation and to provide the best estimator possible at the present time. The delay factor allows to compare figures belonging to the same date of detection.\n\nFast, daily models which can be used and integrated to a filtering stage on the parameter estimator in a complex approach are left out of scope. Continuous models can also be used and interpolation among the data points is another source of noise to be considered, especially when counting methods are suddenly changing as it is the case with COVID-19.\n\nCountries were grouped as found representative for methodology illustration purposes. Results are discussed and compared across the different groups and potential indicators of this behavior are drawn for further study.\n\nFindingsFrom 593.291 cases in the sample, and its 7 representative groups, the recovery time and the local CFR are negatively correlated, having the highest fatality rates (21%, Spain) the countries with shorter recovery time (11 days, Spain). Also, CFR can be an indicator of Infection inconsistencies (i.e. South Korea, CFR 1%, Time to recovery 25 days).\n\nAt the review part, focus is made on the inconsistencies detected in Germany and South Korea datasets as well as the potential misfits on China and Spain.\n\nOverall, the Time to Fatality ranges between 4 and 8 days, and the mean is of 6 days (South Korea, 7 days; Japan, 6days). Only Germany and France are detecting earlier than other countries and admit 10 days before fatality occurs.\n\nTo date, shortening hospital discharge times seem to lead to patient reinfections (COVID-19 positive), and studies are working on this line.\n\nInterpretationOne simple explanation for the local CFR and Recovery time correlation is to define such rate as a measure of the healthcare system overload. Anomalous CFR indexes point to a stressed healthcare system. The higher the overload, the more focus on critical cases and hence the higher local CFR.\n\nThe COVID-19 intrinsic CFR is unlikely to change by a factor of 10x from countries with similar lifestyle, GDP per capita and health services (i.e. the Mediterranean Basin, Northern Europe, etc.). Because of this fact, early CFR measured before Healthcare system overwhelming (COVID-19 free flow) are considered to be more accurate than the measured CFR while the outbreak is still ongoing,\n\nFinally, the synthetic Infection indexes may be a helpful indirect measure of the real population infection rate and also used for data quality audit. Any model built upon inconsistent data will be complex to explain and justify.\n\nFundingNo specific funding is raised.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Oriol Gallemi Rovira", - "author_inst": "Universitat Ramon Llull IQS" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.26.20113761", "rel_title": "Differentiating COVID-19 from other types of pneumonia with convolutional neural networks", @@ -1428888,6 +1431490,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.26.20113431", + "rel_title": "Detection of asymptomatic Leishmania infection in Bangladesh by novel antigen and antibody diagnostic tools shows strong association with PKDL patients", + "rel_date": "2020-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113431", + "rel_abs": "BackgroundAsymptomatic Leishmania infections outnumber clinical infections on the Indian sub-continent (ISC) where disease reservoirs are anthroponotic. Diagnostics which detect active asymptomatic infection, which are suitable for monitoring and surveillance, may be of benefit to the visceral leishmaniasis (VL) elimination campaign on the ISC.\n\nMethodology/Principal FindingsQuantitative polymerase chain reaction (qPCR), loop mediated isothermal amplification (LAMP), the direct agglutination test (DAT), and the Leishmania antigen ELISA were carried out on blood and urine samples collected from 720 household and neighbouring contacts of 276 VL and post kala-azar dermal leishmaniasis (PKDL) index cases, with no symptoms or history of VL and PKDL, in endemic regions of Bangladesh between September 2016 and March 2018. Of the 720 contacts of index cases, asymptomatic infection was detected in 69 (9.6%) participants by a combination of qPCR (1.0%), LAMP (2.1%), DAT (3.9%), and Leishmania antigen ELISA (3.3%). Only 1 (0.1%) participant was detected positive by all 4 diagnostic tests. Poor agreement between tests was calculated using Cohens kappa (k) statistics, however the Leishmania antigen ELISA and DAT in combination capture all participants positive by more than one test. We find strong evidence for association between the index case being a PKDL case (OR 1.94, p = 0.009), specifically macular PKDL (OR 2.12, p = 0.004) and being positive for at least one of the four tests.\n\nConclusions/SignificanceLeishmania antigen ELISA detects active asymptomatic infection, requires a non-invasive sample, and therefore may be of benefit for monitoring transmission and surveillance in an elimination setting in combination with serology. Development of an antigen detection test in RDT format would be of benefit to the elimination campaign.\n\nAuthor summaryInfection with the parasite Leishmania donovani can lead to an asymptomatic infection with only around 5% of asymptomatics converting to visceral leishmaniasis the clinical manifestation of the infection. Serological assays detect anti-Leishmania antibodies and therefore cannot distinguish between past and active infection. Molecular assays and those which detect Leishmania antigens detect active infection. Since the signing of a memorandum of understanding in 2005, visceral leishmaniasis has been targeted for elimination in India, Nepal and Bangladesh. In an elimination setting such as Bangladesh, where disease reservoirs are anthroponotic, a relatively simple test such as the Leishmania antigen ELISA which requires a non-invasive urine sample, may be of benefit in combination with serology for surveillance and monitoring of Leishmania transmission. Development of an antigen test into a field compatible rapid diagnostic test would be of further benefit to the elimination campaign.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sophie I Owen", + "author_inst": "Liverpool School of Tropical Medicine, Liverpool, UK" + }, + { + "author_name": "Faria Hossain", + "author_inst": "International Centre for Diarrhoeal Diseases Research (icddr,b), Dhaka, Bangladesh" + }, + { + "author_name": "Prakash Ghosh", + "author_inst": "International Centre for Diarrhoeal Diseases Research (icddr,b), Dhaka, Bangladesh" + }, + { + "author_name": "Rajashree Chowdhury", + "author_inst": "International Centre for Diarrhoeal Diseases Research (icddr,b), Dhaka, Bangladesh" + }, + { + "author_name": "Md. Sakhawat Hossain", + "author_inst": "International Centre for Diarrhoeal Diseases Research (icddr,b), Dhaka, Bangladesh" + }, + { + "author_name": "Christopher Jewell", + "author_inst": "Lancaster University, Lancaster, UK" + }, + { + "author_name": "Isra Cruz", + "author_inst": "Instituto de Salud Carlos III, Madrid, Spain" + }, + { + "author_name": "Albert Picado", + "author_inst": "Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland" + }, + { + "author_name": "Dinesh Mondal", + "author_inst": "International Centre for Diarrhoeal Diseases Research (icddr,b), Dhaka, Bangladesh" + }, + { + "author_name": "Emily R Adams", + "author_inst": "Liverpool School of Tropical Medicine, Liverpool, UK" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.25.20112599", "rel_title": "Meta-regression of COVID-19 prevalence/fatality on socioeconomic characteristics of data from top 50 U.S. large cities", @@ -1430124,57 +1432781,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.05.20.20106633", - "rel_title": "Clinical and Radiological Evaluations of COVID-19 Patients with Anosmia: Preliminary Report.", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20106633", - "rel_abs": "ObjectiveTo investigate clinical and radiological features of olfactory clefts of patients with mild coronavirus disease 2019 (COVID-19).\n\nMethodsSixteen COVID-19 patients were recruited. The epidemiological and clinical data were extracted. Nasal complaints were assessed through the sino-nasal outcome test 22 (SNOT-22). Patients underwent psychophysical olfactory testing, olfactory cleft examination and CT-scan.\n\nResultsSixteen anosmic patients were included. The mean SniffinSticks score was 4.6{+/-}1.7. The majority of patients had no endoscopical abnormality, with a mean olfactory cleft endoscopy score of 0.6{+/-}0.9. The olfactory clefts were opacified in 3 patients on the CT-scan. The mean radiological olfactory cleft score was 0.7{+/-}0.8. There were no significant correlations between clinical, radiological and psychophysical olfactory testing.\n\nConclusionThe olfactory cleft of anosmic COVID-19 patients is free regarding endoscopic examination and imaging. The anosmia etiology would be not related to edema of the olfactory cleft.\n\nLevel of Evidence4", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jerome R Lechien", - "author_inst": "Department of Otorhinolaryngology and Head and Neck Surgery, CHU de Bruxelles, CHU Saint-Pierre, School of Medicine, Universite Libre de Bruxelles, Brussels, Be" - }, - { - "author_name": "Justin Michel", - "author_inst": "Aix Marseille University, APHM, IUSTI, La Conception University Hospital, Department of Oto-Rhino-Laryngology Head and Neck Surgery, Marseille, France" - }, - { - "author_name": "Thomas Radulesco", - "author_inst": "Aix Marseille University, APHM, IUSTI, La Conception University Hospital, Department of Oto-Rhino-Laryngology Head and Neck Surgery, Marseille, France" - }, - { - "author_name": "Carlos M Chiesa-Estomba", - "author_inst": "Hospital Universitario Donostia" - }, - { - "author_name": "Luigi A Vaira", - "author_inst": "Maxillofacial Surgery Unit, University Hospital of Sassari, Sassari, Italy." - }, - { - "author_name": "Giacomo De Riu", - "author_inst": "Maxillofacial Surgery Unit, University Hospital of Sassari, Sassari, Italy." - }, - { - "author_name": "Leigh J Sowerby", - "author_inst": "Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada" - }, - { - "author_name": "Claire Hopkins", - "author_inst": "Guy's and St Thomas's Hospitals" - }, - { - "author_name": "Sven Saussez", - "author_inst": "University of Mons" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2020.05.19.20106575", "rel_title": "Mitigation Policies and Emergency Care Management in Europe's Ground Zero for COVID-19", @@ -1430502,6 +1433108,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.22.20106724", + "rel_title": "Emergence of Low-density Inflammatory Neutrophils Correlates with Hypercoagulable State and Disease Severity in COVID-19 Patients", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20106724", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel viral pathogen that causes a clinical disease called coronavirus disease 2019 (COVID-19). Approximately 20% of infected patients experience a severe manifestation of the disease, causing bilateral pneumonia and acute respiratory distress syndrome. Severe COVID-19 patients also have a pronounced coagulopathy with approximately 30% of patients experiencing thromboembolic complications. However, the etiology driving the coagulopathy remains unknown. Here, we explore whether the prominent neutrophilia seen in severe COVID-19 patients contributes to inflammation-associated coagulation. We found in severe patients the emergence of a CD16IntCD44lowCD11bInt low-density inflammatory band (LDIB) neutrophil population that trends over time with changes in disease status. These cells demonstrated spontaneous neutrophil extracellular trap (NET) formation, phagocytic capacity, enhanced cytokine production, and associated clinically with D-dimer and systemic IL-6 and TNF- levels, particularly for CD40+ LDIBs. We conclude that the LDIB subset contributes to COVID-19-associated coagulopathy (CAC) and could be used as an adjunct clinical marker to monitor disease status and progression. Identifying patients who are trending towards LDIB crisis and implementing early, appropriate treatment could improve all-cause mortality rates for severe COVID-19 patients.\n\nOne Sentence SummaryIn this study, we discover that low-density neutrophils significantly contribute to COVID-19-associated coagulopathy and inflammation", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Samantha M Morrissey", + "author_inst": "University of Louisville.edu" + }, + { + "author_name": "Anne E Geller", + "author_inst": "University of Louisville" + }, + { + "author_name": "Xiaoling Hu", + "author_inst": "University of Louisville" + }, + { + "author_name": "David Tieri", + "author_inst": "University of Louisville" + }, + { + "author_name": "Elizabeth A Cooke", + "author_inst": "University of Louisville" + }, + { + "author_name": "Chuanlin Ding", + "author_inst": "University of Louisville" + }, + { + "author_name": "Matthew Woeste", + "author_inst": "University of Louisville" + }, + { + "author_name": "Huang-ge Zhange", + "author_inst": "University of Louisville" + }, + { + "author_name": "Rodrigo Cavallazi", + "author_inst": "University of Louisville" + }, + { + "author_name": "Sean P Clifford", + "author_inst": "University of Louisville" + }, + { + "author_name": "James Chen", + "author_inst": "University of Louisville" + }, + { + "author_name": "Maiying Kong", + "author_inst": "University of Louisville" + }, + { + "author_name": "Corey T Watson", + "author_inst": "University of Louisville" + }, + { + "author_name": "Jiapeng Huang", + "author_inst": "University of Louisville" + }, + { + "author_name": "Jun Yan", + "author_inst": "University of Louisville School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.05.19.20106781", "rel_title": "Hypertension and renin-angiotensin system blockers are not associated with expression of Angiotensin Converting Enzyme 2 (ACE2) in the kidney", @@ -1431654,53 +1434335,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.19.20107201", - "rel_title": "Computational Simulation to Assess Patient Safety of Uncompensated COVID-19 Two-patient Ventilator Sharing Using the Pulse Physiology Engine", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107201", - "rel_abs": "BackgroundThe COVID-19 pandemic is stretching medical resources internationally, sometimes creating ventilator shortages that complicate clinical and ethical situations. The possibility of needing to ventilate multiple patients with a single ventilator raises patient health and safety concerns in addition to clinical conditions needing treatment.\n\nWherever ventilators are employed, additional tubing and splitting adaptors may be available. Adjustable flow-compensating resistance for differences in lung compliance on individual limbs may not be readily implementable.\n\nBy exploring a number and range of possible contributing factors using computational simulation without risk of patient harm, this paper attempts to define useful bounds for ventilation parameters when compensatory resistance in limbs of a shared breathing circuit is not possible. This desperate approach to shared ventilation support would be a last resort when alternatives have been exhausted.\n\nMethodsA whole-body computational physiology model (using lumped parameters) was used to simulate each patient being ventilated. The primary model of a single patient with a dedicated ventilator was augmented to model two patients sharing a single ventilator. In addition to lung mechanics or estimation of CO2 and pH expected for set ventilation parameters (considerations of lung physiology alone), full physiological simulation provides estimates of additional values for oxyhemoglobin saturation, arterial oxygen tension, and other patient parameters. A range of ventilator settings and patient characteristics were simulated for paired patients.\n\nFindingsTo be useful for clinicians, attention has been directed to clinically available parameters. These simulations show patient outcome during multi-patient ventilation is most closely correlated to lung compliance, oxygenation index, oxygen saturation index, and end-tidal carbon dioxide of individual patients. The simulated patient outcome metrics were satisfactory when the lung compliance difference between two patients was less than 12 mL/cmH2O, and the oxygen saturation index difference was less than 2 mmHg.\n\nInterpretationIn resource-limited regions of the world, the COVID-19 pandemic will result in equipment shortages. While single-patient ventilation is preferable, if that option is unavailable and ventilator sharing using limbs without flow resistance compensation is the only available alternative, these simulations provide a conceptual framework and guidelines for clinical patient selection.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jeffrey B. Webb", - "author_inst": "Kitware, Inc." - }, - { - "author_name": "Aaron Bray", - "author_inst": "Kitware, Inc." - }, - { - "author_name": "Philip K. Asare", - "author_inst": "Bucknell University" - }, - { - "author_name": "Rachel B. Clipp", - "author_inst": "Kitware, Inc." - }, - { - "author_name": "Yatin B. Mehta", - "author_inst": "Geisinger" - }, - { - "author_name": "Sudheer Penupolu", - "author_inst": "Geisinger" - }, - { - "author_name": "Aalpen A. Patel", - "author_inst": "Geisinger" - }, - { - "author_name": "S. Mark Poler", - "author_inst": "Geisinger" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.21.20108522", "rel_title": "Expanding Covid-19 Testing: Mathematical Guidelines for the Optimal Sample Pool Size Given Positive Test Rate", @@ -1431872,6 +1434506,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.23.20111526", + "rel_title": "Hasty Reduction of COVID-19 Lockdown Measures Leads to the Second Wave of Infection", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111526", + "rel_abs": "The outbreak of COVID-19 has an undeniable global impact, both socially and economically. March 11th, 2020, COVID-19 was declared as a pandemic worldwide. Many governments, worldwide, have imposed strict lockdown measures to minimize the spread of COVID-19. However, these measures cannot last forever; therefore, many countries are already considering relaxing the lockdown measures. This study, quantitatively, investigated the impact of this relaxation in the United States, Germany, the United Kingdom, Italy, Spain, and Canada. A modified version of the SIR model is used to model the reduction in lockdown based on the already available data. The results showed an inevitable second wave of COVID-19 infection following loosening the current measures. The study tries to reveal the predicted number of infected cases for different reopening dates. Additionally, the predicted number of infected cases for different reopening dates is reported.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yara Hazem", + "author_inst": "Department of Mathematics, Western Michigan University" + }, + { + "author_name": "Suchitra Natarajan", + "author_inst": "Department of Advanced Nurse practitioners, West Coast University" + }, + { + "author_name": "Essam Berikaa", + "author_inst": "Department of Electrical and Computer Engineering, McGill University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.22.20108084", "rel_title": "Assessment of small pulmonary blood vessels in COVID-19 patients using HRCT", @@ -1433188,29 +1435849,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.05.24.20111625", - "rel_title": "Comparison of epidemic control strategies using agent-based simulations", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111625", - "rel_abs": "A simulation of the dynamics of a small population is used to assess the impact of different confinement and testing strategies in the control of an epidemic. The simulation considers individuals as agents moving randomly across the habitat according to predefined urban patterns. Agents carry a simple tracing device that identifies signals emitted by other agents, recording the position and time of the encounter. The information of every device is propagated daily to an epidemic observatory based on an online graph database. Infections are simulated as stochastic processes depending on the proximity among individuals. Different epidemic control strategies are tested with and without the information of the tracing device under several scenarios. We observe that the success of the strategies strongly depends on the duration of the period of infectiousness before the presence of symptoms and the fraction of asymptomatic agents. If these values are high, strategies based on the presence of symptoms or on testing campaigns can hardly contain the epidemic. Strategies using massive confinement of the agents are able to control the epidemic at the cost of sending a large fraction of the population into quarantine. In cases with moderate and low values for these parameters, the tracing devices can provide a slightly better performance but only if a large fraction of the agents carry the device. Otherwise, the impact of these devices is found to be negligible in comparison with other strategies not using them. Finally, we provide a methodology allowing to use the information of the graph database to estimate basic parameters of the disease such as the infection probability.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Pablo Martinez Ruiz del Arbol", - "author_inst": "Instituto de Fisica de Cantabria" - }, - { - "author_name": "Lara Lloret Iglesias", - "author_inst": "Instituto de Fisica de Cantabria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.25.20111047", "rel_title": "Characteristics of Ischemic Stroke in COVID-19: A Need for Early Detection and Management", @@ -1433550,6 +1436188,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.24.20111872", + "rel_title": "Predicting COVID-19 Pandemic in Saudi Arabia Using Modified Singular Spectrum Analysis", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111872", + "rel_abs": "This research presents a modified Singular Spectrum Analysis (SSA) approach for the analysis of COVID-19 in Saudi Arabia. We have proposed this approach and developed it in [1-3] for separability and grouping step in SSA, which plays an important role for reconstruction and forecasting in the SSA. The modified SSA mainly enables us to identify the number of the interpretable components required for separability, signal extraction and noise reduction. The approach was examined using different number of simulated and real data with different structures and signal to noise ratio. In this study we examine its capability in analysing COVID-19 data. Then, we use Vector SSA for predicting new data points and the peak of this pandemic. The results shows that the approach can be used as a promising one in decomposing and forecasting the daily cases of COVID-19 in Saudi Arabia.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Nader Alharbi", + "author_inst": "King Saud bin Abdulaziz University for Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.22.20110577", "rel_title": "A COVID-19 Reopening Readiness Index: The Key to Opening up the Economy", @@ -1434742,29 +1437399,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.24.20112128", - "rel_title": "Estimation and monitoring of COVID-19 transmissibility from publicly available data", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20112128", - "rel_abs": "The COVID-19 pandemic began in the city of Wuhan, China, at the end of 2019 and quickly spread worldwide. The disease is caused by contact with the SARS-CoV-2 virus, which probably jumped from an animal host to humans. SARS-CoV-2 infects various tissues in the body, notably the lungs, and patients usually die from respiratory complications. Mathematical models of the disease have been instrumental to guide the implementation of mitigation strategies aimed at slowing the spread of the disease. One of the key parameters of mathematical models is the basic reproduction ratio R0, which measures the degree of infectivity of affected individuals. The goal of mitigation is to reduce R0 as close or below 1 as possible, as it means that new infections are in decline. In the present work, we use the recursive least-squares algorithm to establish the stochastic variability of a time-varying R0(t) from eight different countries: Argentina, Belgium, Brazil, Germany, Italy, New Zealand, Spain, and the United States of America. The proposed system can be implemented as an online tracking application providing information about the dynamics of the pandemic to health officials and the public at large.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Antonio da Silva Silveira", - "author_inst": "Federal University of Para" - }, - { - "author_name": "Antonio Pereira Jr.", - "author_inst": "Federal University of Para" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.23.20110965", "rel_title": "Association of age, sex, comorbidities, and clinical symptoms with the severity and mortality of COVID-19 cases: a meta-analysis with 85 studies and 67299 cases", @@ -1434964,6 +1437598,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.26.20113357", + "rel_title": "Excess mortality in England and Wales during the first wave of the COVID-19 pandemic", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113357", + "rel_abs": "BackgroundDeaths during the COVID-19 pandemic result directly from infection and exacerbation of other diseases and indirectly from deferment of care for other conditions, and are socially and geographically patterned. We quantified excess mortality in regions of England and Wales during the pandemic, for all causes and for non-COVID-19 associated deaths.\n\nMethodsWeekly mortality data for 1 Jan 2010 to 1 May 2020 for England and Wales were obtained from the Office of National Statistics. Mean-dispersion negative binomial regressions were used to model death counts based on pre-pandemic trends and exponentiated linear predictions were subtracted from: i) all-cause deaths; and ii) all-cause deaths minus COVID-19 related deaths for the pandemic period (07-13 March to 25 April to 8 May).\n\nFindingsBetween 7 March and 8 May 2020, there were 47,243 (95%CI: 46,671 to 47,815) excess deaths in England and Wales, of which 9,948 (95%CI: 9,376 to 10,520) were not associated with COVID-19. Overall excess mortality rates varied from 49 per 100,000 (95%CI: 49 to 50) in the South West to 102 per 100,000 (95%CI: 102 to 103) in London. Non-COVID-19 associated excess mortality rates ranged from -1 per 100,000 (95%CI: -1 to 0) in Wales (i.e. mortality rates were no higher than expected) to 26 per 100,000 (95%CI: 25 to 26) in the West Midlands.\n\nInterpretationThe COVID-19 pandemic has had markedly different impacts on the regions of England and Wales, both for deaths directly attributable to COVID-19 infection and for deaths resulting from the national public health response.\n\nFundingNone", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Evangelos Kontopantelis", + "author_inst": "University of Manchester" + }, + { + "author_name": "Mamas A Mamas", + "author_inst": "Keele University" + }, + { + "author_name": "John Deanfield", + "author_inst": "University College London" + }, + { + "author_name": "Miqdad Asaria", + "author_inst": "London School of Economics and Political Science" + }, + { + "author_name": "Tim Doran", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.23.20111369", "rel_title": "The impact of thermal pasteurization on viral load in human milk and other matrices: A rapid review", @@ -1435984,29 +1438653,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.05.23.20111039", - "rel_title": "Worldwide and Regional Forecasting of Coronavirus (Covid-19) Spread using a Deep Learning Model", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111039", - "rel_abs": "In December 2019, Covid-19 epidemic was identified in Wuhan, China. Covid-19 may cause fatality especially among elderly, and people with chronic health problems. After human to human transmissions of the disease, it has rapidly spread throughout China, and then the outbreak has reached to neighboring countries in Asia. Now, the spread of the virus is accelerating in the world, and increasing number of new cases has been reported daily in Europe, Middle East, Africa and America regions. Recently, World Health Organization (WHO) also announced Covid-19 as a Pandemic. As of 3 April, worldwide around more than 1 million cases and around 60,000 fatalities are reported. Thus, forecasting regional and worldwide outbreak size of Covid-19 is important in order to take necessary actions regarding to preparedness plans and mitigation interventions. In this work, we design a deep learning model, which is an effective artificial intelligence method, to provide regional and worldwide forecasts. Particularly for worldwide, our approach predicts the cumulative number of cases, cumulative number of deaths and daily new cases. For Europe and Middle East regions, we predict the cumulative number of cases, and for Mainland China we predict daily new cases and the cumulative number of deaths. We predict the next 10 days based on the previously reported actual time series data of Covid-19. For worldwide forecasts, we use the data provided by Worldometers. For Europe and Middle East forecasts, we use the data provided by World Health Organization, and for China Mainland forecasts, the data is obtained from Chinese Centre for Disease Control and Prevention. This is the first time that a deep learning model has been employed for Covid-19 spread prediction, solely based on the known reported cases of Covid-19. The proposed deep learning architecture consists of Long Short Term Memory (LSTM) layer, dropout layer, and fully connected layers to predict regional and worldwide forecasts. We evaluate our approach with Root Mean Square Error (RMSE) metric. For forecasting, we use the network models that give the minimum RMSE on the last 3 days of actual data. Networks, which achieves the minimum RMSE on the last 3 days, are used to predict the next 10 days. Every day, the spread and situations are changing. Our approach can take into account these realtime changes; the deep learning model can be re-trained with new daily data and perform real-time forecasting. Results show that the proposed deep learning model is promising, it can predict possible scenarios regionally and globally for the spread of Covid-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Cem Direkoglu", - "author_inst": "Middle East Technical University - Northern Cyprus Campus" - }, - { - "author_name": "Melike Sah", - "author_inst": "Near East University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.26.116608", "rel_title": "Structure, function and variants analysis of the androgen-regulated TMPRSS2, a drug target candidate for COVID-19 infection", @@ -1436286,6 +1438932,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.23.20110999", + "rel_title": "Modelling COVID-19 Transmission in the United States through Interstate and Foreign Travels and Evaluating Impact of Governmental Public Health Interventions", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20110999", + "rel_abs": "BackgroundThe first case of COVID-19 was reported in Wuhan, China in December 2019. The disease has spread to 210 countries and has been labelled as pandemic by WHO. Modelling, evaluating, and predicting the rate of disease transmission is crucial for epidemic prevention and control. Our aim is to assess the impact of interstate and foreign travel and public health interventions implemented by the United States government in response to the Covid-19 pandemic.\n\nMethodsA disjoint mutually exclusive compartmental model is developed to study transmission dynamics of the novel coronavirus. A system of non-linear differential equations was formulated and the basic reproduction number R0 was computed. Stability of the model was evaluated at the equilibrium points. Optimal controls were applied in the form of travel restrictions and quarantine. Numerical simulations were conducted.\n\nResultsAnalysis shows that the model is locally asymptomatically stable, at endemic and foreigners free equilibrium points. Without any mitigation measures, infectivity and subsequent hospitalization of the population increases while placing interstates individuals and foreigners under quarantine, decreases the chances of exposure and subsequent infection, leading to an increase in the recovery rate.\n\nConclusionInterstate and foreign travel restrictions, in addition to quarantine, help in effectively controlling the epidemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nita H Shah", + "author_inst": "Gujarat University" + }, + { + "author_name": "Nisha Sheoran", + "author_inst": "Gujarat University" + }, + { + "author_name": "Ekta N Jayswal", + "author_inst": "Gujarat University" + }, + { + "author_name": "Dhairya Shukla", + "author_inst": "Medical College of Georgia" + }, + { + "author_name": "Nehal Shukla", + "author_inst": "Columbus State University" + }, + { + "author_name": "Jagdish Shukla", + "author_inst": "Department Of Medical Education, Piedmont Columbus Regional" + }, + { + "author_name": "Yash Shah", + "author_inst": "GCS Medical College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.26.115790", "rel_title": "AN IMMUNOINFORMATICS STUDY TO PREDICT EPITOPES IN THE ENVELOPE PROTEIN OF SARS-COV-2", @@ -1437454,33 +1440143,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.05.22.20110163", - "rel_title": "Low Covid-19 hospitalisation in Dumfries and Galloway: comparison with other Scottish health boards", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110163", - "rel_abs": "BackgroundCovid-19 virus activity appears to have affected some parts of the United Kingdom more than others. Dumfries and Galloway (D&G) has seen fewer hospitalised cases than predicted. We wondered whether this might be related at least in part to population density.\n\nMethodsWe compared Covid-19 hospitalisation rates/100,000 population in D&G with those of the other 10 mainland Scottish health boards. We chose two time points: 19th April which was the peak of the pandemic in Scotland and 15th May, seven and a half weeks after lockdown. We used chi square and odds ratios with 95% confidence intervals to test for differences in hospitalisation rates and Pearsons correlation coefficient to examine the relation between hospitalisation rates and population density. Population density for each health board was provided by National Records of Scotland.\n\nResultsHospitalisation in D&G was 13.4/100,000 on 19th April, falling to 1.3/100,000 by 15th May. Corresponding hospitalisation rates in Greater Glasgow & Clyde (GGC) were 50.1/100,000 and 38.9/100,000. Compared to GGC, hospitalisation rates in D&G were 3 times lower at peak (OR 0.27, 95% CI 0.17, 0.42) and 30 times lower by 15th May (OR 0.03, 95% CI 0.01, 0.14). Hospitalisation rates for the other health boards lay in between values recorded for D&G and GGC and fell in 10 of the 11 boards between these two dates. There was a positive association between hospitalisation rate and population density (r=0.756, p=0.007 on 19th April and r=0.840, p<0.001 for 15th May).\n\nConclusionWe have confirmed there are large differences in Covid-19 hospitalisation rates across the 11 mainland Scottish health boards, that are in part related to population density. These data support a regional rather than one nation approach to easing Covid-19 restrictions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andrew Rideout", - "author_inst": "Department of Public Health, NHS Dumfries and Galloway." - }, - { - "author_name": "Calum Murray", - "author_inst": "Education Centre, Dumfries and Galloway Royal Infirmary, Dumfries DG2 8RX" - }, - { - "author_name": "Chris Isles", - "author_inst": "Dumfries Royal Infirmary" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.05.22.20109231", "rel_title": "Association of country-wide coronavirus mortality with demographics, testing, lockdowns, and public wearing of masks.", @@ -1437636,6 +1440298,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.21.20108233", + "rel_title": "Performance and impact of disposable and reusable respirators for healthcare workers during pandemic respiratory disease: a rapid evidence review.", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108233", + "rel_abs": "ObjectivesIn the context of the Covid-19 pandemic, to identify the range of filtering respirators that can be used in patient care and synthesise evidence to guide the selection and use of different respirator types.\n\nDesignComparative analysis of international standards for filtering respirators and rapid review of their performance and impact in healthcare.\n\nData sourcesWebsites of international standards organisations, Medline and EMBASE (final search 11th May 2020), with hand-searching of references and citations.\n\nStudy selectionGuided by the SPIDER tool, we included studies whose sample was healthcare workers (including students). The phenomenon of interest was respirators, including disposable and reusable types. Study designs including cross-sectional, observational cohort, simulation, interview and focus group. Evaluation approaches included test of respirator performance, test of clinician performance or adherence, self-reported comfort and impact, and perceptions of use. Research types included quantitative, qualitative and mixed methods. We excluded studies comparing the effectiveness of respirators with other forms of protective equipment.\n\nData extraction, analysis and synthesisTwo reviewers extracted data using a template. Suitability for inclusion in the analysis was judged by two reviewers. We synthesised standards by tabulating data according to key criteria. For the empirical studies, we coded data thematically followed by narrative synthesis.\n\nResultsWe included relevant standards from 8 authorities across Europe, North and South America, Asia and Australasia. 39 research studies met our inclusion criteria. There were no instances of comparable publications suitable for quantitative comparison. There were four main findings. First, international standards for respirators apply across workplace settings and are broadly comparable across jurisdictions. Second, effective and safe respirator use depends on proper fitting and fit-testing. Third, all respirator types carry a burden to the user of discomfort and interference with communication which may limit their safe use over long periods; studies suggest that they have little impact on specific clinical skills in the short term but there is limited evidence on the impact of prolonged wearing. Finally, some clinical activities, particularly chest compressions, reduce the performance of filtering facepiece respirators.\n\nConclusionA wide range of respirator types and models is available for use in patient care during respiratory pandemics. Careful consideration of performance and impact of respirators is needed to maximise protection of healthcare workers and minimise disruption to the delivery of care.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Christopher Burton", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Briana Coles", + "author_inst": "University of Leicester" + }, + { + "author_name": "Anil Anisesh", + "author_inst": "Department of Medicine, Division of Occupational Medicine, University of Toronto" + }, + { + "author_name": "Simon Smith", + "author_inst": "Canadian Standards Biological Aerosols Working Group" + }, + { + "author_name": "Elaine Toomey", + "author_inst": "School of Allied Health, University of Limerick, Limerick, Ireland" + }, + { + "author_name": "Xin Hui Chan", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford" + }, + { + "author_name": "Lawrence Ross", + "author_inst": "Childrens Hospital of Los Angeles" + }, + { + "author_name": "Trisha Greenhalgh", + "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.05.20.20108167", "rel_title": "Decentralized governance may lead to higher infection levels and sub-optimal releases of quarantines amid the COVID-19 pandemic", @@ -1438964,77 +1441673,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.24.113423", - "rel_title": "A comparative study of isothermal nucleic acid amplification methods for SARS-CoV-2 detection at point of care", - "rel_date": "2020-05-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.24.113423", - "rel_abs": "COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread worldwide and put most of the world under lockdown. Despite that there have been emergently approved vaccines for SARS-CoV-2, COVID-19 cases, hospitalizations, and deaths have remained rising. Thus, rapid diagnosis and necessary public health measures are still key parts to contain the pandemic. In this study, the colorimetric isothermal nucleic acid amplification tests (iNAATs) for SARS-CoV-2 detection based on loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and polymerase spiral reaction (PSR) were designed and evaluated. The three methods showed the same limit of detection (LOD) value of 1 copy of the targeted gene per reaction. However, for the direct detection of SARS-CoV-2 genomic-RNA, LAMP outperformed both CPA and PSR, exhibiting the LOD value of roughly 43.14 genome copies/reaction. The results can be read with the naked eye within 45 minutes, without cross-reactivity to closely related coronaviruses. Moreover, the direct detection of SARS-CoV-2 RNA in simulated patient specimens by iNAATs was also successful. Finally, the ready-to-use lyophilized reagents for LAMP reactions were shown to maintain the sensitivity and LOD value of the liquid assays. The results indicate that the colorimetric lyophilized LAMP kit developed herein is highly suitable for detecting SARS-CoV-2 nucleic acids at point-of-care.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Diem Hong Tran", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Quoc Cuong Hoang", - "author_inst": "Directorial Board, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Hau Thi Tran", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Uyen Phuong Le", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Hoang Dang Khoa Do", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Le Minh Bui", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Duc Hai Nguyen", - "author_inst": "Planning Division, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Thuy Linh Hoang", - "author_inst": "Medical Analysis Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Thi Thanh Thao Nguyen", - "author_inst": "Microbiology and Immunology Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Hoang Anh Nguyen", - "author_inst": "Microbiology and Immunology Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Trung Hieu Nguyen", - "author_inst": "Microbiology and Immunology Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Minh Thang Cao", - "author_inst": "Microbiology and Immunology Department, Pasteur Institute in Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Van Van Vu", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Huong Thi Thu Phung", - "author_inst": "NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.05.24.113043", "rel_title": "Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein", @@ -1439242,6 +1441880,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.19.20107458", + "rel_title": "The IGNITE Trial: Participant Recruitment Lessons Prior to SARS-CoV-2", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107458", + "rel_abs": "Full and diverse participant enrollment is critical to the success and generalizability of all large-scale Phase III trials. Recruitment of sufficient participants is among the most significant challenges for many studies. The novel SARS-CoV-2 coronavirus pandemic has further changed and challenged the landscape for clinical trial execution, including screening and randomization. The Investigating Gains in Neurocognition in an Intervention Trial of Exercise (IGNITE) study has been designed as the most comprehensive test of aerobic exercise effects on cognition and brain health. Here we assess recruitment into IGNITE prior to the increased infection rates in the United States, and examine new challenges and opportunities for recruitment with a goal of informing the remaining required recruitment as infection containment procedures are lifted. The results may assist the design and implementation of recruitment for future exercise studies, and outline opportunities for study design that are flexible in the face of emerging threats.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Eric D Vidoni", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "Amanda Szabo-Reed", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "Chaeryon Kang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Jaime Perales-Puchalt", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "Ashley R Shaw", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "George Grove", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Morgan Hamill", + "author_inst": "Northeastern University" + }, + { + "author_name": "Donovan Henry", + "author_inst": "Northeastern University" + }, + { + "author_name": "Jeffrey M Burns", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "Charles Hillman", + "author_inst": "Northeastern University" + }, + { + "author_name": "Arthur F Kramer", + "author_inst": "Northeastern University" + }, + { + "author_name": "Edward McAuley", + "author_inst": "University of Illinois Urbana-Champaign" + }, + { + "author_name": "Kirk I Erickson", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.24.20112326", "rel_title": "Early Impact of COVID-19 Pandemic on Paediatric Surgical Practice in Nigeria: a National Survey of Paediatric Surgeons.", @@ -1440358,177 +1443063,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.23.20110916", - "rel_title": "A systems approach to inflammation identifies therapeutic targets in SARS-CoV-2 infection", - "rel_date": "2020-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20110916", - "rel_abs": "BackgroundInfection with SARS-CoV-2 manifests itself as a mild respiratory tract infection in the majority of individuals, which progresses to a severe pneumonia and acute respiratory distress syndrome (ARDS) in 10-15% of patients. Inflammation plays a crucial role in the pathogenesis of ARDS, with immune dysregulation in severe COVID-19 leading to a hyperinflammatory response. A comprehensive understanding of the inflammatory process in COVID-19 is lacking.\n\nMethodsIn this prospective, multicenter observational study, patients with PCR-proven or clinically presumed COVID-19 admitted to the intensive care unit (ICU) or clinical wards were included. Demographic and clinical data were obtained and plasma was serially collected. Concentrations of IL-6, TNF-, complement components C3a, C3c and the terminal complement complex (TCC) were determined in plasma by ELISA. Additionally, 269 circulating biomarkers were assessed using targeted proteomics. Results were compared between ICU and non ICU patients.\n\nFindingsA total of 119 (38 ICU and 91 non ICU) patients were included. IL-6 plasma concentrations were elevated in COVID-19 (ICU vs. non ICU, median 174.5 pg/ml [IQR 94.5-376.3] vs. 40.0 pg/ml [16.5-81.0]), whereas TNF- concentrations were relatively low and not different between ICU and non ICU patients (median 24.0 pg/ml [IQR 16.5-33.5] and 21.5 pg/ml [IQR 16.0-33.5], respectively). C3a and terminal complement complex (TCC) concentrations were significantly higher in ICU vs. non ICU patients (median 556.0 ng/ml [IQR 333.3-712.5]) vs. 266.5 ng/ml [IQR 191.5-384.0] for C3a and 4506 mAU/ml [IQR 3661-6595] vs. 3582 mAU/ml [IQR 2947-4300] for TCC) on the first day of blood sampling. Targeted proteomics demonstrated that IL-6 (logFC 2.2), several chemokines and hepatocyte growth factor (logFC 1.4) were significantly upregulated in ICU vs. non ICU patients. In contrast, stem cell factor was significantly downregulated (logFC -1.3) in ICU vs. non ICU patients, as were DPP4 (logFC -0.4) and protein C inhibitor (log FC -1.0), the latter two factors also being involved in the regulation of the kinin-kallikrein pathway. Unsupervised clustering pointed towards a homogeneous pathogenetic mechanism in the majority of patients infected with SARS-CoV-2, with patient clustering mainly based on disease severity.\n\nInterpretationWe identified important pathways involved in dysregulation of inflammation in patients with severe COVID-19, including the IL-6, complement system and kinin-kallikrein pathways. Our findings may aid the development of new approaches to host-directed therapy.\n\nFundingVidi grant (F.L.v.d.V.) and Spinoza grant (M.G.N.) from the Netherlands Organization for Scientific Research, and ERC Advanced Grant (#833247 to M.G.N.).", - "rel_num_authors": 39, - "rel_authors": [ - { - "author_name": "Frank L. van de Veerdonk", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Nico A.F. Janssen", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Inge Grondman", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Aline H. de Nooijer", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Valerie A.C.M. Koeken", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Vasiliki Matzaraki", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Collins K. Boahen", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Vinod Kumar", - "author_inst": "Radboud University Medical Center and University Medical Center Groningen" - }, - { - "author_name": "Matthijs Kox", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Hans J.P.M. Koenen", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Ruben L. Smeets", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Irma Joosten", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Roger J.M. Br\u00fcggemann", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Ilse J.E. Kouijzer", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Hans G. van der Hoeven", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Jeroen A. Schouten", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Tim Frenzel", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Monique Reijers", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Wouter Hoefsloot", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Anton S.M. Dofferhoff", - "author_inst": "Canisius Wilhelmina Hospital" - }, - { - "author_name": "Ang\u00e8le P.M. Kerckhoffs", - "author_inst": "Jeroen Bosch Hospital" - }, - { - "author_name": "Marc J.T. Blaauw", - "author_inst": "Bernhoven Hospital" - }, - { - "author_name": "Karin Veerman", - "author_inst": "Sint Maartenskliniek" - }, - { - "author_name": "Coen Maas", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Arjan H. Schoneveld", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Imo E. Hoefer", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Lennie P.G. Derde", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Loek Willems", - "author_inst": "Hycult Biotechnology" - }, - { - "author_name": "Erik Toonen", - "author_inst": "Hycult Biotechnology" - }, - { - "author_name": "Marcel van Deuren", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Jos W.M. van der Meer", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Reinout van Crevel", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Evangelos J. Giamarellos-Bourboulis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Leo A.B. Joosten", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Michel M. van den Heuvel", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Jacobien Hoogerwerf", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Quirijn de Mast", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Peter Pickkers", - "author_inst": "Radboud University Medical Center" - }, - { - "author_name": "Mihai G. Netea", - "author_inst": "Radboud University Medical Center and University of Bonn" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.23.20110866", "rel_title": "Visualizing the COVID-19 pandemic in Bangladesh using coxcombs: A tribute to Florence Nightingale", @@ -1440764,6 +1443298,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.22.20110320", + "rel_title": "Mortality of the COVID-19 outbreak in Sweden in relation to previous severe disease outbreaks", + "rel_date": "2020-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110320", + "rel_abs": "Influenza viruses have caused disease outbreaks in human societies for a long time. Influenza often has rapid onset and relatively short duration, both in the individual and in the population. The case fatality rate varies for different strains of the virus, as do the effects on total mortality. Outbreaks related to coronavirus infections have recently become a global concern but much less is known about the dynamics of these outbreaks and their effects on mortality.\n\nIn this work, disease outbreaks in Sweden, in the time period of 1860-2020, are characterized and compared to the currently ongoing COVID-19 outbreak. The focus is on outbreaks with a sharp increase in all-cause mortality. Outbreak onset is defined as the time point when deaths counts starts to increase consistently for a period of 10 days. The duration of the outbreak is defined as the time period in which mortality rates are elevated. Excess mortality is estimated by standard methods.\n\nIn total there were 15 outbreaks detected in the time period, the first 14 were likely caused by influenza virus infections, the last by SARS-CoV-2. The mortality dynamics of the SARS-CoV-2 outbreak is shown to be similar to outbreaks due to influenza virus, and in terms of the number of excess deaths, it is the worst outbreak in Sweden since the Spanish flu of 1918-1919.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Anders Ledberg", + "author_inst": "Stockholm university" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.22.20110460", "rel_title": "Effects of Government Mandated Social Distancing Measures on Cumulative Incidence of COVID-19 in the United States and its Most Populated Cities", @@ -1441812,29 +1444365,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.21.20108860", - "rel_title": "Immunity after COVID-19: protection or sensitization ?", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108860", - "rel_abs": "Motivated by historical and present clinical observations, we discuss the possible unfavorable evolution of the immunity (similar to documented antibody-dependent enhancement scenarios) after a first infection with COVID-19. More precisely we ask the question of how the epidemic outcomes are affected if the initial infection does not provide immunity but rather sensitization to future challenges. We first provide background comparison with the 2003 SARS epidemic. Then we use a compartmental epidemic model structured by immunity level that we fit to available data; using several scenarios of the fragilization dynamics, we derive quantitative insights into the additional expected numbers of severe cases and deaths.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Antoine Danchin", - "author_inst": "Institut Cochin" - }, - { - "author_name": "Gabriel TURINICI", - "author_inst": "Universite Paris Dauphine - PSL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.20.20108340", "rel_title": "The estimations of the COVID-19 incubation period: a systematic review of the literature", @@ -1442022,6 +1444552,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.21.20108985", + "rel_title": "Congregate Shelter Characteristics and Prevalence of Asymptomatic SARS-CoV-2", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108985", + "rel_abs": "BackgroundIndividuals experiencing homelessness residing in congregate shelters have increased risk for SARS-CoV-2 infection. Prevalence of asymptomatic SARS-CoV-2 in congregate shelters is high, but shelter characteristics associated with SARS-CoV-2 transmission are currently unknown.\n\nMethodsWe conducted a cross-sectional, multicenter cohort study across five congregate shelters in Rhode Island. We tested people 18 years of age and older staying in Rhode Island congregate shelters in April 2020 during the COVID-19 pandemic. A survey instrument was designed and implemented based on an a priori sample size. All consented participants reported basic demographics, recent travel, duration of time at the shelter, any symptomatology, and had their temperature and pulse oximetry measured. Each participant was tested for COVID-19 using nasopharyngeal swabbing. Shelter characteristics about location, occupancy, resident length of stay, and COVID-19 mitigation strategies were collected through structured phone questionnaire with shelter staff.\n\nResultsA total of 302 individuals were screened and 299 participated across five homeless shelters. The median age was 47.9 (range 18-85) and 20% were female. Of the 299 participants, 35 (11.7%) were positive for SARS-CoV-2; rates varied among shelters, ranging from 0% to 35%. Among the participants in the study, 5% had a new cough, 4% shortness of breath, and 3% reported loss of taste or smell. Symptom prevalence did not vary significantly between positive and negative SARS-CoV-2 groups. Regular symptom screening was not associated with lower infection rates. Shelters with higher rates of positivity were in more densely populated areas, cared for a more transient populations, and instituted fewer social distancing practices for sleeping arrangements or mealtimes.\n\nConclusions and RelevanceResidents of congregate shelters are at increased risk for asymptomatic transmission of SARS-CoV-2. To reduce transmission and enable continuation of low-threshold shelter services, there is a need for universal testing, implementation of infection control and physical distancing measures within congregate shelters, and expansion of non-congregate supportive housing.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Elizabeth A Samuels", + "author_inst": "Alpert Medical School of Brown University" + }, + { + "author_name": "Rebecca Karb", + "author_inst": "Department of Emergency Medicine, Warren Alpert Medical School of Brown University" + }, + { + "author_name": "Rahul Vanjani", + "author_inst": "Division of General Internal Medicine, Warren Alpert Medical School of Brown University" + }, + { + "author_name": "M. Catherine Trimbur", + "author_inst": "Division of General Internal Medicine, Warren Alpert Medical School of Brown University" + }, + { + "author_name": "Anthony Napoli", + "author_inst": "Department of Emergency Medicine, Warren Alpert Medical School of Brown University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.20.20108555", "rel_title": "Effects of a DPP-4 inhibitor and RAS blockade on clinical outcomes of patients with diabetes and COVID-19", @@ -1443482,41 +1446047,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, - { - "rel_doi": "10.1101/2020.05.20.20108183", - "rel_title": "A Rapid Review of the Asymptomatic Proportion of PCR-Confirmed SARS-CoV-2 Infections in Community Settings", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108183", - "rel_abs": "BackgroundUp to 80% of active SARS-CoV-2 infections are proposed to be asymptomatic based on cross-sectional studies. However, accurate estimates of the asymptomatic proportion require systematic detection and follow-up to differentiate between truly asymptomatic and pre-symptomatic cases. We conducted a rapid review and meta-analysis of current evidence regarding the asymptomatic proportion of PCR-confirmed SARS-CoV-2 infections based on methodologically-appropriate studies in community settings.\n\nMethodsWe searched Medline and EMBASE for peer-reviewed articles, and BioRxiv and MedRxiv for pre-prints published prior to 05/05/2020. We included studies based in community settings that involved systematic PCR testing on participants and follow-up symptom monitoring regardless of symptom status. We extracted data on study characteristics, frequencies of PCR-confirmed infections by symptom status, and (if available) cycle threshold values and/or duration of viral shedding by symptom status. We computed estimates of the asymptomatic proportion and 95% confidence intervals for each study and overall using random effect meta-analysis.\n\nFindingsWe screened 270 studies and included 6. The pooled estimate for the asymptomatic proportion of SARS-CoV-2 infections was 11% (95% CI 4%-18%). Estimates of baseline viral load appeared to be similar for asymptomatic and symptomatic cases based on available data in three studies, though detailed reporting of cycle threshold values and natural history of viral shedding by symptom status was limited.\n\nInterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted.\n\nFundingMedical Research Council", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sarah Beale", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "University College London" - }, - { - "author_name": "Laura Shallcross", - "author_inst": "University College London" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "University College London" - }, - { - "author_name": "Ellen Fragaszy", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.20.20108068", "rel_title": "Demographic and Clinical Characteristics of the Severe Covid-19 Infections: First Report from Mashhad University of Medical Sciences, Iran", @@ -1443800,6 +1446330,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.20.20108415", + "rel_title": "Underreporting of death by COVID-19 in Brazil's second most populous state", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108415", + "rel_abs": "The COVID-19 pandemic brings to light the reality of the Brazilian health system. The underreporting of COVID-19 deaths in the state of Minas Gerais (MG), where is concentrated the second largest population of the country, reveals government unpreparedness, as there is a low capacity of testing in the population, which prevents the real understanding of the general panorama of Sars-Cov-2 dissemination. The goals of this research are to analyze the causes of deaths in the different Brazilian government databases (ARPEN and SINAN) and to assess whether there are sub-records shown by the unexpected increase in the frequency of deaths from causes clinically similar to COVID-19. A descriptive and quantitative analysis of the number of COVID-19 deaths and similar causes was made in different databases. Ours results demonstrate that the different official sources had a discrepancy of 209.23% between these data referring to the same period. There was also a 648.61% increase in SARS deaths in 2020, when compared to the average of previous years. Finally, it was shown that there was an increase in the rate of pneumonia and respiratory insufficiency (RI) by 5.36% and 5.72%, respectively. In conclusion, there is an underreporting of COVID-19 deaths in MG due to the unexplained excess of SARS deaths, Respiratory insufficiency and pneumonia compared to previous years.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Thiago Henrique Evangelista Alves", + "author_inst": "Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil." + }, + { + "author_name": "Tafarel Andrade de Souza", + "author_inst": "Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil." + }, + { + "author_name": "Samyla de Almeida Silva", + "author_inst": "Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil." + }, + { + "author_name": "Nayani Alves Ramos", + "author_inst": "Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil." + }, + { + "author_name": "Stefan Vilges de Oliveira", + "author_inst": "Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.21.20107946", "rel_title": "The connection of growth and medication of COVID-19 affected people after 30 days of lock down in India", @@ -1444756,65 +1447321,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.18.20105841", - "rel_title": "An Interpretable Machine Learning Framework for Accurate Severe vs Non-severe COVID-19 Clinical Type Classification", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105841", - "rel_abs": "Effectively and efficiently diagnosing COVID-19 patients with accurate clinical type is essential to achieve optimal outcomes for the patients as well as reducing the risk of overloading the healthcare system. Currently, severe and non-severe COVID-19 types are differentiated by only a few clinical features, which do not comprehensively characterize complicated pathological, physiological, and immunological responses to SARS-CoV-2 invasion in different types. In this study, we recruited 214 confirmed COVID-19 patients in non-severe and 148 in severe type, from Wuhan, China. The patients comorbidity and symptoms (26 features), and blood biochemistry (26 features) upon admission were acquired as two input modalities. Exploratory analyses demonstrated that these features differed substantially between two clinical types. Machine learning random forest (RF) models using features in each modality were developed and validated to classify COVID-19 clinical types. Using comorbidity/symptom and biochemistry as input independently, RF models achieved >90% and >95% predictive accuracy, respectively. Input features importance based on Gini impurity were further evaluated and top five features from each modality were identified (age, hypertension, cardiovascular disease, gender, diabetes; D-Dimer, hsTNI, neutrophil, IL-6, and LDH). Combining top 10 multimodal features, RF model achieved >99% predictive accuracy. These findings shed light on how the human body reacts to SARS-CoV-2 invasion as a unity and provide insights on effectively evaluating COVID-19 patients severity and developing treatment plans accordingly. We suggest that symptoms and comorbidities can be used as an initial screening tool for triaging, while biochemistry and features combined are applied when accuracy is the priority.\n\nOne Sentence SummaryWe trained and validated machine learning random forest (RF) models to predict COVID-19 severity based on 26 comorbidity/symptom features and 26 biochemistry features from a cohort of 214 non-severe and 148 severe type COVID-19 patients, identified top features from both feature modalities to differentiate clinical types, and achieved predictive accuracy of >90%, >95%, and >99% when comorbidity/symptom, biochemistry, and combined top features were used as input, respectively.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Yuanfang Chen", - "author_inst": "Institute of HIV/AIDS/STI Prevention and Control, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Liu Ouyang", - "author_inst": "Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China" - }, - { - "author_name": "Sheng Bao", - "author_inst": "Department of Computer Science, Iowa State University, USA" - }, - { - "author_name": "Qian Li", - "author_inst": "Department of Pediatrics, Affiliated Kunshan Hospital of Jiangsu University, Kunshan 215300, China" - }, - { - "author_name": "Lei Han", - "author_inst": "Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Hengdong Zhang", - "author_inst": "Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Baoli Zhu", - "author_inst": "Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Ming Xu", - "author_inst": "Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China" - }, - { - "author_name": "Jie Liu", - "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China" - }, - { - "author_name": "Yaorong Ge", - "author_inst": "Department of Software and Information Systems, UNC Charlotte, Charlotte, NC 28223, USA" - }, - { - "author_name": "Shi Chen", - "author_inst": "Department of Public Health Sciences, College of Health and Human Services, University of North Carolina Charlotte, Charlotte, NC 28262, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20105239", "rel_title": "Risks to Children under-five in India from COVID-19", @@ -1445062,6 +1447568,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.18.20106104", + "rel_title": "Mathematical framework to model Covid-19 daily deaths", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20106104", + "rel_abs": "The novel coronavirus (2019-nCoV) pandemic has caused widespread socio-economic disruption and, as of 04/07/2020, resulted in more than 72,614 confirmed deaths worldwide. Robust prediction of the trajectory of the death incidence curve is helpful for policy decisions during this ongoing crisis. We propose a non-parametric model to fit the number of daily deaths in a region, which hypothesizes that the death incidence curve will have a convex shape in the beginning, a concave shape near the peak, and a convex shape in the final stage of the death incidence curve after the peak. Using this, we performed robust short-term predictions on phases in five countries worldwide and five US states. Our analysis shows while the five states are all at peaks or past their peaks, US as a country is possibly not at peak yet. Our model can be easily fitted on daily death data from any region.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Poulami Barman", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Nabarun Deb", + "author_inst": "Department of Statistics, Columbia University, NY, USA" + }, + { + "author_name": "Sumit Mukherjee", + "author_inst": "Department of Statistics, Columbia University, NY, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.18.20105684", "rel_title": "COVID19-Global: A shiny application to perform a global comparative data visualization for the SARS-CoV-2 epidemic", @@ -1446490,33 +1449023,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.19.20099317", - "rel_title": "Early antibody response to SARS-CoV-2", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20099317", - "rel_abs": "BackgroundThe role and significance of the immune response to SARS-CoV-2 infection is not yet well known.\n\nMethodsWe conducted a study on 46 symptomatic subjects with disease confirmed by laboratory tests, to evaluate the presence of IgG and IgM antibodies in these subjects in relation to the time elapsed since the onset of symptoms. The analytical performance of the method used in the study and the effect of two different serum and plasma matrices were also assessed.\n\nResultsIgG positivity was demonstrated in 100% of cases 15 days after the onset of the disease. IgM show lower concentrations and do not exceed 77% of cases after 15 days. The analytical performance of the method used (Maglumi 800, Snibe, China) was confirmed to be good in terms of imprecision, linearity and commutability in two sample matrix.\n\nConclusionThe serological study through the search for specific IgG for SARS-CoV-2 results to be sensitive and suitable for population research and evidences that this approach can also play an important role in diagnosis.\n\nThe diagnostic performance of specific IgMs are lower.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ruggero Dittadi", - "author_inst": "Laboratory Medicine, Ospedale dell'Angelo, ULSS3 Serenissima, Mestre, Venice, Italy" - }, - { - "author_name": "Haleh Afshar", - "author_inst": "Laboratory Medicine, Ospedale dell'Angelo, Mestre, Italy" - }, - { - "author_name": "Paolo Carraro", - "author_inst": "Laboratory Medicine, Ospedale dell'Angelo, Mestre, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20086157", "rel_title": "COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis", @@ -1446816,6 +1449322,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.05.17.20104604", + "rel_title": "Characterization of Patients Who Return to Hospital Following Discharge from Hospitalization For COVID-19", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104604", + "rel_abs": "BackgroundData on patients with coronavirus disease 2019 (COVID-19) who return to hospital after discharge are scarce. Characterization of these patients may inform post-hospitalization care.\n\nMethods and FindingsRetrospective cohort study of patients with confirmed SARS-CoV-2 discharged alive from five hospitals in New York City with index hospitalization between February 27th-April 12th, 2020, with follow-up of [≥]14 days. Significance was defined as P<0.05 after multiplying P by 125 study-wide comparisons. Of 2,864 discharged patients, 103 (3.6%) returned for emergency care after a median of 4.5 days, with 56 requiring inpatient readmission. The most common reason for return was respiratory distress (50%). Compared to patients who did not return, among those who returned there was a higher proportion of COPD (6.8% vs 2.9%) and hypertension (36% vs 22.1%). Patients who returned also had a shorter median length of stay (LOS) during index hospitalization (4.5 [2.9,9.1] vs. 6.7 [3.5, 11.5] days; Padjusted=0.006), and were less likely to have required intensive care on index hospitalization (5.8% vs 19%; Padjusted=0.001). A trend towards association between absence of in-hospital anticoagulation on index admission and return to hospital was also observed (20.9% vs 30.9%, Padjusted=0.064). On readmission, rates of intensive care and death were 5.8% and 3.6%, respectively.\n\nConclusionsReturn to hospital after admission for COVID-19 was infrequent within 14 days of discharge. The most common cause for return was respiratory distress. Patients who returned had higher proportion of COPD and hypertension with shorter LOS on index hospitalization, and a trend towards lower rates of in-hospital treatment-dose anticoagulation. Future studies should focus on whether these comorbid conditions, longer LOS and anticoagulation are associated with reduced readmissions.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Sulaiman Somani", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Felix Richter", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Valentin Fuster", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jessica De Freitas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nidhi Naik", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Keith Sigel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mount Sinai Covid Informatics Center (MSCIC)", + "author_inst": "" + }, + { + "author_name": "Erwin P. Boettinger", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Matthew A. Levin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Zahi Fayad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Allan C. Just", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Shan Zhao", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Benjamin S. Glicksberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Anuradha Lala", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Girish Nadkarni", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.05.17.20104547", "rel_title": "Meteorological Conditions and Covid-19 in Large U.S. Cities", @@ -1448036,37 +1450621,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.05.17.20104927", - "rel_title": "Prevalence Threshold and Temporal Interpretation of Screening Tests: The Example of the SARS-CoV-2 (COVID-19) Pandemic", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104927", - "rel_abs": "The curvilinear relationship between a screening tests positive predictive value (PPV) and its target disease prevalence is proportional. In consequence, there is an inflection point of maximum curvature in the screening curve defined as a function of the sensitivity (a) and specificity (b) beyond which the rate of change of a tests PPV declines sharply relative to disease prevalence ({phi}). Herein, we demonstrate a mathematical model exploring this phenomenon and define the prevalence threshold point ({phi}e) where this change occurs as:\n\nO_FD O_INLINEFIG[Formula]C_INLINEFIGC_FD\n\nUnderstanding where this prevalence point lies in the curve has important implications for the interpretation of test results, the administration of healthcare systems, the implementation of public health measures, and in cases of pandemics like SARS-CoV-2, the functioning of society at large. To illustrate the methods herein described, we provide the example of the screening strategies used in the SARS-CoV-2 (COVID-19) pandemic, and calculate the prevalence threshold statistic of different tests available today. This concept can help contextualize the validity of a screening test in real time, thereby enhancing our understanding of the dynamics of the current pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jacques Balayla", - "author_inst": "McGill University" - }, - { - "author_name": "Ariane Lasry", - "author_inst": "McGill University" - }, - { - "author_name": "Yaron Gil", - "author_inst": "McGill University" - }, - { - "author_name": "Alexander Volodarsky-Perel", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.17.20104612", "rel_title": "The correspondence between the structure of the terrestrial mobility network and the emergence of COVID-19 in Brazil", @@ -1448298,6 +1450852,121 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.05.18.20105569", + "rel_title": "Who should we test for COVID-19?A triage model built from national symptom surveys", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105569", + "rel_abs": "The gold standard for COVID-19 diagnosis is detection of viral RNA in a reverse transcription PCR test. Due to global limitations in testing capacity, effective prioritization of individuals for testing is essential. Here, we devised a model that estimates the probability of an individual to test positive for COVID-19 based on answers to 9 simple questions regarding age, gender, presence of prior medical conditions, general feeling, and the symptoms fever, cough, shortness of breath, sore throat and loss of taste or smell, all of which have been associated with COVID-19 infection. Our model was devised from a subsample of a national symptom survey that was answered over 2 million times in Israel over the past 2 months and a targeted survey distributed to all residents of several cities in Israel. Overall, 43,752 adults were included, from which 498 self-reported as being COVID-19 positive. We successfully validated the model on held-out individuals from Israel where it achieved a positive predictive value (PPV) of 46.3% at a 10% sensitivity and demonstrated its applicability outside of Israel by further validating it on an independently collected symptom survey dataset from the U.K., U.S. and Sweden, where it achieved a PPV of 34.7% at 10% sensitivity. Moreover, evaluating the models performance on this latter independent dataset on entries collected one week prior to the PCR test and up to the day of the test we found the highest performance on the day of the test. As our tool can be used online and without the need of exposure to suspected patients, it may have worldwide utility in combating COVID-19 by better directing the limited testing resources through prioritization of individuals for testing, thereby increasing the rate at which positive individuals can be identified and isolated.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Saar Shoer", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Tal Karady", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Ayya Keshet", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Smadar Shilo", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Hagai Rossman", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Amir Gavrieli", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Tomer Meir", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Amit Lavon", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Dmitry Kolobkov", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Iris Kalka", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Anastasia Godneva", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Ori Cohen", + "author_inst": "-" + }, + { + "author_name": "Adam Kariv", + "author_inst": "The public knowledge workshop" + }, + { + "author_name": "Ori Hoch", + "author_inst": "The public knowledge workshop" + }, + { + "author_name": "Mushon Zer-Aviv", + "author_inst": "The public knowledge workshop" + }, + { + "author_name": "Noam Castel", + "author_inst": "The public knowledge workshop" + }, + { + "author_name": "Carole Sudre", + "author_inst": "King's College London" + }, + { + "author_name": "Anat Ekka Zohar", + "author_inst": "Epidemiology and Database Research Unit, Maccabi Healthcare Services" + }, + { + "author_name": "Angela Irony", + "author_inst": "Epidemiology and Database Research Unit, Maccabi Healthcare Services" + }, + { + "author_name": "Timothy Spector", + "author_inst": "King's College London" + }, + { + "author_name": "Benjamin Geiger", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Dorit Hizi", + "author_inst": "The public knowledge workshop" + }, + { + "author_name": "Varda Shalev", + "author_inst": "Epidemiology and Database Research Unit, Maccabi Healthcare Services" + }, + { + "author_name": "Ran Balicer", + "author_inst": "Clalit Research Institute, Clalit Health Services" + }, + { + "author_name": "Eran Segal", + "author_inst": "Weizmann Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.18.20105783", "rel_title": "How many patients will need ventilators tomorrow?", @@ -1449506,57 +1452175,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.05.17.20104901", - "rel_title": "Development of an interactive, agent-based local stochastic model of COVID-19 transmission and evaluation of mitigation strategies illustrated for the state of Massachusetts, USA", - "rel_date": "2020-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104901", - "rel_abs": "Since its discovery in the Hubei province of China, the global spread of the novel coronavirus SARS-CoV-2 has resulted in millions of COVID-19 cases and hundreds of thousands of deaths. The spread throughout Asia, Europe, and the Americas has presented one of the greatest infectious disease threats in recent history and has tested the capacity of global health infrastructures. Since no effective vaccine is available, isolation techniques to prevent infection such as home quarantine and social distancing while in public have remained the cornerstone of public health interventions. While government and health officials were charged with implementing stay-at-home strategies, many of which had little guidance as to the consequences of how quickly to begin them. Moreover, as the local epidemic curves have been flattened, the same officials must wrestle with when to ease or cease such restrictions as to not impose economic turmoil. To evaluate the effects of quarantine strategies during the initial epidemic, an agent based modeling framework was created to take into account local spread based on geographic and population data with a corresponding interactive desktop and web-based application. Using the state of Massachusetts in the United States of America, we have illustrated the consequences of implementing quarantines at different time points after the initial seeding of the state with COVID-19 cases. Furthermore, we suggest that this application can be adapted to other states, small countries, or regions within a country to provide decision makers with critical information necessary to best protect human health.\n\nAuthor summaryIn this work we presented a local agent-based geographic model for the epidemic spread of COVID-19 with and without quarantine measures. The model is implemented as an interactive Microsoft Windows application, as a web tool online (summaries only), and the source code is freely available at GitHub. In this article, the model is presented for the state of Massachusetts (United States), but can be easily adopted to other administrative districts, areas and territories where the demographics and population characteristics of the reported cases are known. After calibration, the model predicts the morbidity and mortality of the epidemic as it spreads with different quarantine parameters, which lead to reduction of social contact probabilities between individuals. The model outputs for different quarantine start dates and durations are then summarized and compared to actual disease incidence. These summaries demonstrate the effectiveness of the early quarantine measures on the reduction of the number of new infections and deaths. The model framework can also be adopted for use in future decision making process for government and health officials as plans to cease or ease quarantines continue to evolve using the interactive application.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Alexander Kirpich", - "author_inst": "Georgia State University" - }, - { - "author_name": "Vladimir Koniukhovskii", - "author_inst": "EPAM Systems" - }, - { - "author_name": "Vladimir Shvartc", - "author_inst": "EPAM Systems" - }, - { - "author_name": "Pavel Skums", - "author_inst": "Georgia State University" - }, - { - "author_name": "Thomas A. Weppelmann", - "author_inst": "University of South Florida" - }, - { - "author_name": "Evgeny Imyanitov", - "author_inst": "N.N. Petrov Research Institute of Oncology" - }, - { - "author_name": "Semyon Semyonov", - "author_inst": "Quantori" - }, - { - "author_name": "Konstantin Barsukov", - "author_inst": "EPAM Systems" - }, - { - "author_name": "Yuriy Gankin", - "author_inst": "Quantori" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.16.099242", "rel_title": "Capillary Electrophoresis of PCR fragments with labelled primers for testing the SARS-Cov-2", @@ -1449824,6 +1452442,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.21.107870", + "rel_title": "Unfractionated heparin potently inhibits the binding of SARS-CoV-2 spike protein to a human cell line", + "rel_date": "2020-05-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.107870", + "rel_abs": "The SARS-CoV-2 spike protein is known to bind to the receptor, ACE2, on the surface of target cells. The spike protein is processed by membrane proteases, including TMPRSS2, and either internalises or fuses directly with the cell, leading to infection. We have identified a human cell line that expresses both ACE2 and TMPRSS2, the RT4 urinary bladder transitional carcinoma, and used it to develop a proxy assay for viral interactions with host cells. A tagged recombinant form of the spike protein, containing both the S1 and S2 domains, interacted strongly with RT4 cells as determined by flow cytometry, whereas the S1 domain and the receptor binding domain (RBD) interacted weakly. S1S2 interaction was temperature dependent and increased sharply at 37{degrees}C, suggesting that processing of the intact spike protein is likely to be important in the interaction. S1S2 protein could associate with cells with a low dependence on ACE2 expression, while RBD required the presence of ACE2 for interaction. As the spike protein has previously been shown to bind heparin, a soluble glycosaminoglycan, we used a flow cytometric assay to determine the effect of heparin on spike protein interaction with RT4 cells. Unfractionated heparin inhibited spike protein interaction with an IC50 value of <0.05U/ml whereas two low molecular weight heparins were much less effective. A mutant form of the spike protein, lacking the Arg-rich region proposed to be a furin cleavage site, interacted very weakly with cells and had a lower affinity for unfractionated and lower molecular weight heparin than the wild type spike protein. This indicates that the furin cleavage site might also be a heparin binding site and potentially important in interactions with host cells. Taken together, our data suggest that heparin, particularly unfractionated forms, could be considered to reduce clinical manifestations of COVID-19 by inhibiting continuing viral infection.\n\nAuthor SummarySince the emergence of SARS-CoV-2 in 2019, the world has faced a vast public health crisis. SARS-CoV-2 associates with human cells through interaction of the viral spike protein with the host receptor, ACE2. In the absence of a vaccine, new treatments are required to reduce the morbidity and mortality of SARS-CoV-2. Here, we use a novel technique to demonstrate spike protein interactions with human cells with low levels of ACE2 at the cell surface, suggesting a secondary receptor. We demonstrate the importance of a new heparin-binding site within the viral spike protein for these interactions. We also found that unfractionated heparin was able to bind to the viral spike protein and therefore, potently inhibit viral spike protein interactions with human cells. Our data demonstrate that ACE2 is not absolutely required for spike protein interactions with human cells and furthermore, that unfractionated heparin should be considered as a treatment to reduce SARS-CoV-2 viral infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lynda J Partridge", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Lucy Urwin", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Martin JH Nicklin", + "author_inst": "University of Sheffield" + }, + { + "author_name": "David C James", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Luke R Green", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Peter N Monk", + "author_inst": "University of Sheffield" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.21.108605", "rel_title": "Mechanistic insights into ventricular arrhythmogenesis of hydroxychloroquine and azithromycin for the treatment of COVID-19", @@ -1450876,33 +1453533,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.16.20104133", - "rel_title": "Predicting the COVID-19 positive cases in India with concern to Lockdown by using Mathematical and Machine Learning based Models", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20104133", - "rel_abs": "In this study, we analyze the number of infected positive cases of COVID-19 outbreak with concern to lockdown in India in the time window of February 11th 2020 to Jun 30th 2020. The first case in India was reported in Kerala on January 30th 2020. To break the chain of spreading, Government announced a nationwide lockdown on March 24th 2020, which is increased two times. The Ongoing lockdown 3.0 is over on May 18th, 2020. We derived how the lockdown relaxation is going to impact on containment of the outbreak. Here the Exponential Growth Model has been used to derive the epidemic curve based on the data collected from February 11th 2020, to May 11th 2020, and the Machine Learning based Linear Regression model that gives the epidemic curve to predict the cases with the continuous flow of the lockdown. We estimate that if the lockdown is continuing with more relaxation, then the estimated infected cases reach up to 1.16 crores by June 30th 2020, and the lockdown would persist with current restriction, then the expected predicted infected cases are 5.69 lacs. The Exponential Growth Model and the Linear Regression Model are advantageous to predict the number of affected cases of COVID-19. These models can be used for forecasting in long term intervals. It shows from our result that lockdown with certain restriction has a vital role in preventing the spreading of this epidemic in this current situation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ajit Kumar Pasayat", - "author_inst": "IIT Kharagpur" - }, - { - "author_name": "Satya Narayan Pati", - "author_inst": "Centurion University" - }, - { - "author_name": "Aashirbad Maharana", - "author_inst": "Centurion University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.16.20104489", "rel_title": "A Computer Simulation Study on novel Corona Virus Transmission among the People in a Queue", @@ -1451034,6 +1453664,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.16.20103879", + "rel_title": "The Effects of Stringent Interventions for Coronavirus Pandemic", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20103879", + "rel_abs": "The pandemic of COVID-19 has caused severe public health consequences around the world. Many interventions of COVID-19 have been implemented. It is of great public health and societal importance to evaluate the effects of interventions in the pandemic of COVID-19. In this paper, with help of synthetic control method, regression discontinuity and a Susceptible-Infected and infectious without isolation-Hospitalized in isolation-Removed (SIHR) model, we evaluate the horizontal and longitudinal effects of stringent interventions implemented in Wenzhou, a representative urban city of China, where stringent interventions were enforced to curb its own epidemic situation with rapidly increasing newly confirmed cases. We found that there were statistically significant treatment effects of those stringent interventions which reduced the cumulative confirmed cases of COVID-19. Those reduction effects would increase over time. Also, if the stringent interventions were delayed by 2 days or mild interventions were implemented instead, the expected number of cumulative confirmed cases would have been nearly 2 times or 5 times of the actual number. The effects of stringent interventions are significant in mitigating the epidemic situation of COVID-19. The slower the interventions were implemented, the more severe the epidemic would have been, and the stronger the interventions would have been required.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ting Tian", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Wenxiang Luo", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Yukang Jiang", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Minqiong Chen", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Canhong Wen", + "author_inst": "University of Science and Technology of China" + }, + { + "author_name": "Wenliang Pan", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Xueqin Wang", + "author_inst": "University of Science and Technology of China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.16.20104430", "rel_title": "A Real-Time Statistical Model for Tracking and Forecasting COVID-19 Deaths, Prevalence and Incidence", @@ -1452422,49 +1455095,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.16.20102095", - "rel_title": "Systematic and Statistical Review of COVID19 Treatment Trials", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20102095", - "rel_abs": "ObjectiveThe following systematic review and meta-analysis compiles the current data regarding human controlled COVID-19 treatment trials.\n\nMethodsAn electronic search of the literature compiled studies pertaining to human controlled treatment trials with COVID-19. Medications assessed included lopinavir/ritonavir, arbidol, hydroxychloroquine, favipiravir, and heparin. Statistical analyzes were performed for common viral clearance endpoints whenever possible.\n\nResultsLopinavir/ritonavir showed no significant effect on viral clearance for COVID-19 cases (OR 0.95 [95% CI 0.50-1.83]). Hydroxychloroquine also showed no significant effect on COVID-19 viral clearance rates (OR 2.16 [95% CI 0.80-5.84]). Arbidol showed no seven-day (OR 1.63 [95% CI 0.76-3.50]) or 14-day viral (OR 5.37 [95% CI 0.35-83.30]) clearance difference compared to lopinavir/ritonavir. Review of literature showed no significant clinical improvement with lopinavir/ritonavir, arbidol, hydroxychloroquine, or remdesivir. Favipiravir showed quicker symptom improvement compared to lopinavir/ritonavir and arbidol. Heparin showed improvement with severe COVID-19 cases.\n\nConclusionCurrent medications do not show significant effect on COVID-19 viral clearance rates. Favipiravir shows favorable results compared to other tested medications. Heparin shows benefit for severe cases of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Juan Arturo Siordia Jr.", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Michael Bernaba", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Kenji Yoshino", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Abid Ulhaque", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Sooraj Kumar", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Mario Bernaba", - "author_inst": "Banner University Medical Center" - }, - { - "author_name": "Edward Bergin", - "author_inst": "Banner University Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.14.20102087", "rel_title": "Modeling the Effects of Non-PharmaceuticalInterventions on COVID-19 Spread in Kenya", @@ -1452672,6 +1455302,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.05.17.20097410", + "rel_title": "COVID-19 death rates by age and sex and the resulting mortality vulnerability of countries and regions in the world", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20097410", + "rel_abs": "The growing number of series on COVID-19 deaths classified by age and sex, released by national health authorities, has allowed us to compute age and sex patterns of its mortality, based on 183,619 deaths from Western Europe and the USA. We highlight the specific age schedule of COVID-19 mortality and its pronounced excess male mortality and we then apply these COVID-19 death rates to world populations, in 2020. Our results underscore that considerable variations exist between world regions, as concerns the potential impact of COVID-19 mortality, because of their demographic structures. When compared to younger countries in Sub-Saharan Africa, the vulnerability to COVID-19 mortality is shown to be 17 times higher in several industrialized countries of East Asia and Europe. There is a high correlation (r2= .44) between demographic vulnerability to COVID-19 mortality and current COVID-19 death rates.\n\nAbstractCOVID-19, mortality, age structures, death rates, Europe, USA.\n\nBackgroundThe data available on infection and death rates from COVID-19 have pointed to the elderlys vulnerability to pandemics, especially elderly men. However, current models have not yet incorporated the growing volume of information on deaths by age and sex that is being released by statistical offices and health authorities. These newly available data allow us to examine the specific age and sex patterns of COVID-19 mortality and to estimate the impact of specific demographic structures on potential COVID-19 mortality worldwide.\n\nMethodsWe use the data available on May 15, 2020, from the nine countries with the largest series of deaths, disaggregated by age and sex: Belgium, France, Germany, Italy, Netherlands, Spain, Sweden, the UK, and the USA. Using 183,619 deaths (60.2% of all currently estimated COVID-19 deaths), we estimate the sex-specific death rates, by 5-year ranges, for two large death samples: USA and Western Europe. We compare these mortality rates with Gompertz models and with life tables of the worlds population, estimated by the United Nations. We apply these COVID-19 mortality rates by sex and 5-year group to the 2020 age and sex structures of world countries and regions, and obtain an index summarizing the relative magnitude of their potential vulnerability to COVID-19 mortality because of their demographic structures.\n\nFindingsCOVID-19 death rates cannot be computed below age 15. COVID-19 death rates from age 15-19 years to 90+ increase by a factor of 3 of every ten years, at a rate that is faster than general mortality. Male mortality from COVID-19 is systematically higher than female mortality, with a peak of excess male mortality occurring among 55-59-year-olds. Age and sex structures show considerable variations across countries, in terms of vulnerability to COVID-19 mortality. It transpires that the youngest countries in Central Africa are 17 times less vulnerable than aging countries, such as Japan.\n\nInterpretationWhereas the true intensity of the ongoing COVID-19 pandemic remains underestimated by existing statistics, this unique mortality dataset shows that the regularity of the distribution of COVID deaths by age and sex is in line with the standard Gompertz mortality equation; thus confirming the quality of the first death samples and the unique age and sex patterns of COVID-19 mortality.\n\nCOVID-19 death rates tend to be negligible below age 15 and cannot be used for analysis. The rate of progression of death rates by age is faster than that of general mortality. This feature places the elderly population in a particularly vulnerable situation compared to younger adults. Male excess mortality from COVID-19 also appears far more pronounced than in general mortality patterns, with men aged 40-59 years being almost 2.5 times more likely to die than women of the same age.\n\nOur analysis also points to considerable variations between world regions, as concerns the potential impact of COVID-19 mortality, because of their demographic structures. The COVID-19 structural vulnerability index ranges from .28 in Western or Middle Africa to 2.6 in Southern Europe. There is a high correlation between demographic vulnerability to COVID-19 mortality and current COVID-19 death rates (r2= .44 for 188 countries).", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Christophe Z Z Guilmoto", + "author_inst": "CEPED" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.17.20073189", "rel_title": "Metamorphosis of COVID-19 Pandemic", @@ -1453548,49 +1456197,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.15.20103051", - "rel_title": "Data-driven analysis on the simulations of the spread of COVID-19 under different interventions of China", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103051", - "rel_abs": "Since February 2020, COVID-19 has spread rapidly to more than 200 countries in the world. During the pandemic, local governments in China have implemented different interventions to efficiently control the spread of the epidemic. Characterizing transmission of COVID-19 under some typical interventions is essential to help countries develop appropriate interventions. Based on the pre-symptomatic transmission patterns of COVID-19, we established a novel compartmental model: Baysian SIHR model with latent Markov structure, which treated the numbers of infected and infectious individuals without isolation to be the latent variables and allowed the effective reproduction number to change over time, thus the effects of policies could be reasonably estimated. By using the epidemic data of Wuhan, Wenzhou and Shenzhen, we migrated the corresponding estimated policy modes to South Korea, Italy, and the United States and simulated the potential outcomes for these countries when they adopted similar policy strategies of three cities in China. We found that the mild interventions implemented in Shenzhen were effective to control the epidemic in the early stage, while more stringent policies which were issued in Wuhan and Wenzhou were necessary if the epidemic was more severe and needed to be controlled in a short time.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ting Tian", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Jingwen Zhang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Shiyun Lin", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Yukang Jiang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Jianbin Tan", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Zhongfei Li", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Xueqin Wang", - "author_inst": "University of Science and Technology of China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.16.20103903", "rel_title": "Causal Modeling of Twitter Activity During COVID-19", @@ -1453838,6 +1456444,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.15.20103119", + "rel_title": "Survival of hospitalized COVID-19 patients in Northern Italy: a population-based cohort study by the ITA-COVID19 Network", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103119", + "rel_abs": "BackgroundCOVID-19 case fatality rate in hospitalized patients varies across countries and studies, but reliable estimates specific for age, sex, and comorbidities are needed to design trials for COVID-19 interventions. Aim of this study is to provide population-based survival curves of hospitalized COVID-19 patients.\n\nMethodsA cohort study was conducted in Lombardy, Veneto, and Reggio Emilia using COVID-19 registries linked to hospital discharge databases containing patient clinical histories. All patients with positive SARS-CoV-2 RT-PCR test on oral/nasopharyngeal swabs hospitalized from 21st February to 21st April 2020 were identified. Kaplan Meier survival estimates were calculated at 14 and 30 days for death in any setting, stratifying by age, sex and Charlson Index.\n\nFindingsOverall, 42,926 hospitalized COVID-19 patients were identified. Patients median age was 69 years (IQR: 57-79), 62{middle dot}6% were males, 69{middle dot}4% had a Charlson Index of 0. In total, 11,205 (26{middle dot}1%) patients died over a median follow-up of 24 days (IQR: 10-35). Survival curves showed that 22{middle dot}0% of patients died within 14 days and 27{middle dot}6% within 30 days of hospitalization. Survival was higher in younger patients and in females. Younger patients with comorbidities had a lower survival than older ones with comorbidities.\n\nInterpretationOver 27% of hospitalized COVID-19 patients died within one month in three areas of Northern Italy that were heavily affected by SARS-CoV-2 infection. Such a high fatality rate suggests that trials should focus on survival and have follow-up of at least one month.\n\nFundingThe study did not receive any external funding.\n\nResearch in contextEvidence before this study\n\nTwo recent systematic reviews with meta-analyses report case fatality rates of three to four percent in COVID-19 patients. Most studies on hospitalized cohorts report only slightly higher figures. These figures do not correspond to those derived from routinely collected clinical data in most European countries, reporting a 10% case fatality rate which has been increasing over time since the epidemic started.\n\nRobust and precise survival estimates of hospitalized COVID-19 patients which take into account prognostic factors such as age, sex and burden of comorbidities are needed to design appropriate phase II and phase III clinical studies of drugs targeting COVID-19.\n\nAdded value of this studyIn this study we present the first survival estimates by age, sex and Charlson index for a large population-based cohort of Italian hospitalized COVID-19 patients.\n\nImplications of all the available evidenceOver 27% of COVID-19 patients died within one month from hospital admission. Such a high fatality rate suggests that studies should prioritize mortality as primary outcome. Furthermore, we found that the fatality rate reaches a plateau 30 days after hospitalization, suggesting that studies should have at least one month of follow up to observe deaths; shorter follow-up could lead to overestimation of treatment benefits.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Paolo Giorgi Rossi", + "author_inst": "Azienda Unita' Sanitaria Locale IRCCS di Reggio Emilia, Italy" + }, + { + "author_name": "Eliana Ferroni", + "author_inst": "Azienda Zero of the Veneto Region, Padua, Italy" + }, + { + "author_name": "Stefania Spila Alegiani", + "author_inst": "Italian National Institute of Health, National Center for Drug Research and Evaluation, Rome, Italy" + }, + { + "author_name": "Olivia Leoni", + "author_inst": "Department of Health of Lombardy Region, Milan, Italy" + }, + { + "author_name": "Gisella Pitter", + "author_inst": "Azienda Zero of the Veneto Region, Padua, Italy" + }, + { + "author_name": "Danilo Cereda", + "author_inst": "Department of Health of Lombardy Region, Milan, Italy" + }, + { + "author_name": "Massimiliano Marino", + "author_inst": "Azienda Unita' Sanitaria Locale IRCCS, Reggio Emilia, Italy" + }, + { + "author_name": "Michele Pellizzari", + "author_inst": "Azienda Zero of the Veneto Region, Padua, Italy" + }, + { + "author_name": "Janet Sultana", + "author_inst": "Department of Biomedical and Dental Sciences and Morphofunctional Imaging University of Messina, Messina, Italy" + }, + { + "author_name": "Gianluca Trifiro'", + "author_inst": "Department of Biomedical and Dental Sciences and Morphofunctional Imaging University of Messina, Messina, Italy" + }, + { + "author_name": "Marco Massari", + "author_inst": "Pharmacoepidemiology Unit Italian National Institute of Health, Rome, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.14.20101972", "rel_title": "AI-based multi-modal integration of clinical characteristics, lab tests and chest CTs improves COVID-19 outcome prediction of hospitalized patients", @@ -1455090,73 +1457755,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.13.20100651", - "rel_title": "Efficacy of moist heat decontamination against various pathogens for the reuse of N95 respirators in the COVID-19 emergency", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100651", - "rel_abs": "Decontamination of N95 respirators has become critical to alleviate PPE shortages for healthcare workers in the current COVID-19 emergency. The factors that are considered for the effective reuse of these masks are the fit, filter efficiency and decontamination/disinfection level both for SARS-CoV2, which is the causative virus for COVID-19, and for other organisms of concern in the hospital environment such as Staphylococcus aureus or Clostridium difficile.\n\nThe efficacy of inactivation or eradication against various pathogens should be evaluated thoroughly to understand the level of afforded disinfection. Methods commonly used in the sterilization of medical devices such as ionizing radiation, vaporized hydrogen peroxide, and ethylene oxide can provide a high level of disinfection, defined as a 6 log10 reduction, against bacterial spores, considered the most resistant microorganisms. CDC guidance on the decontamination and reuse of N95s also includes the use of moist heat (60{degrees}C, 80% relative humidity, 15-30 min) as a possible recommendation based on literature showing preservation of fit efficiency and inactivation of H1N1 on spiked masks.\n\nHere, we explored the efficacy of using moist heat under these conditions as a decontamination method for an N95 respirator (3M 1860S, St. Paul, MN) against various pathogens with different resistance; enveloped RNA viruses, Gram (+/-) bacteria, and non-enveloped viruses.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ebru Oral", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Keith K Wannomae", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Dmitry Gil", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Rachel L Connolly", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Joseph Gardecki", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Hui Min Leung", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Orhun K Muratoglu", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Amy Tsurumi", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Laurence G Rahme", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Tareq Jaber", - "author_inst": "Charles River Laboratories" - }, - { - "author_name": "Cassidy Collins", - "author_inst": "Charles River Laboratories" - }, - { - "author_name": "Amanda Budzilowicz", - "author_inst": "Charles River Laboratories" - }, - { - "author_name": "Julian Gjore", - "author_inst": "Charles River Laboratories" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.13.20100602", "rel_title": "Can we use these masks? Rapid Assessment of the Inhalation Resistance Performance of Uncertified Medical Face Masks in the Context of Restricted Resources Imposed during a Public Health Emergency", @@ -1455404,6 +1458002,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.13.20101253", + "rel_title": "The infection fatality rate of COVID-19 inferred from seroprevalence data", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20101253", + "rel_abs": "ObjectiveTo estimate the infection fatality rate of coronavirus disease 2019 (COVID-19) from data of seroprevalence studies.\n\nMethodsPopulation studies with sample size of at least 500 and published as peer-reviewed papers or preprints as of July 11, 2020 were retrieved from PubMed, preprint servers, and communications with experts. Studies on blood donors were included, but studies on healthcare workers were excluded. The studies were assessed for design features and seroprevalence estimates. Infection fatality rate was estimated from each study dividing the number of COVID-19 deaths at a relevant time point by the number of estimated people infected in each relevant region. Correction was also attempted accounting for the types of antibodies assessed. Secondarily, results from national studies were also examined from preliminary press releases and reports whenever a country had no other data presented in full papers of preprints.\n\nResults36 studies (43 estimates) were identified with usable data to enter into calculations and another 7 preliminary national estimates were also considered for a total of 50 estimates. Seroprevalence estimates ranged from 0.222% to 47%. Infection fatality rates ranged from 0.00% to 1.63% and corrected values ranged from 0.00% to 1.31%. Across 32 different locations, the median infection fatality rate was 0.27% (corrected 0.24%). Most studies were done in pandemic epicenters with high death tolls. Median corrected IFR was 0.10% in locations with COVID-19 population mortality rate less than the global average (<73 deaths per million as of July 12, 2020), 0.27% in locations with 73-500 COVID-19 deaths per million, and 0.90% in locations exceeding 500 COVID-19 deaths per million. Among people <70 years old, infection fatality rates ranged from 0.00% to 0.57% with median of 0.05% across the different locations (corrected median of 0.04%).\n\nConclusionsThe infection fatality rate of COVID-19 can vary substantially across different locations and this may reflect differences in population age structure and case-mix of infected and deceased patients as well as multiple other factors. Estimates of infection fatality rates inferred from seroprevalence studies tend to be much lower than original speculations made in the early days of the pandemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "John Ioannidis", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.13.20101303", "rel_title": "An integrated deterministic-stochastic approach for predicting the long-term trajectories of COVID-19", @@ -1456268,57 +1458885,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.06.20076687", - "rel_title": "COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20076687", - "rel_abs": "BackgroundCurrent management efforts of COVID-19 include: early diagnosis, use of antivirals and immune modulation. After the initial viral phase of the illness, identification of the patients developing cytokine storm syndrome is critical. Treatment of this hyper-inflammation in these patients using existing, approved therapies with proven safety profiles could address the immediate need to reduce the rising mortality.\n\nMethodsUsing data from an A549 cell line, primary human bronchial epithelial (NBHE), as well as from COVID-19-infected lung, we compare the changes in the gene expression, pathways and mechanisms between SARS-CoV2, influenza A, and respiratory syncytial virus.\n\nResultsWe identified FDA-approved drugs that could be repurposed to help COVID-19 patients with severe symptoms related to hyper-inflammation. An important finding is that drugs in the same class will not achieve similar effects. For instance methylprednisolone and prednisolone were predicted to be effective in reverting many of the changes triggered by COVID-19, while other closely related steroids, such as prednisone or dexamethasone, were not. An independent clinical study evaluated 213 subjects, 81 (38%) and 132 (62%) in pre-and post-methylprednisolone groups, respectively. The composite end point was composed of escalation to intensive care units, need for mechanical ventilation, and death. The composite endpoint occurred at a significantly lower rate in post-methylprednisolone group compared to pre-methylprednisolone group (34.9% vs. 54.3%, p=0.005).\n\nConclusionClinical results confirmed the efficacy of the in silico prediction that indicated methylprednisolone could improve outcomes in severe COVID-19. These findings are important for any future pandemic regardless of the virus.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sorin Draghici", - "author_inst": "Wayne State University" - }, - { - "author_name": "Tuan-Minh Nguyen", - "author_inst": "Wayne State University" - }, - { - "author_name": "Larry A Sonna", - "author_inst": "Bon Air Consulting" - }, - { - "author_name": "Cordelia Ziraldo", - "author_inst": "Advaita Bioinformatics" - }, - { - "author_name": "Radu L Vanciu", - "author_inst": "Advaita Bioinformatics" - }, - { - "author_name": "Raef Fadel", - "author_inst": "Henry Ford Health System" - }, - { - "author_name": "Austin Morrison", - "author_inst": "Henry Ford Health System" - }, - { - "author_name": "Mayur Ramesh", - "author_inst": "Henry Ford Health System" - }, - { - "author_name": "Gil Mor", - "author_inst": "Wayne State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20105197", "rel_title": "SARS-CoV-2 seroconversion in health care workers", @@ -1456610,6 +1459176,73 @@ "type": "contradictory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.19.103630", + "rel_title": "Transcriptional profiling of immune and inflammatory responses in the context of SARS-CoV-2 fungal superinfection in a human airway epithelial model", + "rel_date": "2020-05-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.19.103630", + "rel_abs": "Superinfections of bacterial/fungal origin are known to affect the course and severity of respiratory viral infections. An increasing number of evidence indicate a relatively high prevalence of superinfections associated with COVID-19, including invasive aspergillosis, but the underlying mechanisms remain to be characterized. In the present study, to better understand the biological impact of superinfection we sought to determine and compare the host transcriptional response to SARS-CoV-2 versus Aspergillus superinfection, using a model of reconstituted humain airway epithelium. Our analyses reveal that both simple infection and superinfection induce a strong deregulation of core components of innate immune and inflammatory responses, with a stronger response to superinfection in the bronchial epithelial model compared to its nasal counterpart. Our results also highlight unique transcriptional footprints of SARS-CoV-2 Aspergillus superinfection, such as an imbalanced type I/type III IFN, and an induction of several monocyte- and neutrophil associated chemokines, that could be useful for the understanding of Aspergillus-associated COVID-19 and but also management of severe forms of aspergillosis in this specific context.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Claire Nicolas de Lamballerie", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Andres Pizzorno", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Julien Fouret", + "author_inst": "Signia Therapeutics" + }, + { + "author_name": "Lea szpiro", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Blandine Padey", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Julia Dubois", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Thomas Julien", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Aurelien Traversier", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Victoria Duliere", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Pauline Brun", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Bruno Lina", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Manuel Rosa-Calatrava", + "author_inst": "CIRI, Centre International de Recherche en Infectiologie, (Team VirPath)" + }, + { + "author_name": "Olivier Terrier", + "author_inst": "Centre International de Recherche en Infectiologie" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.19.104042", "rel_title": "High Throughput Designing and Mutational Mapping of RBD-ACE2 Interface Guide Non-Conventional Therapeutic Strategies for COVID-19", @@ -1458142,29 +1460775,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.12.20099366", - "rel_title": "A pitfall in estimating the effective reproductivenumber Rt for COVID-19", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099366", - "rel_abs": "The effective reproductive number Rt of COVID-19 is determined indirectly from data that are only incompletely known. Approaches based on reconstructing these data by sampling time lags from suitable distributions introduce noise effects that can result in distorted estimates of Rt. This, in turn, may lead to misleading interpretations of the efficacy of the various measures taken to limit COVID-19 transmission. We discuss in some detail a study used for real time monitoring of the reproductive number in Switzerland; see https://ncs-tf.ch/en/situation-report.\n\nWe argue that the method used to derive the above curve is systematically flawed and leads to an underestimation of the efficacy of the lockdown. The method adopted by the Robert Koch Institute suffers from similar deficiencies, their impact is however smaller.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "daniel wyler", - "author_inst": "University of Zurich" - }, - { - "author_name": "markus petermann", - "author_inst": "Pud Consulting Zurich" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.11.20092692", "rel_title": "Household transmission of COVID-19, Shenzhen, January-February 2020", @@ -1458444,6 +1461054,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.14.20093633", + "rel_title": "Evaluation of the US governors decision when to issue stay-at-home orders", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20093633", + "rel_abs": "ObjectivesTo evaluate if the US governors decision to issue the stay-at-home orders reflects the classic Weber-Fechner law of psychophysics, the amount by which a stimulus (such as number of cases or deaths) must increase in order to be noticed-the \"just noticeable difference\"-as a fraction of the intensity of that stimulus.\n\nDesignA prospective observational study using data on the daily number of infected patients and deaths from the New York Times daily database.\n\nSetting50 States and the District of Columbia\n\nParticipantsAll individuals judged to be positive for the coronavirus or to have died from COVID19.\n\nMain outcome measuresNumber of people diagnosed with or died from COVID19.\n\nResultsWe found that the decision to issue the state-at-home order reflects the Weber-Fechner law of psychophysics. Both the number of infections (p=<0.0001; R2=0.79) and deaths (p<0.0001; R2=0.63) were highly statistically significantly associated with the decision to issue the stay-at-home orders. The results indicate that for each doubling of infections or deaths within their state, an additional four to six governors will issue the stay-at-home order. We also observed a clear dose-response relationship in the Cox model: the larger the number of cases, or deaths, the higher the probability that the stay-at-home order will be made. When the number of deaths reached 256 or the number of infected people was greater than 16,384, the probability of issuing a \"stay-at-home\" order was close to 100%.\n\nConclusionsWhen there are not clearly articulated rules to follow, decision-makers in times of crisis such as COVID19 resort to use of simple heuristics consistent with the Weber-Fechner law of psychophysics. The findings are important for the public to understand how their elected officials make important public health decisions.\n\nStrengths and limitations of this studyO_LIThe study was based on individual, publicly available patient data accessible to both researchers and policy-makers.\nC_LIO_LIThe US governors seemed to be wired to act according to the Weber-Fechner law of psychophysics\nC_LIO_LIThe Weber-Fechner function explained 60-80% of the variance in the governors decisions. Typically, explanatory factors in decision-making fields capture at best 30% of such variance.\nC_LIO_LIThe accuracy of data and reporting practices could not be independently verified.\nC_LIO_LIWe demonstrated an association but not a causal relation-we have identified the stimulus that underlies the decision, but we do not know why some governors acted more quickly than others.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Benjamin Djulbegovic", + "author_inst": "City of Hope" + }, + { + "author_name": "David J Weiss", + "author_inst": "California State University, Los Angeles, CA" + }, + { + "author_name": "Iztok Hozo", + "author_inst": "Indiana University, IN" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.05.15.20103341", "rel_title": "Symptomatic SARS-CoV-2 infections display specific IgG Fc structures", @@ -1460012,77 +1462649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.12.20073577", - "rel_title": "Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20073577", - "rel_abs": "BackgroundDetermining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a polyester swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, polyester, and foam) and one clinical grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients with 16 COVID-19+. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent.\n\nResultsCompared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2-4x higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved polyester swab. The limit of detection (LoD) of SARs-CoV-2 from floor samples collected using the CGp or TMI swabs was similar or better than the CDC standard, further suggesting that swab type does not impact RNA recovery as measured by SARs-CoV-2. The LoD for TMI was between 0-362.5 viral particles while PE and CGp were both between 725-1450 particles. Lastly microbiome analyses (16S rRNA) of paired samples (e.g., environment to host) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type but instead driven by the patient and sample type (floor or nasal).\n\nConclusionsCompared to using a clinical-grade polyester swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity in these samples makes it possible to perform concomitant microbiome analysis.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jeremiah J Minich", - "author_inst": "Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Farhana Ali", - "author_inst": "Division of Gastroenterology, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Clarisse Marotz", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Pedro Belda-Ferre", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Leslie Chiang", - "author_inst": "Division of Infectious Diseases, Department of Pediatrics, University of California San Diego" - }, - { - "author_name": "Justin P. Shaffer", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Carolina S. Carpenter", - "author_inst": "Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Daniel McDonald", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Jack A Gilbert", - "author_inst": "Department of Pediatrics, School of Medicine; Scripps Institution of Oceanography; Center for Microbiome Innovation,University of California San Diego, La Jolla" - }, - { - "author_name": "Sarah M. Allard", - "author_inst": "Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Eric E Allen", - "author_inst": "Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego" - }, - { - "author_name": "Rob Knight", - "author_inst": "Departments of Pediatrics, Computer Science and Engineering, & Bioengineering, University of California San Diego, La Jolla, CA USA." - }, - { - "author_name": "Daniel A Sweeney", - "author_inst": "Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, San Diego, La Jolla, CA, USA." - }, - { - "author_name": "Austin D. Swafford", - "author_inst": "Center for Microbiome Innovation, University of California, San Diego" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.12.20094524", "rel_title": "Perceived versus proven SARS-CoV-2 specific immune responses in health care workers", @@ -1460274,6 +1462840,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.11.20097865", + "rel_title": "MODELING COVID19 IN INDIA (MAR 3 - MAY 7, 2020): HOW FLAT IS FLAT, AND OTHER HARD FACTS", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20097865", + "rel_abs": "A time-series model was developed for Number of Total Infected Cases in India, using data from Mar 3 to May 7, 2020. Two models developed in the early phases were discarded when they lost statistical validity, The third, current, model is a 3rd-degree polynomial that has remained stable over the last 30 days (since Apr 8), with R2 > 0.998 consistently. This model is used to forecast Total Covid cases, after cautionary discussion of triggers that would invalidate the model. The purpose of all forecasts in the study is to provide a comparator to evaluate policy initiatives to control the pandemic - the forecasts are not objectives by themselves. Actual observations less than forecasts mean successful policy interventions. Figures of Doubling Time, Fatality Rate and Recovery Rate used by authorities are questioned. Elongation of doubling rates is inherent in the model, and worthy of mention only when the time actually exceeds what the model predicts. The popular Fatality Rate and Recovery Rate metrics are shown to be illogical. The study defines two terms Ongoing Fatality Rate (OFR), and Ongoing Recovery Rate (ORR) and determines these currently to be ~9% and ~76% respectively in India. Over time, OFR will decline to the eventual Case Fatality Rate (CFR), while ORR will eventually climb to (1-CFR). There is no statistical basis to assume eventual Indian CFR, and Chinas 5.5% CFR is used as a proxy. Using these metrics, the current model forecasts by May-end, >150000 Total Infected, ~5000 Deaths and >85000 Active Cases. There is no pull-back evident in the current model in the foreseeable future, and cases continue to rise at progressively slower rates. Subject to usual caveats, the model is used to forecast till Sep 15. The study argues that Indian hospital infrastructure is reasonably ready to handle Active Cases as predicted for Sept 15 - in that sense, the curve is \"flat enough\". However, the curve is NOT flat enough with respect to fatalities - nearly 100000 by Sept 15. Setting an arbitrary limit that Total Deaths must be within 50,000 by Sept 15, the study retrofits a model that shows what the desired growth of Covid19 cases should be. It is seen that overall doubling time of 38 days is required in period June 1 to Sep 15, if deaths are to remain below 50000.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Smarajit Dey", + "author_inst": "Independent Consultant" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.15.20102657", "rel_title": "The differential impact of physical distancing strategies on social contacts relevant for the spread of COVID-19", @@ -1461230,61 +1463815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.15.20102608", - "rel_title": "Fusing a Bayesian case velocity model with random forest for predicting COVID-19 in the U.S.", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20102608", - "rel_abs": "Predictions of COVID-19 case growth and mortality are critical to the decisions of political leaders, businesses, and individuals grappling with the pandemic. This predictive task is challenging due to the novelty of the virus, limited data, and dynamic political and societal responses. We embed a Bayesian nonlinear mixed model and a random forest algorithm within an epidemiological compartmental model for empirically grounded COVID-19 predictions. The Bayesian case model fits a location-specific curve to the velocity (first derivative) of the transformed cumulative case count, borrowing strength across geographic locations and incorporating prior information to obtain a posterior distribution for case trajectory. The compartmental model uses this distribution and predicts deaths using a random forest algorithm trained on COVID-19 data and population-level characteristics, yielding daily projections and interval estimates for infections and deaths in U.S. states. We evaluate forecasting accuracy on a two-week holdout set, finding that the model predicts COVID-19 cases and deaths well, with a mean absolute scaled error of 0.40 for cases and 0.32 for deaths throughout the two-week evaluation period. The substantial variation in predicted trajectories and associated uncertainty between states is illustrated by comparing three unique locations: New York, Ohio, and Mississippi. The sophistication and accuracy of this COVID-19 model offer reliable predictions and uncertainty estimates for the current trajectory of the pandemic in the U.S. and provide a platform for future predictions as shifting political and societal responses alter its course.\n\nAuthor summaryCOVID-19 models can be roughly classified as mathematical models that simulate disease within a population, including epidemiological compartmental models, or statistical curve-fitting models that fit a function to observed data and extrapolate forward into the future. Bridging this divide, we combine the strengths of curve-fitting statistical models and the structure of epidemiological models, by embedding a Bayesian nonlinear mixed model for case velocity and a machine learning algorithm (random forest) into the framework of a compartmental model. Fusing these models together exploits the particular strengths of each to glean as much information as possible from the currently available data. We also identify the velocity of log cumulative cases as an excellent target for modeling and extrapolating COVID-19 case trajectories. We empirically evaluate the predictive performance of the model and provide predicted trajectories with credible intervals for cumulative confirmed case count, active confirmed infections and COVID-19 deaths for each of the 50 U.S. states. Combining sophisticated data analytic methods with proven epidemiological models offers an empirically grounded strategy for making realistic predictions and quantifying their uncertainty. These predictions indicate substantial variation in the COVID-19 trajectories of U.S. states.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Gregory L Watson", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Di Xiong", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Lu Zhang", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Joseph A Zoller", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "John Shamshoian", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Phillip Sundin", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Teresa Bufford", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Anne W Rimoin", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Marc A Suchard", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Christina M Ramirez", - "author_inst": "University of California Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.13.20098186", "rel_title": "Excess Out-Of-Hospital Mortality and Declining Oxygen Saturation Documented by EMS During the COVID-19 Crisis in Tijuana, Mexico", @@ -1461468,6 +1463998,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.13.20098426", + "rel_title": "Analytical performance of lateral flow immunoassay for SARS-CoV-2 exposure screening on venous and capillary blood samples", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20098426", + "rel_abs": "ObjectivesNumerous serologic immunoassays have been launched to detect antibodies to SARS-CoV-2, including rapid tests. Here, we validate use of a lateral flow immunoassay (LFI) intended for rapid screening and qualitative detection of anti-SARS-CoV-2 IgM and IgG in serum, plasma, and whole blood, and compare results with ELISA. We also seek to establish the value of LFI testing on blood obtained from a capillary blood sample.\n\nMethodsSamples collected by venous blood draw and capillary finger stick were obtained from patients with SARS-CoV-2 detected by RT-qPCR and control patients negative for SARS-CoV-2. Samples were tested with the 2019-nCoV IgG/IgM Detection Kit (Colloidal Gold) lateral flow immunoassay, and antibody calls were compared with results obtained by ELISA.\n\nResultsThe Biolidics LFI kit shows clinical sensitivity of 92% at 7 days after PCR diagnosis of SARS-CoV-2 on venous blood. Test specificity was 92% for IgM and 100% for IgG. There was no significant difference in detecting IgM and IgG with Biolidics LFI and ELISA at D0 and D7 (p=1.00), except for detection of IgM at D7 (p=0.04). Finger stick whole blood of SARS-CoV-2 patients showed 93% sensitivity for antibody detection.\n\nConclusionsClinical performance of Biolidics 2019-nCoV IgG/IgM Detection Kit (Colloidal Gold) is comparable to ELISA and showed consistent results across different sample types. Furthermore, we show that capillary blood obtained by finger stick shows similar sensitivity for detecting anti-SARS-CoV-2 IgM and IgG antibodies as venous blood samples. This provides an opportunity for decentralized rapid testing in the community and may allow point-of-care and longitudinal self-testing for the presence of anti-SARS-CoV-2 antibodies.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Margaret A Black", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Guomiao Shen", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Xiaojun Feng", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Wilfredo Garcia Beltran", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Yang Feng", + "author_inst": "New York University" + }, + { + "author_name": "Varshini Vasudevaraja", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Douglas Allison", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Lawrence H. Lin", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Tatyana Gindin", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Michael Astudillo", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Diane Yang", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Mandakolathur Murali", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "A. John Iafrate", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "George Jour", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Paolo Cotzia", + "author_inst": "NYU Langone Health" + }, + { + "author_name": "Matija Snuderl", + "author_inst": "NYU Langone Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.05.11.20098806", "rel_title": "Higher Body Mass Index is an Important Risk factor in COVID-19 patients: A Systematic Review", @@ -1462520,81 +1465129,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.05.17.100289", - "rel_title": "Establishment of an African green monkey model for COVID-19", - "rel_date": "2020-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.17.100289", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for an unprecedented global pandemic of COVID-19. Animal models are urgently needed to study the pathogenesis of COVID-19 and to screen candidate vaccines and treatments. Nonhuman primates (NHP) are considered the gold standard model for many infectious pathogens as they usually best reflect the human condition. Here, we show that African green monkeys support a high level of SARS-CoV-2 replication and develop pronounced respiratory disease that may be more substantial than reported for other NHP species including cynomolgus and rhesus macaques. In addition, SARS-CoV-2 was detected in mucosal samples of all animals including feces of several animals as late as 15 days after virus exposure. Importantly, we show that virus replication and respiratory disease can be produced in African green monkeys using a much lower and more natural dose of SARS-CoV-2 than has been employed in other NHP studies.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Courtney B. Woolsey", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Viktoriya Borisevich", - "author_inst": "1Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Abhishek N Prasad", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Krystle N. Agans", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Daniel J. Deer", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Natalie S. Dobias", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "John C. Heymann", - "author_inst": "Department of Radiology, University of Texas Medical Branch, Galveston, TX 77555, USA." - }, - { - "author_name": "Stephanie L. Foster", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Corri B. Levine", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Liana Medina", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Kevin Melody", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Joan B. Geisbert", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Karla A. Fenton", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Thomas W. Geisbert", - "author_inst": "Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555" - }, - { - "author_name": "Robert W. Cross", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.16.099747", "rel_title": "REMBRANDT: A high-throughput barcoded sequencing approach for COVID-19 screening.", @@ -1462794,6 +1465328,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.05.12.20099184", + "rel_title": "Modelling and data-based analysis of COVID-19 outbreak in India : a study on impact of social distancing measures", + "rel_date": "2020-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099184", + "rel_abs": "In this manuscript, we model and visualize the region-wise trends of the evolution to COVID-19 infections employing a SIR epidemiological model. The SIR dynamics are expressed using stochastic differential equations. We first optimize the parameters of the model using RMSE as loss function on the available data using L-BFGS-B gradient descent optimisation to minimise this loss function. This helps to gain better approximation of the models parameter for specific country or region. The derived parameters are aggregated to project future trends for the Indian subcontinent for next 180 days, which is currently at an early stage within the infection cycle. The projections are meant to function a suggestion for strategies for the socio-political counter measures to mitigate COVID-19. This study considers the current data for India from various open sources. The SIR models prediction is found following the actual trends till date. The inflection point analysis is important to find out which countries have reached their inflection point of the number of infection.\n\nWe found that if current restrictions like lockdown in India continues with same control, then India will observe it[s] peak in active patients count on 22 May 2020, it will take 28 August 2020 for 90% of the peak active infections to end. Inspired from the study of DDI Lab at Singapore university of technology and design (SUTD), this study additionally tries to model and quantify the variations in the count of active patients in the country which might occur due to effect of waiver in restrictions. It should be noted that these results were predicted using COVID-19 data of India till 03 May 2020.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "ANURADHA SINGH", + "author_inst": "INDIAN INSTITUETE OF INFORMATION TECHNOLOGY, NAGPUR" + }, + { + "author_name": "Ankit Khushal Barai", + "author_inst": "INDIAN INSTITUTE OF INFORMATION TECHNOLOGY NAGPUR" + }, + { + "author_name": "Amol Shinde", + "author_inst": "DMIMS, Sawangi, Wardha, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.12.20099093", "rel_title": "Evaluating the determinants of COVID-19 mortality: A cross-country study", @@ -1463782,53 +1466343,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.05.12.20099267", - "rel_title": "The impact of containment measures and air temperature on mitigating the transmission of COVID-19: a novel data-based comprehensive modeling analysis", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099267", - "rel_abs": "Early non-pharmaceutical interventions (NPIs) are crucial to prevent and control of COVID-19 pandemic. We established a stochastic non-classical SEIR NPIs model (ScEIQRsh) which can quantify the three kinds of NPIs measures simultaneously to mimic the clustered intra-family or intra-acquaintance spreading pattern of COVID-19 under the effective integrated NPIs in Mainland China. Model simulation demonstrated that measures to diminish contactable susceptible (Sc), such as home confinement, travel constraint, social distancing etc. and measures to avoid delay of diagnosis and hospitalized isolation ({eta}) were more effective but consumptive than contact tracing ({kappa}, {rho}). From fitted model by MCMC method, the proportion of asymptomatic infectors was 14.88% (IQR 8.17%, 25.37%). The association between air temperature and the fitted transmission rate ({beta}) of COVID-19 suggests that COVID-19 pandemic would be seasonal with the optimal temperature range of 5{degrees}C-14{degrees}C and peak of 10{degrees}C for spreading, and vaccine is indispensable to ultimate prevention COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Di Liu", - "author_inst": "Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, PR China" - }, - { - "author_name": "Qidong Tai", - "author_inst": "Shanghai Pulmonary Hospital, Tongji University School of Medicine" - }, - { - "author_name": "Yaping Wang", - "author_inst": "Public Health and Preventive Medicine, Tongji University School of Medicine" - }, - { - "author_name": "Miao Pu", - "author_inst": "Public Health and Preventive Medicine, Tongji University School of Medicine" - }, - { - "author_name": "Sikai Ge", - "author_inst": "Division of biostatistics, School of public health, University of Minnesota, Minneapolis" - }, - { - "author_name": "Tingting Ji", - "author_inst": "Department of Liver Disease, The Second Hospital of Nanjing Southeast University School of Medicine" - }, - { - "author_name": "Lei Zhang", - "author_inst": "Shanghai Pulmonary Hospital, Tongji University School of Medicine" - }, - { - "author_name": "Bo Su", - "author_inst": "Shanghai Pulmonary Hospital, Tongji University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.12.20099481", "rel_title": "The Evaluation of Deep Neural Networks and X-Ray as a Practical Alternative for Diagnosis and Management of COVID-19", @@ -1464008,6 +1466522,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.13.20100677", + "rel_title": "Number of International Arrivals Predicts Severity of the first Global Wave of the COVID-19 Pandemic", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100677", + "rel_abs": "ObjectiveWe aimed to identify the country-level determinants of the severity of the first wave of the COVID-19 pandemic.\n\nDesignAn ecological study design of publicly available data was employed. Countries reporting >25 COVID-related deaths until 08/06/2020 were included. The outcome was log mean mortality rate from COVID-19, an estimate of the country-level daily increase in reported deaths during the ascending phase of the epidemic curve. Potential determinants assessed were most recently published demographic parameters (population and population density, percentage population living in urban areas, median age, average body mass index, smoking prevalence), Economic parameters (Gross Domestic Product per capita); environmental parameters: pollution levels, mean temperature (January-May)), co-morbidities (prevalence of diabetes, hypertension and cancer), health system parameters (WHO Health Index and hospital beds per 10,000 population); international arrivals, the stringency index, as a measure of country-level response to COVID-19, BCG vaccination coverage, UV radiation exposure and testing capacity. Multivariable linear regression was used to analyse the data.\n\nPrimary OutcomeCountry-level mean mortality rate: the mean slope of the COVID-19 mortality curve during its ascending phase.\n\nParticipantsThirty-seven countries were included: Algeria, Argentina, Austria, Belgium, Brazil, Canada, Chile, Colombia, the Dominican Republic, Ecuador, Egypt, Finland, France, Germany, Hungary, India, Indonesia, Ireland, Italy, Japan, Mexico, the Netherlands, Peru, the Philippines, Poland, Portugal, Romania, the Russian Federation, Saudi Arabia, South Africa, Spain, Sweden, Switzerland, Turkey, Ukraine, the United Kingdom and the United States.\n\nResultsOf all country-level predictors included in the multivariable model, total number of international arrivals (beta 0.033 (95% Confidence Interval 0.012,0.054)) and BCG vaccination coverage (-0.018 (-0.034,-0.002)), were significantly associated with the mean death rate.\n\nConclusionsInternational travel was directly associated with the mortality slope and thus potentially the spread of COVID-19. Very early restrictions on international travel should be considered to control COVID outbreak and prevent related deaths.\n\nARTICLE SUMMARYO_ST_ABSStrengths and limitationsC_ST_ABSO_LIA comparable and relevant outcome variable quantifying country-level increases in the COVID-19 death rate was derived which is largely independent of different testing policies adopted by each country\nC_LIO_LIOur multivariable regression models accounted for public health and economic measures which were adopted by each country in response to the COVID-19 pandemic by adjusting for the Stringency Index\nC_LIO_LIThe main limitation of the study stems from the ecological study design which does not allow for conclusions to be drawn for individual COVID-19 patients\nC_LIO_LIOnly countries that had reported at least 25 daily deaths over the analysed period were included, which reduced our sample and consequently the power.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tiberiu A Pana", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "Sohinee Bhattacharya", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "David T Gamble", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "Zahra Pasdar", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "Weronika A Szlachetka", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "Jesus A Perdomo-Lampignano", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "David McLernon", + "author_inst": "University of Aberdeen" + }, + { + "author_name": "Phyo K Myint", + "author_inst": "University of Aberdeen" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.13.20100727", "rel_title": "National estimates of critical care capacity in 54 African countries.", @@ -1465352,45 +1467913,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.14.095885", - "rel_title": "Predicting the Immunogenicity of T cell epitopes: From HIV to SARS-CoV-2", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.095885", - "rel_abs": "We describe a physics-based learning model for predicting the immunogenicity of Cytotoxic T Lymphocyte (CTL) epitopes derived from diverse pathogens, given a Human Leukocyte Antigen (HLA) genotype. The model was trained and tested on experimental data on the relative immunodominance of CTL epitopes in Human Immunodeficiency Virus infection. The method is more accurate than publicly available models. Our model predicts that only a fraction of SARS-CoV-2 epitopes that have been predicted to bind to HLA molecules is immunogenic. The immunogenic CTL epitopes across all SARS-CoV-2 proteins are predicted to provide broad population coverage, but the immunogenic epitopes in the SARS-CoV-2 spike protein alone are unlikely to do so. Our model predicts that several immunogenic SARS-CoV-2 CTL epitopes are identical to those contained in low-pathogenicity coronaviruses circulating in the population. Thus, we suggest that some level of CTL immunity against COVID-19 may be present in some individuals prior to SARS-CoV-2 infection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ang Gao", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Zhilin Chen", - "author_inst": "Ragon Insitute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard" - }, - { - "author_name": "Mary Carrington", - "author_inst": "Frederick National Laboratory for Cancer Research" - }, - { - "author_name": "Hendrik Streeck", - "author_inst": "Institute of Virology" - }, - { - "author_name": "Arup K. Chakraborty", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Boris Juelg", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.14.095620", "rel_title": "Unveiling diffusion pattern and structural impact of the most invasive SARS-CoV-2 spike mutation", @@ -1465574,6 +1468096,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.10.20088369", + "rel_title": "Medical overuse in the Iranian healthcare system: a systematic scoping review and practical recommendations for decreasing medical overuse during unexpected COVID-19 pandemic opportunity", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20088369", + "rel_abs": "BackgroundOveruse of medical care is a major problem across health systems as well as in Iran. By our knowledge, this is the first scoping review in which medical overuse in the Iranian healthcare system was investigated.\n\nObjectiveTo perform an inclusive search for original studies that report medical overuse in the Iranian healthcare system.\n\nMethodsA systematic search of the literature conducted in bibliographic databases including PubMed, Embase, Scopus, Web of Sciences, Cochrane and Scientific Information Database using a comprehensive search strategy without time limit until the end of 2018, accomplished by reference tracking, author contacting and expert consultation to identify studies on the overuse of medical care.\n\nResultsWe reviewed 4124 published articles based on predetermined inclusion criteria. The authors consensus included a total of 40 articles. Of these, 31 were in English and 9 in Farsi, published between 19975-2018. The result categorized into two distinct clinical areas: treatment (17 articles), and diagnostic (23 articles) services. Almost all of the studies only described the magnitude of unnecessary overuse. Unnecessary overuse of Antibiotics, MRI, and CT-scan were the most reported topics. The ranges of their overuse proportion were as follows; Antibiotic (31 to 97%); MRI (33 to 88%), and CT-scan (19 to 50%).\n\nConclusionsOur review showed, even so, the magnitude of unnecessary overuse of medical services is high but there are only a few interventional studies in clinical and administrative level for finding effective methods for decreasing these unnecessary services. Researchers should be encouraged to conducting interventional studies. We suggest the ministry of health to use the golden opportunity of COVID-19 epidemic for designing Iran national policy and action plan for controlling and preventing unnecessary health care services and including a section for \"Interventional Research\" in the action plan.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mohammad Zakaria Pezeshki", + "author_inst": "Tabriz university of Medical Sciences" + }, + { + "author_name": "Ali Janati", + "author_inst": "Tabriz University of Medical Sciences" + }, + { + "author_name": "Morteza Arab-Zozani", + "author_inst": "Birjand University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.05.11.20092338", "rel_title": "Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting", @@ -1466937,53 +1469486,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.05.10.20096925", - "rel_title": "NON-WHITE ETHNICITY, MALE SEX, AND HIGHER BODY MASS INDEX, BUT NOT MEDICATIONS ACTING ON THE RENIN-ANGIOTENSIN SYSTEM ARE ASSOCIATED WITH CORONAVIRUS DISEASE 2019 (COVID-19) HOSPITALISATION: REVIEW OF THE FIRST 669 CASES FROM THE UK BIOBANK", - "rel_date": "2020-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20096925", - "rel_abs": "BackgroundCardiometabolic morbidity and medications, specifically Angiotensin Converting Enzyme inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs), have been linked with adverse outcomes from coronavirus disease 2019 (COVID-19). This study aims to investigate factors associated with COVID-19 positivity for the first 669 UK Biobank participants; compared with individuals who tested negative, and with the untested, presumed negative, rest of the population.\n\nMethodsWe studied 1,474 participants from the UK Biobank who had been tested for COVID-19. Given UK testing policy, this implies a hospital setting, suggesting at least moderate to severe symptoms. We considered the following exposures: age, sex, ethnicity, body mass index (BMI), diabetes, hypertension, hypercholesterolaemia, ACEi/ARB use, prior myocardial infarction (MI), and smoking. We undertook comparisons between: 1) COVID-19 positive and COVID-19 tested negative participants; and 2) COVID-19 tested positive and the remaining participants (tested negative plus untested, n=501,837). Logistic regression models were used to investigate univariate and mutually adjusted associations.\n\nResultsAmong participants tested for COVID-19, non-white ethnicity, male sex, and greater BMI were independently associated with COVID-19 positive result. Non-white ethnicity, male sex, greater BMI, diabetes, hypertension, prior MI, and smoking were independently associated with COVID-19 positivity compared to the remining cohort (test negatives plus untested). However, similar associations were observed when comparing those who tested negative for COVID-19 with the untested cohort; suggesting that these factors associate with general hospitalisation rather than specifically with COVID-19.\n\nConclusionsAmong participants tested for COVID-19 with presumed moderate to severe symptoms in a hospital setting, non-white ethnicity, male sex, and higher BMI are associated with a positive result. Other cardiometabolic morbidities confer increased risk of hospitalisation, without specificity for COVID-19. Notably, ACE/ARB use did not associate with COVID-19 status.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Zahra Raisi-Estabragh", - "author_inst": "William Harvey Research Institute" - }, - { - "author_name": "Celeste McCracken", - "author_inst": "William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK" - }, - { - "author_name": "Maddalena Ardissino", - "author_inst": "Sir Alexander Fleming Building, Imperial College London, London, UK" - }, - { - "author_name": "Mae S Bethell", - "author_inst": "North West Anglia NHS Foundation Trust, Hinchingbrooke Hospital, Huntingdon, UK" - }, - { - "author_name": "Jackie Cooper", - "author_inst": "William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK" - }, - { - "author_name": "Cyrus Cooper", - "author_inst": "MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK" - }, - { - "author_name": "Nicholas C Harvey", - "author_inst": "MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK" - }, - { - "author_name": "Steffen E Petersen", - "author_inst": "William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, London, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.05.15.097741", "rel_title": "Analysis of SARS-CoV-2 RNA-Sequences by Interpretable Machine Learning Models", @@ -1467239,6 +1469741,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.09.20096818", + "rel_title": "Hemogram Data as a Tool for Decision-making in COVID-19 Management: Applications to Resource Scarcity Scenarios", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096818", + "rel_abs": "BackgroundCOVID-19 pandemics has challenged emergency response systems worldwide, with widespread reports of essential services breakdown and collapse of health care structure. A critical element involves essential workforce management since current protocols recommend release from duty for symptomatic individuals, including essential personnel. Testing capacity is also problematic in several countries, where diagnosis demand outnumbers available local testing capacity.\n\nPurposeThis work describes a machine learning model derived from hemogram exam data performed in symptomatic patients and how they can be used to predict qRT-PCR test results.\n\nMethodsA Naive-Bayes model for machine learning is proposed for handling different scarcity scenarios, including managing symptomatic essential workforce and absence of diagnostic tests. Hemogram result data was used to predict qRT-PCR results in situations where the latter was not performed, or results are not yet available. Adjusts in assumed prior probabilities allow fine-tuning of the model, according to actual prediction context.\n\nResultsProposed models can predict COVID-19 qRT-PCR results in symptomatic individuals with high accuracy, sensitivity and specificity. Data assessment can be performed in an individual or simultaneous basis, according to desired outcome. Based on hemogram data and background scarcity context, resource distribution is significantly optimized when model-based patient selection is observed, compared to random choice. The model can help manage testing deficiency and other critical circumstances.\n\nConclusionsMachine learning models can be derived from widely available, quick, and inexpensive exam data in order to predict qRT-PCR results used in COVID-19 diagnosis. These models can be used to assist strategic decision-making in resource scarcity scenarios, including personnel shortage, lack of medical resources, and testing insufficiency.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Marcio Dorn", + "author_inst": "Federal University of Rio Grande do Sul" + }, + { + "author_name": "Eduardo Avila", + "author_inst": "Pontifical Catholic University of Rio Grande do Sul" + }, + { + "author_name": "Clarice Sampaio Alho", + "author_inst": "Pontifical Catholic University of Rio Grande do Sul" + }, + { + "author_name": "Alessandro Kahmann", + "author_inst": "Federal University of Rio Grande" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.09.20096644", "rel_title": "Critical levels of mask efficiency and of mask adoption that theoretically extinguish respiratory virus epidemics", @@ -1468751,61 +1471284,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.05.14.096016", - "rel_title": "Transcriptional profiling reveals TRPM5-expressing cells involved in viral infection in the olfactory epithelium", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.096016", - "rel_abs": "BackgroundUnderstanding viral infection of the olfactory epithelium is essential because the olfactory nerve is an important route of entry for viruses to the central nervous system. Specialized chemosensory epithelial cells that express the transient receptor potential cation channel subfamily M member 5 (TRPM5) are found throughout the airways and intestinal epithelium and are involved in responses to viral infection.\n\nResultsHerein we performed deep transcriptional profiling of olfactory epithelial cells sorted by flow cytometry based on the expression of mCherry as a marker for olfactory sensory neurons and for eGFP in OMP-H2B::mCherry/TRPM5-eGFP transgenic mice (Mus musculus). We find profuse expression of transcripts involved in inflammation, immunity and viral infection in TRPM5-expressing microvillous cells.\n\nConclusionOur study provides new insights into a potential role for TRPM5-expressing microvillous cells in viral infection of the olfactory epithelium. We find that, as found for solitary chemosensory cells (SCCs) and brush cells in the airway epithelium, and for tuft cells in the intestine, the transcriptome of TRPM5-expressing microvillous cells indicates that they are likely involved in the inflammatory response elicited by viral infection of the olfactory epithelium.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Eric D Larson", - "author_inst": "University of Colorado" - }, - { - "author_name": "Laetitia Merle", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Paul Feinstein", - "author_inst": "Hunter College, CUNY" - }, - { - "author_name": "Arianna Gentile Polese", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Andrew N Bubak", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Christy S Niemeyer", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Douglas Shepherd", - "author_inst": "Arizona State University" - }, - { - "author_name": "Vijay R Ramakrishnan", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Maria A Nagel", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Diego Restrepo", - "author_inst": "Universtiy of Colorado Anschutz Medical Campus" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2020.05.15.096511", "rel_title": "Broad sarbecovirus neutralizing antibodies define a key site of vulnerability on the SARS-CoV-2 spike protein", @@ -1469285,6 +1471763,45 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.05.14.097311", + "rel_title": "Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection", + "rel_date": "2020-05-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.097311", + "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first identified in December 2019 and has quickly become a worldwide pandemic. In response, many diagnostic manufacturers have developed molecular assays for SARS-CoV-2 under the Food and Drug Administration (FDA) Emergency Use Authorization (EUA) pathway. This study compared three of these assays: the Hologic Panther Fusion SARS-CoV-2 assay (Fusion), the Hologic Aptima SARS-CoV-2 assay (Aptima) and the BioFire Diagnostics COVID-19 test (BioFire), to determine analytical and clinical performance, as well as workflow. All three assays showed a similar limit of detection (LOD) using inactivated virus, with 100% detection ranging from 500-1,000 genome equivalents/ml, whereas use of a quantified RNA transcript standard showed the same trend, but had values ranging from 62.5 to 125 copies/ml, confirming variability in absolute quantification of reference standards. The clinical correlation found that the Fusion and BioFire assays had a positive percent agreement (PPA) of 98.7%, followed by the Aptima assay at 94.7% when compared to the consensus result. All three assays exhibited 100% negative percent agreement (NPA). Analysis of discordant results revealed that all four samples missed by the Aptima assay had Ct values >37 on the Fusion assay.\n\nIn conclusion, while all three assays showed similar relative LODs, we showed differences in absolute LODs depending on which standard was employed. In addition, the Fusion and BioFire assays showed better clinical performance, while the Aptima assay showed a modest decrease in overall PPA. These findings should be kept in mind when making platform testing decisions.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Elizabeth Smith", + "author_inst": "Northwell Health Laboratories" + }, + { + "author_name": "Wei Zhen", + "author_inst": "Northwell Health Laboratories" + }, + { + "author_name": "Ryhana Manji", + "author_inst": "Northwell Health Laboratories" + }, + { + "author_name": "Deborah Schron", + "author_inst": "Northwell Health Laboratories" + }, + { + "author_name": "Scott Duong", + "author_inst": "Northwell Health Laboratories" + }, + { + "author_name": "Gregory J Berry", + "author_inst": "Northwell Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.10.20097394", "rel_title": "Outbreak of Kawasaki disease in children during COVID-19 pandemic: a prospective observational study in Paris, France", @@ -1470493,37 +1473010,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.14.093757", - "rel_title": "Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome", - "rel_date": "2020-05-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.093757", - "rel_abs": "A novel coronavirus (SARS-CoV-2) emerged from China in late 2019 and rapidly spread across the globe, infecting millions of people and generating societal disruption on a level not seen since the 1918 influenza pandemic. A safe and effective vaccine is desperately needed to prevent the continued spread of SARS-CoV-2; yet, rational vaccine design efforts are currently hampered by the lack of knowledge regarding viral epitopes targeted during an immune response, and the need for more in-depth knowledge on betacoronavirus immunology. To that end, we developed a computational workflow using a series of open-source algorithms and webtools to analyze the proteome of SARS-CoV-2 and identify putative T cell and B cell epitopes. Using increasingly stringent selection criteria to select peptides with significant HLA promiscuity and predicted antigenicity, we identified 41 potential T cell epitopes (5 HLA class I, 36 HLA class II) and 6 potential B cell epitopes, respectively. Docking analysis and binding predictions demonstrated enrichment for peptide binding to HLA-B (class I) and HLA-DRB1 (class II) molecules. Overlays of predicted B cell epitopes with the structure of the viral spike (S) glycoprotein revealed that 4 of 6 epitopes were located in the receptor-binding domain of the S protein. To our knowledge, this is the first study to comprehensively analyze all 10 (structural, non-structural and accessory) proteins from SARS-CoV-2 using predictive algorithms to identify potential targets for vaccine development.\n\nSignificance StatementThe novel coronavirus SARS-CoV-2 recently emerged from China, rapidly spreading and ushering in a global pandemic. Despite intensive research efforts, our knowledge of SARS-CoV-2 immunology and the proteins targeted by the immune response remains relatively limited, making it difficult to rationally design candidate vaccines. We employed a suite of bioinformatic tools, computational algorithms, and structural modeling to comprehensively analyze the entire SARS-CoV-2 proteome for potential T cell and B cell epitopes. Utilizing a set of stringent selection criteria to filter peptide epitopes, we identified 41 T cell epitopes (5 HLA class I, 36 HLA class II) and 6 B cell epitopes that could serve as promising targets for peptide-based vaccine development against this emerging global pathogen.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Stephen N. Crooke", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Inna G. Ovsyannikova", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Richard B. Kennedy", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Gregory A. Poland", - "author_inst": "Mayo Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.13.093971", "rel_title": "Insights into molecular evolution recombination of pandemic SARS-CoV-2 using Saudi Arabian sequences", @@ -1470767,6 +1473253,33 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.05.10.20097428", + "rel_title": "Will an imperfect vaccine curtail the COVID-19 pandemic in the U.S.?", + "rel_date": "2020-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20097428", + "rel_abs": "The novel coronavirus (COVID-19) that emerged from Wuhan city of China in late December 2019 continue to pose devastating public health and economic challenges across the world. Although the community-wide implementation of basic non-pharmaceutical intervention measures, such as social-distancing, quarantine of suspected COVID-19 cases, isolation of confirmed cases, use of face masks in public, and contact-tracing, have been quite effective in curtailing and mitigating the burden of the pandemic, it is universally believed that the use of an anti-COVID-19 vaccine is necessary to build the community herd immunity needed to effectively control and eliminate the pandemic. This study is based on the design and use of a mathematical model for assessing the population-level impact of a hypothetical imperfect anti-COVID-19 vaccine on the control of COVID-19. An analytical expression for the minimum number of unvaccinated susceptible individuals needed to be vaccinated to achieve vaccine-induced community herd immunity is derived. The epidemiological consequence of the herd immunity threshold is that the disease can be effectively controlled or eliminated if the minimum herd immunity threshold is achieved in the community. Simulations of the model, using baseline parameter values obtained from fitting the model with mortality data relevant to COVID-19 dynamics in the US states of New York and Florida, as well as for the entire US, show that, for an anti-COVID-19 vaccine with an assumed protective efficacy of 80%, the minimum herd immunity threshold for the entire US, state of New York and state of Florida are, respectively, 90%, 84% and 85%. Furthermore, it was shown that, while a significantly large increase in vaccination rate (from baseline) is necessarily needed to eliminate COVID-19 from the entire US, the pandemic can be eliminated from the states of New York and Florida if the vaccination rate is marginally increased (by as low as 10%) from its baseline value. The prospect of COVID-19 elimination in the US or in the two states of New York and Florida is greatly enhanced if the vaccination program is combined with a public mask use program or an effective social-distancing measure. Such combination of strategies significantly reduces the vaccine-induced herd immunity threshold. Finally, it is shown that the vaccination program is more likely to lead to COVID-19 elimination in the state of Florida, followed by the state of New York and then the entire US.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Enahoro Amos Iboi", + "author_inst": "Arizona State University" + }, + { + "author_name": "Calistus N. Ngonghala", + "author_inst": "University of Florida" + }, + { + "author_name": "Abba B Gumel", + "author_inst": "Arizona State University" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.10.20097485", "rel_title": "The far side of the COVID-19 epidemic curve: local re-openings based on globally coordinated triggers may work best", @@ -1472063,57 +1474576,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.09.20091454", - "rel_title": "Early Awake Prone and Lateral Position in Non-intubated Severe and Critical Patients with COVID-19 in Wuhan: A Respective Cohort Study", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20091454", - "rel_abs": "BackgroundPrevious studies suggest applying prone position (PP) and lateral position (LP) in patients with severe acute respiratory distress syndrome (ARDS) for their efficacy in improving oxygenation and lung recruitment.This paper aims to share clinical experiences and outcome of using PP and LP in combination with oxygen therapy (OT) and Non-invasive ventilation (NIV) in severe and critical patients with COVID-19.\n\nMethodsClinical data of 48 severe and critical patients have been retrieved from medical records and reviewed. The primary outcome is the survival rate. Secondary outcome is the rate of patients requiring intubation.\n\nResultsIn total, 25 patients were finally included in the study. The mean respiratory rate of all 25 patients decreased from 28.4 breaths/min to 21.3 breaths/min. CT results showed increase in lung recruitment. All patients tolerated PP and LP well. No deterioration or severe adverse events associated with PP and LP occurred. All patients recovered and survived without intubation. Follow-up to date showed that all patients have been discharged except one with mild symptoms and positive RNA test.\n\nConclusionClinical outcomes of early application of PP and LP in combination with OT and NIV in severe and critical patients with COVID-19 indicated well tolerance of the therapy and resulted in improving patients oxygenation in a safe and effective manner. Therefore, this strategy can be explored as an early intervention in managing patients in early stage of disease development under the context of pandemic and limited medical resources.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Wei Dong", - "author_inst": "1.Critical Care Medicine Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Techno" - }, - { - "author_name": "Yiping Gong", - "author_inst": "1.\tDepartment of Infectious Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, China" - }, - { - "author_name": "Juan Feng", - "author_inst": "1.\tDepartment of Infectious Disease, Renmin Hospital of Wuhan University,Wuhan,Hubei, China" - }, - { - "author_name": "Lang Bai", - "author_inst": "1.Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan, China; 2.Department of Infectious Disease, Renmin Hospital of Wuhan " - }, - { - "author_name": "Haomiao Qing", - "author_inst": "Radiology Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, " - }, - { - "author_name": "Peng Zhou", - "author_inst": "Radiology Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, " - }, - { - "author_name": "Yu Du", - "author_inst": "1.Emergency department and intensive care unit, West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China; 2.D" - }, - { - "author_name": "Junchen Zhu", - "author_inst": "1.Intensive Care Unit, Affiliated Hospital of Chengdu University, Chengdu, Sichuan, China; 2.Department of Infectious Disease, Renmin Hospital of Wuhan Universi" - }, - { - "author_name": "Shanling Xu", - "author_inst": "1.Critical Care Medicine Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Techno" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.08.20095877", "rel_title": "Forecasting Transmission Dynamics of COVID-19 Epidemic in India under Various Containment Measures- A Time-Dependent State-Space SIR Approach", @@ -1472405,6 +1474867,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2020.05.08.20095604", + "rel_title": "MIGRANTS IN TRANSIT AND ASYLUM SEEKERS IN MEXICO: AN EPIDEMIOLOGICAL ANALYSIS OF THE COVID-19 PANDEMIC", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095604", + "rel_abs": "BACKGROUNDMigrants could be disproportionately affected by the COVID-19 pandemic, yet little is known so far of the epidemiology of the disease among them, especially in low- and middle-income countries.\n\nOBJECTIVETo describe the epidemiology of suspect cases of COVID-19 in migrants in transit and asylum seekers in Mexico, and to compare their characteristics with those of non-migrants.\n\nMETHODSThis was a secondary analysis of information from the surveillance system of Mexico from January 1 to May 3 2020, identifying persons from the main sending countries of mixed migrant flows in Mexico (Central America, the Caribbean, Venezuela and African countries), in northern and southern Mexican border states. We compared the demographic and clinical characteristics, risk conditions, and epidemic curves for migrants and non-migrants. Also, we estimated the cumulative incidence for non-migrants, and for migrants in two scenarios defined by different estimations of their population size.\n\nRESULTSMigrants were on average younger, had less accompanying risk conditions, and a lower percentage of suspect cases tested positive for COVID-19. The odds of hospitalization were lower among migrants, but the difference disappeared after adjusting by age, gender and underlying risk conditions. The cumulative incidence ratios comparing migrants with non-migrants were 6.12 (CI95% 4.75,7.77) for the first scenario, and 1.49 (CI95% 1.15,1.89) for the second scenario.\n\nCONCLUSIONMigrants and asylum seekers in Mexico are at increased risk for infectious respiratory diseases, and could be disproportionately affected by COVID-19. It is important to continue monitoring the situation, with more detailed information about migration status, living conditions and other determinants of migrants health.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ietza Bojorquez", + "author_inst": "El Colegio de la Frontera Norte" + }, + { + "author_name": "Cesar Infante", + "author_inst": "Instituto Nacional de Salud Publica" + }, + { + "author_name": "Isabel Vieitez", + "author_inst": "Population Council" + }, + { + "author_name": "Silvana Larrea", + "author_inst": "Population Council" + }, + { + "author_name": "Chiara Santoro", + "author_inst": "Medicos del Mundo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.08.20095596", "rel_title": "The timing of contact restrictions and pro-active testing balances the socio-economic impact of a lockdown with the control of infections", @@ -1473313,73 +1475810,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, - { - "rel_doi": "10.1101/2020.05.11.20092528", - "rel_title": "ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20092528", - "rel_abs": "Serologic assays are needed to determine SARS-CoV-2 seroprevalence, but poor specificity can overestimate exposures. Here, we built a pan-human coronavirus proteome-wide programmable phage display assay (VirScan) to profile coronavirus antigens specifically enriched by 20 COVID-19 patient serum IgG. With ReScan, a new diagnostic development workflow which combines the isolation of phage expressing the most immunogenic peptides with paper-based microarrays manufactured via acoustic liquid handling, we identified 9 candidate antigens from a library of 534 SARS-CoV-2 peptides. These arrays could form the basis of a multiplexed COVID-19 serologic assay with enhanced specificity. ReScan has broad applicability for serologic assay development.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Colin R. Zamecnik", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jayant V. Rajan", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kevin A. Yamauchi", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Sabrina A. Mann", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Gavin M. Sowa", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kelsey C. Zorn", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Bonny D. Alvarenga", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mars Stone", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Philip J. Norris", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Wei Gu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Charles Y Chiu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joseph L. DeRisi", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Michael R Wilson", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.09.20096123", "rel_title": "Breaking the back of COVID-19: Is Bangladesh doing enough testing?", @@ -1473539,6 +1475969,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.10.20096933", + "rel_title": "Increased levels of anxiety among medical and non-medical university students during the COVID-19 pandemic in the United Arab Emirates.", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20096933", + "rel_abs": "IntroductionThe COVID-19 pandemic is likely to increase anxiety levels within the community and in particular medical students who are already considered psychologically vulnerable groups. Since the COVID-19 outbreak, no study has yet estimated the effect of this pandemic on university students in the UAE or its impact on the psychological well-being of medical students.\n\nMethodsIn this study, we surveyed 1485 medical (comprising medical and dental) and non-medical university students across 4 emirates within the UAE. We used an online platform to assess knowledge, sources of information, changes in hygienic behavior, perceptions of fear and worry and anxiety levels using the generalized anxiety disorder 7 (GAD-7) scale. The GAD-7 score was measured at three time points; during hospital visits for medical/dental students, before the introduction of online learning and after online learning for all students.\n\nResultsThe majority of students demonstrated high levels of knowledge and utilized reliable sources of information. Non-medical students exercised higher compliance with social restrictions, while medical students practiced better hand hygiene. Almost half of students reported anxiety levels ranging from mild to severe with females reporting higher anxiety scores during hospital visits (OR=2.02, 95% CI, 1.41 to 2.91) and medical students reporting lower anxiety levels in comparison to dental students (OR=0.61, 95% CI, 0.45 to 0.84). Medical students reported higher levels of anxiety during their clinical rotations which decreased with the introduction of online learning, yet, non-medical students anxiety levels increased with online learning.\n\nConclusionsThis is the first study to provide important information on the initial response and anxiety levels in university students across the UAE. The findings from our study can be used to support the development of effective screening strategies and interventions to build psychological resilience among university students during the COVID-19 pandemic or any other public health emergencies in the future.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Basema Saddik", + "author_inst": "The University of Sharjah" + }, + { + "author_name": "Amal Hussein", + "author_inst": "The University of Sharjah" + }, + { + "author_name": "Fatemeh Saheb Sharif-Askari", + "author_inst": "The University of Sharjah" + }, + { + "author_name": "Waad Kheder", + "author_inst": "The University of Sharjah" + }, + { + "author_name": "Mohamad-Hani Temsah", + "author_inst": "King Saud University" + }, + { + "author_name": "Rim Adnan Koutaich", + "author_inst": "The University of Sharjah" + }, + { + "author_name": "Enad Sami Haddad", + "author_inst": "The University of Sharjah" + }, + { + "author_name": "Nora Marwan Al-Roub", + "author_inst": "The University of Sharjah" + }, + { + "author_name": "Fatema Adel Marhoon", + "author_inst": "The University of Sharjah" + }, + { + "author_name": "Qutayba Hamid", + "author_inst": "The University of Sharjah" + }, + { + "author_name": "Rabih Halwani", + "author_inst": "The University of Sharjah" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.09.20096438", "rel_title": "Lifestyle Risk Factors for Cardiovascular Disease in Relation to COVID-19 Hospitalization: A Community-Based Cohort Study of 387,109 Adults in UK", @@ -1474903,25 +1477392,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.05.08.20092080", - "rel_title": "SELF-POLICING COVID-19 AND CIVIC RESPONSIBILITIES IN LAGOS METROPOLIS, NIGERIA", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20092080", - "rel_abs": "This study investigated self-policing COVID-19 and civic responsibilities in Lagos Metropolis, Nigeria adopting an online qualitative interview due to the current lockdown that denied field (face to face) interview. Fifty out of the feedbacks from the online interview were picked randomly to arrive at the conclusion of this study. The feedbacks suggested that there is adequate awareness of the COVID-19 pandemic among the people living in Lagos Metropolis, Nigeria and that they are following the directives of federal and state governments in an effort to reduce the community transmission of the infectious diseases. However, the ban on public gatherings and movements has made it impossible for many homes to meet their basic needs especially feeding. The government provided palliatives have also been largely insufficient to cater for the vulnerable. There could be a crisis (such as hunger) and the breakdown of law and order if the government does not increase their capacity to mitigate the hardship which the ongoing lockdown has imposed on the people.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ayomide Ilori", - "author_inst": "University of Ibadan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.05.08.20095521", "rel_title": "Expected impact of reopening schools after lockdown on COVID-19 epidemic in Ile-de-France", @@ -1475169,6 +1477639,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.07.20094839", + "rel_title": "Compassionate drug (mis)use during pandemics: lessons for COVID-19 from 2009.", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094839", + "rel_abs": "BackgroundNew emerging infections have no known treatment. Assessing potential drugs for safety and efficacy enables clinicians to make evidence-based treatment decisions, and contributes to overall outbreak control. However, it is difficult to launch clinical trials in the unpredictable environment of an outbreak. We conducted a bibliometric systematic review for the 2009 influenza pandemic to determine the speed, and quality of evidence generation for treatments. This informs approaches to high-quality evidence generation in this and future pandemics.\n\nMethodsWe searched PubMed for all clinical data (including clinical trial, observational and case series) describing treatment for patients with influenza A(H1N1)pdm09 and ClinicalTrials.gov for research that aimed to enrol patients with the disease.\n\nFindings33869 treatment courses for patients hospitalised with A(H1N1)pdm09 were detailed in 160 publications. Most were retrospective observational studies or case series. 592 patients received treatment (or placebo) as participants in a registered interventional clinical trial with results publicly available. None of these registered trial results were available during the timeframe of the pandemic, and the median date of publication was 213 days after the Public Health Emergency of International Concern ended.\n\nInterpretationPatients were frequently treated for pandemic influenza with drugs not registered for this indication, but rarely under circumstances of high-quality data capture. The result was a reliance on use under compassionate circumstances, resulting in continued uncertainty regarding the potential benefits and harms of anti-viral treatment. Rapid scaling of clinical trials is critical for generating a quality evidence base during pandemics.\n\nFundingWellcome Trust.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Amanda Rojek", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Genevieve Martin", + "author_inst": "Alfred Hospital" + }, + { + "author_name": "Peter Horby", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.07.20094805", "rel_title": "Stability of SARS-CoV-2 on environmental surfaces and in human excreta", @@ -1476385,153 +1478882,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.12.088716", - "rel_title": "Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability", - "rel_date": "2020-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.088716", - "rel_abs": "The rapid spread of SARS-CoV-2 has a significant impact on global health, travel and economy. Therefore, preventative and therapeutic measures are urgently needed. Here, we isolated neutralizing antibodies from convalescent COVID-19 patients using a SARS-CoV-2 stabilized prefusion spike protein. Several of these antibodies were able to potently inhibit live SARS-CoV-2 infection at concentrations as low as 0.007 {micro}g/mL, making them the most potent human SARS-CoV-2 antibodies described to date. Mapping studies revealed that the SARS-CoV-2 spike protein contained multiple distinct antigenic sites, including several receptor-binding domain (RBD) epitopes as well as previously undefined non-RBD epitopes. In addition to providing guidance for vaccine design, these mAbs are promising candidates for treatment and prevention of COVID-19.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Philip Brouwer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Tom Caniels", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Karlijn van Straten", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jonne Snitselaar", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Yoann Aldon", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Sandhya Bangaru", - "author_inst": "Scripps Research" - }, - { - "author_name": "Jonathan Torres", - "author_inst": "Scripps Research" - }, - { - "author_name": "Nisreen Okba", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Mathieu Claireaux", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Gius Kerster", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Arthur Bentlage", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marlies van Haaren", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Denise Guerra", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Judith Burger", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Edith Schermer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Kirsten Verheul", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Niels van der Velde", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Alex van der Kooi", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jelle van Schooten", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marielle van Breemen", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Tom Bijl", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Kwinten Sliepen", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Aafke Aartse", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Ronald Derking", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Ilja Bontjer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Neeltje Kootstra", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Joost Wiersinga", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Gestur Vidarsson", - "author_inst": "Sanquin Research" - }, - { - "author_name": "Bart Haagmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Andrew Ward", - "author_inst": "Scripps Research" - }, - { - "author_name": "Godelieve de Bree", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Rogier Sanders", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marit van Gils", - "author_inst": "Amsterdam UMC" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.12.091090", "rel_title": "Static All-Atom Energetic Mappings of the SARS-Cov-2 Spike Protein with Potential Latch Identification of the Down State Protomer", @@ -1476726,6 +1479076,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.11.088179", + "rel_title": "SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant", + "rel_date": "2020-05-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.11.088179", + "rel_abs": "One of the features distinguishing SARS-CoV-2 from its more pathogenic counterpart SARS-CoV is the presence of premature stop codons in its ORF3b gene. Here, we show that SARS-CoV-2 ORF3b is a potent interferon antagonist, suppressing the induction of type I interferon more efficiently than its SARS-CoV ortholog. Phylogenetic analyses and functional assays revealed that SARS-CoV-2-related viruses from bats and pangolins also encode truncated ORF3b gene products with strong anti-interferon activity. Furthermore, analyses of more than 15,000 SARS-CoV-2 sequences identified a natural variant, in which a longer ORF3b reading frame was reconstituted. This variant was isolated from two patients with severe disease and further increased the ability of ORF3b to suppress interferon induction. Thus, our findings not only help to explain the poor interferon response in COVID-19 patients, but also describe a possibility of the emergence of natural SARS-CoV-2 quasispecies with extended ORF3b that may exacerbate COVID-19 symptoms.\n\nHighlightsO_LIORF3b of SARS-CoV-2 and related bat and pangolin viruses is a potent IFN antagonist\nC_LIO_LISARS-CoV-2 ORF3b suppresses IFN induction more efficiently than SARS-CoV ortholog\nC_LIO_LIThe anti-IFN activity of ORF3b depends on the length of its C-terminus\nC_LIO_LIAn ORF3b with increased IFN antagonism was isolated from two severe COVID-19 cases\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yoriyuki Konno", + "author_inst": "Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the" + }, + { + "author_name": "Izumi Kimura", + "author_inst": "Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the" + }, + { + "author_name": "Keiya Uriu", + "author_inst": "Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the" + }, + { + "author_name": "Masaya Fukushi", + "author_inst": "Institute of Biomedical and Health Sciences, Hiroshima University" + }, + { + "author_name": "Takashi Irie", + "author_inst": "Institute of Biomedical and Health Sciences, Hiroshima University" + }, + { + "author_name": "Yoshio Koyanagi", + "author_inst": "Institute for Frontier Life and Medical Sciences, Kyoto University" + }, + { + "author_name": "So Nakagawa", + "author_inst": "Department of Molecular Life Science, Tokai University School of Medicine" + }, + { + "author_name": "Kei Sato", + "author_inst": "Institute of Medical Science, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.07.20091769", "rel_title": "Evolving Transmission Network Dynamics of COVID-19 Cluster Infections in South Korea: a descriptive study", @@ -1477858,129 +1480255,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.07.20073817", - "rel_title": "The majority of male patients with COVID-19 present low testosterone levels on admission to Intensive Care in Hamburg, Germany: a retrospective cohort study.", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20073817", - "rel_abs": "Males develop more severe SARS-CoV-2 infection related disease outcome than females. Herein, sex hormones were repeatedly proposed to play an important role in Covid-19 pathophysiology and immunity. However, it is yet unclear whether sex hormones are associated with Covid-19 outcome in males and females. In this study, we analyzed sex hormones, cytokine and chemokine responses as well as performed a large profile analysis of 600 metabolites in critically-ill male and female Covid-19 patients in comparison to healthy controls and patients with coronary heart diseases as a prime Covid-19 comorbidity. We here show that dysregulated sex hormones, IFN-{gamma} levels and unique metabolic signatures are associated with critical illness in Covid-19 patients. Both, male and female Covid-19 patients, present elevated estradiol levels which positively correlates with IFN-{gamma} levels. Male Covid-19 patients additionally display severe testosterone and triglyceride deficiencies as compared to female patients and healthy controls. Our results suggest that male Covid-19 patients suffer from multiple metabolic disorders, which may lead to higher risk for fatal outcome. These findings will help to understand molecular pathways involved in Covid-19 pathophysiology.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Maria Schroeder", - "author_inst": "Department for Intensive Care Medicine, University Hospital Hamburg-Eppendorf" - }, - { - "author_name": "Berfin Schaumburg", - "author_inst": "Department for Viral Zoonoses-One Health, Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Zacharias Mueller", - "author_inst": "Department for Viral Zoonoses-One Health, Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Ann Parplys", - "author_inst": "Department for Viral Zoonoses-One Health, Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Dominik Jarczak", - "author_inst": "Department for Critical Care Medicine, University Hospital Hamburg Eppendorf" - }, - { - "author_name": "Axel Nierhaus", - "author_inst": "Department for Critical Care Medicine, University Hospital Hamburg Eppendorf" - }, - { - "author_name": "Andreas Kloetgen", - "author_inst": "Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig" - }, - { - "author_name": "Bettina Schneider", - "author_inst": "Department of Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover" - }, - { - "author_name": "Manuela Peschka", - "author_inst": "Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Fabian Stoll", - "author_inst": "Department for Viral Zonoses-One Health, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg" - }, - { - "author_name": "Tian Bai", - "author_inst": "Department for Viral Zoonoses-One Health, Heinrich Pette Institute, Leibniz Institute for EXperimental Virology" - }, - { - "author_name": "Henning Jacobsen", - "author_inst": "Department for Viral Zoonoses-One Health at the Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Martin Zickler", - "author_inst": "Department for Viral Zoonoses-One Health at the Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Stephanie Stanelle-Bertram", - "author_inst": "Department for Viral Zoonoses-One Health at the Heinrich Pette Institute, Leibniz Institute for Experimental Virology" - }, - { - "author_name": "Geraldine de Heer", - "author_inst": "Department for Intensive Care Medicine, University Hospital Hamburg-Eppendorf" - }, - { - "author_name": "Thomas Renne", - "author_inst": "Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Andreas Meinhardt", - "author_inst": "Institute of Anatomy and Cell Biology, Justus-Liebig University of Giessen, Germany" - }, - { - "author_name": "Joerg Heeren", - "author_inst": "Institute for Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Jens Aberle", - "author_inst": "Department of Endocrinology, University Hospital Hamburg Eppendorf" - }, - { - "author_name": "Alice C McHardy", - "author_inst": "Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig" - }, - { - "author_name": "Hartmut Schlueter", - "author_inst": "Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Jens Hiller", - "author_inst": "Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Sven Peine", - "author_inst": "Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Lothar Kreienbrock", - "author_inst": "Department of Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover" - }, - { - "author_name": "Karin Klingel", - "author_inst": "Institute for Pathology and Neuropathology, University Hospital Tuebingen" - }, - { - "author_name": "Stefan Kluge", - "author_inst": "Department for Intensive Care Medicine, University Hospital Hamburg Eppendorf" - }, - { - "author_name": "Guelsah Gabriel", - "author_inst": "Department for Viral Zoonoses-One Health at the Heinrich Pette Institute, Leibniz Institute for Experimental Virology; University for Veterinary Medicine, Hanno" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.06.20073742", "rel_title": "Evaluating transmission heterogeneity and super-spreading event of COVID-19 in a metropolis of China", @@ -1478244,6 +1480518,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2020.05.07.20090225", + "rel_title": "Anxiety among the general population during Coronavirus-19 Disease in Saudi Arabia: Implications for a Mental Support Program", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20090225", + "rel_abs": "BackgroundThe 2019 outbreak of coronavirus disease (COVID-19) is an worldwide health emergency that threatens mental health of general public. Research data are required to establish evidence-based approaches to alleviate the symptoms of anxiety during the outbreak. This study aimed to survey the general public in Saudi Arabia to help in understanding their levels of anxiety during the COVID-19 outbreak.\n\nMethodsThe researchers performed an on-line survey using snowball sampling methods from April 1 through April 10, 2020. The online survey collected demographics information data, while the Social Anxiety Questionnaire for Adults (SAQ-A30) was used to measure anxiety level.\n\nResultsThis study consisted of 709 respondents from different regions of Saudi Arabia. The general population reported mild to moderate rates of anxiety. Married respondents were associated with a significantly higher level of anxiety (p<0.05).\n\nConclusionsThe respondents reported mild to moderate anxiety during the outbreak of COVID-19 in Saudi Arabia.\n\nImplication for practiceThe results of this study identify the implications to lower levels of anxiety that may be used during the COVID-19 outbreak to develop mental health support programs to improve the mental health of vulnerable groups.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mohannad Alkwiese Sr.", + "author_inst": "Universiti Sultan Zainal Abidin (UniSZA)" + }, + { + "author_name": "Salman H. Alsaqri Sr.", + "author_inst": "University of Hail" + }, + { + "author_name": "Mohammed Aldalaykeh Sr.", + "author_inst": "Jordan University of Science and Technology" + }, + { + "author_name": "Mada Hamzi", + "author_inst": "Ministry of health ; Jazan Health" + }, + { + "author_name": "Mada Mahdi", + "author_inst": "Ministry of health ; Jazan Health" + }, + { + "author_name": "Zainab Shafie", + "author_inst": "Universiti Sultan Zainal Abidin (UniSZA)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2020.05.04.20087072", "rel_title": "St George's COVID shield for use by ENT surgeons performing tracheostomies", @@ -1479484,65 +1481797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2020.05.06.20093724", - "rel_title": "Variations in Personal Protective Equipment Preparedness in Intensive Care Units during the COVID-19 Pandemic: A Survey of Asia-Pacific Countries", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093724", - "rel_abs": "ObjectivesTo evaluate PPE-preparedness across intensive care units (ICUs) in 6 Asia-Pacific countries. PPE-preparedness was defined as the adherence to guidelines, training HCWs, procuring PPE stocks and responding appropriately to a suspected case (transportation and admission to hospital).\n\nDesignCross-sectional web-based survey.\n\nSettingICUs in Australia, New Zealand (NZ), Singapore, Hong Kong (HK), India and Philippines with a 24/7 Emergency/Casualty Department, and capable of mechanically ventilating patients for >24 hours.\n\nInterventionsQuestionnaire sent to intensivists in 633 Level ll/lll ICUs in 6 Asia-Pacific countries by email, WhatsApp and text messaging.\n\nMain outcome measures263 intensivists responded, of whom 231 were eligible for analysis. Response rates were 68%-100% in all countries except India, where it was 24%. 97% either conformed to or exceeded WHO recommendations for PPE-practice. 59% employed airborne precautions irrespective of aerosol-generation-procedures. There were variations in negative-pressure room use (highest in HK/Singapore), training (best in NZ), and PPE stock-awareness (best in HK/Singapore/NZ). High-flow-nasal-oxygenation and non-invasive ventilation were not options in most HK (66.7%, 83.3% respectively) and Singapore ICUs (50%, 80% respectively), but were considered in other countries to a greater extent. 38% reported not having specialized airway teams. Showering and \"buddy-systems\" were underutilized. Clinical waste disposal training was suboptimal (38%).\n\nConclusionsMost intensivists from six Asia-Pacific countries appeared to be aware of the WHO PPE-guidelines by either conforming to/exceeding the recommendations. Despite this, there were widespread variabilities across ICUs and countries in several domains, particularly related to PPE-training and preparedness. Standardising PPE guidelines may translate to better training, better compliance and policies that improve HCW safety. Adopting low-cost approaches such as buddy-systems should be encouraged. More importantly, better pandemic preparedness and building systems with deeply embedded culture of safety is essential to ensure the safety and well-being of HCWs during such pandemics.\n\nAuthor Contributorship\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@1f291aorg.highwire.dtl.DTLVardef@1c388ccorg.highwire.dtl.DTLVardef@4a1a65org.highwire.dtl.DTLVardef@10af39aorg.highwire.dtl.DTLVardef@1ff1eaa_HPS_FORMAT_FIGEXP M_TBL C_TBL Summary BoxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIPersonal-protective equipment (PPE) is the cornerstone to preventing HCW- infections. A search was done on March 23, 2020 on PubMed, Embase or Google Scholar using the mesh terms \"personal protective equipment\", \"PPE\", \"preparedness OR practice OR training\". It revealed no previous studies on PPE preparedness in intensive care units (ICUs). No filters were used for the search.\nC_LIO_LISeveral guidelines/recommendations issued by health organisations on PPE practice exist\nC_LI\n\nWhat are the new findingsO_LIAs the first study to evaluate PPE-preparedness in ICUs, it demonstrated major concerns on PPE-preparedness across several ICUs, particularly in Australia, India and Philippines. There was suboptimal PPE-training, under-utilisation of low-cost interventions such as buddy-systems/team-training, and stock-awareness.\nC_LIO_LIThe guidelines by health organisations on PPE practice have several conflicting recommendations.\nC_LI\n\nHow might it impact on clinical practice in the foreseeable futureO_LIStandardising PPE guidelines by health organisations may translate to better training, better compliance and policies that improve HCW safety.\nC_LIO_LITo ensure the safety and well-being of HCWs, urgent measures are needed to improve PPE-preparedness and building systems with deeply embedded culture of safety. By helping ICUs evaluate and improve their current state of PPE preparedness, the study may help prevent healthcare worker infections and save lives.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Arvind Rajamani", - "author_inst": "Nepean Clinical School University of Sydney" - }, - { - "author_name": "Ashwin SUBRAMANIAM", - "author_inst": "Frankston Hospital and Monash University, VIC" - }, - { - "author_name": "Kiran Shekar", - "author_inst": "The Prince Charles Hospital" - }, - { - "author_name": "Jumana Haji", - "author_inst": "ECMO program director, Consultant anesthesia and critical care 8.\tAster CMI hospital Bangalore" - }, - { - "author_name": "Jinghang Luo", - "author_inst": "Basic Physician Trainee 9.\tWestern Health, VIC" - }, - { - "author_name": "Shailesh BIHARI", - "author_inst": "Flinders university and Flinders Medical center, Bedford Park SA 5042" - }, - { - "author_name": "Wai Tat Wong", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Navya GULLAPALLI", - "author_inst": "Final Year Medical Student Monash University, Clayton VIC" - }, - { - "author_name": "Markus RENNER", - "author_inst": "Senior clinical lecturer Otago University, NZ." - }, - { - "author_name": "Claudia Maria ALCANCIA", - "author_inst": "Makati Medical Center, Philippines" - }, - { - "author_name": "Kollengode RAMANATHAN", - "author_inst": "National University Hospital, Singapore" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.05.07.20094094", "rel_title": "Epidemiology of CoVID-19 and predictors of recovery in the Republic of Korea", @@ -1479798,6 +1482052,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.06.20093658", + "rel_title": "Disinfection effect of pulsed xenon ultraviolet irradiation on SARS-CoV-2 and implications for environmental risk of COVID-19 transmission", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093658", + "rel_abs": "Prolonged survival of SARS-CoV-2 on environmental surfaces and personal protective equipment (PPE) may lead to these surfaces transmitting disease to others. This article reports the effectiveness of a pulsed xenon ultraviolet (PX-UV) disinfection system in reducing the load of SARS-CoV-2 on hard surfaces and N95 respirators. Chamber slides and N95 respirator material were directly inoculated with SARS-CoV-2 and exposed to different durations of PX-UV disinfection. For hard surfaces, disinfection for 1, 2, and 5 minutes resulted in 3.53 Log10, >4.54 Log10, and >4.12 Log10 reductions in viral load, respectively. For N95 respirators, disinfection for 5 minutes resulted in >4.79 Log10 reduction in viral load. We found that PX-UV significantly reduces SARS-CoV-2 on hard surfaces and N95 respirators. With the potential to rapidly disinfectant environmental surfaces and N95 respirators, PX-UV devices are a promising technology for the reduction of environmental and PPE bioburden and to enhance both HCW and patient safety by reducing the risk of exposure to SARS-CoV-2.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Sarah Simmons", + "author_inst": "Xenex Disinfection Services, Inc., San Antonio, TX" + }, + { + "author_name": "Ricardo Carrion Jr.", + "author_inst": "Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX" + }, + { + "author_name": "Kendra Alfson", + "author_inst": "Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX" + }, + { + "author_name": "Hilary Staples", + "author_inst": "Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX" + }, + { + "author_name": "Chetan Jinadatha", + "author_inst": "Department of Medicine, Central Texas Veterans Healthcare System, Temple, TX, Department of Medicine, College of Medicine, Texas A&M Health Science Center, Brya" + }, + { + "author_name": "William Jarvis", + "author_inst": "Jason and Jarvis Associates, Hilton Head Island, SC" + }, + { + "author_name": "Priya Sampathkumar", + "author_inst": "Mayo Clinic, Rochester, MN" + }, + { + "author_name": "Roy Chemaly", + "author_inst": "Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX" + }, + { + "author_name": "Fareed Khawaja", + "author_inst": "Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX" + }, + { + "author_name": "Mark Povroznik", + "author_inst": "Department of Quality, WVU Medicine: United Hospital Center, Bridgeport, WV" + }, + { + "author_name": "Stephanie Jackson", + "author_inst": "Department of Quality, HonorHealth, Scottsdale, AZ" + }, + { + "author_name": "Keith Kaye", + "author_inst": "School of Medicine, Department of Infectious Diseases, University of Michigan, Ann Arbor, MI" + }, + { + "author_name": "Robert Rodriguez", + "author_inst": "Department of Emergency Medicine, University of California San Francisco, San Francisco, CA" + }, + { + "author_name": "Mark Stibich", + "author_inst": "Xenex Disinfection Services, Inc., San Antonio, TX" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.07.20093674", "rel_title": "Coronavirus Disease 2019 (COVID-19): An Evidence Map of Medical Literature", @@ -1481086,61 +1483411,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.08.20095075", - "rel_title": "A rapid review of available evidence on the serial interval and generation time of COVID-19", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095075", - "rel_abs": "BackgroundThe serial interval is the time between symptom onsets in an infector-infectee pair. The generation time, also known as the generation interval, is the time between infection events in an infector-infectee pair. The serial interval and the generation time are key parameters for assessing the dynamics of a disease. A number of scientific papers reported information pertaining to the serial interval and/or generation time for COVID-19.\n\nObjectivesConduct a rapid review of available evidence to advise on appropriate parameter values for serial interval and generation time in national COVID-19 transmission models for Ireland and on methodological issues relating to those parameters.\n\nMethodsA review of scientific literature was conducted covering the period between December 1, 2019 and April 27, 2020. Nineteen scientific papers were evaluated in detail from 27 papers that contained information on the serial interval and/or generation time for COVID-19.\n\nResultsThe mean of the serial interval ranged from 3.1 to 7.5 days, based on 22 estimates, and the median from 1.9 to 6.0 days (based on 7 estimates). Only three estimates were provided for the mean of the generation time. These ranged from 3.9 to 5.2 days. One estimate of 5.0 days was provided for the median of the generation time.\n\nDiscussionThe values of the estimates for serial interval and generation time are heavily influenced by the contact rates between infectious and susceptible individuals. Mitigation measures that are introduced in a country or region are of paramount importance in this regard. The serial interval estimate of 6.6 days (95% confidence interval: 0.7 - 19.0) from the paper by Cereda et al.[10] is likely to be the most relevant to European countries. National estimates should be obtained as soon as possible.\n\nStrengths and limitations of this studyO_LIThe study provides timely information on serial interval and generation time for those involved in the development of models and in the implementation of control measures against COVID-19.\nC_LIO_LIThis is a rapid review of available evidence in the scientific literature between December 1, 2019 and April 27, 2020 on the serial interval and/or the generation time and it contains the usual limitations associated with such a review.\nC_LIO_LIEleven of the 19 papers reviewed in detail were pre-print articles.\nC_LIO_LIThe statistical methods used in the different papers were not analysed in detail.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "John M Griffin", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Aine B Collins", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Kevin Hunt", - "author_inst": "School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "David McEvoy", - "author_inst": "School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland" - }, - { - "author_name": "Miriam Casey", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Andrew W Byrne", - "author_inst": "One Health Scientific Support Unit, Department of Agriculture, Food and the Marine (DAFM), Kildare Street, Dublin 2, Ireland" - }, - { - "author_name": "Conor G McAloon", - "author_inst": "Section of Herd Health and Animal Husbandry, UCD School of Veterinary Medicine, University College Dublin, Dublin D04 W6F6, Ireland" - }, - { - "author_name": "Ann Barber", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Elizabeth Ann Lane", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - }, - { - "author_name": "Simon J More", - "author_inst": "Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 W6F6, Ireland." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.07.20094714", "rel_title": "DOUBLE POWER LAW FOR COVID-19: PREDICTION OF NEW CASES AND DEATH RATES IN ITALY AND SPAIN", @@ -1481348,6 +1483618,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.05.07.20094086", + "rel_title": "Transmission in Latent Period Causes A Large Number of Infected People in the United States", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094086", + "rel_abs": "The cumulative number of confirmed cases in the United States exceeded one million on 29 April 2020, becoming the country of the most serious pandemic in the world. We proposed a model to analyze the real situation and follow-up trend of the epidemic in the US.\n\nThe proposed model divides the epidemic period into two phases, and includes three different categories of transmitters: the latent population, the documented infectious population, and the undocumented infectious population. We use metapopulation network to simulate the spread of the COVID-19 in the US, and apply the Bayesian inference to estimate the key parameters of the model. We also perform component analysis and sensitivity analysis, researching the compositions of the people with COVID-19.\n\nThe results show that the basic reproduction number in the early period of propagation is 4.06. As of April 13, 2020, only 45% (95% CI: 35% - 73%) of symptom onset cases in the United States were documented. The incubation period of COVID-19 is 10.69 days (95% CI: 10.02 - 11.74). If the current level of interventions is continued, the cumulative number of confirmed cases is expected to reach more than 1.7 million in July and continue to grow.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Qinghe Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Junkai Zhu", + "author_inst": "Southeast University" + }, + { + "author_name": "Zhicheng Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Yuhao Zhu", + "author_inst": "Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, the Netherlands" + }, + { + "author_name": "Liuling Zhou", + "author_inst": "Southeast University" + }, + { + "author_name": "Zefei Gao", + "author_inst": "Southeast University" + }, + { + "author_name": "Deqiang Li", + "author_inst": "Southeast Univesity" + }, + { + "author_name": "Yuanbo Tang", + "author_inst": "Southeast University" + }, + { + "author_name": "Xiang Zhang", + "author_inst": "Southeast University" + }, + { + "author_name": "Junyan Yang", + "author_inst": "Southeast University" + }, + { + "author_name": "Qiao Wang", + "author_inst": "Southeast University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.08.20095174", "rel_title": "Effect of underlying comorbidities on the infection and severity of COVID-19 in South Korea", @@ -1482376,49 +1484705,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.05.09.085613", - "rel_title": "Potential modes of COVID-19 transmission from human eye revealed by single-cell atlas", - "rel_date": "2020-05-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.09.085613", - "rel_abs": "There is a pressing urgency to understand the entry route of SARS-CoV-2 viruses into the human body. SARS-CoV-2 viruses enter through ACE2 receptors after the S proteins of the virus are primed by proteases such as TMPRSS2. Most studies focused on the airway epithelial and lung alveolar cells as the route of infection, while the mode of transmission through the ocular route is not well established. Here, we profiled the presence of SARS-CoV-2 receptors and receptor-associated enzymes at single-cell resolution of thirty-three human ocular cell types. We identified unique populations of corneal cells with high ACE2 expression, among which the conjunctival cells co-expressed both ACE2 and TMPRSS2, suggesting that they could serve as the entry points for the virus. Integrative analysis further models the signaling and transcription regulon networks involved in the infection of distinct corneal cells. Our work constitutes a unique resource for the development of new treatments and management of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kiyofumi Hamashima", - "author_inst": "Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore 138673" - }, - { - "author_name": "Pradeep Gautam", - "author_inst": "Institute of Molecular and Cell Biology (IMCB)" - }, - { - "author_name": "Katherine Anne Lau", - "author_inst": "Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore 138673" - }, - { - "author_name": "Chan Woon Khiong", - "author_inst": "Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore" - }, - { - "author_name": "Timothy A Blenkinsop", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" - }, - { - "author_name": "Hu Li", - "author_inst": "Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA" - }, - { - "author_name": "Yuin Han Loh", - "author_inst": "Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore 138673" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.09.086249", "rel_title": "Cholesterol and COVID19 lethality in elderly.", @@ -1482734,6 +1485020,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.05.06.20093104", + "rel_title": "How to Flatten the post-lockdown epidemic trajectory", + "rel_date": "2020-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093104", + "rel_abs": "Populations are locked down during an epidemic to slow down the rate of infection so that epidemic trajectory is \"flattened\". This helps to keep cases at a manageable level. Given the enormous economic damage and misery caused by a lockdown, it is imperative to keep the lockdown period limited. A lockdown is useful only if it can be ensured that after the lockdown is lifted, the epidemic trajectory does not rise sharply again. We present here the results from a mathematical model of the epidemic which examines how the timing, strength and duration of the lockdown affects the post-lockdown epidemic trajectory. Our results show the following:\n\nO_LIA early lockdown (imposed when less than 1% of the population has been infected), of any reasonable duration, cannot prevent the return of the epidemic when the lockdown is lifted. The curve starts climbing soon after lifting the lockdown and reaches a peak of the same height as the no-lockdown curve\nC_LIO_LIThe post-lockdown trajectory can be flattened only if the lockdown is imposed after about 10% of the population has recovered after infection.\nC_LIO_LIThe slope of the post-lockdown epidemic curve depends on the level of immunity built up in the population before and during the lockdown period. Application of lockdown around the inflexion point of the epidemic curve (the point of maximum slope of the curve) ensures that the post-lockdown curve is also flattened.\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ajit Haridas", + "author_inst": "individual" + }, + { + "author_name": "Roschen Sasikumar", + "author_inst": "CSIR-NIIST" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.06.20093757", "rel_title": "Prepared and highly committed despite the risk of COVID-19 infection: A cross-sectional survey of primary care physicians' concerns and coping strategies in Singapore", @@ -1484214,53 +1486523,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.05.20088906", - "rel_title": "Predicting Disease Progression in COVID19: A Score Based On Lab Tests At Time Of Diagnosis", - "rel_date": "2020-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20088906", - "rel_abs": "BackgroundCOVID19 is worldwide pandemic that is mild in the majority of patients but can result in a pneumonia like illness with progression to acute respiratory distress syndrome and death. Predicting the disease severity at time of diagnosis can be helpful in prioritizing hospital admission and resources.\n\nMethodsWe prospectively recruited 1096 consecutive patients with COVID19 from the Jaber Hospital, a COVID19 facility in Kuwait, between 24 February and 20 April 2020. The primary endpoint of interest was disease severity defined algorithmically. Predefined risk variables were collected at the time of PCR based diagnosis of the infection. Prognostic model development used 5-fold cross-validated regularized logit regression. The cohort was divided into a training and validation cohort and all model development proceeded on the training cohort.\n\nResultsThere were 643 patients with clinical course data of whom 94 developed severe COVID19. In the final model, age, CRP, procalcitonin, lymphocyte and monocyte percentages and serum albumin were independent predictors of a more severe illness course. The final prognostic model demonstrated good discrimination, calibration and internal validity.\n\nConclusionWe developed and validated a simple score calculated at time of diagnosis that can predict patients with severe COVID19 disease.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Mohammad H. Jamal", - "author_inst": "Kuwait University School Of Medicine" - }, - { - "author_name": "Suhail Doi", - "author_inst": "Qatar University College of Medicine" - }, - { - "author_name": "Sarah Al Youha", - "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health of Kuwait" - }, - { - "author_name": "Sulaiman AlMazeedi", - "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health of Kuwait" - }, - { - "author_name": "Muhannad AlHaddad", - "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health of Kuwait" - }, - { - "author_name": "Ali AlMuhaini", - "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health of Kuwait" - }, - { - "author_name": "Fahad AlGhimlas", - "author_inst": "Public Health Administration, Ministry of Health of Kuwait" - }, - { - "author_name": "Salman K. AlSabah", - "author_inst": "Kuwait University,College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20091918", "rel_title": "Identification and Analysis of Shared Risk Factors in Sepsis and High Mortality Risk COVID-19 Patients", @@ -1484560,6 +1486822,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.05.20092346", + "rel_title": "IKONOS: An intelligent tool to support diagnosis of Covid-19 by texture analysis of x-ray images", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092346", + "rel_abs": "In late 2019, the SARS-Cov-2 spread worldwide. The virus has high rates of proliferation and causes severe respiratory symptoms, such as pneumonia. There is still no specific treatment and diagnosis for the disease. The standard diagnostic method for pneumonia is chest X-ray image. There are many advantages to using Covid-19 diagnostic X-rays: low cost, fast and widely available. We propose an intelligent system to support diagnosis by X-ray images. We tested Haralick and Zernike moments for feature extraction. Experiments with classic classifiers were done. Support vector machines stood out, reaching an average accuracy of 89.78%, average recall and sensitivity of 0.8979, and average precision and specificity of 0.8985 and 0.9963 respectively. The system is able to differentiate Covid-19 from viral and bacterial pneumonia, with low computational cost.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Juliana Carneiro Gomes", + "author_inst": "Escola Politecnica da Universidade de Pernambuco" + }, + { + "author_name": "Valter Augusto de Freitas Barbosa", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Maira Araujo de Santana", + "author_inst": "Escola Politecnica da Universidade de Pernambuco" + }, + { + "author_name": "Jonathan Bandeira", + "author_inst": "Escola Politecnica da Universidade de Pernambuco" + }, + { + "author_name": "Meuser Jorge Silva Valenca", + "author_inst": "Escola Politecnica da Universidade de Pernambuco" + }, + { + "author_name": "Ricardo Emmanuel de Souza", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Aras Masood Ismael", + "author_inst": "Information Technology Department, Technical College of Informatics, Sulaimani Polytechnic University" + }, + { + "author_name": "Wellington Pinheiro dos Santos", + "author_inst": "Universidade Federal de Pernambuco" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.05.20091702", "rel_title": "Elevated RDW is Associated with Increased Mortality Risk in COVID-19", @@ -1485600,41 +1487909,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.02.20088013", - "rel_title": "Social distancing and movement constraint as the most likely factors for COVID-19 outbreak control in Brazil", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088013", - "rel_abs": "As thousands of new cases of COVID-19 have been confirmed, there is an increasing demand to understand the factors underlying the spread of this disease. Using country-level data, we modeled the early growth in the number of cases for over 480 cities in all Brazilian states. As the main findings, we found that the percentage of people respecting social distancing protocols was the main explanatory factor for the observed growth rate of COVID-19. Those cities that presented the highest spread of the new coronavirus were also those that had lower averages of social distancing. We also underline that total population of cities and connectivity, represented by the city-level importance to the air transportation of people across the country, plays important roles in the dissemination of SARS-CoV-2. Climate and socioeconomic predictors had little contribution to the big-picture scenario. Our results show that different States had high variability in their growth rates, mostly due to quite different public health strategies to retain the outbreak of COVID-19. In spite of all limitations of such a large-scale approach, our results underline that climatic conditions are likely weak limiting factors for the spread of the new coronavirus, and the circulation of people in the city- and country-level are the most responsible factors for the early outbreak of COVID-19 in Brazil. Moreover, we reinforce that social distancing protocols are fundamental to avoid critical scenarios and the collapse of healthcare systems. We also predict that economic-induced decisions for relaxing social distancing might have catastrophic consequences, especially in large cities.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Matheus T Baumgartner", - "author_inst": "Universidade Estadual de Maringa" - }, - { - "author_name": "Fernando M Lansac-Toha", - "author_inst": "Universidade Estadual de Maringa" - }, - { - "author_name": "Marco Tulio P Coelho", - "author_inst": "Universidade Federal de Goias" - }, - { - "author_name": "Ricardo Dobrovolski", - "author_inst": "Universidade Federal da Bahia" - }, - { - "author_name": "Jose Alexandre F Diniz-Filho", - "author_inst": "Universidade Federal de Goias" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.02.20086314", "rel_title": "Testing lags and emerging COVID-19 outbreaks in federal penitentiaries in Canada", @@ -1485762,6 +1488036,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.04.20090050", + "rel_title": "Hospitalization and 30-day fatality in 121,263 COVID-19 outpatient cases", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090050", + "rel_abs": "BackgroundTo date, characterisation studies of COVID-19 have focussed on hospitalised or intensive care patients. We report for the first time on the natural history of COVID-19 disease from first diagnosis, including both outpatient and hospital care.\n\nMethodsData was obtained from SIDIAP, a primary care records database covering >6 million people (>80% of the population of Catalonia), linked to COVID-19 RT-PCR tests, hospital emergency and inpatient, and mortality registers. All participants >=15 years, diagnosed with COVID-19 in outpatient between 15th March and 24th April 2020 (10th April for outcome studies) were included. Baseline characteristics, testing, and 30-day outcomes (hospitalisation for COVID-19 and all-cause fatality) were analysed.\n\nResultsA total of 121,263 and 95,467 COVID-19 patients were identified for characterisation and outcome studies, respectively. Women (57.8%) and age 45-54 (20.2%) were predominant. 44,709 were tested, with 32,976 (73.8%) PCR+. From 95,467 cases, a 14.6% [14.4-14.9] were hospitalised in the month after diagnosis, with male predominance (19.2% vs 11.3%), peaking at age 75-84. Overall 30-day fatality was 4.0% [95%CI 3.9%-4.2%], higher in men (4.8%) than women (3.4%), increasing with age, and highest in those residing in nursing homes (25.3% [24.2% to 26.4%]).\n\nConclusionsCOVID-19 is seen in all age-sex strata, but severe forms of disease cluster in older men and nursing home residents. Although initially managed in primary care, 15% of cases require hospitalization within a month, with overall fatality of 4%.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "DANIEL PRIETO-ALHAMBRA", + "author_inst": "University of Oxford" + }, + { + "author_name": "Elisabet Ballo", + "author_inst": "Institut Catala de la Salut" + }, + { + "author_name": "Ermengol Coma-Redon", + "author_inst": "Institut Catala de la Salut" + }, + { + "author_name": "Nuria Mora", + "author_inst": "Idiap Jordi Gol" + }, + { + "author_name": "Maria Aragon", + "author_inst": "Idiap Jordi Gol" + }, + { + "author_name": "Albert Prats-Uribe", + "author_inst": "University of Oxford" + }, + { + "author_name": "Francesc Fina-Aviles", + "author_inst": "Institut Catala de la Salut" + }, + { + "author_name": "Mencia Benitez", + "author_inst": "Institut Catala de la Salut" + }, + { + "author_name": "Carolina Guiriguet", + "author_inst": "Institut Catala de la Salut" + }, + { + "author_name": "Mireia Fabregas", + "author_inst": "Institut Catala de la Salut" + }, + { + "author_name": "Manuel Medina-Peralta", + "author_inst": "Institut Catala de la Salut" + }, + { + "author_name": "Talita Duarte-Salles", + "author_inst": "Idiap Jordi Gol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.02.20088872", "rel_title": "Assessment of Hydroxychloroquine and Chloroquine Safety Profiles: A Systematic Review and Meta-Analysis", @@ -1487450,81 +1489787,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.04.20091231", - "rel_title": "Point-of-care testing for COVID-19 using SHERLOCK diagnostics", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20091231", - "rel_abs": "The recent outbreak of the novel coronavirus SARS-CoV-2, which causes COVID-19, can be diagnosed using RT-qPCR, but inadequate access to reagents and equipment has slowed disease detection and impeded efforts to mitigate viral spread. Alternative approaches based on combinations of isothermal amplification and CRISPR-mediated detection, such as the SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing) technique, offer reduced dependence on RT-qPCR equipment, but previously reported methods required multiple fluid handling steps, complicating their deployment outside clinical labs. Here we developed a simple test chemistry called STOP (SHERLOCK Testing in One Pot) for detecting SARS-CoV-2 in one hour that is suitable for point-of-care use. This simplified test, STOPCovid, provides sensitivity comparable to RT-qPCR-based SARS-CoV-2 tests and has a limit of detection of 100 copies of viral genome input in saliva or nasopharyngeal swabs per reaction. Using lateral flow readout, the test returns result in 70 minutes, and using fluorescence readout, the test returns result in 40 minutes. Moreover, we validated STOPCovid using nasopharyngeal swabs from COVID-19 patients and were able to correctly diagnose 12 positive and 5 negative patients out of 3 replicates. We envision that implementation of STOPCovid will significantly aid \"test-trace-isolate\" efforts, especially in low-resource settings, which will be critical for long-term public health safety and effective reopening of the society.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Julia Joung", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Department of Biological Engineering at MIT" - }, - { - "author_name": "Alim Ladha", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Department of Biological Engineering at MIT" - }, - { - "author_name": "Makoto Saito", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Departments of Biological Engineering and Bra" - }, - { - "author_name": "Michael Segel", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Departments of Biological Engineering and Bra" - }, - { - "author_name": "Robert Bruneau", - "author_inst": "University of Washington, Seattle" - }, - { - "author_name": "Meei-li W Huang", - "author_inst": "University of Washington, Seattle" - }, - { - "author_name": "Nam-Gyun Kim", - "author_inst": "University of Washington, Seattle" - }, - { - "author_name": "Xu Yu", - "author_inst": "Ragon Institute of MGH, MIT and Harvard; Massachusetts General Hospital; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Jonathan Li", - "author_inst": "Ragon Institute of MGH, MIT and Harvard; Brigham and Women's Hospital; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Bruce D. Walker", - "author_inst": "Howard Hughes Medical Institute; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Alexander L. Greninger", - "author_inst": "University of Washington, Seattle; Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Keith R. Jerome", - "author_inst": "University of Washington, Seattle; Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jonathan S. Gootenberg", - "author_inst": "McGovern Institute for Brain Research at MIT; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Omar O. Abudayyeh", - "author_inst": "McGovern Institute for Brain Research at MIT; Massachusetts Consortium for Pathogen Readiness" - }, - { - "author_name": "Feng Zhang", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Departments of Biological Engineering and Bra" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.04.20091132", "rel_title": "Phenomenological Modelling of COVID-19 epidemics in Sri Lanka, Italy and Hebei Province of China", @@ -1488156,6 +1490418,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.05.20091553", + "rel_title": "Health seeking behaviors of patients with acute respiratory infections during the outbreak of novel coronavirus disease 2019 in Wuhan, China", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091553", + "rel_abs": "We conducted two surveys to evaluate the health-seeking behaviors of individuals with acute respiratory infections (ARI) during the COVID-19 outbreak in Wuhan, China. Among 351 participants reporting ARI (10.3%, 351/3,411), 36.5% sought medical assistance. Children were more likely to seek medical assistance than other age groups (66.1% vs. 28.0%-35.1%).", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Juan Yang", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Hui Gong", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Xinhua Chen", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Zhiyuan Chen", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Xiaowei Deng", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Mengcen Qian", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Zhiyuan Hou", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA" + }, + { + "author_name": "Hongjie Yu", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.05.20091686", "rel_title": "Forecasting the spread of COVID-19 in Nigeria using Box-Jenkins Modeling Procedure", @@ -1489292,41 +1491609,6 @@ "type": "confirmatory results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.05.05.079400", - "rel_title": "Massive Multiplexing Can Deliver a $1 Test for COVID-19", - "rel_date": "2020-05-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.079400", - "rel_abs": "The severe acute respiratory syndrome virus, SARS-CoV-2 (hereafter COVID-19), rapidly achieved global pandemic status, provoking large-scale screening programs in many nations. Their activation makes it imperative to identify methods that can deliver a diagnostic result at low cost. This paper describes an approach which employs sequence variation in the gene coding for its envelope protein as the basis for a scalable, inexpensive test for COVID-19. It achieves this by coupling a simple RNA extraction protocol with low-volume RT-PCR, followed by E-Gel screening and sequencing on high-throughput platforms to analyze 10,000 samples in a run. Slight modifications to the protocol could support screening programs for other known viruses and for viral discovery. Just as the $1,000 genome is transforming medicine, a $1 diagnostic test for viral and bacterial pathogens would represent a major advance for public health.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Paul DN Hebert", - "author_inst": "Centre for Biodiversity Genomics, University of Guelph" - }, - { - "author_name": "Sean WJ Prosser", - "author_inst": "Centre for Biodiversity Genomics, University of Guelph" - }, - { - "author_name": "Natalia V Ivanova", - "author_inst": "Centre for Biodiversity Genomics, University of Guelph" - }, - { - "author_name": "Evgeny V. Zakharov", - "author_inst": "University of Guelph" - }, - { - "author_name": "Sujeevan Ratnasingham", - "author_inst": "Centre for Biodiversity Genomics, University of Guelph" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.03.20089755", "rel_title": "Who maintains a good mental health in a locked-down country? A French nationwide online survey of 11,391 participants", @@ -1489486,6 +1491768,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.06.050260", + "rel_title": "SARS-CoV-2 proteins exploit host's genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology", + "rel_date": "2020-05-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.050260", + "rel_abs": "The constant rise of the death toll and cases of COVID-19 has made this pandemic a serious threat to human civilization. Understanding of host-SARS-CoV-2 interaction in viral pathogenesis is still in its infancy. In this study we aimed to correlate how SARS-CoV-2 utilizes its proteins for tackling the host immune response; parallelly, how host epigenetic factors might play a role in this pathogenesis was also investigated. We have utilized a blend of computational and knowledgebase approach to elucidate the interplay between host and SARS-CoV-2. Integrating the experimentally validated host interactome proteins and differentially expressed host genes due to SARS-CoV-2 infection, we have taken a blend of computational and knowledgebase approach to delineate the interplay between host and SARS-CoV-2 in various signaling pathways. Also, we have shown how host epigenetic factors are involved in the deregulation of gene expression. Strikingly, we have found that several transcription factors and other epigenetic factors can modulate some immune signaling pathways, helping both host and virus. We have identified miRNA hsa-miR-429 whose transcription factor was also upregulated and targets were downregulated and this miRNA can have pivotal role in suppression of host immune responses. While searching for the pathways in which viral proteins interact with host proteins, we have found pathways like-HIF-1 signaling, autophagy, RIG-I signaling, Toll-like receptor signaling, Fatty acid oxidation/degradation, Il-17 signaling etc significantly associated. We observed that these pathways can be either hijacked or suppressed by the viral proteins, leading to the improved viral survival and life-cycle. Moreover, pathways like-Relaxin signaling in lungs suggests aberration by the viral proteins might lead to the lung pathophysiology found in COVID-19. Also, enrichment analyses suggest that deregulated genes in SARS-CoV-2 infection are involved in heart development, kidney development, AGE-RAGE signaling pathway in diabetic complications etc. might suggest why patients with comorbidities are becoming more prone to SARS-CoV-2 infection. Our results suggest that SARS-CoV-2 integrates its proteins in different immune signaling pathway and other cellular signaling pathways for developing efficient immune evasion mechanisms, while leading the host to more complicated disease condition. Our findings would help in designing more targeted therapeutic interventions against SARS-CoV-2.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Md. Abdullah-Al-Kamran Khan", + "author_inst": "Department of Mathematics and Natural Sciences, BRAC University" + }, + { + "author_name": "Abul B.M.M.K. Islam", + "author_inst": "Department of Genetic Engineering and Biotechnology, University of Dhaka" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.05.02.20089086", "rel_title": "Quantitative Estimation of Covid-19 Related Unemployment On Suicide and Excess Mortality in the United States", @@ -1490870,49 +1493175,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.03.20089342", - "rel_title": "Temperature and relative humidity are not major contributing factor on the occurrence of COVID-19 pandemic: An observational study in 57 countries", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089342", - "rel_abs": "The world searching for hope has already experienced a huge loss of lives due to COVID-19 caused by SARS-CoV-2 started in Wuhan, China. There are speculations that climatic conditions can slowdown the transmission of COVID-19. Findings from the early outbreak indicated the possible association of air temperature and relative humidity in COVID-19 occurrence in China. Current study focused on whether climatic conditions (temperature and relative humidity) are having any influence in the occurrence of COVID-19 when the outbreak has been classified as pandemic. To determine the effect of daily average temperature and average relative humidity on log-transformed total daily cases of COVID-19, polynomial regression as a quadratic term and linear regression were done. Linear regression analysis was also carried out to explore the same effect on selected countries. Present study observed no correlation between the climatic conditions (the daily average temperature and relative humidity) and the number of cases of COVID-19. Similar result was found in relation between daily average temperature and average number of cases per day in country-wise analysis. However, about 93.5% cases of COVID-19 occurred between 1{degrees}C to 16{degrees}C and the average number of cases per day was lower in high temperature country than low temperature country with exceptions. The minimum effect of summer temperature may not be effective to control the pandemic rather need to apply the control measures of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Md.Abdus Sobur", - "author_inst": "Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - }, - { - "author_name": "Md.Saiful Islam", - "author_inst": "Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - }, - { - "author_name": "Md.Emdadul Haque", - "author_inst": "Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - }, - { - "author_name": "AMM Taufiquer Rahman", - "author_inst": "Naogaon District Hospital, Naogaon, Bangladesh." - }, - { - "author_name": "Md.Taohidul Islam", - "author_inst": "Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - }, - { - "author_name": "Antonio Toniolo", - "author_inst": "Global Virus Network, University of Insubria, 21100 Varese, Italy." - }, - { - "author_name": "Md.Tanvir Rahman", - "author_inst": "Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20092635", "rel_title": "Studies of Novel Coronavirus Disease 19 (COVID-19) Pandemic: A Global Analysis of Literature", @@ -1491212,6 +1493474,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.05.20084889", + "rel_title": "Sensitivity of Nasopharyngeal, Nasal and Throat Swab for the Detection of SARS-CoV-2", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20084889", + "rel_abs": "Nasopharyngeal (NP), nasal and throat swabs are the most practical specimen sources to test for upper respiratory pathogens. We compared the sensitivity of NP, nasal and throat swabs to detect SARS-CoV-2 in community patients. Using detection at any site as the standard, the sensitivities were 90%, 80% and 87% for NP, nasal and throat respectively (n=30 positive at any site). Throat swabs are likely a suitable alternative to NP swabs for the detection of COVID-19 infections.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Byron Michael Berenger", + "author_inst": "University of Calgary" + }, + { + "author_name": "Kevin Fonseca", + "author_inst": "Provincial Laboratory of Public Health" + }, + { + "author_name": "Angela R Schneider", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jia Hu", + "author_inst": "Alberta Health Services" + }, + { + "author_name": "Nathan Zelyas", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.01.20086694", "rel_title": "Famotidine Use is Associated with Improved Clinical Outcomes in Hospitalized COVID-19 Patients: A Retrospective Cohort Study", @@ -1492564,53 +1494861,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.04.20090258", - "rel_title": "Safe Blues: A Method for Estimation and Control in the Fight Against COVID-19", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090258", - "rel_abs": "How do fine modifications to social distancing measures really affect COVID-19 spread? A major problem for health authorities is that we do not know.\n\nIn an imaginary world, we might develop a harmless biological virus that spreads just like COVID-19, but is traceable via a cheap and reliable diagnosis. By introducing such an imaginary virus into the population and observing how it spreads, we would have a way of learning about COVID-19 because the benign virus would respond to population behaviour and social distancing measures in a similar manner. Such a benign biological virus does not exist. Instead, we propose a safe and privacy-preserving digital alternative.\n\nOur solution is to mimic the benign virus by passing virtual tokens between electronic devices when they move into close proximity. As Bluetooth transmission is the most likely method used for such inter-device communication, and as our suggested \"virtual viruses\" do not harm individuals software or intrude on privacy, we call these Safe Blues.\n\nIn contrast to many app-based methods that inform individuals or governments about actual COVID-19 patients or hazards, Safe Blues does not provide information about individuals locations or contacts. Hence the privacy concerns associated with Safe Blues are much lower than other methods. However, from the point of view of data collection, Safe Blues has two major advantages:\n\nO_LIData about the spread of Safe Blues is uploaded to a central server in real time, which can give authorities a more up-to-date picture in comparison to actual COVID-19 data, which is only available retrospectively.\nC_LIO_LISampling of Safe Blues data is not biased by being applied only to people who have shown symptoms or who have come into contact with known positive cases.\nC_LI\n\nThese features mean that there would be real statistical value in introducing Safe Blues. In the medium term and end game of COVID-19, information from Safe Blues could aid health authorities to make informed decisions with respect to social distancing and other measures.\n\nIn this paper we outline the general principles of Safe Blues and we illustrate how Safe Blues data together with neural networks may be used to infer characteristics of the progress of the COVID-19 pandemic in real time. Further information is on the Safe Blues website: https://safeblues.org/.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Raj Abhijit Dandekar", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Shane G. Henderson", - "author_inst": "Cornell University" - }, - { - "author_name": "Marijn Jansen", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Sarat Moka", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Yoni Nazarathy", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Christopher Rackauckas", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Peter G. Taylor", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Aapeli Vuorinen", - "author_inst": "The University of Queensland and The University of Melbourne" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.04.20090324", "rel_title": "Estimating Excess Deaths in the United States Early in the COVID-19 Pandemic", @@ -1492762,6 +1495012,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.03.20089623", + "rel_title": "Risk of secondary infection waves of COVID-19 in an insular region: the case of the Balearic Islands, Spain", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089623", + "rel_abs": "The Spanish government declared the lockdown on March 14th, 2020 to tackle the fast-spreading of COVID-19. As a consequence the Balearic Islands remained almost fully isolated due to the closing of airports and ports, These isolation measures and the home-based confinement have led to a low prevalence of COVID-19 in this region. We propose a compartmental model for the spread of COVID-19 including five compartments (Susceptible, Latent, Infected, Diseased, and Recovered), and the mobility between municipalities. The model parameters are calibrated with the temporal series of confirmed cases provided by the Spanish Ministry of Health. After calibration, the proposed model captures the trend of the official confirmed cases before and after the lockdown. We show that the estimated number of cases depends strongly on the initial dates of the local outbreak onset and the number of imported cases before the lockdown. Our estimations indicate that the population has not reached the level of herd immunization necessary to prevent future outbreaks. While the low prevalence, in comparison to mainland Spain, has prevented the saturation of the health system, this low prevalence translates into low immunization rates, therefore facilitating the propagation of new outbreaks that could lead to secondary waves of COVID-19 in the region. These findings warn about scenarios regarding after-lockdown-policies and the risk of second outbreaks, emphasize the need for widespread testing, and could potentially be extrapolated to other insular and continental regions.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Victor M. Eguiluz", + "author_inst": "IFISC (CSIC-UIB)" + }, + { + "author_name": "Juan Fernadez-Gracia", + "author_inst": "IFSIC (CSIC-UIB)" + }, + { + "author_name": "Jorge P. Rodriguez", + "author_inst": "ISI Foundation" + }, + { + "author_name": "Juan M. Pericas", + "author_inst": "Infectious Disease Department, Hospital Clinic de Barcelona" + }, + { + "author_name": "Carlos J. Melian", + "author_inst": "EAWAG" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.03.20089615", "rel_title": "Forecasting COVID-19 new cases in Algeria using Autoregressive fractionally integrated moving average Models (ARFIMA)", @@ -1494217,65 +1496502,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.04.20090746", - "rel_title": "Urban Air Pollution May Enhance COVID-19 Case-Fatality and Mortality Rates in the United States", - "rel_date": "2020-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090746", - "rel_abs": "BackgroundThe novel human coronavirus disease 2019 (COVID-19) pandemic has claimed more than 240,000 lives worldwide, causing tremendous public health, social, and economic damages. While the risk factors of COVID-19 are still under investigation, environmental factors, such as urban air pollution, may play an important role in increasing population susceptibility to COVID-19 pathogenesis.\n\nMethodsWe conducted a cross-sectional nationwide study using zero-inflated negative binomial models to estimate the association between long-term (2010-2016) county-level exposures to NO2, PM2.5 and O3 and county-level COVID-19 case-fatality and mortality rates in the US. We used both single and multipollutant models and controlled for spatial trends and a comprehensive set of potential confounders, including state-level test positive rate, county-level healthcare capacity, phase-of-epidemic, population mobility, sociodemographic, socioeconomic status, behavior risk factors, and meteorological factors.\n\nResults1,027,799 COVID-19 cases and 58,489 deaths were reported in 3,122 US counties from January 22, 2020 to April 29, 2020, with an overall observed case-fatality rate of 5.8%. Spatial variations were observed for both COVID-19 death outcomes and long-term ambient air pollutant levels. County-level average NO2 concentrations were positively associated with both COVID-19 case-fatality rate and mortality rate in single-, bi-, and tri-pollutant models (p-values<0.05). Per inter-quartile range (IQR) increase in NO2 (4.6 ppb), COVID-19 case-fatality rate and mortality rate were associated with an increase of 7.1% (95% CI 1.2% to 13.4%) and 11.2% (95% CI 3.4% to 19.5%), respectively. We did not observe significant associations between long-term exposures to PM2.5 or O3 and COVID-19 death outcomes (p-values>0.05), although per IQR increase in PM2.5 (3.4 ug/m3) was marginally associated with 10.8% (95% CI: -1.1% to 24.1%) increase in COVID-19 mortality rate.\n\nDiscussions and ConclusionsLong-term exposure to NO2, which largely arises from urban combustion sources such as traffic, may enhance susceptibility to severe COVID-19 outcomes, independent of longterm PM2.5 and O3 exposure. The results support targeted public health actions to protect residents from COVID-19 in heavily polluted regions with historically high NO2 levels. Moreover, continuation of current efforts to lower traffic emissions and ambient air pollution levels may be an important component of reducing population-level risk of COVID-19 deaths.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Donghai Liang", - "author_inst": "Emory University" - }, - { - "author_name": "Liuhua Shi", - "author_inst": "Emory University" - }, - { - "author_name": "Jingxuan Zhao", - "author_inst": "American Cancer Society" - }, - { - "author_name": "Pengfei Liu", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Joel Schwartz", - "author_inst": "Harvard University" - }, - { - "author_name": "Song Gao", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Jeremy A Sarnat", - "author_inst": "Emory University" - }, - { - "author_name": "Yang Liu", - "author_inst": "Emory University" - }, - { - "author_name": "Stefanie T Ebelt", - "author_inst": "Emory University" - }, - { - "author_name": "Noah C Scovronick", - "author_inst": "Emory University" - }, - { - "author_name": "Howard Chang", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.04.20090670", "rel_title": "Projection of COVID-19 Cases and Deaths in the US as Individual States Re-open May 4,2020", @@ -1494439,6 +1496665,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.05.02.20088997", + "rel_title": "Predictive Model with Analysis of the Initial Spread of COVID-19 in India", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088997", + "rel_abs": "The Coronavirus Disease 2019 (COVID-19) has currently ravaged through the world, resulting in over three million confirmed cases and over two hundred thousand deaths, a complete change in daily life as we know it, worldwide lock-downs, travel restrictions, as well as heightened hygiene measures and physical distancing. Being able to analyse and predict the spread of this epidemic-causing disease is hence of utmost importance now, especially as it would help in the reasoning behind important decisions drastically affecting countries and their people, as well as in ensuring efficient resource and utility management. However, the needs of the people and specific conditions of the spread are varying widely from country to country. In this article, we have conducted an in-depth analysis of the spread of COVID-19 in India, patient statistics, as well as proposed a mathematical prediction system that has succeeded in predicting the following days number of cases with 83% accuracy, ever since the first COVID-19 case was declared in India.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Shinjini Ghosh", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.02.20088765", "rel_title": "Potential biases arising from epidemic dynamics in observational seroprotection studies", @@ -1495523,33 +1497768,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.03.20081380", - "rel_title": "FACTORS INFLUENCING MENTAL HEALTH DURING COVID-19 OUTBREAK: AN EXPLORATORY SURVEY AMONG INDIAN POPULATION", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20081380", - "rel_abs": "PurposeResearch on the impact of social distancing on mental health during epidemics is limited, especially in India. The purpose of this study is to scale the association between anxiety and socio-demographic factors during Covid19 lockdown among the general Indian population.\n\nDesign/methodology/approachA descriptive cross-sectional nationwide study was designed to enrol the general population. The inclusion criteria for this study were Indian citizens aged 18 years and above. The study was conducted from 29th March to 12th April 2020, using an online google questionnaire. The anxiety among respondents was detected and measured using a Generalised Anxiety Disorder Scale which consists of 7 questions (in English), i.e. GAD-7.\n\nFindingsRespondees were 392, and from these participants, the prevalence of anxiety was 25.3 per cent. Based on the bivariate logistic regression analysis, the predictors of anxiety were gender, religion, occupation as business/self-employed, marital status, family size, health status and sleep deprivation.\n\nConclusionThis study reports the prevalence of anxiety among Indian population who were grounded at their homes during lockdown due to coronavirus pandemic in the country.\n\nLimitations(1) The selection of participants through non-random sampling. (2) Because of the cross-sectional character of the study, causal conclusions cannot be drawn.\n\nOriginality/ValueThis paper fulfils an identified need to study the mental health status of the population under situations like lockdown, thereby helping fill a persistent gap in Indian research on this issue.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Absar Ahmad", - "author_inst": "Career Institute of Medical Sciences and Hospital, Lucknow, India" - }, - { - "author_name": "Ishrat Rahman", - "author_inst": "College of Dentistry, Princess Nourah Bint Abdulrahman University Riyadh, KSA" - }, - { - "author_name": "Maitri Agarwal", - "author_inst": "Career Institute of Medical Sciences & Hospital, Lucknow, India" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.05.01.20081034", "rel_title": "Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies.", @@ -1495869,6 +1498087,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.03.20089680", + "rel_title": "The Impact of Social Distancing on TheCourse of The Covid-19 Pandemic in FourEuropean Countries", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089680", + "rel_abs": "In this article the mortality data from four European countries arising from the Covid-19 pandemic is modelled using logistic functions. The countries chosen for examination are Spain, Italy, France and the UK. They have been selected because in each the pandemic is advanced, mortality high and any prospect of containment has passed. They have also been selected because in each social distancing has been used in an attempt to reduce peak daily mortality with relatively strict enforcement following a defined date. The choices of data set and model type is justified. The impact, if any, of social distancing is examined.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Andrew Michael Shardlow", + "author_inst": "The Open University, Milton Keynes, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.03.20089300", "rel_title": "Functional alteration of innate T cells in critically ill Covid-19 patients", @@ -1497041,97 +1499278,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2020.05.01.20087080", - "rel_title": "Early phases of COVID-19 are characterized by a reduction of lymphocyte populations and the presence of atypical monocytes", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087080", - "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 is a recently discovered pathogen responsible of coronavirus disease 2019 (COVID-19). The immunological changes associated with this infection are largely unknown.\n\nMethodsWe evaluated the peripheral blood mononuclear cells profile of 63 patients with COVID-19 at diagnosis and the presence of association with inflammatory biomarkers and 28-days mortality.\n\nResultsLymphocytopenia was present in 51 of 63 (80.9%) patients. This reduction was mirrored also on CD8+ lymphocytes (128 cells/L), natural killer cells (67 cells/L) and natural killer T cells (31 cells/L). Monocytes were preserved in total number but displayed a subpopulation composed mainly of cells with a reduced expression of both CD14 and HLA-DR. A direct correlation was found between serum values of IL-6 and the frequency of Th2 lymphocytes (R=0.17; p=0.04) but not with the monocytes count (R=0.01; p=0.60). Patients who died in the 28 days from admission (N=10, 15.9%), when compared to those who did not, displayed lower mean values of CD3+ (p=0.028) and CD4+ cells (p=0.042) and higher mean percentages of CD8+/CD38+/HLA-DR+ lymphocytes (p=0.026).\n\nConclusionsThe early phases of COVID-19 are characterized by lymphocytopenia, predominance of Th2 lymphocytes and less immunocompetent monocytes, which include atypical mononuclear cells.\n\neTOC-At diagnosis patients with COVID-19 have lymphocytopenia\n-Monocytes with both normal or altered scatter properties display a reduced expression of CD14 and HLA-DR in most of COVID-19 patients\n-Patients who die in the 28 days from admission have lower values of CD3+ and CD4+ cells and higher percentages of activated CTL cells compared to those who survive", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "ANDREA LOMBARDI", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Elena Trombetta", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Alessandra Cattaneo", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Valeria Castelli", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Emanuele Palomba", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Mario Tirone", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Davide Mangioni", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Giuseppe Lamorte", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Maria Manunta", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Daniele Prati", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Ferruccio Ceriotti", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Roberta Gualtierotti", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Giorgio Costantino", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Stefano Aliberti", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Vittorio Scaravilli", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Giacomo Grasselli", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Andrea Gori", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Laura Porretti", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - }, - { - "author_name": "Alessandra Bandera", - "author_inst": "Foundation IRCCS Ca Granda Ospedale Maggiore Policlinico" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.01.20087114", "rel_title": "Lung disease severity, Coronary Artery Calcium, Coronary inflammation and Mortality in Coronavirus Disease 2019.", @@ -1497387,6 +1499533,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.01.20087411", + "rel_title": "COVID-19 Related Mortality: Is the BCG Vaccine Truly Effective?", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087411", + "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has become a worldwide emergency. In the attempt to search for interventions that would improve outcomes, some studies have looked at the potential benefit of BCG vaccination. These past studies have found a statistically significant reduction in COVID-19 related mortality in countries with a current universal bacille Calmette-Guerin (BCG) vaccination policy. However, just as the authors themselves noted, the nature of ecological studies make them very prone to the presence of several confounders. This paper took into account demographic differences, economic differences and the different stages of the pandemic in each country; gathering data from publicly available sources. It was found that no statistically significant difference exists in mortality rates between countries with a current or prior BCG vaccination policy when compared to those that never had such a program. Nevertheless, the immunostimulatory potential of the BCG vaccine might still prove useful in the development of future vaccines or other prophylactic measures.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jan Alberto Paredes Mogica", + "author_inst": "Anahuac University" + }, + { + "author_name": "Valeria Nava", + "author_inst": "Anahuac University" + }, + { + "author_name": "Julian Torres", + "author_inst": "Central Military Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20087403", "rel_title": "Who is more susceptible to Covid-19 infection and mortality in the States?", @@ -1498371,61 +1500544,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2020.05.01.20087973", - "rel_title": "COVID-19 Utilization and Resource Visualization Engine (CURVE) to Forecast In-Hospital Resources", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087973", - "rel_abs": "BackgroundThe emergence of COVID-19 has created an urgent threat to public health worldwide. With rapidly evolving demands on healthcare resources, it is imperative that healthcare systems have the ability to access real-time local data to predict, plan, and effectively manage resources.\n\nObjectiveTo develop an interactive COVID-19 Utilization and Resource Visualization Engine (CURVE) as a data visualization tool to inform decision making and guide a large health systems proactive pandemic response.\n\nMethodsWe designed and implemented CURVE using R Shiny to display real-time parameters of healthcare utilization at Atrium Health with projections based upon locally derived models for the COVID-19 pandemic. We used the CURVE app to compare predictions from two of our models -one created before and one after the statewide stay-at-home and social distancing orders (denoted before- and after-SAH-order model). We established parameter settings for best-, moderate-, and worst-case scenarios for pandemic spread and resource use, leveraging two locally developed forecasting models to determine peak date trajectory, resource use, and root mean square error (RMSE) between observed and predicted results.\n\nResultsCURVE predicts and monitors utilization of hospital beds, ICU beds, and number of ventilators in the context of up-to-date local resources and provides Atrium Health leadership with timely, actionable insights to guide decision-making during the COVID-19 pandemic. The after-SAH-order model demonstrated the lowest RMSE in total bed, ICU bed, and patients on ventilators.\n\nConclusionsCURVE provides a powerful, interactive interface that provides locally relevant, dynamic, timely information to guide health system decision making and pandemic preparedness.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Shih-Hsiung Chou", - "author_inst": "Atrium Health" - }, - { - "author_name": "James T. Kearns", - "author_inst": "Atrium Health" - }, - { - "author_name": "Philip Turk", - "author_inst": "Atrium Health" - }, - { - "author_name": "Marc Kowalkowski", - "author_inst": "Atrium Health" - }, - { - "author_name": "Jason Roberge", - "author_inst": "Atrium Health" - }, - { - "author_name": "Jennifer S. Priem", - "author_inst": "Atrium Health" - }, - { - "author_name": "Yhenneko J Taylor", - "author_inst": "Atrium Health" - }, - { - "author_name": "Ryan Burns", - "author_inst": "Atrium Health" - }, - { - "author_name": "Pooja Palmer", - "author_inst": "Atrium Health" - }, - { - "author_name": "Andrew D. McWilliams", - "author_inst": "Atrium Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.01.20088179", "rel_title": "Impact of policy interventions and social distancing on SARS-CoV-2 transmission in the United States", @@ -1498749,6 +1500867,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.01.20088260", + "rel_title": "Impact of non-pharmaceutical interventions against COVID-19 in Europe: a quasi-experimental study", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20088260", + "rel_abs": "The current epidemic of COVID-19 is unparalleled in recent history as are the social distancing interventions that have led to a significant halt on the economic and social life of so many countries. However, there is very little empirical evidence about which social distancing measures have the most impact. We report a quasi-experimental study of the impact of various interventions for control of the outbreak. Data on case numbers and deaths were taken from the daily published figures by the European Centre for Disease Control and dates of initiation of various control strategies from the Institute of Health Metrics and Evaluation website and published sources. Our complementary analyses were modelled in R using Bayesian generalised additive mixed models (GAMM) and in Stata using multi-level mixed effects regression models. From both sets of modelling, we found that closure of education facilities, prohibiting mass gatherings and closure of some non-essential businesses were associated with reduced incidence whereas stay at home orders and closure of all non-businesses was not associated with any independent additional impact. Our results could help inform strategies for coming out of lockdown.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Paul Raymond Hunter", + "author_inst": "Norwich Medical School, University of East Anglia" + }, + { + "author_name": "Felipe Colon-Gonzalez", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Julii Suzanne Brainard", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Steve Rushton", + "author_inst": "Newcastle University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.02.20088823", "rel_title": "Pharmacological interventions for COVID-19: Protocol for a Rapid Living Systematic Review with network meta-analysis", @@ -1500005,29 +1502154,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2020.04.29.20085787", - "rel_title": "A systematic review to evaluate the clinical outcomes in COVID -19 patients on angiotensin converting enzyme inhibitors or angiotensin receptor blockers", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085787", - "rel_abs": "IntroductionAngiotensin converting enzyme inhibitors (ACEI) and angiotensin receptor blockers (ARB) share their target receptor site with the SARS-CoV-2 virus, that may cause ACE2 receptor upregulation which raised concerns regarding ACEI and ARB use in COVID-19 patients. However, many medical professional societies recommended their continued use given the paucity of clinical evidence but there is need for an updated systematic review of latest clinical studies.\n\nMethodsA search was conducted on PubMed, Google Scholar, EMBASE and various preprint servers for studies comparing clinical outcomes and mortality in COVID-19 patients on ACEI and/or ARB and a meta-analysis was performed.\n\nResultsA total of sixteen studies were included for review and meta-analysis. There were conflicting findings reported in several studies as Meng J. et al, Liu Y. et al, Feng Y. et al, Zhang P. et al, Mancia G. et al and Reynolds H.R. et al reported that patients on ACE inhibitors/ARB had lower rates of severe outcomes whereas Richardson S. et al reported higher rates of invasive ventilation and intensive care unit (ICU) admissions in patients on ACE inhibitors/ARB as compared to non-users. Similarly, there were conflicting results in the rate of mortality reported in the various studies. Meng J. et al, Li J. et al, Zhang P. et al, Yang G. et al, Zeng Z. et al and Andrew Ip et al reported lower rates of mortality in ACE inhibitors/ARB users versus non-users whereas Richardson S. et al and Guo T. et al reported higher rates of mortality. In a pooled analysis of 9 studies, there was a statistically significant reduction (OR = 0.86, 95% CI = 0.75-0.99, I2 = 53.25, p value = 0.03) in the odds of death in those on ACEI/ARB as compared to patients not on ACEI/ARB. In a pooled analysis of five studies, there was a statistically non-significant reduction (OR = 0.90, 95% CI: 0.63-1.23, I2=70.36) in the odds of developing severe disease in patients on ACEI/ARB versus non-users.\n\nConclusionIt is concluded that ACEI and ARB should be continued in COVID-19 patients. Additionally, the individual patient factors like ACE2 polymorphisms which might confer higher risk of adverse outcomes need to be evaluated further.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Abhinav Grover", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Mansi Oberoi", - "author_inst": "Internal Medicine, University of South Dakota, Sanford School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.04.29.20085563", "rel_title": "Public knowledge, attitudes and practices towards COVID-19: A cross-sectional study in Malaysia", @@ -1500283,6 +1502409,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.29.20085449", + "rel_title": "Preliminary Results of Seroprevalence of SARS-CoV-2 at Community Clinics in Tokyo", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085449", + "rel_abs": "Serological evaluation with SARS-CoV-2 specific IgG antibody will be an alternative way to know the pandemic of novel coronavirus disease (COVID-19) if the capacity for diagnostic PCR test is limited. The point-of-care test to detect SARS-CoV-2 specific IgG antibody in peripheral blood (n =202) was performed in two community clinics in Tokyo, Japan. The overall positive rate of SRAS-CoV-2 IgG antibody was 5.9% (95% confidence interval[CI]: 3.1-10.1). Higher rate was observed for healthcare workers (n =55, 9.1 [3.0-20.0]). The limitation on antibody tests includes low sensitivity and potent cross-reactivity with the previous coronavirus. Robust healthcare policy to efficiently monitor COVID-19 spread is warranted in Tokyo.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Morihito Takita", + "author_inst": "Navitas Clinic Tachikawa" + }, + { + "author_name": "Tomoko Matsumura", + "author_inst": "Navitas Clinic Tachikawa" + }, + { + "author_name": "Kana Yamamoto", + "author_inst": "Navitas Clinic Shinjuku" + }, + { + "author_name": "Erika Yamashita", + "author_inst": "Navitas Clinic Shinjuku" + }, + { + "author_name": "Kazutaka Hosoda", + "author_inst": "Navitas Clinic Tachikawa" + }, + { + "author_name": "Tamae Hamaki", + "author_inst": "Navitas Clinic Shinjuku" + }, + { + "author_name": "Eiji Kusumi", + "author_inst": "Navitas Clinic Tachikawa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.29.20085415", "rel_title": "Clinical characteristics of 106 patients with neurological diseases and co-morbid coronavirus disease 2019: a retrospective study", @@ -1501399,29 +1503568,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.30.20086181", - "rel_title": "A Simple Method for Estimating the Number of Unconfirmed COVID-19 Cases in a Local Area that Includes a Confidence Interval: A Case Study of Whatcom County, Washington", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086181", - "rel_abs": "Along with many other data problems affecting the unfolding of the COVID-10 pandemic in the United States, virtually nothing is known about the number of positive, unconfirmed cases, especially in local areas. We show that it is possible to estimate the number of positive, unconfirmed COVID-19 cases using a simple, long-established method employed by demographers to estimate a population in the absence of a census count. We go on to show how a confidence interval can be constructed around an estimate of positive, unconfirmed COVID-19 cases constructed from this method, using Whatcom County, Washington as a case study.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "David A Swanson", - "author_inst": "University of California Riverside" - }, - { - "author_name": "Ronald E. Cossman", - "author_inst": "Social Science Research Center, Mississippi State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.30.20086652", "rel_title": "Perspectives of Cancer Patients and Their Health during the COVID-19 Pandemic", @@ -1501617,6 +1503763,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.30.20086751", + "rel_title": "Prediction of the Epidemic Peak of Covid19 in Egypt, 2020", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086751", + "rel_abs": "ObjectivesSince December 2019 a pandemic of new novel coronavirus has started from Wuhan, China, in Egypt, the first case reported on February 14, 2020. In this study we aimed to predict the time of possible peak and simulate the changes could be happen by the social behavior of Egyptians during Ramadan (the holy month).\n\nMethodsSIR and SEIR compartmental models were used to predict the peak time. We simulated different expected scenarios based to examine their effects on the peak timing.\n\nResultsWe found that the peak most likely to be in middle of June 2020. Simulating different transmission rate probability and R0 the earliest peak could to be in the May 20 and latest one could be in 18 July. The peak shifted much earlier to 11th April 2020 without lockdown and other mitigation strategies.\n\nConclusionSocial behaviors of citizens during the holy month will dramatically affect the peak timing. Mitigations strategies and other lockdown measure helped to delay the expected peak.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Eman D. El Desouky", + "author_inst": "National Cancer Institute , Cairo University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20086009", "rel_title": "Presence and vitality of SARS-CoV-2 virus in wastewaters and rivers", @@ -1502669,61 +1504834,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.04.28.20083956", - "rel_title": "Sensitivity evaluation of 2019 novel coronavirus (SARS-CoV-2) RT-PCR detection kits and strategy to reduce false negative", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083956", - "rel_abs": "An ongoing outbreak of pneumonia associated with SARS-CoV-2 has now been confirmed globally. In absence of effective vaccines, infection prevention and control through diagnostic testing and quarantine is critical. Early detection and differential diagnosis of respiratory infections increases the chances for successful control of COVID-19 disease. The nucleic acid RT-PCR test is regarded as the current standard for molecular diagnosis with high sensitivity. However, the highest specificity confirmation target ORF1ab gene is considered to be less sensitive than other targets in clinical application. In addition, a large amount of recent evidence indicates that the initial missed diagnosis of asymptomatic patients with SARS-CoV-2 and discharged patients with \"re-examination positive\" may be due to low viral load, and the ability of rapid mutation of coronavirus also increases the rate of false negative results. We aimed to evaluate the sensitivity of different nucleic acid detection kits so as to make recommendations for the selection of validation kit, and amplify the suspicious result to be reportable positive by means of simple continuous amplification, which is of great significance for the prevention and control of the current epidemic and the discharge criteria of low viral load patients.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "yunying zhou", - "author_inst": "Jinan Central Hospital, Cheeloo College of Medicine, Shandong University" - }, - { - "author_name": "Fengyan Pei", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Li Wang", - "author_inst": "inan Infectious Disease Hospital, Shandong University" - }, - { - "author_name": "Huailong Zhao", - "author_inst": "Jinan Center for Disease Control and Prevention" - }, - { - "author_name": "Huanjie Li", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Mingyu Ji", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Weihua Yang", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Qingxi Wang", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Qianqian Zhao", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - }, - { - "author_name": "Yunshan Wang", - "author_inst": "Jinan Central Hospital Affiliated to Shandong University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.30.20082172", "rel_title": "Monitoring social distancing and SARS-CoV-2 transmission in Brazil using cell phone mobility data", @@ -1503075,6 +1505185,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20082263", + "rel_title": "Modeling and predicting the spread of COVID-19 in Lebanon: A Bayesian perspective", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20082263", + "rel_abs": "In this article, we investigate the problem of modelling the trend of the current Coronavirus disease 2019 pandemic in Lebanon along time. Two different models were developed using Bayesian Markov chain Monte Carlo simulation methods. The models fitted included Poisson autoregressive as a function of a short-term dependence only and Poisson autoregressive as a function of both a short-term dependence and a long-term dependence. The two models are compared in terms of their predictive ability using root mean squared error and deviance information criterion. The Poisson autoregressive model that allows to capture both short and long term memory effects performs best under all criterions. The use of such a model can greatly improve the estimation of number of new infections, and can indicate whether disease has an upward/downward trend, and where about every country is on that trend, so that containment measures can be applied and/or relaxed.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Samer Kharroubi", + "author_inst": "American University of Beirut" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.30.20086074", "rel_title": "COVID-19, smoking, and inequalities: a cross-sectional survey of adults in the UK", @@ -1504371,117 +1506500,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.05.02.20084673", - "rel_title": "Disruption of the CCL5/RANTES-CCR5 Pathway Restores Immune Homeostasis and Reduces Plasma Viral Load in Critical COVID-19", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20084673", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is now pandemic with nearly three million cases reported to date1. Although the majority of COVID-19 patients experience only mild or moderate symptoms, a subset will progress to severe disease with pneumonia and acute respiratory distress syndrome (ARDS) requiring mechanical ventilation2. Emerging results indicate a dysregulated immune response characterized by runaway inflammation, including cytokine release syndrome (CRS), as the major driver of pathology in severe COVID-193,4. With no treatments currently approved for COVID-19, therapeutics to prevent or treat the excessive inflammation in severe disease caused by SARS-CoV-2 infection are urgently needed. Here, in 10 terminally-ill, critical COVID-19 patients we report profound elevation of plasma IL-6 and CCL5 (RANTES), decreased CD8+ T cell levels, and SARS-CoV-2 plasma viremia. Following compassionate care treatment with the CCR5 blocking antibody leronlimab, we observed complete CCR5 receptor occupancy on macrophage and T cells, rapid reduction of plasma IL-6, restoration of the CD4/CD8 ratio, and a significant decrease in SARS-CoV-2 plasma viremia. Consistent with reduction of plasma IL-6, single-cell RNA-sequencing revealed declines in transcriptomic myeloid cell clusters expressing IL-6 and interferon-related genes. These results demonstrate a novel approach to resolving unchecked inflammation, restoring immunologic deficiencies, and reducing SARS-CoV-2 plasma viral load via disruption of the CCL5-CCR5 axis, and support randomized clinical trials to assess clinical efficacy of leronlimab-mediated inhibition of CCR5 for COVID-19.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Bruce K Patterson", - "author_inst": "IncellDX" - }, - { - "author_name": "Harish Seethamraju", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Kush Dhody", - "author_inst": "Amarex Clinical Research, LLC" - }, - { - "author_name": "Michael J Corley", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Kazemm Kazempour", - "author_inst": "Amarex Clinical Research" - }, - { - "author_name": "Jay P Lalezari", - "author_inst": "Quest Clinical Research" - }, - { - "author_name": "Alina PS Pang", - "author_inst": "University of Hawaii" - }, - { - "author_name": "Christopher Sugai", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Edgar B Francisco", - "author_inst": "IncellDX" - }, - { - "author_name": "Amruta Pise", - "author_inst": "IncellDX" - }, - { - "author_name": "Hallison Rodrigues", - "author_inst": "IncellDX" - }, - { - "author_name": "Matthew Ryou", - "author_inst": "IncellDX" - }, - { - "author_name": "Helen L Wu", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Gabriela M Webb", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Byung S Park", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Scott Kelly", - "author_inst": "CytoDyn, Inc" - }, - { - "author_name": "Nadar Pourhassan", - "author_inst": "CytoDyn, Inc" - }, - { - "author_name": "Alena Lelic", - "author_inst": "Beckman Coulter" - }, - { - "author_name": "Lama Kdouh", - "author_inst": "Beckman Coulter" - }, - { - "author_name": "Monica Herrera", - "author_inst": "Bio-Rad, Inc" - }, - { - "author_name": "Eric Hall", - "author_inst": "Bio-Rad, Inc" - }, - { - "author_name": "Enver Aklin", - "author_inst": "Montefiore Medical Center" - }, - { - "author_name": "Lishomwa Ndhlovu", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Jonah B Sacha", - "author_inst": "Oregon Health and Science University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.29.20084533", "rel_title": "Pre-Existing Characteristics Associated with Covid-19 Illness Severity", @@ -1504721,6 +1506739,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.28.20075036", + "rel_title": "A simulation-based procedure to estimate base rates from Covid-19 antibody test results I: Deterministic test reliabilities", + "rel_date": "2020-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20075036", + "rel_abs": "We design a procedure (the complete Python code may be obtained at https://github.com/abhishta91/antibody_montecarlo) using Monte Carlo (MC) simulation to establish the point estimators described below and confidence intervals for the base rate of occurence of an attribute (e.g., antibodies against Covid-19) in an aggregate population (e.g., medical care workers) based on a test. The requirements for the procedure are the tests sample size (N) and total number of positives (X), and the data on tests reliability.\n\nThe modus is the prior which generates the largest frequency of observations in the MC simulation with precisely the number of test positives (maximum-likelihood estimator). The median is the upper bound of the set of priors accounting for half of the total relevant observations in the MC simulation with numbers of positives identical to the tests number of positives.\n\nO_LSTOur rather preliminary findings areC_LSTO_LIThe median and the confidence intervals suffice universally.\nC_LIO_LIThe estimator [Formula] may be outside of the two-sided 95% confidence interval.\nC_LIO_LIConditions such that the modus, the median and another promising estimator which takes the reliability of the test into account, are quite close.\nC_LIO_LIConditions such that the modus and the latter estimator must be regarded as logically inconsistent.\nC_LIO_LIConditions inducing rankings among various estimators relevant for issues concerning over-or underestimation.\nC_LI\n\nJEL-codes: C11, C13, C63", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Reinoud Joosten", + "author_inst": "University of Twente" + }, + { + "author_name": "Abhishta Abhishta", + "author_inst": "University of Twente" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.03.20072207", "rel_title": "Sensitivity assessment of SARS-CoV-2 PCR assays developed by WHO referral laboratories", @@ -1506469,41 +1508510,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.03.075473", - "rel_title": "Computational analysis on the ACE2-derived peptides for neutralizing the ACE2 binding to the spike protein of SARS-CoV-2", - "rel_date": "2020-05-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.03.075473", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19, is spreading globally and has infected more than 3 million people. It has been discovered that SARS-CoV-2 initiates the entry into cells by binding to human angiotensin-converting enzyme 2 (hACE2) through the receptor binding domain (RBD) of its spike glycoprotein. Hence, drugs that can interfere the SARS-CoV-2-RBD binding to hACE2 potentially can inhibit SARS-CoV-2 from entering human cells. Here, based on the N-terminal helix 1 of human ACE2, we designed nine short peptides that have potential to inhibit SARS-CoV-2 binding. Molecular dynamics simulations of peptides in the their free and SARS-CoV-2 RBD-bound forms allow us to identify fragments that are stable in water and have strong binding affinity to the SARS-CoV-2 spike proteins. The important interactions between peptides and RBD are highlighted to provide guidance for the design of peptidomimetics against the SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "cecylia s. lupala", - "author_inst": "beijing computational science research center" - }, - { - "author_name": "Vikash Kumar", - "author_inst": "Beijing computational science research center" - }, - { - "author_name": "xuanxuan li", - "author_inst": "tsinghua university" - }, - { - "author_name": "xiaodong su", - "author_inst": "peking university" - }, - { - "author_name": "haiguang liu", - "author_inst": "beijing computational science research center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.04.29.20084061", "rel_title": "Psychological Stress and Gender Differences during COVID-19 Pandemic in Chinese Population", @@ -1506679,6 +1508685,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.04.29.20081174", + "rel_title": "Brazilian Modeling of COVID-19 (BRAM-COD): a Bayesian Monte Carlo approach for COVID-19 spread in a limited data set context", + "rel_date": "2020-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20081174", + "rel_abs": "11.1 BackgroundThe new coronavirus respiratory syndrome disease (COVID-19) pandemic has become a major health problem worldwide. Many attempts have been devoted to modeling the dynamics of new infection rates, death rates, and the impact of the disease on health systems and the world economy. Most of these modeling concepts use the Susceptible-Infectious-Susceptible (SIS) and Susceptible-Exposed-Infected-Recovered (SEIR) compartmental models; however, wide imprecise outcomes in forecasting can occur with these models in the context of poor data, low testing levels, and a nonhomogeneous population.\n\n1.2 ObjectivesTo predict Brazilian ICU beds demand over time and during COVID-19 pandemic \"peak\".\n\n1.3 MethodsIn the present study, we describe a Bayesian COVID-19 model combined with a Hamiltonian Monte Carlo algorithm to forecast quantitative predictions of infections, number of deaths and the demand for critical care beds in the next month in the Brazilian context of scarce data availability. We also estimated COVID-19 spread tendency in the state of Sao Paulo and forecasted the demand for critical care beds, as Sao Paulo is the epicenter of the Latin America pandemic.\n\n1.4 ResultsOur model estimated that the number of infected individuals would be approximately 6.5 million (median) on April 25, 2020, and would reach 16 to 17 million (median) by the end of August 2020 in Brazil. The probability that an infected individual requires ICU-level care in Brazil is 0.5833%. Our model suggests that the current level of mitigation seen in Sao Paulo is sufficient to reach Rt < 1, thus attaining a \"peak\" in the short term. In Sao Paulo state, the total number of deaths is estimated to be around 9,000 (median) with the 2.5% quantile being 6,600 deaths and the 97.5% quantile being around 13,350 deaths. Also, Sao Paulo will not attain its maximum capacity of ICU beds if the current trend persists over the long term.\n\n1.5 ConclusionsThe COVID-19 pandemic should peak in Brazil between May 8 and May 20, 2020 with a fatality rate lower than that suggested in the literature. The northern and northeastern regions of Brazil will suffer from a lack of available ICU beds, the southern and central-western regions appear to have sufficient ICU beds, finally, the southeastern region seems to have enough ICU beds only if it shares private beds with the publicly funded Unified Health System (SUS). The model predicts that, if the current policies and population behavior are maintained throughout the forecasted period, by the end of August 2020, Brazil will have around 7.6% to 8.2% of its population immune to COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Samy Dana", + "author_inst": "Fundacao Getulio Vargas (EASP-FGV), Brazil" + }, + { + "author_name": "Alexandre B Simas", + "author_inst": "Mathematics Department, Federal University of Paraiba, Brazil" + }, + { + "author_name": "Bruno A Filardi", + "author_inst": "Scientific Director of Cancer Institute, Brazil" + }, + { + "author_name": "Rodrigo N Rodriguez", + "author_inst": "Director of Ubarana Hospital, Taubate, Brazil" + }, + { + "author_name": "Leandro Lane da Costa Valiengo", + "author_inst": "University of Sao Paulo, Institute of Psychiatry, Brazil" + }, + { + "author_name": "Jose Gallucci-Neto", + "author_inst": "University of Sao Paulo, Institute of Psychiatry, Brazil" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.04.27.20081356", "rel_title": "Predictive value of sudden olfactory loss in the diagnosis of COVID-19", @@ -1508091,65 +1510136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.27.20081711", - "rel_title": "Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study", - "rel_date": "2020-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081711", - "rel_abs": "BackgroundThe health impact of COVID-19 may differ in African settings as compared to countries in Europe or China due to demographic, epidemiological, environmental and socio-economic factors. We evaluated strategies to reduce SARS-CoV-2 burden in African countries, so as to support decisions that balance minimising mortality, protecting health services and safeguarding livelihoods.\n\nMethodsWe used a Susceptible-Exposed-Infectious-Recovered mathematical model, stratified by age, to predict the evolution of COVID-19 epidemics in three countries representing a range of age distributions in Africa (from oldest to youngest average age: Mauritius, Nigeria and Niger), under various effectiveness assumptions for combinations of different non-pharmaceutical interventions: self-isolation of symptomatic people, physical distancing, and shielding (physical isolation) of the high-risk population. We adapted model parameters to better represent uncertainty about what might be expected in African populations, in particular by shifting the distribution of severity risk towards younger ages and increasing the case-fatality ratio.\n\nResultsWe predicted median clinical attack rates over the first 12 months of 17% (Niger) to 39% (Mauritius), peaking at 2-4 months, if epidemics were unmitigated. Self-isolation while symptomatic had a maximum impact of about 30% on reducing severe cases, while the impact of physical distancing varied widely depending on percent contact reduction and R0. The effect of shielding high-risk people, e.g. by rehousing them in physical isolation, was sensitive mainly to residual contact with low-risk people, and to a lesser extent to contact among shielded individuals. Response strategies incorporating self-isolation of symptomatic individuals, moderate physical distancing and high uptake of shielding reduced predicted peak bed demand by 46% to 54% and mortality by 60% to 75%. Lockdowns delayed epidemics by about 3 months. Estimates were sensitive to differences in age-specific social mixing patterns, as published in the literature.\n\nDiscussionIn African settings, as elsewhere, current evidence suggests large COVID-19 epidemics are expected. However, African countries have fewer means to suppress transmission and manage cases. We found that self-isolation of symptomatic persons and general physical distancing are unlikely to avert very large epidemics, unless distancing takes the form of stringent lockdown measures. However, both interventions help to mitigate the epidemic. Shielding of high-risk individuals can reduce health service demand and, even more markedly, mortality if it features high uptake and low contact of shielded and unshielded people, with no increase in contact among shielded people. Strategies combining self-isolation, moderate physical distancing and shielding will probably achieve substantial reductions in mortality in African countries. Temporary lockdowns, where socioeconomically acceptable, can help gain crucial time for planning and expanding health service capacity.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kevin van Zandvoort", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Christopher I Jarvis", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Carl Pearson", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Nicholas G Davies", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "CMMID COVID-19 working group", - "author_inst": "" - }, - { - "author_name": "Timothy W Russell", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Adam J Kucharski", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Mark J Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "LSHTM" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Francesco Checchi", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.28.20083378", "rel_title": "Ocular toxicity and Hydroxychloroquine: A Rapid Meta-Analysis", @@ -1508665,6 +1510651,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20084483", + "rel_title": "A surprising formula for the spread of Covid-19 under aggressive management", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084483", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWWe propose an algebraic-type formula that describes with high accuracy the total number of detected infections for the Covid-19 pandemic in many countries. Our 2-phase formula can be used as a powerful forecasting tool. It is based on the authors new theory of momentum management of epidemics; Bessel functions are employed. Its 3 parameters are the initial transmission rate, reflecting the viral fitness and \"normal\" frequency of contacts in the infected areas, and the intensity of prevention measures at phases 1, 2. Austria, Brazil, Germany, Japan, India, Israel, Italy, the Netherlands, Sweden, Switzerland, UK, and the USA are considered. For the USA, all states are processed independently and some \"interaction\" is added; the forecasting software is provided.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ivan Cherednik", + "author_inst": "UNC at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.29.20084517", "rel_title": "How and when to end the COVID-19 lockdown: an optimisation approach", @@ -1509905,77 +1511910,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.05.02.071811", - "rel_title": "Structural and Functional Implications of Non-synonymous Mutations in the Spike protein of 2,954 SARS-CoV-2 Genomes", - "rel_date": "2020-05-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.02.071811", - "rel_abs": "Protein-protein interactions between virus and host are crucial for infection. SARS-CoV-2, the causative agent of COVID-19 pandemic is an RNA virus prone to mutations. Formation of a stable binding interface between the Spike (S) protein Receptor Binding Domain (RBD) of SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) of host actuates viral entry. Yet, how this binding interface evolves as virus acquires mutations during pandemic remains elusive. Here, using a high fidelity bioinformatics pipeline, we analysed 31,403 SARS-CoV-2 genomes across the globe, and identified 444 non-synonymous mutations that cause 49 distinct amino acid substitutions in the RBD. Molecular phylogenetic analysis suggested independent emergence of these RBD mutants during pandemic. In silico structure modelling of interfaces induced by mutations on residues which directly engage ACE2 or lie in the near vicinity revealed molecular rearrangements and binding energies unique to each RBD mutant. Comparative structure analysis using binding interface from mouse that prevents SARS-CoV-2 entry uncovered minimal molecular determinants in RBD necessary for the formation of stable interface. We identified that interfacial interaction involving amino acid residues N487 and G496 on either ends of the binding scaffold are indispensable to anchor RBD and are well conserved in all SARS-like corona viruses. All other interactions appear to be required to locally remodel binding interface with varying affinities and thus may decide extent of viral transmission and disease outcome. Together, our findings propose the modalities and variations in RBD-ACE2 interface formation exploited by SARS-CoV-2 for endurance.\n\nImportanceCOVID-19, so far the worst hit pandemic to mankind, started in January 2020 and is still prevailing globally. Our study identified key molecular arrangements in RBD-ACE2 interface that help virus to tolerate mutations and prevail. In addition, RBD mutations identified in this study can serve as a molecular directory for experimental biologists to perform functional validation experiments. The minimal molecular requirements for the formation of RBD-ACE2 interface predicted using in silico structure models may help precisely design neutralizing antibodies, vaccines and therapeutics. Our study also proposes the significance of understanding evolution of protein interfaces during pandemic.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Shijulal Nelson-Sathi", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Perunthottathu K Umasankar", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Sreekumar Easwaran", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Radhakrishnan R Nair", - "author_inst": "Rajiv Gandhi Centre for Biotechnolgoy" - }, - { - "author_name": "Iype Joseph", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Sai Ravi Chandra Nori", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Jamiema Sara Philip", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Roshny Prasad", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Kolaparamba V Navyasree", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Shikha Ramesh", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Heera Pillai", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Sanu Gosh", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Santhosh Kumar TR", - "author_inst": "RajiV Gandhi Centre for Biotechnology" - }, - { - "author_name": "M Radhakrishna Pillai", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.05.01.071050", "rel_title": "CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization", @@ -1510123,6 +1512057,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.29.20085100", + "rel_title": "Using different epidemiological models to modeling the epidemic dynamics in Brazil", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085100", + "rel_abs": "In this paper we provide forecasts of the cumulative number of confirmed reported cases in Brazil, specifically in Pernambuco and Ceara, by using the generalized logistic growth model, the Richards growth model and Susceptible, Un-quanrantined infected, Quarantined infected, Confirmed infected (SUQC) phenomenological model. We rely on the Nash-Sutcliffe efficiency (NSE), root-mean-square error (RMSE) and mean absolute relative error (MARE) to quantify the quality of the models fits during the calibrationAll of these analyzes have been valid until the present date, April 14, 2020. The different models provide insights of our scenario predictions.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Lucas Ravellys Pyrrho de Alcantara", + "author_inst": "UFPE" + }, + { + "author_name": "Lucio Silva", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Anderson Rodrigues de Almeida", + "author_inst": "UFPE" + }, + { + "author_name": "Maira Galdino da Rocha Pitta", + "author_inst": "UFPE" + }, + { + "author_name": "Artur Paiva Coutinho", + "author_inst": "UFPE" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.28.20083154", "rel_title": "A Model of Workflow in the Hospital During a Pandemic to Assist Management", @@ -1511519,33 +1513488,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.26.20075937", - "rel_title": "Using the COVID-19 to influenza ratio to estimate the numbers of symptomatic COVID-19 cases in Wuhan prior to the lockdown", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20075937", - "rel_abs": "A recent study tested 45 throat swabs taken from adults over age 30 who sought outpatient care at one of two central Wuhan hospitals for influenza-like-illness between December 30, 2019 and January 19, 2020. Although none were confirmed COVID-19 cases, nine retrospectively tested positive for the virus. Using the fact that Wuhan has 393 other hospitals, we extrapolate the total number of undetected cases of symptomatic COVID-19 in adults during this period. we estimate that there were 5,558 [95% CI: 2,761-9,864] adults with symptomatic COVID-19 infections in Wuhan between December 30th and January 19th, 2020.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Zhanwei Du", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.27.20080309", "rel_title": "Serial measurements in COVID-19-induced acute respiratory disease to unravel heterogeneity of the disease course: design of the Maastricht Intensive Care COVID cohort; MaastrICCht", @@ -1511949,6 +1513891,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.25.20080002", + "rel_title": "Performance & Quality Evaluation of Marketed COVID-19 RNA Detection Kits", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20080002", + "rel_abs": "Compared to other coronaviruses, COVID-19 has a longer incubation period and features asymptomatic infection at a high rate (>25%)1,2. Therefore, early detection of infection is the key to early isolation and treatment. Direct detection of the virus itself has advantages over indirect detection. Currently, the most sensitive and commercially validated method for COVID-19 testing is RT-qPCR, designed to detect amplified virus-specific RNA. Reliable testing has proven to be a bottleneck in early diagnosis of virus infection in all countries dealing with the pandemic. Significant performance and quality issues with available testing kits have caused confusion and serious health risks. In order to provide better understanding of the Quality and performance of COVID-19 RNA detection kits on the market, we designed a system to evaluate the specificity (quantitation), sensitivity (LOD) and robustness of the kits using positive RNA and pseudovirus controls based on COVID-19 genomic sequence3,4. We evaluated 8 Nucleic Acid qPCR Kits approved in China, some of which are also approved in the US and EU. Our study showed that half of these 8 kits lack 1:1 linear relationship for virus RNA copy: qPCR signal. Of the 4 with linear response, 2 demonstrated sensitivity at 1 Copy viral RNA/Reaction, suitable for early detection of virus infection. Furthermore, we established the best RNA extraction, handling and qPCR procedures allowing highly sensitive and consistent performance using BGI qPCR kits. Our study provides an effective method to assess and compare performance quality of all COVID-19 nucleic acid testing kits, globally.\n\nSignificance StatementTesting for COVID-19 has been a critical topic in the pandemic management since the first outbreak reported in China, and now globally. Despite of focused efforts from global biomedical industries and regulatory authorities, testing tools currently available on the market are not satisfying the huge and most important needs for virus control, which is specific, sensitive, affordable, and commercially viable early diagnosis of infected populations. We have designed an experimental system to assess and compare all nucleic acid-based COVID-19 testing kits from quality control perspectives. The results reported here demonstrate the suitability of using our system as an objective QC system for all commercial kits, including any future kits. We also identified the best testing method using commercially available reagents.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "David Surace Kapitula", + "author_inst": "Jade Biomedical LTD" + }, + { + "author_name": "Zhuopu Jiang", + "author_inst": "Jade Biomedical LTD" + }, + { + "author_name": "Jianhao Jiang", + "author_inst": "Gene Pharma" + }, + { + "author_name": "Jing Zhu", + "author_inst": "Jade Biomedical LTD" + }, + { + "author_name": "Xiangyong Chen", + "author_inst": "Gene Pharma" + }, + { + "author_name": "Claudia Qiao Lin", + "author_inst": "Jade Biomedical LTD" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.04.28.20073767", "rel_title": "COVID-19 in people living with human immunodeficiency virus: A case series of 33 patients", @@ -1513041,33 +1515022,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.26.20080648", - "rel_title": "Risk assessment via layered mobile contact tracing for epidemiological intervention", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080648", - "rel_abs": "There is strong interest globally amidst the current COVID-19 pandemic in tracing contacts of infectious patients using mobile technologies, both as a warning system to individuals and as a targeted intervention strategy for governments. Several governments, including India, have introduced mobile apps for this purpose, which give a warning when the individuals phone establishes bluetooth contact with the phone of an infected person. We present a methodology to probabilistically evaluate risk of infection given the network of contacts that individuals are likely to encounter in real life. Instead of binary \"infected\" or \"uninfected\" statuses, an infection risk probability is maintained which can be efficiently calculated based on probabilities of recent contacts, and updated when a recent contact is diagnosed with a disease. We demonstrate on realistic networks that this method sharply outperforms a naive immediate-contact method even in an ideal circumstance that all infected persons are known to the naive method. We demonstrate robustness to missing contact information (such as when phones fail to make bluetooth contact or the app is not installed). We show, within our model, a strong flattening of the infectious peak when even a small fraction of cases are identified, tested and isolated. In the real world, where most known-infected persons are isolated or quarantined and where many individuals may not carry their mobiles in public, we believe the improvement offered by our method warrants consideration. Importantly, in view of widespread concerns on privacy and contact-tracing, our method relies mainly on direct contact data that can be stored locally on users phones, and uses limited communication via intermediary servers only upon testing, mitigating privacy concerns.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Vishwesha Guttal", - "author_inst": "Indian Institute of Science, Bengaluru, India" - }, - { - "author_name": "Sandeep Krishna", - "author_inst": "National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India" - }, - { - "author_name": "Rahul Siddharthan", - "author_inst": "The Institute of Mathematical Sciences, Chennai, India" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.26.20080655", "rel_title": "Preparedness and Mitigation by projecting the risk against COVID-19 transmission using Machine Learning Techniques", @@ -1513243,6 +1515197,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.26.20081307", + "rel_title": "Fast SARS-CoV-2 detection protocol based on RNA precipitation and RT-qPCR in nasopharyngeal swab samples", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20081307", + "rel_abs": "The SARS-CoV-2 pandemic has evolved far more aggressively in countries lacking a robust testing strategy to identify infected individuals. Given the global demand for fast and reliable diagnosis to determine the carrier individuals, a stock-out scenario for a number of essential reagents/kits used along the diagnostic process has been foreseen by many organizations. Having identified the RNA extraction step as one of the key bottlenecks, we tested several alternatives that avoid the use of commercial kits for this step. The analysis showed that 2-propanol precipitation of the viral RNA, followed by one-step RT-qPCR results in a sensitivity and specificity comparable to that provided currently by automatized systems such as the COBAS 6800 system. Therefore, this simple protocol allows SARS-CoV-2 testing independently of commercial kit providers in a time and cost-effective manner. It can be readily implemented in research and/or diagnostic laboratories worldwide, provided that patient confidentiality and researcher safety are ensured. Scaling up the testing capabilities of hospitals and research facilities will identify larger numbers of infected individuals to paint a clear picture of the COVID-19 prevalence, a pre-requisite for informed policy decision making.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Xabier Guruceaga", + "author_inst": "University of the Basque Country UPV/EHU" + }, + { + "author_name": "Amanda Sierra", + "author_inst": "Achucarro Basque Center for Neuroscience" + }, + { + "author_name": "Daniel Marino", + "author_inst": "University of the Basque Country UPV/EHU" + }, + { + "author_name": "Izortze Santin", + "author_inst": "University of the Basque Country UPV/EHU" + }, + { + "author_name": "Jon Ander Nieto-Garai", + "author_inst": "University of the Basque Country UPV/EHU" + }, + { + "author_name": "Jose Ramon Bilbao", + "author_inst": "University of the Basque Country UPV/EHU" + }, + { + "author_name": "Maier Lorizate", + "author_inst": "University of the Basque Country UPV/EHU" + }, + { + "author_name": "Patricia Aspichueta", + "author_inst": "University of the Basque Country EHU/UPV" + }, + { + "author_name": "coBIG (COVID19 Basque Inter-institutional Group)", + "author_inst": "" + }, + { + "author_name": "Ugo Mayor", + "author_inst": "University of the Basque Country EHU/UPV" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.26.20080846", "rel_title": "Spatial-temporal variations of atmospheric factors contribute to SARS-CoV-2 outbreak", @@ -1514423,37 +1516432,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.01.067769", - "rel_title": "Heat inactivation of the Severe Acute Respiratory Syndrome Coronavirus 2", - "rel_date": "2020-05-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.01.067769", - "rel_abs": "Supernatants of cells infected with SARS-CoV-2, nasopharyngeal and sera samples containing SARS-CoV-2 were submitted to heat inactivation for various periods of time, ranging from 30 seconds to 60 minutes. Our results showed that SARS-CoV-2 could be inactivated in less than 30 minutes, 15 minutes and 3 minutes at 56{degrees}C, 65{degrees}C and 95{degrees}C respectively. These data could help laboratory workers to improve their protocols with handling of the virus in biosafety conditions.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Christophe Batejat", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Quentin Grassin", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean-Claude Manuguerra", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "India Leclercq", - "author_inst": "Universite de Paris" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.01.071654", "rel_title": "Mutational spectra of SARS-CoV-2 orf1ab polyprotein and Signature mutations in the United States of America", @@ -1514629,6 +1516607,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.28.20082917", + "rel_title": "Tuberculosis and COVID-19 in 2020: lessons from the past viral outbreaks and possible future outcomes", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20082917", + "rel_abs": "BackgroundThe threat of contagious infectious diseases is constantly evolving, as demographic explosion, travel globalization and changes in human lifestyle increase the risk of spreading pathogens, leading to accelerated changes in disease landscape. Of particular interest is the aftermath of superimposing viral epidemics (especially SARS-CoV-2) over long-standing diseases, such as tuberculosis (TB), which remains a significant disease for public health worldwide and especially in emerging economies.\n\nMethods and ResultsPubMed electronic database was requested for relevant articles linking TB, influenza and SARS-CoV viruses and subsequently assessed eligibility according to inclusion criteria. Using a data mining approach, we also queried the COVID-19 Open Research Dataset (CORD-19). We aimed to answer the following questions: What can be learned from other coronavirus outbreaks (with a focus on TB patients)? Is coinfection (TB and SARS-CoV-2) more severe? Is there a vaccine for SARS-CoV-2? How does the TB vaccine affect COVID19? How does one diagnosis affect the other?\n\nDiscussionsFew essential elements about TB and SARS-CoV coinfections were discussed. First, lessons from the past outbreaks (other coronaviruses), as well as influenza pandemic / seasonal outbreaks have taught the importance of infection control to avoid the severe impact on TB patients. Second, although challenging due to data scarcity, investigating the pathological pathways linking TB and SARS-CoV-2 leads to the idea that their coexistence might yield a more severe clinical evolution. Finally, we addressed the issues of vaccination and diagnostic reliability in the context of coinfection.\n\nConclusionsBecause viral respiratory infections and TB impede the hosts immune responses, it can be assumed that their harmful synergism may contribute to more severe clinical evolution. Despite the rapidly growing number of cases, the data needed to predict the impact of the COVID-19 pandemic on patients with latent TB and TB sequelae still lies ahead.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Radu Crisan-Dabija", + "author_inst": "University of Medicine and Pharmacy \"Grigore T. Popa\" Iasi, Pulmonology Department, Head of Clinic of Pulmonary Diseases Iasi, Romania" + }, + { + "author_name": "Cristina Grigorescu", + "author_inst": "University of Medicine and Pharmacy \"Grigore T. Popa\" Iasi, Department Thoracic Surgery, Clinic of Thoracic Surgery Iasi, Hospital of Pulmonary Diseases Iasi, R" + }, + { + "author_name": "Cristina Alice Pavel", + "author_inst": "Clinic of Pulmonary Diseases Iasi, Romania" + }, + { + "author_name": "Bogdan Artene", + "author_inst": "Department of Interventional Cardiology - Cardiovascular Diseases Institute, Iasi, Romania" + }, + { + "author_name": "Iolanda Valentina Popa", + "author_inst": "Institute of Gastroenterology and Hepatology, Iasi, Romania, and \"Grigore T. Popa\" University of Medicine, Iasi, Romania" + }, + { + "author_name": "Andrei Cernomaz", + "author_inst": "University of Medicine and Pharmacy \"Grigore T. Popa\" Iasi, Pulmonology Department, Institute of Oncology Iasi" + }, + { + "author_name": "Alexandru Burlacu", + "author_inst": "Head of Department of Interventional Cardiology - Cardiovascular Diseases Institute, and \"Grigore T. Popa\" University of Medicine, Iasi, Romania" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.04.29.20085738", "rel_title": "Rapidly fatal pneumonitis from immunotherapy and concurrent SARS-CoV-2 infection in a patient with newly diagnosed lung cancer", @@ -1515753,29 +1517774,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.25.20079996", - "rel_title": "Public perceptions of COVID-19 in Australia: perceived risk, knowledge, health-protective behaviours, and vaccine intentions", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079996", - "rel_abs": "Widespread and sustained engagement with health-protective behaviours (i.e., hygiene and distancing) is critical to successfully managing the COVID-19 pandemic. Evidence from previous emerging infectious disease outbreaks points to the role of perceived risk, worry, media coverage, and knowledge in shaping engagement with health-protective behaviours as well as vaccination intentions. The current study examined these factors in 2,174 Australian residents. An online survey was completed between 2-9 March 2020, at an early stage of the COVID-19 outbreak in Australia. Results revealed that two thirds of respondents were at least moderately worried about a widespread COVID-19 outbreak in Australia (which subsequently occurred). Worry about the outbreak and closely following media coverage were consistent predictors of health-protective behaviours (both over the previous month, and intended behaviours in the case of a widespread outbreak) as well as vaccination intentions. Health-behaviour engagement over the previous month was lower in some demographic groups, including males and younger individuals (18-29 age group). These was a substantial mismatch between respondents expected symptoms of infection and emerging evidence that a meaningful proportion of people who contract the novel coronavirus will experience asymptomatic infection (i.e., they will not experience symptoms associated with COVID-19). Only 0.3% of those in the current study believed that they personally would not experience any symptoms if they were infected. Uncertainty and misconceptions about COVID-19 were common, including one third of respondents who reported being unsure whether people are likely have natural or existing immunity. There was also uncertainty around whether specific home remedies (e.g., vitamins, saline rinses) would offer protection, whether the virus could spread via the airborne route, and whether the virus was human made and deliberately released. Such misconceptions are likely to cause concern for members of the public. These results point to areas of uncertainty that could be usefully targeted by public education campaigns, as well as psychological and demographic factors associated with engagement with health-protective behaviours. These findings offer potential pathways for interventions to encourage health-protective behaviours to reduce the spread of COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Kate Faasse", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Jill M Newby", - "author_inst": "UNSW" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.24.20077487", "rel_title": "SUCCESSFUL MANUFACTURING OF CLINICAL-GRADE SARS-CoV-2 SPECIFIC T CELLS FOR ADOPTIVE CELL THERAPY", @@ -1515995,6 +1517993,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.25.20074419", + "rel_title": "Increased travel times to United States SARS-CoV-2 testing sites: a spatial modeling study", + "rel_date": "2020-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20074419", + "rel_abs": "ImportanceAccess to testing is key to a successful response to the COVID-19 pandemic.\n\nObjectiveTo determine the geographic accessibility to SARS-CoV-2 testing sites in the United States, as quantified by travel time.\n\nDesignCross-sectional analysis of SARS-CoV-2 testing sites as of April 7, 2020 in relation to travel time.\n\nSettingUnited States COVID-19 pandemic.\n\nParticipantsThe United States, including the 48 contiguous states and the District of Columbia.\n\nExposuresPopulation density, percent minority, percent uninsured, and median income by county from the 2018 American Community Survey demographic data.\n\nMain OutcomeSARS-CoV-2 testing sites identified in two national databases (Carbon Health and CodersAgainstCovid), geocoded by address. Median county 1 km2 gridded friction surface of travel times, as a measure of geographic accessibility to SARS-CoV-2 testing sites.\n\nResults6,236 unique SARS-CoV-2 testing sites in 3,108 United States counties were identified. Thirty percent of the U.S. population live in a county (N = 1,920) with a median travel time over 20 minutes. This was geographically heterogeneous; 86% of the Mountain division population versus 5% of the Middle Atlantic population lived in counties with median travel times over 20 min. Generalized Linear Models showed population density, percent minority, percent uninsured and median income were predictors of median travel time to testing sites. For example, higher percent uninsured was associated with longer travel time ({beta} = 0.41 min/percent, 95% confidence interval 0.3-0.53, p = 1.2x10-12), adjusting for population density.\n\nConclusions and RelevanceGeographic accessibility to SARS-Cov-2 testing sites is reduced in counties with lower population density and higher percent of minority and uninsured, which are also risk factors for worse healthcare access and outcomes. Geographic barriers to SARS-Cov-2 testing may exacerbate health inequalities and bias county-specific transmission estimates. Geographic accessibility should be considered when planning the location of future testing sites and interpreting epidemiological data.\n\nKey PointsO_LISARS-CoV-2 testing sites are distributed unevenly in the US geography and population.\nC_LIO_LIMedian county-level travel time to SARS-CoV-2 testing sites is longer in less densely populated areas, and in areas with a higher percentage of minority or uninsured populations.\nC_LIO_LIImproved geographic accessibility to testing sites is imperative to manage the COVID-19 pandemic in the United States.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Benjamin Rader", + "author_inst": "Boston University" + }, + { + "author_name": "Christina M. Astley", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Karla Therese L. Sy", + "author_inst": "Boston University" + }, + { + "author_name": "Kara Sewalk", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Yulin Hswen", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "John S. Brownstein", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Moritz U.G. Kraemer", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.25.20079483", "rel_title": "A HEURISTIC MODEL FOR SPREAD OF COVID-19 INFECTION CASES IN INDIA", @@ -1517175,49 +1519216,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.28.20083998", - "rel_title": "Assessment of the outbreak risk, mapping and infestation behavior of COVID-19: Application of the autoregressive and moving average (ARMA) and polynomial models", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083998", - "rel_abs": "Infectious disease outbreaks pose a significant threat to human health worldwide. The outbreak of pandemic coronavirus disease 2019 (COVID-2019) has caused a global health emergency. Identification of regions with high risk for COVID-19 outbreak is a major priority of the governmental organizations and epidemiologists worldwide. The aims of the present study were to analyze the risk factors of coronavirus outbreak and identify areas with a high risk of human infection with virus in Fars Province, Iran. A geographic information system (GIS)-based machine learning algorithm (MLA), support vector machine (SVM), was used for the assessment of the outbreak risk of COVID-19 in Fars Province, Iran. The daily observations of infected cases was tested in the third-degree polynomial and the autoregressive and moving average (ARMA) models to examine the patterns of virus infestation in the province and in Iran. The results of disease outbreak in Iran were compared with the data for Iran and the world. Sixteen effective factors including minimum temperature of coldest month (MTCM), maximum temperature of warmest month (MTWM), precipitation in wettest month (PWM), precipitation of driest month (PDM), distance from roads, distance from mosques, distance from hospitals, distance from fuel stations, human footprint, density of cities, distance from bus stations, distance from banks, distance from bakeries, distance from attraction sites, distance from automated teller machines (ATMs), and density of villages - were selected for spatial modelling. The predictive ability of an SVM model was assessed using the receiver operator characteristic - area under the curve (ROC-AUC) validation technique. The validation outcome reveals that SVM achieved an AUC value of 0.786 (March 20), 0.799 (March 29), and 86.6 (April 10) a good prediction of change detection. The growth rate (GR) average for active cases in Fars for a period of 41 days was 1.26, whilst it was 1.13 in country and the world. The results of the third-degree polynomial and ARMA models revealed an increasing trend for GR with an evidence of turning, demonstrating extensive quarantines has been effective. The general trends of virus infestation in Iran and Fars Province were similar, although an explosive growth of the infected cases is expected in the country. The results of this study might assist better programming COVID-19 disease prevention and control and gaining sorts of predictive capability would have wide-ranging benefits.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Hamid Reza Pourghasemi", - "author_inst": "Shiraz University" - }, - { - "author_name": "Soheila Pouyan", - "author_inst": "Yazd University" - }, - { - "author_name": "Zakariya Farajzadeh", - "author_inst": "Shiraz University" - }, - { - "author_name": "Nitheshnirmal Sadhasivam", - "author_inst": "Bharathidasan University" - }, - { - "author_name": "Bahram Heidari", - "author_inst": "Shiraz University" - }, - { - "author_name": "Sedigheh Babaei", - "author_inst": "Shiraz University" - }, - { - "author_name": "John P Tiefenbacher", - "author_inst": "Texas State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.28.20083873", "rel_title": "Bayesian Inference of COVID-19 Spreading Rates in South Africa", @@ -1517365,6 +1519363,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.04.24.20078287", + "rel_title": "The reproductive index from SEIR model of Covid-19 epidemic in Asean", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078287", + "rel_abs": "As we calculate analytic to link the coefficient of third-order polynomial equations from raw data of an Asean to the SEIR model. The Reproductive index depending on the average incubation period and the average infection period and the coefficient polynomial equations fitted from raw are derived. We also consider the difference of the average incubation period as 5 days and 3 days with the average infection period as 10 day of an Asean. We find that the value of R0 are Indonesia (7.97), Singapore (6.22), Malaysia (3.86), Thailand (2.48), respectively. And we also find that Singapore has 2 values of R0 as 1.54 (16 Feb to 37 March) and 6.22 (31 March-4 April).The peak of infection rate are not found for Singapore and Indonesia at the time of consideration. The model of external stimulus is added into raw data of Singapore and Indonesia to find the maximum rate of infection. We find that Singapore need more magnitude of external stimulus than Indonesia. And the external stimulus for 14 days can stimulate to occur the peak of infected daily case of both country.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "pongkaew udomsamuthirun", + "author_inst": "Srinakharinwirot University" + }, + { + "author_name": "Grittichon Chanilkul", + "author_inst": "Department of Physics, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand." + }, + { + "author_name": "Pongkarn Tongkhonburi", + "author_inst": "Department of Physics, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand." + }, + { + "author_name": "Chatcharawan Meesubthong", + "author_inst": "Faculty of Business Administration, Huachiew Chalermprakiet University, Samutprakan province, 10540, Thailand" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.24.20078154", "rel_title": "Predicting COVID-19 peaks around the world", @@ -1518257,37 +1520286,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.04.24.20078923", - "rel_title": "Real-time time-series modelling for prediction of COVID-19 spread and intervention assessment", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078923", - "rel_abs": "Substantial amount of data about the COVID-19 pandemic is generated every day. Yet, data streaming, while considerably visualized, is not accompanied with advanced modelling techniques to provide real-time insights. This study introduces a unified platform which integrates visualization capabilities with advanced statistical methods for predicting the virus spread in the short run, using real-time data. The platform is backed up by advanced time series models to capture any possible non-linearity in the data which is enhanced by the capability of measuring the expected impact of preventive interventions such as social distancing and lockdowns. The platform enables lay users, and experts, to examine the data and develop several customized models with different restriction such as models developed for specific time window of the data. Our policy assessment of the case of Australia, shows that social distancing and travel ban restriction significantly affect the reduction of number of cases, as an effective policy.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Taha Hossein Rashidi", - "author_inst": "UNSW Sydney" - }, - { - "author_name": "Siroos Shahriari", - "author_inst": "UNSW Sudney" - }, - { - "author_name": "AKM Azad", - "author_inst": "UNSW Sydney" - }, - { - "author_name": "Fatemeh Vafaee", - "author_inst": "UNSW Sydney" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.25.20079830", "rel_title": "FIRST DETECTION OF SARS-COV-2 IN UNTREATED WASTEWATERS IN ITALY", @@ -1518459,6 +1520457,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.20078949", + "rel_title": "Reconstructed diagnostic sensitivity and specificity of the RT-PCR test for COVID-19", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078949", + "rel_abs": "Real-time reverse transcription polymerase chain reaction (RT-PCR) targeting select genes of the SARS-CoV-2 RNA has been the main diagnostic tool in the global response to the COVID-19 pandemic. This study was aimed at the estimation of diagnostic sensitivity and specificity of the first RT-PCR test developed by China CDC in January 2020. The study design is a secondary analysis of published findings on 1014 patients in Wuhan, China, of whom 59.3% tested positive for COVID-19 in RT-PCR tests and 87.6% tested positive in chest CT exams. We utilized previously ignored expert opinions in the form of verbal probability classifications of patients with conflicting test results to estimate the informative prior distribution of the infected proportion. It was then used in a Bayesian version of a previously developed model to reconstruct the sensitivity and specificity of the diagnostic tests without the need for specifying an inaccurate test as the gold standard. The sensitivity of the RT-PCR diagnostic test was estimated to be 0.707 (95% CI: 0.668, 0.749), while the specificity was 0.851 (95% CI: 0.774, 0.941). Caution is advised in generalizing these findings to other versions of the RT-PCR test that are being used in diverse geographic regions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Nikhil S Padhye", + "author_inst": "The University of Texas Health Science Center at Houston" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.25.20079095", "rel_title": "Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: a reliable, faster and economical method.", @@ -1519847,37 +1521864,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.04.29.067728", - "rel_title": "An engineered stable mini-protein to plug SARS-Cov2 Spikes", - "rel_date": "2020-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.067728", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe novel betacoronavirus SARS-CoV-2 is the etiological agent of the current pandemic COVID-19. Like other coronaviruses, this novel virus relies on the surface Spike glycoprotein to access the host cells, mainly through the interaction of its Receptor Binding Domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2). Therefore, molecular entities able to interfere with binding of the SARS-CoV-2 Spike protein to ACE2 have a great potential to inhibit viral entry. Starting from the available structural data on the interaction between SARS-CoV-2 Spike protein and the host ACE2 receptor, we here engineered a mini-protein with the aim of creating a soluble and stable Spike interactor. This mini-protein, which was recombinantly produced in high yields, possesses a stable helical conformation and is able to interact with the RBD of glycosylated Spike protein from SARS-CoV-2 with nanomolar affinity, as measured by microscale thermophoresis. By plugging the Spike protein, our mini-protein constitutes a valid tool for the development of treatments against different types of coronavirus.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maria Romano", - "author_inst": "Institute of Biostructures and Bioimaging, CNR" - }, - { - "author_name": "Alessia Ruggiero", - "author_inst": "Institute of Biostructures and Bioimaging, CNR" - }, - { - "author_name": "Flavia Squeglia", - "author_inst": "Institute of Biostructures and Bioimaging, CNR" - }, - { - "author_name": "Rita Berisio", - "author_inst": "CNR IBB" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.04.29.068098", "rel_title": "Mass spectrometry analysis of newly emerging coronavirus HCoV-19 spike S protein and human ACE2 reveals camouflaging glycans and unique post-translational modifications", @@ -1520077,6 +1522063,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.04.25.20079079", + "rel_title": "Lopinavir-ritonavir alone or combined with arbidol in the treatment of 73 hospitalized patients with COVID-19: a pilot retrospective study", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079079", + "rel_abs": "ObjectivesThis study aimed to evaluate the antiviral efficacy of lopinavir/ritonavir alone or combined with arbidol in the treatment of hospitalized patients with common coronavirus disease-19 (COVID-19).\n\nMethodsIn this retrospective observational study, COVID-19 hospitalized patients were identified and divided into two groups based on the antiviral agents used during their hospitalization. Group-LR patients were treated with single antiviral drug of lopinavir-ritonavir. Group-LR+Ar patients were treated with lopinavir-ritonavir combined with arbidol for antiviral therapy at least 3 days. Patients were assessed for different clinical outcomes.\n\nResultsA total of 34 and 39 patients were identified for Group-LR and Group-LR+Ar, respectively. Treatment with lopinavir-ritonavir alone was not difference from lopinavir-ritonavir combined with arbidol in overall cure rate of COVID-19 hospitalized patients (92.3% and 97.1%, respectively). In a modified intention-to-treat analysis, lopinavir-ritonavir combined with abidol led to a median time of hospital stay that was shorter by 1.5 days than group-LR (12.5 days vs. 14 days). The percentages of COVID-19 RNA clearance was 92.3 in group-LR and 97.1 in group-LR+Ar. The mean time of virus turning negative was 11.5{+/-}9.0 days in group-LR+Ar that were longer than group-LR. Treatment of lopinavir-ritonavir combined with arbidol did not significantly accelerate main symptoms improvement and promote the image absorption of pulmonary inflammation.\n\nConclusionNo benefit was observed in the anti-virus effect of lopinavir-ritonavir combined with arbidol compared with lopinavir-ritonavir alone in the hospitalized patients with COVID-19. More clinical observations in COVID-19 patients may help to confirm or exclude the effect of antiviral agents.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Xiu Lan", + "author_inst": "Lishui Hospital of Zhejiang University" + }, + { + "author_name": "Chuxiao Shao", + "author_inst": "Lishui Hospital of Zhejiang University" + }, + { + "author_name": "Xu Zeng", + "author_inst": "Lishui Hospital of Zhejiang University" + }, + { + "author_name": "Zhenbo Wu", + "author_inst": "Lishui Hospital of Zhejiang University" + }, + { + "author_name": "Yanyan Xu", + "author_inst": "Lishui Hospital of Zhejiang University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.25.20079335", "rel_title": "The nexus of travel restriction, air pollution and COVID-19 infection: Investigation from a megacity of the southern China", @@ -1521469,37 +1523490,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.23.20077271", - "rel_title": "Enacting national social distancing policies corresponds with dramatic reduction in COVID19 infection rates", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077271", - "rel_abs": "The outbreak the SARS-CoV-2 (CoV-2) virus has resulted in over 2.5 million cases of COVID19, greatly stressing global healthcare infrastructure. Lacking medical prophylactic measures to combat disease spread, many nations have adopted social distancing policies in order to mitigate transmission of CoV-2. While mathematical models have suggested the efficacy of social distancing to curb the spread of CoV-2, there is a lack of systematic studies to quantify the real-world efficacy of these approaches. Here, we quantify the spread rate of COVID19 before and after national social distancing measures were implemented in 26 nations and compare this to the changes in COVID19 spread rate over equivalent time periods in 27 nations that did not enact social distancing policies. We find that social distancing policies significantly reduced the COVID19 spread rate. Using mixed linear regression models we estimate that social distancing policies reduced the spread of COVID19 by 66%. These data suggest that social distancing policies may be a powerful tool to prevent spread of COVID19 in real-world scenarios.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Daniel J McGrail", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Jianli Dai", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Kathleen M McAndrews", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Raghu Kalluri", - "author_inst": "The University of Texas MD Anderson Cancer Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20077446", "rel_title": "On the estimation of the total number of SARS-CoV-2 infections", @@ -1521639,6 +1523629,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.23.20077172", + "rel_title": "Instantaneous R calculation for COVID-19 epidemic in Brazil", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077172", + "rel_abs": "COVID-19 pandemic represents a major challenge to health systems of all countries. Brazilian regions habe been showing marked differences in onset and number of cases. Health authorities instituted widespread social distancing and lockdown measures but their implementation has also varied. The authors used data on confirmed cases of COVID-19 in Brazil and its states to calculate the value of instantaneous reproduction number at these regions. The results show a reduction of instantaneous reproduction number with time, probably due to social distancing measures put in place in the last weeks by brazillian authorities. It seems logical to maintain restrictions to social contact until the epidemic peak has occurred in Brazil.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Francisco H. C. Felix", + "author_inst": "Hospital Infantil Albert Sabin" + }, + { + "author_name": "Juvenia B. Fontenele", + "author_inst": "Federal University of Cear" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.23.20077115", "rel_title": "An age-structured epidemiological model of the Belgian COVID-19 epidemic", @@ -1523127,37 +1525140,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.24.20070649", - "rel_title": "Performance of temporal artery temperature measurement in ruling out fever: implications for COVID-19 screening.", - "rel_date": "2020-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20070649", - "rel_abs": "The use of non-invasive temperature testing methods like temporal artery thermometers (TATs) is growing exponentially in the face of the ongoing COVID-19 pandemic. We performed a retrospective analysis of over 1.8 million emergency department electronic health records to identify assess the performance of TAT measurement using patients with near-contemporaneous temperature measurements taken via rectal or oral approaches. Using over 17,000 matched measurements, we show poor fever sensitivity using TAT. We show that sensitivity is significantly improved by lowering the fever threshold and describe limits of agreement between methods of measurement. Our findings suggest that private, public, and healthcare delivery organizations may need to reconsider how we perform high-volume screening during this time of crisis and has implications for return-to-work protocols.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Adrian Haimovich", - "author_inst": "Yale University" - }, - { - "author_name": "Richard Andrew Taylor", - "author_inst": "Yale University" - }, - { - "author_name": "Harlan Krumholz", - "author_inst": "Yale University" - }, - { - "author_name": "Arjun K Venkatesh", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.24.20069633", "rel_title": "Lung injury in patients with or suspected COVID-19 : a comparison between lung ultrasound and chest CT-scanner severity assessments, an observational study", @@ -1523413,6 +1525395,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.23.20076562", + "rel_title": "COVID-19 spreading: a model", + "rel_date": "2020-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076562", + "rel_abs": "This communication describes a recursive mathematical model of the spreading COVID-19 infection, which allows estimating the effectiveness of quarantine measures. This model takes into account the contagiousness of infected people during the incubation period of the disease and the conditionally non-contagiousness of sick people due to their isolation. The model was used to analyze the situation in eight countries and to find the viral transmissibility, which made it possible to give a brief prediction of the COVID-19 spreading.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sergey O Ilyin", + "author_inst": "A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.22.20075630", "rel_title": "Multi-chain Fudan-CCDC model for COVID-19 in Iran", @@ -1524521,25 +1526522,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.22.20076166", - "rel_title": "Early detection of superspreaders by mass group pool testing can mitigate COVID-19 pandemic", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20076166", - "rel_abs": "BackgroundMost of epidemiological models applied for COVID-19 do not consider heterogeneity in infectiousness and impact of superspreaders, despite the broad viral loading distributions amongst COVID-19 positive people (1 - 106 per mL). Also, mass group testing is not used regardless to existing shortage of tests. I propose new strategy for early detection of superspreaders with reasonable number of RT-PCR tests, which can dramatically mitigate development COVID-19 pandemic and even turn it endemic.\n\nMethodsI used stochastic social-epidemiological SEIAR model, where S-suspected, E-exposed, I-infectious, A-admitted (confirmed COVID-19 positive, who are admitted to hospital or completely isolated), R-recovered. The model was applied to real COVID-19 dynamics in London, Moscow and New York City.\n\nFindingsViral loading data measured by RT-PCR were fitted by broad log-normal distribution, which governed high importance of superspreaders. The proposed full scale model of a metropolis shows that top 10% spreaders (100+ higher viral loading than median infector) transmit 45% of new cases. Rapid isolation of superspreaders leads to 4-8 fold mitigation of pandemic depending on applied quarantine strength and amount of currently infected people. High viral loading allows efficient group \"matrix\" pool testing of population focused on detection of the superspreaders requiring remarkably small amount of tests.\n\nInterpretationThe model and new testing strategy may prevent thousand or millions COVID-19 deaths requiring just about 5000 daily RT-PCR test for big 12 million city such as Moscow. Though applied to COVID-19 pandemic the results are universal and can be used for other infectious heterogenous epidemics.\n\nFundingNo funding", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Maxim B Gongalsky", - "author_inst": "Lomonosov Moscow State University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.21.20044594", "rel_title": "Smart Pooled sample Testing for COVID-19: A Possible Solution for Sparsity of Test Kits", @@ -1524819,6 +1526801,137 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.04.27.064279", + "rel_title": "Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice.", + "rel_date": "2020-04-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.27.064279", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 as the causative agent of the novel pandemic viral disease COVID-19. With no approved therapies, this pandemic illustrates the urgent need for safe, broad-spectrum antiviral countermeasures against SARS-CoV-2 and future emerging CoVs. We report that remdesivir (RDV), a monophosphoramidate prodrug of an adenosine analog, potently inhibits SARS-CoV-2 replication in human lung cells and primary human airway epithelial cultures (EC50 = 0.01 M). Weaker activity was observed in Vero E6 cells (EC50 = 1.65 M) due to their low capacity to metabolize RDV. To rapidly evaluate in vivo efficacy, we engineered a chimeric SARS-CoV encoding the viral target of RDV, the RNA-dependent RNA polymerase, of SARS-CoV-2. In mice infected with chimeric virus, therapeutic RDV administration diminished lung viral load and improved pulmonary function as compared to vehicle treated animals. These data provide evidence that RDV is potently active against SARS-CoV-2 in vitro and in vivo, supporting its further clinical testing for treatment of COVID-19.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Andrea J Pruijssers", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Amelia S George", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Alexandra Sch\u00e4fer", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Sarah R Leist", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Lisa E Gralinski", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kenneth H Dinnon III", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Boyd L Yount", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Maria L Agostini", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Laura J Stevens", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "James D Chappell", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Xiaotao Lu", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Tia M Hughes", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Kendra L Gully", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "David R Martinez", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ariane J Brown", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Rachel L Graham", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Jason K Perry", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Venice Du Pont", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Jared Pitts", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Bin Ma", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Darius Babusis", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Eisuke Murakami", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Joy Y Feng", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "John P Bilello", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Danielle P Porter", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Tomas Cihlar", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Ralph S Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Mark R Denison", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Timothy P Sheahan", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.27.063180", "rel_title": "Structure of replicating SARS-CoV-2 polymerase", @@ -1525851,37 +1527964,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.23.20076075", - "rel_title": "How fast does the SARS-Cov-2 virus really mutate in heterogeneous populations?", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076075", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe problem of estimating unknown features of viral species using a limited collection of observations is of great relevance in computational biology. We consider one such particular problem, concerned with determining the mutational support and distribution of the SARS-Cov-2 viral genome and its open reading frames (ORFs). The mutational support refers to the unknown number of sites that is expected to be eventually mutated in the SARS-Cov-2 genome. It may be used to assess the virulence of the virus or guide primer selection for real-time RT-PCR tests during the early stages of an outbreak. Estimating the unknown distribution of mutations in the genome of different subpopulations while accounting for the unseen may aid in discovering adaptation mechanisms used by the virus to evade the immune system. To estimate the mutational support in the small-sample regime, we use GISAID sequencing data and new state-of-the-art polynomial estimation techniques based on weighted and regularized Chebyshev approximations. For distribution estimation, we adapt the well-known Good-Turing estimator. We also perform a differential analysis of mutations and their sites across different populations. Our analysis reveals several findings: First, the mutational supports exhibit significant differences in the ORF6 and ORF7a regions (older vs younger patients), ORF1b and ORF10 regions (females vs males) and as may be expected, in almost all ORFs (for Asia versus Europe and North America). Second, despite the fact that the N region of SARS-Cov-2 has a predicted 10% mutational support, almost all observed mutations fall outside of the two regions of paired primers recommended for testing by the CDC.\n\nAuthor SummaryWe introduce the new problem of small-sample estimation of the number of mutations and the distribution of mutations in viral and bacterial genomes, and in particular, in the SARS-Cov-2 genome. The approach is of interest due to the fact that it aims to predict which regions in the genome will mutate in the future and with what frequency, given only a very limited number of complete viral sequences. This setting is usually encountered during the early stages of an outbreak when it is critical to assess the potential of the virus to gain mutations advantageous for its spreading. The results may also be used to guide the selection of genomic (primer) regions that are not subject to mutational pressure and can consequently be used as identifiers in the process of testing for the disease. They can also highlight differences in the mutation rates and locations of the SARS-Cov-2 virus affecting diverse subpopulations and therefore potentially suggest the role of certain mutations in evading the immune system. Our approach uses a new class of estimation methods that may find other applications in bioinformatics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Vishal Rana", - "author_inst": "University of Illinois, Urbana-Champaign" - }, - { - "author_name": "Eli Chien", - "author_inst": "University of Illinois, Urbana-Champaign" - }, - { - "author_name": "Jianhao Peng", - "author_inst": "University of Illinois, Urbana-Champaign" - }, - { - "author_name": "Olgica Milenkovic", - "author_inst": "University of Illinois, Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20075861", "rel_title": "The Potential Impact of Interruptions to HIV Services: A Modelling Case Study for South Africa", @@ -1525997,6 +1528079,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.23.20076463", + "rel_title": "The First Month Spread of COVID-19 in Madagascar", + "rel_date": "2020-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076463", + "rel_abs": "Using the officially published data and aware of the unclear source and insufficient number of samples, we present a first and (for the moment) unique attempt to study the spread of the pandemic COVID-19 in Madagascar. The approach has been tested by predicting the number of contaminated persons until 20 days after fitting the inputs data collected within 15 days using standard least,{chi} 2-fit method. Encouraged by this first test, we add the new data collected within 30 days and give prevision until 33 days. We complete the analysis by using the updated data until 46 days. The data below 30 days show an approximate linear or quadratic polynomial increase of about (4-5) infected persons per day. A comparison with some other SI-like models is done. However, newer additional data collected until 46 days favours a cubic polynomial behaviour which signals an eventual near future stronger growth as confirmed by the data on the 48th day received after our study and our estimate including this new data for the next days. The analysis of the numbers of cured persons for 38 and 46 days shows behaviours similar to the ones of the infected persons. They indicate about 3 cured persons per day. These results for infected and cured persons may also be interpreted as the lowest values of the real cases due to the insufficient number of samples (about 3968 for 27 million inhabitants on 07/05/2020). Some social, economical and political impacts of COVID-19 and confinement for Madagascar and Worldwide are shortly discussed.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Stephan Narison", + "author_inst": "LUPM/CNRS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.22.20075663", "rel_title": "Ethnic and socioeconomic differences in SARS-CoV2 infection in the UK Biobank cohort study", @@ -1526877,37 +1528978,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.04.19.048991", - "rel_title": "CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2", - "rel_date": "2020-04-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.19.048991", - "rel_abs": "The ability to detect the SARS-CoV-2 in a widespread epidemic is crucial for screening of carriers and for the success of quarantine efforts. Methods based on real-time reverse transcription polymerase chain reaction (RT-qPCR) and sequencing are being used for virus detection and characterization. However, RNA viruses are known for their high genetic diversity which poses a challenge for the design of efficient nucleic acid-based assays. The first SARS-CoV-2 genomic sequences already showed novel mutations, which may affect the efficiency of available screening tests leading to false-negative diagnosis or inefficient therapeutics. Here we describe the CoV2ID (http://covid.portugene.com/), a free database built to facilitate the evaluation of molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates the available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Updated sequences alignments are used to constantly verify the theoretical efficiency of available testing methods. Detailed information on available detection protocols are also available to help laboratories implementing SARS-CoV-2 testing.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jo\u00e3o Carneiro", - "author_inst": "Interdisciplinary Centre of Marine and Environmental Research (CIIMAR)" - }, - { - "author_name": "Catarina Gomes", - "author_inst": "IDENTIFICA University of Porto" - }, - { - "author_name": "Catia Couto", - "author_inst": "IDENTIFICA University of Porto" - }, - { - "author_name": "Filipe Pereira", - "author_inst": "IDENTIFICA genetic testing" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.25.060947", "rel_title": "MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples", @@ -1527271,6 +1529341,81 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.04.25.061499", + "rel_title": "A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing", + "rel_date": "2020-04-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.25.061499", + "rel_abs": "Early detection of infection with SARS-CoV-2 is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). Almost all diagnostic methods currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require larger concentrations of the virus to achieve this degree of accuracy. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy. The genotypic data contained in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of both positive and negative clinical nasopharyngeal swab samples 100% match the diagnoses obtained in a clinical diagnostic lab using the Center for Disease Controls 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8- hour experiment at the cost of [~]$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity in this approach.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Per A Adastra", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Neva C. Durand", + "author_inst": "Broad Institute" + }, + { + "author_name": "Namita Mitra", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Saul Godinez", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Ragini Mahajan", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Alyssa Blackburn", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Zane Colaric", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Joshua W. Theisen", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "David Weisz", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Olga Dudchenko", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Andreas Gnirke", + "author_inst": "Broad Institute" + }, + { + "author_name": "Suhas S.P. Rao", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Parwinder Kaur", + "author_inst": "The University of Western Australia" + }, + { + "author_name": "Erez Aiden", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Aviva Aiden", + "author_inst": "Baylor College of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.04.25.061200", "rel_title": "Elevated expression of ACE2 in tumor-adjacent normal tissues of cancer patients", @@ -1528451,53 +1530596,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.21.20074435", - "rel_title": "The spatio-temporal epidemic dynamics of COVID-19 outbreak in Africa", - "rel_date": "2020-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074435", - "rel_abs": "The novel coronavirus (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the city of Wuhan, China in December 2019. Although, the disease appears on the African continent late, it has spread to virtually all the countries. We provide early spatio-temporal dynamics of COVID-19 within the first 62 days of the diseases appearance on the African continent. We used a two-parameter hurdle Poisson model to simultaneously analyze the zero counts and the frequency of occurrence. We investigate the effects of important healthcare capacities including hospital beds and number of medical doctors in the different countries. The results show that cases of the pandemic vary geographically across Africa with notable high incidence in neighboring countries particularly in West and North Africa. The burden of the disease (per 100,000) was most felt in Djibouti Tunisia, Morocco and Algeria. Temporally, during the first 4 weeks, the burden was highest in Senegal, Egypt and Mauritania, but by mid-April it shifted to Somalia, Chad, Guinea, Tanzania, Gabon, Sudan, and Zimbabwe. Currently, Namibia, Angola, South Sudan, Burundi and Uganda have the least burden. The findings could be useful in implementing epidemiological intervention and allocation of scarce resources based on heterogeneity of the disease patterns.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ezra Gayawan", - "author_inst": "Federal University of Technology, Akure, Nigeria" - }, - { - "author_name": "Olawale Awe", - "author_inst": "Anchor University, Lagos, Nigeria" - }, - { - "author_name": "Bamidele M Oseni", - "author_inst": "Federal University of Technology, Akure, Nigeria" - }, - { - "author_name": "Ikemefuna C Uzochukwu", - "author_inst": "Nnamdi Azikiwe University, Nigeria" - }, - { - "author_name": "Adeshina I Adekunle", - "author_inst": "James Cook University" - }, - { - "author_name": "Gemisola Samuel", - "author_inst": "covenant university, Nigeria" - }, - { - "author_name": "Damon Eisen", - "author_inst": "James Cook University" - }, - { - "author_name": "Oyelola Adegboye", - "author_inst": "James Cook University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20074914", "rel_title": "Antibody tests in detecting SARS-CoV-2 infection: a meta-analysis", @@ -1528665,6 +1530763,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.21.20064147", + "rel_title": "Conspiracy beliefs are associated with lower knowledge and higher anxiety levels regarding COVID-19 among students at the University of Jordan", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20064147", + "rel_abs": "BackgroundThe world has been afflicted heavily by the burden of coronavirus disease 2019 (COVID-19) that overwhelmed health care systems and caused severe economic and educational deficits, in addition to anxiety among the public. The main aim of this study was to evaluate the mutual effects of belief that the pandemic was the result of a global conspiracy on knowledge and anxiety levels among students at the University of Jordan (UJ).\n\nMethodsAn electronic-based survey was conducted between March 29th 2020 and March 31st 2020. The targeted population involved all undergraduate and postgraduate students from Health, Scientific and Humanities Schools at UJ. Survey sections included 26 items on: socio-demographic information, knowledge and sources of information about the disease, attitude towards the false notion that COVID-19 stemmed from a global conspiracy and items to assess the anxiety level among students during the quarantine period.\n\nResultsThe total number of participants was 1540 students. The majority of participants perceived the disease as moderately dangerous (n=1079, 70.1%), with males, Jordanians and participants with lower income being more inclined to feel that the disease is very dangerous (p<0.001, 0.020, and <0.001, respectively). Lower level of knowledge and higher level of anxiety about COVID-19 were associated with the belief that the disease is part of a global conspiracy (p<0.001 and p=0.004, respectively). Females and participants with lower income were more likely to believe that the disease is related to conspiracy (p=0.001 and p<0.001, respectively). Belief in global conspiracy regarding the origin of COVID-19 was associated with misinformation about the availability of vaccine and the therapeutic use of antibiotics for COVID-19 treatment (p=0.001 and p<0.001, respectively). Ministry of Health in Jordan was the most common source of information about COVID-19 reported by the participants (n=1018).\n\nConclusionsThe false belief that COVID-19 was the result of a global conspiracy could be the consequence of lower level of knowledge about the virus and could lead to higher level of anxiety, which should be considered in the awareness tools of various media platforms about the current pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Malik Sallam", + "author_inst": "University of Jordan" + }, + { + "author_name": "Deema Dababseh", + "author_inst": "University of Jordan" + }, + { + "author_name": "Alaa' Yaseen", + "author_inst": "University of Jordan" + }, + { + "author_name": "Ayat Al-Haidar", + "author_inst": "University of Jordan" + }, + { + "author_name": "Nidaa A. Ababneh", + "author_inst": "University of Jordan" + }, + { + "author_name": "Faris G. Bakri", + "author_inst": "University of Jordan" + }, + { + "author_name": "Azmi Mahafzah", + "author_inst": "University of Jordan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.23.056309", "rel_title": "SARS-CoV-2 Isolation and Propagation from Turkish COVID-19 patients", @@ -1530057,77 +1532198,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2020.04.20.20065953", - "rel_title": "The production of antibodies for SARS-CoV-2 and its clinical implication", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20065953", - "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2(SARS-CoV-2), a novel betacoronavirus, has caused an outburst of pneumonia cases in Wuhan, China. We report the production of specific IgM and IgG antibodies after the infection of SARS-CoV-2 and its implication for the diagnosis, pathology and the course of the disease as well as the recurrence of positive nucleic acid tests after discharge.\n\nMethodsTest results for SARS-CoV-2 IgM and IgG antibodies of 221 confirmed COVID-19 patients were retrospectively examined, and their clinical data were collected and analyzed based on various subgroups. SARS-CoV-2 IgM and IgG antibodies were determined with the chemiluminescence method.\n\nFindingsThe concentration (S/CO) of SARS-CoV-2 IgM and IgG antibodies peaked on day 19-21 after symptom onset, with a median of 17.38 (IQR 4.39-36.4) for IgM and 5.59 (IQR 0.73-13.65) for IgG. Detection rates reached highest on day 16-18 and day 19-21 for IgM and IgG, which were 73.6% and 98.6%, respectively, with significantly higher concentration of IgG in critically ill patients than in those with mild to moderate disease (P=0.027). The concentration of the antibodies on day 16-21 is not correlated with the course or outcome of the disease (Spearman r < 0.20, P > 0.05). Nasopharyngeal swabs revealed positive SARS-CoV-2 RNA in up to 52.7% of recovered patients after discharge, whose IgG proved to be significantly lower than that of those with negative RNA results (P = 0.009). IgG and IgM were tested twice within 14 days after discharge with a 7-day interval, and the second testing of these antibodies displayed a decrease in concentration of 21.2% (IQR, 11.2%,34.48%) for IgG and 23.05% (IQR, -27.96%,46.13%) for IgM, without statistical significance between the patients with re-detectable positive RNA results and those with negative RNA results after discharge. However, those with positive results experienced a count decrease in lymphocyte subsets.\n\nInterpretationThe concentration of SARS-CoV-2 IgM and IgG antibodies peaked on day 19-21 after symptom onset, and antibody testing on day 16-21 is associated with increased detection rates, but the antibody concentration does not affect the course and outcome of the infection. Recovering patients with re-detectable positive SARS-CoV-2 RNA displayed lower concentration of IgG, but the downward trend of IgG during recovery indicated its limited duration of protection, and the protective effect of IgG remains to be investigated.\n\nFundingChongqing Education Board, Chongqing Science and Technology Bureau, Famous teacher project of Chongqing talent plan", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Qianfang Hu", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Xiaoping Cui", - "author_inst": "Department of Medical Laboratory, Chongqing Three Gorges Central Hospital" - }, - { - "author_name": "Xinzhu Liu", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Bin Peng", - "author_inst": "Department of Health Statistics, School of Public Health and Management, Chongqing Medical University" - }, - { - "author_name": "Jinyue Jiang", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Xiaohui Wang", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Yan Li", - "author_inst": "Department of Health Management Centre, Chongqing Three Gorges Central Hospital," - }, - { - "author_name": "Wenhui Hu", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Zhi Ao", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Jun Duan", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Xue Wang", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Linxiao Zhu", - "author_inst": "Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University" - }, - { - "author_name": "Shuliang Guo", - "author_inst": "the First Affiliated Hospital of Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Guicheng Wu", - "author_inst": "Department of Hepatopathy, Chongqing Three Gorges Central Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.04.21.20066761", "rel_title": "Risk of drug-induced Long QT Syndrome associated with the use of repurposed COVID-19 drugs: a systematic review", @@ -1530383,6 +1532453,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.04.22.20070441", + "rel_title": "CT in relation to RT-PCR in diagnosing COVID-19 in the Netherlands: a prospective study", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20070441", + "rel_abs": "IntroductionEarly differentiation between emergency department (ED) patients with and without corona virus disease (COVID-19) is very important. Chest CT scan may be helpful in early diagnosing of COVID-19. We investigated the diagnostic accuracy of CT using RT-PCR for SARS-CoV-2 as reference standard and investigated reasons for discordant results between the two tests.\n\nMethodsIn this prospective single centre study in the Netherlands, all adult symptomatic ED patients had both a CT scan and a PCR upon arrival at the ED. CT results were compared with PCR test(s). Diagnostic accuracy was calculated. Discordant results were investigated using discharge diagnoses.\n\nResultsBetween March 13th and March 24th 2020, 193 symptomatic ED patients were included. In total, 43.0% of patients had a positive PCR and 56.5% a positive CT, resulting in a sensitivity of 89.2%, specificity 68.2%, likelihoodratio (LR) + 2.81 and LR-0.16. Sensitivity was higher in patients with high risk pneumonia (CURB-65 score [≥]3; n=17, 100%) and with sepsis (SOFA score [≥]2; n=137, 95.5%).\n\nOf the 35 patients (31.8%) with a suspicious CT and a negative PCR, 9 had another respiratory viral pathogen, and in 7 patients, COVID-19 was considered likely. One of nine patients with a non-suspicious CT and a positive PCR had developed symptoms within 48 hours before scanning.\n\nDiscussionThe accuracy of chest CT in symptomatic ED patients is high, but used as a single diagnostic test, CT can not safely diagnose or exclude COVID-19. However, CT can be used as a quick first screening tool.\n\nO_TEXTBOXKey messages\n\nWhat is the key question?\n\nO_LIWe investigated the diagnostic accuracy of the chest CT scan using the PCR test for diagnosing COVID-19 as reference.\nC_LI\n\nWhat is the bottom line?\n\nO_LISensitivity of chest CT is high, especially in severely ill patients, but with moderate specificity, which could in part be explained by other respiratory viruses and false negative PCR tests.\nC_LI\n\nWhy read on?\n\nEarly differentation between patients with and without COVID-19 is extremely important, and CT scan should be considered a quick screening test, and may help to overcome suboptimal sensitivity of PCR tests.\n\nC_TEXTBOX", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Hester A Gietema", + "author_inst": "Department of Radiology, Maastricht University Medical Centre, Grow school for oncology and developmental biology, Maastricht University, Maastricht" + }, + { + "author_name": "Noortje Zelis", + "author_inst": "Department of Internal Medicine, Division of General Internal Medicine, Section Acute Medicine, Maastricht University Medical Centre, CARIM School for Cardiovas" + }, + { + "author_name": "J. Martijn Nobel", + "author_inst": "Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre, School of Health Professions Education, Maastricht University, Maastricht, t" + }, + { + "author_name": "Lars J.G. Lambriks", + "author_inst": "Department of Internal Medicine, Division of General Internal Medicine, Section Acute Medicine, Maastricht University Medical Centre" + }, + { + "author_name": "Lieke B van Alphen", + "author_inst": "Department of Medical Microbiology, Maastricht University Medical Centre, School CAPHRI, Care and Public Health Research Institute, Maastricht University, Maast" + }, + { + "author_name": "Astrid M.L. Oude Lashof", + "author_inst": "Department of Medical Microbiology, Maastricht University Medical Centre, School of Nutrition and Translational Research in Metabolism, Maastricht University, M" + }, + { + "author_name": "Joachim E Wildberger", + "author_inst": "Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht" + }, + { + "author_name": "Irene C Nelissen", + "author_inst": "Department of Internal Medicine, Division of General Internal Medicine, Section Acute Medicine, Maastricht University Medical Centre, Maastricht" + }, + { + "author_name": "Patricia M Stassen", + "author_inst": "Department of Internal Medicine, Division of General Internal Medicine, Section Acute Medicine, Maastricht University Medical Centre, School CAPHRI, Care and Pu" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.21.20066258", "rel_title": "No Clear Benefit to the Use of Corticosteroid as Treatment in Adult Patients with Coronavirus Disease 2019 : A Retrospective Cohort Study", @@ -1531815,25 +1533936,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.19.20071761", - "rel_title": "Minimising lockdown periods for regional elimination of covid-19", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071761", - "rel_abs": "There seems to be widespread pessimism regarding the ability of a nation to eliminate covid. One factor in this pessimism seems to be concern that covid might always be able to re-emerge because of the ongoing presence of unrecognised asymptomatic cases. However, it is shown here that it should be possible to eliminate covid more easily than anticipated, for a reason that at first glance seems paradoxical - the presence of superspreaders. If superspreaders are responsible for most of the spread, then, with the average number of secondary cases fixed at say R0 = 2.5, we have to conclude that superspreaders are relatively rare. When towards the end of an elimination program, there are very few infected people, whether symptomatic or asymptomatic, that small number of people may well not include any superspreaders. As a result, chance effects may make extinction likely. Nevertheless it is clear an attempt at elimination will require a rather onerous \"lockdown\". In this paper we use a branching processes model to look at the tradeoff between risk of disease re-emergence and the length of \"lockdown\" required after a program of elimination has dropped the number of symptomatic cases in a region to just one.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "David Abraham Kault", - "author_inst": "James Cook University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.20.20072470", "rel_title": "Prevalence of SARS-CoV-2 infection in previously undiagnosed health care workers at the onset of the U.S. COVID-19 epidemic", @@ -1532109,6 +1534211,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.21.20073049", + "rel_title": "What can trends in hospital deaths from COVID-19 tell us about the progress and peak of the pandemic? An analysis of death counts from England announced up to 20 April 2020", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073049", + "rel_abs": "BackgroundReporting of daily hospital COVID-19 deaths in the UK are promoted by the government and scientific advisers alike as a key metric for assessing the progress in the control of the epidemic. These data, however, have certain limitations, among which one of the most significant concerns the fact that the daily totals span deaths that have occurred between 1 and 10 days or more in the past.\n\nData and methodsWe obtained daily data published published by NHS England up to and including April 25 in the form of Excel spreadsheets in which deaths counts are presented by date of death according to age and region. Simple descriptive analyses were conducted and presented in graphical and tabular form which were aimed at illustrating the biases inherent in focussing on daily counts regardless of when the deaths occurred. We then looked at how a less biased picture could be obtained by looking at trends in death counts stratifying by individual period of delay in days between occurrence of death and when the death was included in the daily announcement.\n\nFindingsThe number of hospital COVID-19 deaths announced daily overestimates the maximum number of deaths actually occurring so far in the epidemic in the UK, and also obscures the pattern of decline in deaths. Taking account of reporting delays suggests that for England as a whole a peak in hospital COVID-19 deaths may have been reached on April 8 with a subsequent gradual decline suggested. The same peak is also seen among those aged 60-79 and 80+, although there is slightly shallower decline in the oldest age group (80+ years). Among those aged 40-59 years a later peak on April 11 is evident. London shows a peak on April 8 and a clearer and steeper pattern of subsequent decline compared to England as a whole.\n\nInterpretationAnalyses of mortality trends must take account of delay, and in communication with the public more emphasis should be placed on looking at trends based on deaths that occurred 5 or more days prior to the announcement day. The slightly weaker decline seen at age 80+ may reflect increased hospitalisation of people from care homes, whereas the later peak under the age of 60 years may reflect the higher proportions at these younger ages being admitted to critical care resulting in an extension of life of several days.\n\nCompeting interestsAll authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: no support from any organization for the submitted work; no financial relationships with any organizations that might have an interest in the submitted work in the previous three years other than LS who reported grants from Wellcome, MRC, NIHR, GSK, BHF, Diabetes UK all outside the submitted work; no other relationships or activities that could appear to have influenced the submitted work other than LS who is a Trustee of the British Heart Foundation and AJM who is a member of the Royal Society Delve Committee.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "David A Leon", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Christopher I Jarvis", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Anne M Johnson", + "author_inst": "University College London" + }, + { + "author_name": "Liam Smeeth", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Vladimir M Shkolnikov", + "author_inst": "Max Planck Institute for Demographic Research" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.20.20072801", "rel_title": "The Association of Lymphocyte count and levels of CRP, D-Dimer, and LDH with severe coronavirus disease 2019 (COVID-19): A Meta-Analysis", @@ -1533389,41 +1535526,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.16.20067744", - "rel_title": "Psychiatric Symptoms Related to the COVID-19 Pandemic", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067744", - "rel_abs": "The COVID-19 pandemic and the consequential societal changes are likely to have major health consequences way beyond those caused by the virus infection. One of the medical fields that may experience significant consequences of the pandemic is that of psychiatry. Importantly, individuals who already live with mental disorders may be particularly vulnerable to the psychological stress associated with the pandemic. However, data on how the COVID-19 pandemic affects this group of people is largely absent from the literature.\n\nHere, we report data from a quality development project conducted at the psychiatric services of the Central Denmark Region (CDR), which has a catchment area of approximately 1.3 million people covered by five psychiatric hospitals providing inpatient and outpatient treatment of all types of mental disorders. Based on a manual screening of all clinical notes from the period from February 1st to March 23rd 2020 that contained at least one of the following words: corona, COVID, virus, epidemic, pandemic, and contaminate/contamination (including compound words), we found 1357 notes from 918 adult patients that described pandemic-related psychopathology (symptoms that appeared to be caused/deteriorated by the pandemic and/or its societal consequences).\n\nTo our knowledge, this is the first investigation of COVID-19 pandemic-related psychopathology from a large psychiatric treatment setting. The results clearly suggest that this phenomenon exists among individuals with mental illness. However, as the data from this investigation stems from standard clinical practice where the patients were not systematically assessed for pandemic-related psychopathology, we cannot speak to its overall prevalence. Nevertheless, we believe that our findings underline the necessity of taking urgent action to mitigate the negative effects of the COVID-19 pandemic on patients with mental disorders. A low-cost intervention would be to simply discuss the ongoing pandemic and its societal consequences with patients seeking care in psychiatric settings - as this may lead to relief of pandemic-related symptoms via general comforting, and clarification of misunderstandings/false beliefs regarding the pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christopher Rohde", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Oskar Hougaard Jefsen", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Bettina Noerremark", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "Andreas Aalkjaer Danielsen", - "author_inst": "Aarhus University Hospital" - }, - { - "author_name": "S\u00f8ren Dinesen \u00d8stergaard", - "author_inst": "Aarhus University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.04.17.20070219", "rel_title": "From Community Acquired Pneumonia to COVID-19: A Deep Learning Based Method for Quantitative Analysis of COVID-19 on thick-section CT Scans", @@ -1533647,6 +1535749,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.20073213", + "rel_title": "A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20073213", + "rel_abs": "We present a stochastic compartmental network model of SARS-CoV-2 and COVID-19 exploring the effects of policy choices in three domains: social distancing, hospital triaging, and testing. We distinguished between high-risk and low-risk members of the population, and modeled differences in social interactions due to context, risk level, infection status, and testing status. The model incorporates many of the currently important characteristics of the disease, including overcapacity in the healthcare system and uncertainties surrounding the proportion and transmission potential of asymptomatic cases. We compared current policy guidelines from public health agencies with alternative options, and investigated the effects of policy decisions on the overall proportion of COVID-19-related deaths. Our results support current policies to contain the outbreak but also suggest possible refinements, including emphasizing the need to reduce public, random contacts more than private contacts, and testing low-risk symptomatic individuals before high-risk symptomatic individuals. Our model furthermore points to interactions among the three policy domains; the efficacy of a particular policy choice depends on other implemented policies. Finally, our results provide an explanation for why societies like Germany, with lower average rates of social contact, are more successful at containing the outbreak than highly social societies such as Italy, despite the implementation of similar policy measures.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Audrey McCombs", + "author_inst": "Iowa State University" + }, + { + "author_name": "Claus Kadelka", + "author_inst": "Iowa State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.20.20073031", "rel_title": "An Interactive Tool to Forecast US Hospital Needs in the Coronavirus 2019 Pandemic", @@ -1534967,81 +1537092,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, - { - "rel_doi": "10.1101/2020.04.17.20069930", - "rel_title": "A single-cell atlas of the peripheral immune response to severe COVID-19", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069930", - "rel_abs": "There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2. Here, we apply single-cell RNA sequencing (scRNA-seq) to peripheral blood mononuclear cells (PBMCs) of 7 patients hospitalized with confirmed COVID-19 and 6 healthy controls. We identify substantial reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene (ISG) signature, HLA class II downregulation, and a novel B cell-derived granulocyte population appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines, suggesting that circulating leukocytes do not significantly contribute to the potential COVID-19 cytokine storm. Collectively, we provide the most thorough cell atlas to date of the peripheral immune response to severe COVID-19.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Aaron J Wilk", - "author_inst": "Stanford University" - }, - { - "author_name": "Arjun Rustagi", - "author_inst": "Stanford University" - }, - { - "author_name": "Nancy Q Zhao", - "author_inst": "Stanford University" - }, - { - "author_name": "Jonasel Roque", - "author_inst": "Stanford University" - }, - { - "author_name": "Giovanny J Martinez-Colon", - "author_inst": "Stanford University" - }, - { - "author_name": "Julia L McKechnie", - "author_inst": "Stanford University" - }, - { - "author_name": "Geoffrey T Ivison", - "author_inst": "Stanford University" - }, - { - "author_name": "Thanmayi Ranganath", - "author_inst": "Stanford University" - }, - { - "author_name": "Rosemary Vergara", - "author_inst": "Stanford University" - }, - { - "author_name": "Taylor Hollis", - "author_inst": "Stanford University" - }, - { - "author_name": "Laura J Simpson", - "author_inst": "Stanford University" - }, - { - "author_name": "Philip Grant", - "author_inst": "Stanford University" - }, - { - "author_name": "Aruna Subramanian", - "author_inst": "Stanford University" - }, - { - "author_name": "Angela J Rogers", - "author_inst": "Stanford University" - }, - { - "author_name": "Catherine A Blish", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.18.20070565", "rel_title": "Clinical Characteristics of 20,662 Patients with COVID-19 in mainland China: A Systemic Review and Meta-analysis", @@ -1535325,6 +1537375,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.19.20068072", + "rel_title": "COVID-19 Asymptomatic Infection Estimation", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20068072", + "rel_abs": "BackgroundMounting evidence suggests that there is an undetected pool of COVID-19 asymptomatic but infectious cases. Estimating the number of asymptomatic infections has been crucial to understand the virus and contain its spread, which is, however, hard to be accurately counted.\n\nMethodsWe propose an approach of machine learning based fine-grained simulator (ML-Sim), which integrates multiple practical factors including disease progress in the incubation period, cross-region population movement, undetected asymptomatic patients, and prevention and containment strength. The interactions among these factors are modeled by virtual transmission dynamics with several undetermined parameters, which are determined from epidemic data by machine learning techniques. When MLSim learns to match the real data closely, it also models the number of asymptomatic patients. MLSim is learned from the open Chinese global epidemic data.\n\nFindingsMLSim showed better forecast accuracy than the SEIR and LSTM-based prediction models. The MLSim learned from the data of Chinas mainland reveals that there could have been 150,408 (142,178-157,417) asymptomatic and had self-healed patients, which is 65% (64% - 65%) of the inferred total infections including undetected ones. The numbers of asymptomatic but infectious patients on April 15, 2020, were inferred as, Italy: 41,387 (29,037 - 57,151), Germany: 21,118 (11,484 - 41,646), USA: 354,657 (277,641 - 495,128), France: 40,379 (10,807 - 186,878), and UK: 144,424 (127,215 - 171,930). To control the virus transmission, the containment measures taken by the government were crucial. The learned MLSim also reveals that if the date of containment measures in Chinas mainland was postponed for 1, 3, 5, and 7 days later than Jan. 23, there would be 109,039 (129%), 183,930 (218%), 313,342 (371%), 537,555 (637%) confirmed cases on June 12.\n\nConclusionsMachine learning based fine-grained simulators can better model the complex real-world disease transmission process, and thus can help decision-making of balanced containment measures. The simulator also revealed the potential great number of undetected asymptomatic infections, which poses a great risk to the virus containment.\n\nFundingNational Natural Science Foundation of China.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Yang Yu", + "author_inst": "Nanjing University" + }, + { + "author_name": "Yu-Ren Liu", + "author_inst": "Nanjing University" + }, + { + "author_name": "Fan-Ming Luo", + "author_inst": "Nanjing University" + }, + { + "author_name": "Wei-Wei Tu", + "author_inst": "4Paradigm" + }, + { + "author_name": "De-Chuan Zhan", + "author_inst": "Nanjing University" + }, + { + "author_name": "Guo Yu", + "author_inst": "Northern Jiangsu People's Hospital" + }, + { + "author_name": "Zhi-Hua Zhou", + "author_inst": "Nanjing University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.19.20070805", "rel_title": "Epidemiological impact of SARS-CoV-2 vaccination: mathematical modeling analyses", @@ -1536801,93 +1538894,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.04.17.20064469", - "rel_title": "Effectiveness and Safety of Glucocorticoids to Treat COVID-19: A Rapid Review and Meta-Analysis", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20064469", - "rel_abs": "BackgroundGlucocorticoids are widely used in the treatment of various pulmonary inflammatory diseases, but they are also often accompanied by significant adverse reactions. Published guidelines point out that low dose and short duration systemic glucocorticoid therapy may be considered for patients with rapidly progressing COVID-19 while the evidence is still limited.\n\nMethodsWe comprehensively searched electronic databases and supplemented the screening by conducting a manual search. We included RCTs and cohort studies evaluating the effectiveness and safety of glucocorticoids in children and adults with COVID-19, SARS and MERS, and conducted meta-analyses of the main indicators that were identified in the studies.\n\nResultsOur search retrieved 23 studies, including one RCT and 22 cohort studies, with a total of 13,815 patients. In adults with COVID-19, the use of systemic glucocorticoid did not reduce mortality (RR=2.00, 95% CI: 0.69 to 5.75, I2=90.9%) or the duration of lung inflammation (WMD=-1 days, 95% CI: -2.91 to 0.91), while a significant reduction was found in the duration of fever (WMD=-3.23 days, 95% CI: -3.56 to -2.90). In patients with SARS, glucocorticoids also did not reduce the mortality (RR=1.52, 95% CI: 0.89 to 2.60, I2=84.6%), duration of fever (WMD=0.82 days, 95% CI: -2.88 to 4.52, I2=97.9%) or duration of lung inflammation absorption (WMD=0.95 days, 95% CI: -7.57 to 9.48, I2=94.6%). The use of systemic glucocorticoid therapy prolonged the duration of hospital stay in all patients (COVID-19, SARS and MERS).\n\nConclusionsGlucocorticoid therapy was found to reduce the duration of fever, but not mortality, duration of hospitalization or lung inflammation absorption. Long-term use of high-dose glucocorticoids increased the risk of adverse reactions such as coinfections, so routine use of systemic glucocorticoids for patients with COVID-19 cannot be recommend.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Shuya Lu", - "author_inst": "Department of Pediatric, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China" - }, - { - "author_name": "Qi Zhou", - "author_inst": "The First School of Clinical Medicine, Lanzhou University, Lanzhou" - }, - { - "author_name": "Liping Huang", - "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Qianling Shi", - "author_inst": "The First School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Siya Zhao", - "author_inst": "School of Public Health, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Zijun Wang", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Weiguo Li", - "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Yuyi Tang", - "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Yanfang Ma", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Xufei Luo", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Toshio Fukuoka", - "author_inst": "Emergency and Critical Care Center, the Department of General Medicine, Department of Research and Medical Education at Kurashiki Central Hospital, Japan" - }, - { - "author_name": "Hyeong Sik Ahn", - "author_inst": "Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea" - }, - { - "author_name": "Myeong Soo Lee", - "author_inst": "Korea Institute of Oriental Medicine, Daejeon, Korea" - }, - { - "author_name": "Zhengxiu Luo", - "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Enmei Liu", - "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Yaolong Chen", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Chenyan Zhou", - "author_inst": "Department of Pediatric, Sichuan Provincial People Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China" - }, - { - "author_name": "Donghong Peng", - "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.04.13.20064287", "rel_title": "Does TB Vaccination Reduce COVID-19 Infection?: No Evidence from a Regression Discontinuity Analysis", @@ -1537055,6 +1539061,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20064444", + "rel_title": "Effectiveness of Intravenous Immunoglobulin for Children with Severe COVID-19: A Rapid Review", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20064444", + "rel_abs": "BackgroundIntravenous immunoglobulin (IVIG) is usually used as supportive therapy, but the treatment of COVID-19 by IVIG is controversial. This rapid review aims to explore the clinical effectiveness and safety of IVIG in the treatment of children with severe COVID-19.\n\nMethodsWe systematically searched the literature on the use of IVIG in patients with COVID-19, Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS), including both adults and children. We assessed the risk of bias and quality of evidence and reported the main findings descriptively.\n\nResultsA total of 1519 articles were identified by initial literature search, and finally six studies, included one randomized controlled trial (RCT), four case series and one case report involving 198 patients. One case series showed the survival of COVID-19 patients with acute respiratory distress syndrome (ARDS) was not improved by IVIG. One case report showed high-dose IVIG could improve the outcome of COVID-19 adults. Three observational studies showed inconsistent results of the effect of IVIG on SARS patients. One RCT showed that IVIG did not reduce mortality or the incidence of nosocomial infection in adults with severe SARS. The quality of evidence was between low and very low.\n\nConclusionsThe existing evidence is insufficient to support the efficacy or safety of IVIG in the treatment of COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jingyi Zhang", + "author_inst": "School of Public Health, Lanzhou University, Lanzhou 730000, China; Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzho" + }, + { + "author_name": "Yinmei Yang", + "author_inst": "Children Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Nan Yang", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Yanfang Ma", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Qi Zhou", + "author_inst": "The First School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Weiguo Li", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China; National Clinical Research Center for Child Heal" + }, + { + "author_name": "Xia Wang", + "author_inst": "Children Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Liping Huang", + "author_inst": "Children Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Xufei Luo", + "author_inst": "School of Public Health, Lanzhou University, Lanzhou 730000, China; Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzho" + }, + { + "author_name": "Toshio Fukuoka", + "author_inst": "Emergency and Critical Care Center, the Department of General Medicine, Department of Research and Medical Education at Kurashiki Central Hospital, Japan;Adviso" + }, + { + "author_name": "Hyeong Sik Ahn", + "author_inst": "Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea; Korea Cochrane Centre, Korea" + }, + { + "author_name": "Myeong Soo Lee", + "author_inst": "Korea Institute of Oriental Medicine, Daejeon, Korea; University of Science and Technology, Daejeon, Korea" + }, + { + "author_name": "Zhengxiu Luo", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China; National Clinical Research Center for Child Heal" + }, + { + "author_name": "Yaolong Chen", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; Lanzhou University, an Affiliate of the Cochrane Ch" + }, + { + "author_name": "Enmei Liu", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China; National Clinical Research Center for Child Heal" + }, + { + "author_name": "Kehu Yang", + "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Zhou Fu", + "author_inst": "Department of Respiratory Medicine, Children Hospital of Chongqing Medical University, Chongqing 400014, China; National Clinical Research Center for Child Heal" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.17.20064907", "rel_title": "COVID-19 diagnosis and study of serum SARS-CoV-2 specific IgA, IgM and IgG by a quantitative and sensitive immunoassay", @@ -1538271,33 +1540360,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.17.20070052", - "rel_title": "Surveying Tenants of Permanent Supportive Housing in Skid Row about COVID-19", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20070052", - "rel_abs": "Permanent supportive housing (PSH) enrolls highly vulnerable homeless adults who experience early onset of geriatric conditions and require in-home support. Thus, there is potentially a high risk for COVID-19 within PSH, which may necessitate tenants to take protective measures. This study reports on survey results collected from 532 PSH tenants in Los Angeles, California during the 4th week of March in 2020. Results show that nearly all tenants were aware of COVID-19, and 65% considered it to be a very serious health threat. The latter characteristic was a strong predictor of taking protective measures (i.e., handwashing and social distancing). Tenants in units with shared bathroom facilities had lower odds of social distancing than those in studio apartments. Tenants with mental health diagnoses had lower odds of consistent handwashing. Lack of access to food, hygiene items, and medication delivery were commonly reported barriers to sheltering in place.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Benjamin F Henwood", - "author_inst": "USC Suzanne Dworak-Peck School of Social Work, University of Southern California" - }, - { - "author_name": "Brian Redline", - "author_inst": "USC Suzanne Dworak-Peck School of Social Work, University of Southern California" - }, - { - "author_name": "Jack Lahey", - "author_inst": "Skid Row Housing Trust" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.17.20069823", "rel_title": "An ecological study of socioeconomic predictors in detection of COVID-19 cases across neighborhoods in New York City", @@ -1538509,6 +1540571,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.16.20067728", + "rel_title": "Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067728", + "rel_abs": "BackgroundThe role of aerosols in the transmission of SARS-CoV-2 remains debated. We analysed an outbreak involving three non-associated families in Restaurant X in Guangzhou, China, and assessed the possibility of aerosol transmission of SARS-CoV-2 and characterize the associated environmental conditions.\n\nMethodsWe collected epidemiological data, obtained a video record and a patron seating-arrangement from the restaurant, and measured the dispersion of a warm tracer gas as a surrogate for exhaled droplets from the suspected index patient. Computer simulations were performed to simulate the spread of fine exhaled droplets. We compared the in-room location of subsequently infected cases and spread of the simulated virus-laden aerosol tracer. The ventilation rate was measured using the tracer decay method.\n\nResultsThree families (A, B, C), 10 members of which were subsequently found to have been infected with SARS-CoV-2 at this time, or previously, ate lunch at Restaurant X on Chinese New Years Eve (January 24, 2020) at three neighboring tables. Subsequently, three members of family B and two members of family C became infected with SARS-CoV-2, whereas none of the waiters or 68 patrons at the remaining 15 tables became infected. During this occasion, the ventilation rate was 0.75-1.04 L/s per person. No close contact or fomite contact was observed, aside from back-to-back sitting by some patrons. Our results show that the infection distribution is consistent with a spread pattern representative of exhaled virus-laden aerosols.\n\nConclusionsAerosol transmission of SARS-CoV-2 due to poor ventilation may explain the community spread of COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yuguo Li", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Hua Qian", + "author_inst": "Southeast University" + }, + { + "author_name": "Jian Hang", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Xuguang Chen", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Ling Hong", + "author_inst": "Sun Yat-sen University" + }, + { + "author_name": "Peng Liang", + "author_inst": "Ganzi Tibetan Autonomous Prefecture Center for Disease Control and Prevention" + }, + { + "author_name": "Jiansen Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Shenglan Xiao", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Jianjian Wei", + "author_inst": "Zhejiang University" + }, + { + "author_name": "Li Liu", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Min Kang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.17.20069526", "rel_title": "Persistent viral shedding of SARS-CoV-2 in faeces - a rapid review", @@ -1539737,221 +1541858,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.16.20067835", - "rel_title": "Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067835", - "rel_abs": "Rapid and accurate SARS-CoV-2 diagnostic testing is essential for controlling the ongoing COVID-19 pandemic. The current gold standard for COVID-19 diagnosis is real-time RT-PCR detection of SARS-CoV-2 from nasopharyngeal swabs. Low sensitivity, exposure risks to healthcare workers, and global shortages of swabs and personal protective equipment, however, necessitate the validation of new diagnostic approaches. Saliva is a promising candidate for SARS-CoV-2 diagnostics because (1) collection is minimally invasive and can reliably be self-administered and (2) saliva has exhibited comparable sensitivity to nasopharyngeal swabs in detection of other respiratory pathogens, including endemic human coronaviruses, in previous studies. To validate the use of saliva for SARS-CoV-2 detection, we tested nasopharyngeal and saliva samples from confirmed COVID-19 patients and self-collected samples from healthcare workers on COVID-19 wards. When we compared SARS-CoV-2 detection from patient-matched nasopharyngeal and saliva samples, we found that saliva yielded greater detection sensitivity and consistency throughout the course of infection. Furthermore, we report less variability in self-sample collection of saliva. Taken together, our findings demonstrate that saliva is a viable and more sensitive alternative to nasopharyngeal swabs and could enable at-home self-administered sample collection for accurate large-scale SARS-CoV-2 testing.", - "rel_num_authors": 50, - "rel_authors": [ - { - "author_name": "Anne Louise Wyllie", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "John Fournier", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Arnau Casanovas-Massana", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Melissa Campbell", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Maria Tokuyama", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Pavithra Vijayakumar", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Bertie Geng", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "M. Catherine Muenker", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Adam J. Moore", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Chantal B. F. Vogels", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Mary E. Petrone", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Isabel M. Ott", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Peiwen Lu", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Alice Lu-Culligan", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jonathan Klein", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Arvind Venkataraman", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Rebecca Earnest", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Michael Simonov", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Rupak Datta", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Ryan Handoko", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Nida Naushad", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Lorenzo R. Sewanan", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jordan Valdez", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Elizabeth B. White", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Sarah Lapidus", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Chaney C. Kalinich", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Xiaodong Jiang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Daniel J. Kim", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Eriko Kudo", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Melissa Linehan", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Tianyang Mao", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Miyu Moriyama", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Ji Eun Oh", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Annsea Park", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Julio Silva", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Eric Song", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Takehiro Takahashi", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Manabu Taura", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Orr-El Weizman", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Patrick Wong", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Yexin Yang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Santos Bermejo", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Camila Odio", - "author_inst": "Yale-New Haven Health" - }, - { - "author_name": "Saad B. Omer", - "author_inst": "Yale University, Yale Institute of Global Health" - }, - { - "author_name": "Charles S. Dela Cruz", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Shelli Farhadian", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Richard A. Martinello", - "author_inst": "Yale School of Medicine, Yale-New Haven Health" - }, - { - "author_name": "Akiko Iwasaki", - "author_inst": "Yale University, Howard Hughes Medical Institute" - }, - { - "author_name": "Nathan D. Grubaugh", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Albert I. Ko", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.17.20068577", "rel_title": "Aerosolized Hydrogen Peroxide Decontamination of N95 Respirators, with Fit-Testing and Virologic Confirmation of Suitability for Re-Use During the COVID-19 Pandemic", @@ -1540183,6 +1542089,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20069898", + "rel_title": "A multivariate spatiotemporal spread model of COVID-19 using ensemble of ConvLSTM networks", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069898", + "rel_abs": "The high R-naught factor of SARS-CoV-2 has created a race against time for mankind and it necessitates rapid containment actions to control the spread. In such scenario short term accurate spatiotemporal predictions can help understanding the dynamics of the spread in a geographic region and identify hotspots. However due to the novelty of the disease there is very little disease specific data generated yet. This poses a difficult problem for machine learning methods to learn a model of the epidemic spread from data. A proposed ensemble of convolutional LSTM based spatiotemporal model can forecast the spread of the epidemic with high resolution and accuracy in a large geographic region. A data preparation method is proposed to convert available spatial causal features into set of 2D images with or without temporal component. The model has been trained with available data for USA and Italy. It achieved 5.57% and 0.3% mean absolute percent error for total number of predicted infection cases in a 5day prediction period for USA and Italy respectively.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "swarna kamal paul", + "author_inst": "Tata Consultancy Services" + }, + { + "author_name": "Saikat Jana", + "author_inst": "Tata Consultancy Services" + }, + { + "author_name": "Parama Bhaumik", + "author_inst": "Jadavpur University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.17.20069724", "rel_title": "A Retrospective Analysis of Clinical Recovery-Period of the First 1000 COVID-19 Patients in Singapore for Estimating Recovery Rate", @@ -1541243,37 +1543176,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.19.20071852", - "rel_title": "A Bayesian analysis of the total number of cases of the COVID 19 when only a few data is available. A case study in the state of Goias, Brazil", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071852", - "rel_abs": "The outbreak of COVID 19 has been provoking several problems to the health system around the world. One of the concerning is the crash of the health system due to the increasing demand suddenly. To avoid it, knowing the total number and daily new cases is crucial. In this study, we fitted curves growth models using a Bayesian approach. We extracted information obtained from some countries to build the prior distribution of the model. The total number of cases of the COVID 19 in the state of Goias was analyzed. Results from analysis indicated that the date of the outbreak peak is between 51 and 68 days after the beginning. Moreover, the total number of cases is around 3180 cases. The analysis did not take into consideration possibles changes in government control measures. We hope this study can provide some valuable information to public health management.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Renato Rodrigues Silva", - "author_inst": "Federal University of Goias" - }, - { - "author_name": "Wisley Donizetti Velasco", - "author_inst": "Health Department of the State of Goias" - }, - { - "author_name": "Wanderson da Silva Marques", - "author_inst": "Health Department of the State of Goias" - }, - { - "author_name": "Carlos Augusto Goncalves Tibirica", - "author_inst": "Health Department of the State of Goias" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.19.20071951", "rel_title": "Seasonality and uncertainty in COVID-19 growth rates", @@ -1541461,6 +1543363,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.20071928", + "rel_title": "Lies, Gosh Darn Lies, and Not Enough Good Statistics: Why Epidemic Model Parameter Estimation Fails", + "rel_date": "2020-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20071928", + "rel_abs": "An opportunity exists in exploring epidemic modeling as a novel way to determine physiological and demic parameters for genetic association studies on a population/environmental (quasi) epidemiological study level. First, the spread of SARS-COV-2 has produced population specific lineages; second, epidemic spread model parameters are tied directly to these physiological and demic rates (e. g. incubation time, recovery time, transmission rate); and third, these parameters may serve as novel phenotypes to associate with region-specific genetic mutations as well as demic characteristics (e. g. age structure, cultural observance of personal space, crowdedness). Therefore, we sought to understand whether the parameters of epidemic models could be determined from the trajectory of infections, recovery, and hospitalizations prior to peak, and also to evaluate the quality and comparability of data between jurisdictions reporting their statistics necessary for the analysis of model parameters across populations. We found that, analytically, the pre-peak growth of an epidemic is limited by a subset of the model variates, and that the rate limiting variables are dominated by the expanding eigenmode of their equations. The variates quickly converge to the ratio of eigenvector components of the positive growth rate, which determines the doubling time. There are 9 parameters and 4 independent components in the eigenmode, leaving 5 undetermined parameters. Those parameters can be strikingly population dependent, and can have significant impact on estimates of hospital loads downstream. Without a sound framework, measurements of infection rates and other parameters are highly corrupted by uneven testing rates to uneven counting and reporting of relevant values. From the standpoint of phenotype parameters, this means that structured experiments must be performed to estimate these parameters in order to perform genetic association studies, or to construct viable models that accurately predict critical quantities such as hospitalization loads.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Daniel E Platt", + "author_inst": "IBM" + }, + { + "author_name": "Laxmi E Parida", + "author_inst": "IBM Research" + }, + { + "author_name": "Pierre Zalloua", + "author_inst": "TH Chan Harvard School of Public Health; School of Medicine, Lebanese American University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.17.20070284", "rel_title": "COVID-19: An Update on the Epidemiological, Genomic Origin, Phylogenetic study, Indiacentric to Worldwide current status", @@ -1542765,29 +1544694,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.16.20066159", - "rel_title": "Susceptibility and Sustainability of India against CoVid19: a multivariate approach", - "rel_date": "2020-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20066159", - "rel_abs": "PurposeWe are currently in the middle of a global crisis. Covid19 pandemic has suddenly threatened the existence of human life. Till date, as no medicine or vaccine is discovered, the best way to fight against this pandemic is prevention. The impact of different environmental, social, economic and health parameters is unknown and under research. It is important to identify the factors which can weaken the virus, and the nations which are more vulnerable to this virus.\n\nMaterials and MethodsData of weather, vaccination trends, life expectancy, lung disease, number of infected people in the pre-lockdown and post-lockdown period of highly infected nations are collected. These are extracted from authentic online resources and published reports. Analysis is done to find the possible impact of each parameter on CoVid19.\n\nResultsCoVid19 has no linear correlation with any of the selected parameters, though few parameters have depicted non-linear relationship in the graphs. Further investigations have shown better result for some parameters. A combination of the parameters results in a better correlation with infection rate.\n\nConclusionsThough depending on the study outcome, the impact of CoVid19 in India can be predicted, the required lockdown period cannot be calculated due to data limitation.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Soumi Ray", - "author_inst": "IIT Roorkee" - }, - { - "author_name": "Mitu Roy", - "author_inst": "Haldia Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.16.20067553", "rel_title": "Early forecasts of the evolution of the COVID-19 outbreaks and quantitative assessment of the effectiveness of countering measures.", @@ -1543039,6 +1544945,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2020.04.17.20060251", + "rel_title": "Two patients with acute meningo-encephalitis concomitant to SARS-CoV-2 infection", + "rel_date": "2020-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20060251", + "rel_abs": "Human coronaviruses are known for their tropism for central nervous system and to be associated with neurological complications. SARS-CoV-2 pandemy represent a major health issue and if respiratory symptoms are at the forefront, neurological symptoms should be expected. Here we report the case of two patient that developed encephalitic symptoms with neuropsychological impairment and pathologic cerebrospinal fluid features concomitantly to SARS-CoV-2 documented infection. Both patient recovered promptly without treatment. This report raises the question of central nervous system involvement in SARS-CoV-2 infection and the need for investigation of neuropsychological complications in infected patient.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Raphael Bernard-Valnet", + "author_inst": "Centre Hospitalier Universitaire Vaudois, Lausanne, CH" + }, + { + "author_name": "Beatrice Pizzarotti", + "author_inst": "Centre Hospitalier Universitaire Vaudois, Lausanne, CH" + }, + { + "author_name": "Angelica Anichini", + "author_inst": "Centre Hospitalier Universitaire Vaudois, Lausanne, CH" + }, + { + "author_name": "Yoris Demars", + "author_inst": "Centre Hospitalier Universitaire Vaudois, Lausanne, CH" + }, + { + "author_name": "Enrico Russo", + "author_inst": "Centre Hospitalier Universitaire Vaudois, Lausanne, CH" + }, + { + "author_name": "Marie Schmidhauser", + "author_inst": "Centre Hospitalier Universitaire Vaudois, Lausanne, CH" + }, + { + "author_name": "Jonathan Cerruti-Sola", + "author_inst": "Centre Hospitalier Universitaire Vaudois, Lausanne, CH" + }, + { + "author_name": "Andrea O. Rossetti", + "author_inst": "Centre Hospitalier Universitaire Vaudois, Lausanne, CH" + }, + { + "author_name": "Renaud Du Pasquier", + "author_inst": "Centre Hospitalier Universitaire Vaudois, Lausanne, CH" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.04.16.20068148", "rel_title": "COVID-19-Associated Acute Disseminated Encephalomyelitis: A Case Report", @@ -1544787,53 +1546744,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2020.04.15.20067066", - "rel_title": "Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys", - "rel_date": "2020-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20067066", - "rel_abs": "Establishing how many people have already been infected by SARS-CoV-2 is an urgent priority for controlling the COVID-19 pandemic. Patchy virological testing has hampered interpretation of confirmed case counts, and unknown rates of asymptomatic and mild infections make it challenging to develop evidence-based public health policies. Serological tests that identify past infection can be used to estimate cumulative incidence, but the relative accuracy and robustness of various sampling strategies has been unclear. Here, we used a flexible framework that integrates uncertainty from test characteristics, sample size, and heterogeneity in seroprevalence across tested subpopulations to compare estimates from sampling schemes. Using the same framework and making the assumption that serological positivity indicates immune protection, we propagated these estimates and uncertainty through dynamical models to assess the uncertainty in the epidemiological parameters needed to evaluate public health interventions. We examined the relative accuracy of convenience samples versus structured surveys to estimate population seroprevalence and found that sampling schemes informed by demographics and contact networks outperform uniform sampling. The framework can be adapted to optimize the design of serological surveys given particular test characteristics and capacity, population demography, sampling strategy, and modeling approach, and can be tailored to support decision-making around introducing or removing interventions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Daniel B Larremore", - "author_inst": "University of Colorado Boulder" - }, - { - "author_name": "Bailey K Fosdick", - "author_inst": "Colorado State University" - }, - { - "author_name": "Kate M Bubar", - "author_inst": "University of Colorado Boulder" - }, - { - "author_name": "Sam Zhang", - "author_inst": "University of Colorado Boulder" - }, - { - "author_name": "Stephen M Kissler", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "C. Jessica E. Metcalf", - "author_inst": "Princeton University" - }, - { - "author_name": "Caroline Buckee", - "author_inst": "Harvard School of Public Health" - }, - { - "author_name": "Yonatan Grad", - "author_inst": "Harvard T. H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.15.20066407", "rel_title": "Evaluation of antibody testing for SARS-Cov-2 using ELISA and lateral flow immunoassays", @@ -1545273,6 +1547183,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.15.20066100", + "rel_title": "Estimation of true number of COVID-19 infected people in Japan using LINE questionnaire", + "rel_date": "2020-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066100", + "rel_abs": "The authors estimated the true number of COVID-19 infected people in Japan using the LINE questionnaire data and the PCR test results. A statistically significant correlation was observed between the infection rate per prefecture with PCR test and the rate of high fever. Using this correlation, true number of COVID-19 infected people in Japan was estimated approximately twenty thousand ({+/-}ten thousand) as of April 1, 2020.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Shin-ichiro Tanaka", + "author_inst": "Osaka University" + }, + { + "author_name": "Shinya Oku", + "author_inst": "Die Revolution Group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.15.20066845", "rel_title": "Why lockdown? Simplified arithmetic tools for decision-makers, health professionals, journalists and the general public to explore containment options for the novel coronavirus", @@ -1546549,73 +1548482,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.04.16.045419", - "rel_title": "Synthetic nanobodies targeting the SARS-CoV-2 receptor-binding domain", - "rel_date": "2020-04-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.16.045419", - "rel_abs": "The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has resulted in a global health and economic crisis of unprecedented scale. The high transmissibility of SARS-CoV-2, combined with a lack of population immunity and prevalence of severe clinical outcomes, urges the rapid development of effective therapeutic countermeasures. Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2. In an expeditious process taking only twelve working days, sybodies were selected entirely in vitro from three large combinatorial libraries, using ribosome and phage display. We obtained six strongly enriched sybody pools against the isolated RBD and identified 63 unique anti-RBD sybodies which also interact in the context of the full-length SARS-CoV-2 spike ectodomain. Among the selected sybodies, six were found to bind to the viral spike with double-digit nanomolar affinity, and five of these also showed substantial inhibition of RBD interaction with human angiotensin-converting enzyme 2 (ACE2). Additionally, we identified a pair of anti-RBD sybodies that can simultaneously bind to the RBD. It is anticipated that compact binders such as these sybodies could feasibly be developed into an inhalable drug that can be used as a convenient prophylaxis against COVID-19. Moreover, generation of polyvalent antivirals, via fusion of anti-RBD sybodies to additional small binders recognizing secondary epitopes, could enhance the therapeutic potential and guard against escape mutants. We present full sequence information and detailed protocols for the identified sybodies, as a freely accessible resource.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Justin D Walter", - "author_inst": "Institute of Medical Microbiology, University of Zurich" - }, - { - "author_name": "Cedric A.J. Hutter", - "author_inst": "Institute of Medical Microbiology, University of Zurich" - }, - { - "author_name": "Iwan Zimmermann", - "author_inst": "Institute of Medical Microbiology, University of Zurich and Linkster Therapeutics AG, Zurich" - }, - { - "author_name": "Marianne Wyss", - "author_inst": "Division of Experimental and Clinical Research, Vetsuisse Faculty, University of Bern, Switzerland" - }, - { - "author_name": "Pascal Egloff", - "author_inst": "Institute of Medical Microbiology, University of Zurich and Linkster Therapeutics AG, Zurich" - }, - { - "author_name": "Mich\u00e8le Sorgenfrei", - "author_inst": "Institute of Medical Microbiology, University of Zurich" - }, - { - "author_name": "Lea M H\u00fcrlimann", - "author_inst": "Institute of Medical Microbiology, University of Zurich" - }, - { - "author_name": "Imre Gonda", - "author_inst": "Institute of Medical Microbiology, University of Zurich" - }, - { - "author_name": "Gianmarco Meier", - "author_inst": "Institute of Medical Microbiology, University of Zurich" - }, - { - "author_name": "Sille Remm", - "author_inst": "Institute of Medical Microbiology, University of Zurich" - }, - { - "author_name": "Sujani Thavarasah", - "author_inst": "Institute of Medical Microbiology, University of Zurich" - }, - { - "author_name": "Philippe Plattet", - "author_inst": "Division of Experimental and Clinical Research, Vetsuisse Faculty, University of Bern, Switzerland" - }, - { - "author_name": "Markus A Seeger", - "author_inst": "Institute of Medical Microbiology, University of Zurich" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.04.13.20064295", "rel_title": "Benefits and Risks of Chloroquine and Hydroxychloroquine in The Treatment of Viral Diseases: A Meta-Analysis of Placebo Randomized Controlled Trials", @@ -1546863,6 +1548729,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.17.046185", + "rel_title": "Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies.", + "rel_date": "2020-04-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.17.046185", + "rel_abs": "The recent severe acute respiratory syndrome, known as Corona Virus Disease 2019 (COVID-19) has spread so much rapidly and severely to induce World Health Organization (WHO) to declare state of emergency over the new coronavirus SARS-CoV-2 pandemic. While several countries have chosen the almost complete lock-down for slowing down SARS-CoV-2 spread, scientific community is called to respond to the devastating outbreak by identifying new tools for diagnosis and treatment of the dangerous COVID-19. With this aim we performed an in silico comparative modeling analysis, which allows to gain new insights about the main conformational changes occurring in the SARS-CoV-2 spike protein, at the level of the receptor binding domain (RBD), along interactions with human cells angiotensin converting enzyme 2 (ACE2) receptor, that favour human cell invasion. Furthermore, our analysis provides i) an ideal pipeline to identify already characterized antibodies that might target SARS-CoV-2 spike RBD, for preventing interactions with the human ACE2, and ii) instructions for building new possible neutralizing antibodies, according to chemical/physical space restraints and complementary determining regions (CDR) mutagenesis of the identified existing antibodies. The proposed antibodies show in silico a high affinity for SARS-CoV-2 spike RBD and can be used as reference antibodies also for building new high affinity antibodies against present and future coronavirus able to invade human cells through interactions of their spike proteins with the human ACE2. More in general, our analysis provides indications for the set-up of the right biological molecular context for investigating spike RBD-ACE2 interactions for the development of new vaccines, diagnosis kits and other treatments based on the usage or the targeting of SARS-CoV-2 spike protein.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ivan Mercurio", + "author_inst": "University of Bari" + }, + { + "author_name": "Vincenzo Tragni", + "author_inst": "University of Bari" + }, + { + "author_name": "Francesco Busto", + "author_inst": "University of Bari" + }, + { + "author_name": "Anna De Grassi", + "author_inst": "University of Bari" + }, + { + "author_name": "Ciro Leonardo Pierri", + "author_inst": "University of Bari" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.16.043224", "rel_title": "Transcriptional Difference between SARS-COV-2 and other Human Coronaviruses Revealed by Sub-genomic RNA Profiling", @@ -1548375,29 +1550276,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.15.20065425", - "rel_title": "A consideration of publication-derived immune-related associations in Coronavirus and related lung damaging diseases", - "rel_date": "2020-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20065425", - "rel_abs": "The severe acute respiratory syndrome virus SARS-CoV-2, a close relative of the SARS-CoV virus, is the cause of recent COVID-19 pandemic affecting, to date, nearly 2 million individuals across the globe and demonstrating relatively high rates of infection and mortality. A third virus, the H5N1, responsible for avian influenza, has caused infection with some clinical similarities to those in COVID-19 infections.\n\nCytokines, small proteins that modulate immune responses, have been directly implicated in some of the severe responses seen in COVID-19 patients, e.g. cytokine storms.\n\nUnderstanding the immune processes related to COVID-19, and other similar infections, could help identify diagnostic markers and therapeutic targets.\n\nHere we examine data of cytokine, immune cell types, and disease associations captured from biomedical literature associated with coronavirus, SARS, and H5N1 influenza, with the objective of identifying potentially useful relationships and areas for future research. Cytokine and cell-type associations captured from MeSH terms linked to thousands of PubMed abstracts, has identified differing patterns of associations between the three corpuses of abstracts (coronavirus, SARS, or H5N1 influenza). Clustering of cytokine-disease co-occurrences in the context of coronavirus has identified compelling clusters of co-morbidities and symptoms, some of which already known to be linked to COVID-19. Finally, network analysis identified sub-networks of cytokines and immune cell types associated with different manifestations, co-morbidities and symptoms of coronavirus, SARS, and H5N1.\n\nSystematic review of research in medicine is essential to facilitate evidence-based choices about health interventions. In a fast moving pandemic the approach taken here will identify trends and enable rapid comparison to the literature of related diseases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Nophar Geifman", - "author_inst": "University of Manchester" - }, - { - "author_name": "Anthony D Whetton", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.15.20065995", "rel_title": "SARS-Cov-2 RNA Found on Particulate Matter of Bergamo in Northern Italy: First Preliminary Evidence", @@ -1548613,6 +1550491,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.14.20065896", + "rel_title": "Significantly longer Covid-19 incubation times for the elderly, from a case study of 136 patients throughout China", + "rel_date": "2020-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065896", + "rel_abs": "ObjectiveTo infer Covid-19 incubation time distribution from a large sample.\n\nMethodBased on individual case data published online by 21 cities of China, we investigated a total of 136 COVID-19 patients who traveled to Hubei from 21 cities of China between January 5 and January 31, 2020, remained there for 48 hours or less, and returned to these cities with onset of symptoms between January 10 and February 6, 2020. Among these patients, 110 were found to be aged 15 - 64, 22 aged 65 - 86, and 4 aged under 15.\n\nFindingsThe differential incubation time histogram of the two age groups 15 - 64 and 65 - 86 are adequately fitted by the log normal model. For the 15 - 64 age group, the median incubation time of [Formula] days (uncertainties are 95 -0.90 % CL) is broadly consistent with previous literature. For the 65-86 age group, the median is [Formula] days is statistically significantly longer. Moreover, for -2.0 this group, the 95 % confidence contour indicates the data cannot constrain the upper bound of the log normal parameters {micro}, {sigma} by failing to close there; this is because the sample has a maximum incubation time of 17 days, beyond which we ran out of data even though the histogram has not yet peaked. Thus there is the potential of a much longer incubation time for the 65-86 age group than 10 - 14 days. Only a much larger sample can settle this.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ally Bi-zhu Jiang", + "author_inst": "Shenzhen RAK wireless Technology Co., Ltd., China" + }, + { + "author_name": "Richard Lieu", + "author_inst": "Department of Physics and Astronomy, University of Alabama in Huntsville, Huntsville, AL 35899, USA" + }, + { + "author_name": "Siobhan Quenby", + "author_inst": "Division of Reproductive Health, Warwick Medical School, The University of Warwick, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.15.20066431", "rel_title": "Estimating the early death toll of COVID-19 in the United States", @@ -1549985,37 +1551890,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.13.20063412", - "rel_title": "Analysis of COVID-19 spread in South Korea using the SIR model with time-dependent parameters and deep learning", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063412", - "rel_abs": "Mathematical modeling is a process aimed at finding a mathematical description of a system and translating it into a relational expression. When a system is continuously changing over time (e.g., infectious diseases) differential equations, which may include parameters, are used for modeling the system. The process of finding those parameters that best fit the given data from the system is called an inverse problem. This study aims at analyzing the novel coronavirus infection (COVID-19) spread in South Korea using the susceptible-infected-recovered (SIR) model. We collect the data from Korea Centers for Disease Control & Prevention (KCDC). We assume that each parameter in the SIR model is a function of time so that we can compute important parameters, such as the basic reproduction number (R0), more delicately. Using neural networks, we propose a method to find the best time-varying parameters and the solution for the model simultaneously. Moreover, using time-dependent parameters, we find that traditional numerical algorithms, such as the Runge-Kutta methods, can successfully approximate the SIR model while fitting the COVID-19 data, thus modeling the propagation patterns of COVID-19 more precisely.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Hyeontae Jo", - "author_inst": "POSTECH" - }, - { - "author_name": "Hwijae Son", - "author_inst": "POSTECH" - }, - { - "author_name": "Se Young Jung", - "author_inst": "Seoul National University Bundang Hospital" - }, - { - "author_name": "Hyung Ju Hwang", - "author_inst": "POSTECH" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.14.20065375", "rel_title": "Informing Homemade Emergency Facemask Design: The Ability of Common Fabrics to Filter Ultrafine Particles", @@ -1550271,6 +1552145,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.04.14.20064808", + "rel_title": "Coronavirus PPE: a positive pressure hood assembled from ubiquitous,low-cost materials", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20064808", + "rel_abs": "A positive pressure protective hood system was purposefully constructed only from materials commonly found worldwide, including bendable aluminum mesh, elastic head straps, velcro tape, a plastic sheet, a furnace filter and two computer central processing unit (CPU) cooling fans. The practical advantages of this system are that the materials are readily available in the inventories of most electronics and hardware outlets, ease of assembly (particularly if choosing to employ 3D printing for the fan enclosure and/or making several units at once with a defined workflow), and high probability of the materials being available in current or prospective personal protective equipment (PPE)-deplete regions. An experiment with identical fire detectors showed adequate inner isolation of the hood prototype from paper combustion particulates, which have a size range slightly smaller than putative coronavirus aerosols, for at least 90 seconds. The theoretical advantages of this system include significant reduction in healthcare provider exposure to coronavirus-containing respiratory fomites, respiratory droplets and aerosols (vs. traditional static masks and shields) during high risk procedures such as endotracheal intubation or routine care of an upright and coughing patient. Additionally, the assembly eliminates contact exposure to coronavirus fomites due to whole-head coverage from a hood system.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mark A Crawford", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.04.15.20066068", "rel_title": "The socio-economic determinants of the coronavirus disease (COVID-19) pandemic", @@ -1551343,33 +1553236,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.14.20065300", - "rel_title": "The Easter and Passover Blip in New York City", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065300", - "rel_abs": "Abstract and Executive SummaryWhen it comes to pandemics such as the currently present COVID-19 [1], various issues and problems arise for infrastructures and institutions. Due to possible extreme effects, such as hospitals potentially running out of beds or medical equipment, it is essential to lower the infection rate to create enough space to attend to the affected people and allow enough time for a vaccine to be developed. Unfortunately, this requires that measures put into place are upheld long enough to reduce the infection rate sufficiently.\n\nIn this paper, we describe research simulating the influences of the contact rate on the spread of the pandemic using New York City as an example (Section IV) and especially already observed effects of contact rate increases during holidays [2-4] (Section V). In multiple simulations scenarios for Passover and Easter holidays, we evaluated 25%, 50%, 75%, and 100% temporary increases in contact rates using a scenario close to the currently reported numbers as reference and contact rates based on bioterrorism research as a \"normal\" baseline for NYC.\n\nThe first general finding from the simulations is that singular events of increased visits/contacts amplify each other disproportionately if they are happening in close proximity (time intervals) together. The second general observation was that contact rate spikes leave a permanently increased and devastating infection rate behind, even after the contact rate returns to the reduced one. In case of a temporary sustained increase of contact rate for just three days in a row, the aftermath results in an increase of infection rate up to 40%, which causes double the fatalities in the long run.\n\nIn numbers, given that increases of 25% and 50% seem to be most likely given the data seen in Germany for the Easter weekend for example [2, 3], our simulations show the following increases (compared to the realistic reference run): for a temporary 25% surge in contact rate, the total cases grew by 215,880, the maximum of required hospitalizations over time increased to 63,063, and the total fatalities climbed by 8,844 accumulated over 90 days. As for the 50% surge, we saw the total number of cases rise by 461,090, the maximum number of required hospitalizations increase to 79,733, and the total number of fatalities climb by 19,125 over 90 days in NYC.\n\nAll in all, we conclude that even very short, temporary increases in contact rates can have disproportionate effects and result in unrecoverable phenomena that can hardly be reversed or managed later. The numbers show possible phenomena before they might develop effects in reality. This is important because phenomena such as the described blip can impact the hospitals in reality. Therefore, we warn that a wave of infections due to increased contact rates during Passover/Easter might come as a result!", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Maximilian Vierlboeck", - "author_inst": "Stevens Institute of Technology" - }, - { - "author_name": "Roshanak R Nilchiani", - "author_inst": "Stevens Institute of Technology" - }, - { - "author_name": "Christine M Edwards", - "author_inst": "Stevens Institute of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.14.20065318", "rel_title": "State-level variation of initial COVID-19 dynamics in the United States: The role of local government interventions", @@ -1551509,6 +1553375,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.14.20065698", + "rel_title": "Using Feedback on Symptomatic Infections to Contain the Coronavirus Epidemic: Insight from a SPIR Model", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065698", + "rel_abs": "A study is presented on the use of real-time information about symptomatic infectious individuals to adjust restrictions of human contacts at two basic levels, the stricter being on the symptomatic infectious group. Explicit analytical formulas as well as numerical results are presented to rapidly elucidate what-if questions on averting resurgence of the coronavirus epidemic after the first wave wanes. Implementation of related ideas would rely on a mix of several factors, including personal initiative and sophisticated technology for monitoring and testing. For robust decision making on the subject, detailed multidisciplinary studies remain indispensable.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Michael Nikolaou", + "author_inst": "University of Houston" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.11.20054643", "rel_title": "Improving Coronavirus (COVID-19) Diagnosis using Deep Transfer Learning", @@ -1552541,69 +1554426,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.14.20059733", - "rel_title": "Distinct early IgA profile may determine severity of COVID-19 symptoms: an immunological case series", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20059733", - "rel_abs": "SARS-CoV-2 is the causative agent of COVID-19 and is a severe threat to global health. Patients infected with SARS-CoV-2 show a wide range of symptoms and disease severity, while limited data is available on its immunogenicity.\n\nHere, the kinetics of the development of SARS-CoV-2-specific antibody responses in relation to clinical features and dynamics of specific B-cell populations are reported. Immunophenotyping of B cells was performed by flow cytometry with longitudinally collected PBMCs. In parallel, serum samples were analyzed for the presence of SARS-CoV-2-specific IgA, IgG, and IgM antibodies using whole proteome peptide microarrays. Soon after disease onset in a mild case, we observed an increased frequency of plasmablasts concomitantly with a strong SARS-CoV-2-specific IgA response. In contrast, a case with more severe progression showed a delayed, but eventually very strong and broad SARS-CoV-2-specific IgA response.\n\nThis case study shows that determining SARS-CoV-2-specific antibody epitopes can be valuable to monitor the specificity and magnitude of the early B-cell response, which could guide the development of vaccine candidates. Follow-up studies are required to evaluate whether the kinetics and strength of the SARS-CoV-2-specific IgA response could be potential prognostic markers of viral control.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Christine Dahlke", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Jasmin Heidepriem", - "author_inst": "Max Planck Institute of Colloids and Interfaces" - }, - { - "author_name": "Robin Kobbe", - "author_inst": "University Medical Center Eppendorf" - }, - { - "author_name": "Rene Santer", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Till Koch", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Anahita Fathi", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "My L. Ly", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Stefan Schmiedel", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Peter H. Seeberger", - "author_inst": "Max Planck Institute of Colloids and Interfaces" - }, - { - "author_name": "ID-UKE COVID-19 study group", - "author_inst": "" - }, - { - "author_name": "Marylyn M. Addo", - "author_inst": "University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Felix F. Loeffler", - "author_inst": "Max Planck Institute of Colloids and Interfaces" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.12.20061929", "rel_title": "Ad-hoc Assembly of Lean Extracorporeal Membrane Oxygenation Systems for COVID-19", @@ -1552723,6 +1554545,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.11.20062232", + "rel_title": "BCG VACCINES MAY NOT REDUCE COVID-19 MORTALITY RATES", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20062232", + "rel_abs": "The reason for the observed country-wise variability in incidence and severity of the COVID-19 outcome remains unknown. Few recent studies have suggested a positive protective correlation of the BCG vaccination policy of the countries with the observed COVID-19 severity. The current study was undertaken to reassess the existing data as of 4th April 2020. The incidence rates (cases per million population), Case Fatality Rates (CFR) and inherently more robust Infection Fatality Rates (IFR) were calculated across countries accounting for about 99% COVID-19 deaths. The initial scrutiny suggested a weaker association with BCG vaccination policy or BCG coverage, so positivity to the Tuberculin Sensitivity Test (TST)/ Interferon Gamma Release Assay (IGRA) as a measure of the potential protective effect of the resident populations exposure to Mycobacterium spp. whether from BCG vaccination or as a result of exposure to environmental mycobacteria was analyzed. The incidence rates (the number of cases per million population) decreased with an increase in % LTBI (TST/IGRA positivity) for the analyzed countries with R2 =0.6343, suggesting an exponentially negative covariation. However, the covariation of CFR estimates that ranged from 0.29% to 12.25 % (average 5.39%) among countries, was tenuous. Interim estimates of IFR (i-IFR), a more dependable measure for such studies, for the best and worst-case scenarios, i.e., i-IFR-l and i-IFR-h, predict on an average 20.57% to 30.15 % COVID-19 fatality rates globally, but individual country estimates display huge variation. Among countries accounting for 92.14% deaths (11 countries; top 20% countries included in current study) the estimate for lowest IFRs (i-IFR-l=4.16 (China) & i-IFR-h=4.61 (China)) and highest IFRs (i-IFR-l=96.39% (UK); & i-IFR-h=96.54% (UK)) displayed huge difference (average for the group: CFR=6.8{+/-}3.6%; i-IFR-l=34.97{+/-}30.55%; & i-IFR-h=44.20{+/-}29.08%). Currently, the worst affected countries Italy (CFR=12.25%; i-IFR-l=42.63%; i-IFR-h=48.69%) and Spain (CFR=9.39%; i- IFR-l=26.85%; i-IFR-h=36.60%) would seemingly cope with COVID-19 better than UK, Netherlands and USA while the countries Germany (CFR=1.40%; i-IFR-l=4.93%; i-IFR-h=17.49%) and Switzerland (CFR=3.01%; i-IFR-l=10.87%; i-IFR-h=16.23%) along with China could fare the best. The rest of the 80% countries (accounting for 6.74% deaths), seemed to have reduced mortality (CFR=2.45{+/-}2.01; i-IFR-l= 30.62{+/-}28.24%; i-IFR-h=40.99{+/-}30.47%) with associated high % LTBI (17.28{+/-}8.87) than top 20% countries. The inherent issues in the data set (e.g., heterogeneity, non- random sampling, different criteria of sampling and reporting, access to health care, genetic composition, underlying co-morbidities, etc) need to be taken into account for making informed decisions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Samer Singh", + "author_inst": "Institute of Medical Sciences, Banaras Hindu University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.13.20063099", "rel_title": "Comparison of psychological distress and demand induced by COVID-19 during the lockdown period in patients undergoing peritoneal dialysis and hemodialysis: a cross-section study in a tertiary hospital", @@ -1553699,29 +1555540,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.12.20062927", - "rel_title": "MARKOVIAN RANDOM WALK MODELING AND VISUALIZATION OF THE EPIDEMIC SPREAD OF COVID-19", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20062927", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe epidemic spread of CoVID-19 has resulted in confirmed cases of viral respiratory illness in more than 1.4 million people around the world as of April 7th, 2020 [1]. However, different regions have experienced the spread of this disease differently. Here, we develop a Markovian random-walk spatial extension of a quarantine-enhanced SIR model to measure, visualize and forecast the effect of susceptible population density, testing rate, and social distancing and quarantine policies on epidemic spreading. The model is used to simulate the spread of CoVID-19 in the regions of Hubei, China; South Korea; Iran; and Spain. The model allows for evaluating the results of different policies both quantitatively and visually as means of better understanding and controlling the spread of the disease.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Haluk Akay", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "George Barbastathis", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.13.20062760", "rel_title": "Estimates of regional infectivity of COVID-19in the United Kingdom following imposition of social distancingmeasures", @@ -1553985,6 +1555803,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.13.20063305", + "rel_title": "Nowcasting and Forecasting the Spread of COVID-19 and Healthcare Demand In Turkey, A Modelling Study", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063305", + "rel_abs": "BackgroundThis study aims to estimate the total number of infected people, evaluate the effects of NPIs on the healthcare system, and predict the expected number of cases, deaths, hospitalizations due to COVID-19 in Turkey.\n\nMethodsThis study was carried out according to three dimensions. In the first, the actual number of infected people was estimated. In the second, the expected total numbers of infected people, deaths, hospitalizations have been predicted in the case of no intervention. In the third, the distribution of the expected number of infected people and deaths, and ICU and non-ICU bed needs over time has been predicted via a SEIR-based simulator (TURKSAS) in four scenarios.\n\nResultsAccording to the number of deaths, the estimated number of infected people in Turkey on March 21 was 123,030. In the case of no intervention the expected number of infected people is 72,091,595 and deaths is 445,956, the attack rate is 88 {middle dot} 1%, and the mortality ratio is 0{middle dot}54%. The ICU bed capacity in Turkey is expected to be exceeded by 4{middle dot}4-fold and non-ICU bed capacity by 3{middle dot}21-fold. In the second and third scenarios compliance with NPIs makes a difference of 94,303 expected deaths. In both scenarios, the predicted peak value of occupied ICU and non-ICU beds remains below Turkeys capacity.\n\nDiscussionPredictions show that around 16 million people can be prevented from being infected and 94,000 deaths can be prevented by full compliance with the measures taken. Modelling epidemics and establishing decision support systems is an important requirement.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Seyma Arslan", + "author_inst": "Istanbul University, Istanbul Medical Faculty, Public Health Department" + }, + { + "author_name": "Muhammed Yusuf Ozdemir", + "author_inst": "Queen Mary University of London, Centre for Primary Care and Public Health" + }, + { + "author_name": "Abdullah Ucar", + "author_inst": "Istanbul University, Health Sciences Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.13.20063479", "rel_title": "Machine Learning Analysis of Chest CT Scan Images as a Complementary Digital Test of Coronavirus (COVID-19) Patients", @@ -1554777,77 +1556622,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.12.20062943", - "rel_title": "Incidence, clinical outcomes, and transmission dynamics of hospitalized 2019 coronavirus disease among 9,596,321 individuals residing in California and Washington, United States: a prospective cohort study", - "rel_date": "2020-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20062943", - "rel_abs": "BackgroundThe United States is now the country reporting the highest number of 2019 coronavirus disease (COVID-19) cases and deaths. However, little is known about the epidemiology and burden of severe COVID-19 to inform planning within healthcare systems and modeling of intervention impact.\n\nMethodsWe assessed incidence, duration of hospitalization, and clinical outcomes of acute COVID-19 inpatient admissions in a prospectively-followed cohort of 9,596,321 individuals enrolled in comprehensive, integrated healthcare delivery plans from Kaiser Permanente in California and Washington state. We also estimated the effective reproductive number (RE) describing transmission in the study populations.\n\nResultsData covered 1277 hospitalized patients with laboratory- or clinically-confirmed COVID-19 diagnosis by April 9, 2020. Cumulative incidence of first COVID-19 acute inpatient admission was 10.6-12.4 per 100,000 cohort members across the study regions. Mean censoring-adjusted duration of hospitalization was 10.7 days (2.5-97.5%iles: 0.8-30.1) among survivors and 13.7 days (2.5-97.5%iles: 1.7-34.6) among non-survivors. Among all hospitalized confirmed cases, censoring-adjusted probabilities of ICU admission and mortality were 41.9% (95% confidence interval: 34.1-51.4%) and 17.8% (14.3-22.2%), respectively, and higher among men than women. We estimated RE was 1.43 (1.17-1.73), 2.09 (1.63-2.69), and 1.47 (0.07-2.59) in Northern California, Southern California, and Washington, respectively, for infections acquired March 1, 2020. RE declined to 0.98 (0.76-1.27), 0.89 (0.74-1.06), and 0.92 (0.05-1.55) respectively, for infections acquired March 20, 2020.\n\nConclusionsWe identify high probability of ICU admission, long durations of stay, and considerable mortality risk among hospitalized COVID-19 cases in the western United States. Reductions in RE have occurred in conjunction with implementation of non-pharmaceutical interventions.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Joseph A Lewnard", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Vincent X Liu", - "author_inst": "Division of Research, Kaiser Permanente" - }, - { - "author_name": "Michael L Jackson", - "author_inst": "Health Research Institute, Kaiser Permanente Washington" - }, - { - "author_name": "Mark A Schmidt", - "author_inst": "Center for Health Research, Kaiser Permanente Northwest" - }, - { - "author_name": "Britta L Jewell", - "author_inst": "Imperial College, London" - }, - { - "author_name": "Jean P Flores", - "author_inst": "The Care Management Institute, Kaiser Permanente" - }, - { - "author_name": "Chris Jentz", - "author_inst": "The Care Management Institute, Kaiser Permanente" - }, - { - "author_name": "Graham R Northrup", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Ayesha Mahmud", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Arthur L Reingold", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Maya Petersen", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Nicholas P Jewell", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Scott Young", - "author_inst": "The Permanente Foundation, Kaiser Permanente" - }, - { - "author_name": "Jim Bellows", - "author_inst": "The Care Management Institute, Kaiser Permanente" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.13.20063669", "rel_title": "Smoking is Associated with COVID-19 Progression: A Meta-Analysis", @@ -1555099,6 +1556873,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.11.20062158", + "rel_title": "Rapid diagnosis of SARS-CoV-2 infection by detecting IgG and IgM antibodies with an immunochromatographic device: a prospective single-center study", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20062158", + "rel_abs": "ObjectivesSARS-CoV-2 infection diagnosis is challenging in patients from 2-3 weeks after the onset of symptoms, due to the low positivity rate of the PCR. Serologic tests could be complementary to PCR in these situations. The aim of our study was to analyze the diagnostic performance of one serologic rapid test in COVID-19 patients.\n\nMethodsWe evaluated an immunochromatographic test (AllTest COVID-19 IgG / IgM) which detects IgG and IgM antibodies. We validated the serologic test using serum samples from 45 negative patients (group 1) and 55 patients with COVID-19 confirmed by PCR (group 2). Then, we prospectively evaluated the test in 63 patients with clinical diagnosis of pneumonia of unknown etiology that were COVID-19 negative by PCR (group 3).\n\nResultsAll 45 patients from group 1 were negative for the serologic test (specificity = 100%). Regarding group 2 (PCR-positive), the median time from their symptom onset until testing was 11 days. For these 55 group-2 patients, the test was positive for either IgM or IgG in 26 (overall sensitivity = 47%), and in patients tested 14 days or more after the onset of symptoms, the sensitivity was 74%. Regarding the 63 group-3 patients, median time after symptom onset was 17 days, and the test was positive in 56 (89% positivity).\n\nConclusionsOur study shows that serologic rapid tests could be used as a complement of PCR to diagnose SARS-CoV-2 infection after 14 days from the onset of symptoms and in patients with pneumonia and negative PCR for SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Felipe Perez Garcia", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Ramon Perez Tanoira", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Juan Pedro Romanyk Cabrera", + "author_inst": "Hospital Universitario Principe de Asturias y Universidad de Alcala de Henares" + }, + { + "author_name": "Teresa Arroyo Serrano", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Pe\u00f1a Gomez Herruz", + "author_inst": "Hospital Universitario Principe de Asturias" + }, + { + "author_name": "Juan Cuadros Gonzalez", + "author_inst": "Hospital Universitario Principe de Asturias y Universidad de Alcala de Henares" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.12.20062380", "rel_title": "The clinical characteristics and mortal causes analysis of COVID-19 death patients", @@ -1556110,77 +1557923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.11.20061465", - "rel_title": "Hospitalization time and outcome in patients with Coronavirus Disease 2019 (COVID-19): analysis data from China", - "rel_date": "2020-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061465", - "rel_abs": "ObjectiveThe mean hospitalization time and outcome among patients with coronavirus disease 2019 (COVID-19) was estimated with the purpose of providing evidence for decision-making in medical institutions and governments in epidemic areas.\n\nMethodThe data of COVID-19 patients in china were collected from the websites of provincial and municipal health commissions. The mean hospitalization time and mortality in the mild or severe patients and the mean time from severe to mild illness were calculated by Gaussian mixture modeling.\n\nResultsThe mean hospitalization time among mild patients in Hubei province, other areas except Hubei province, and the national areas was 20.71{+/-} 9.30, 16.86 {+/-} 8.24, and 19.34 {+/-} 9.29 days, respectively. The mean transition time from severe to mild group in the above three areas were 15.00, 17.00, and 14.99 days, respectively. The death rate of mild and severe patients in Hubei province and the national areas were 1.10% and 18.14%, and 1.10% and 17.70%, respectively. Among those patients who died of COVID-19, the mean time from severe transition to death in Hubei province and the national areas was 6.22 {+/-} 5.12 and 6.35 {+/-} 5.27 days, respectively.\n\nConclusionThere were regional differences in the average length of stay between Hubei province and other regions, which may be related to different medical configurations. For those severe patients who died of COVID-19, the average time from hospitalization to death was about one week, and proper and effective treatments in the first week were critical.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Songshan Chai", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Dongdong Xiao", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Qikai Cheng", - "author_inst": "School of information and management; Wuhan university" - }, - { - "author_name": "Shengzhi Huang", - "author_inst": "School of information and management; Wuhan university" - }, - { - "author_name": "Yihao Wang", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Jiajia Qian", - "author_inst": "School of information and management; Wuhan university" - }, - { - "author_name": "Jiajing Wang", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Junjun Li", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Peng Fu", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Qiangping Wang", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Jing Rao", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Hongyang Zhao", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Fangcheng Zhang", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Nanxiang Xiong", - "author_inst": "Wuhan union hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.11.20061408", "rel_title": "A Preliminary Assessment of Novel Coronavirus (COVID-19) Knowledge and Perceptions in Nigeria", @@ -1556444,6 +1558186,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.10.20060632", + "rel_title": "FFP-2 respirator masks in times of crisis", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060632", + "rel_abs": "Given the current shortage of respirator masks and the resulting lack of personal protective equipment for use by clinical staff, we examined bottom-up solutions that would allow hospitals to fabricate respirator masks that: (i) meet requirements in terms of filtering capacities, (ii) are easy to produce rapidly and locally, and (iii) can be constructed using materials commonly available in hospitals worldwide. We found that Halyard H300 material used for wrapping of surgical instruments and routinely available in hospitals, met these criteria. Specifically, three layers of material achieved a filter efficiency of 94%, 99%, and 100% for 0.3 m, 0.5 m, and 3.0 m particles, respectively; importantly, these values are close to the efficiency provided by FFP2 and N95 masks. After re-sterilization up to 5 times, the filters efficiency remains sufficiently high for use as an FFP1 respirator mask. Finally, using only one layer of the material satisfies the criteria for use as a surgical mask. This material can therefore be used to help protect hospital staff and other healthcare professionals who require access to suitable masks but lack commercially available solutions.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Johanna H. Meijer", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Timo J.C. Oude Vrielink", + "author_inst": "Leiden University Medical Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.15.20060095", "rel_title": "COVID-19 is an emergent disease of aging", @@ -1557696,49 +1559461,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.20059113", - "rel_title": "Transmission routes of Covid-19 virus in the Diamond Princess Cruise ship", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059113", - "rel_abs": "BackgroundAn outbreak of COVID-19 occurred on the Diamond Princess cruise ship in January and February 2020. We analysed information about cases to infer transmission dynamics and potential modes of transmission.\n\nMethodsWe collected the daily number of 197 symptomatic cases, and that of the 146 passenger cases in two categories, i.e. those who stayed and did not stay in the same stateroom. We retrieved the quarantine details and the ships 14-day itinerary. We searched the websites of national/local health authority along the cruise routes and local news using Google for locally confirmed cases associated with the ship. We obtained the design of air conditioning and sewage treatment of the ship from literature. We back-calculated the dates of infection from the epidemic curve and compared with the start of on-board quarantine.\n\nResultsMajor infections started on Jan 28 and completed by Feb 6 for passengers except those who stayed in the same stateroom with infected individual(s). No other confirmed cases were identified among the disembarked people in Hong Kong except an 80 years old passenger. No confirmed cases were reported in three other stopovers between Jan 27-31 associated with disembarked passengers or visitors from the ship, however two Okinawa taxi drivers became confirmed cases in association with driving the ship passengers. Infection among passengers after Feb 6 was limited to those who stayed in the same stateroom with an infected passenger. Infections in crew members peaked on Feb 7, suggesting significant transmission among crew members after quarantine on Feb 5.\n\nConclusionsWe infer that the ship central air conditioning system did not play a role, i.e. the long-range airborne route was absent in the outbreak. Most transmission appears to have occurred through close contact and fomites.\n\nSignificance StatementTransmission by the long-range airborne route for SARS-CoV-2 in the 2020 Diamond Princess Covid-19 outbreak has been debated with significant implication for intervention. We found that the transmission by close contact and fomite explains the outbreak, and the central air-conditioning system did not play a role, demonstrating the importance of social distancing, good hygiene and maintaining good building ventilation for intervention.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Pengcheng Xu", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Hua Qian", - "author_inst": "Southeast University" - }, - { - "author_name": "Te Miao", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hui-ling Yen", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hongwei Tan", - "author_inst": "Tongji University" - }, - { - "author_name": "Benjamin J. Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yuguo J Li", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.09.20059311", "rel_title": "Real-time forecasts and risk assessment of novel coronavirus (COVID-19) cases: A data-driven analysis", @@ -1557902,6 +1559624,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.04.09.20059204", + "rel_title": "Myocyte Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2 mediated myocarditis", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059204", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a global pandemic caused by a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 infection of host cells occurs predominantly via binding of the viral surface spike protein to the human angiotensin-converting enzyme 2 (ACE2) receptor.1 Hypertension and pre-existing cardiovascular disease are risk factors for morbidity from COVID-19,2 and it remains uncertain whether the use of angiotensin converting enzyme inhibitors (ACEi) or angiotensin receptor blockers (ARB) impacts infection and disease. Here, we aim to shed light on this question by assessing ACE2 expression in normal and diseased human myocardial samples profiled by bulk and single nucleus RNA-seq.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Nathan R Tucker", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Mark Chaffin", + "author_inst": "Precision Cardiology Laboratory, The Broad Institute" + }, + { + "author_name": "Kenneth C Bedi Jr.", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Irinna Papangeli", + "author_inst": "Precision Cardiology Laboratory, Bayer US LLC" + }, + { + "author_name": "Amer-Denis Akkad", + "author_inst": "Precision Cardiology Laboratory, Bayer US LLC" + }, + { + "author_name": "Alessandro Arduini", + "author_inst": "Precision Cardiology Laboratory, The Broad Institute" + }, + { + "author_name": "Sikander Hayat", + "author_inst": "Precision Cardiology Laboratory, Bayer US LLC" + }, + { + "author_name": "G\u00f6kcen Eraslan", + "author_inst": "The Broad Institute" + }, + { + "author_name": "Christoph Muus", + "author_inst": "The Broad Institute" + }, + { + "author_name": "Roby Bhattacharyya", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Christian M Stegmann", + "author_inst": "Precision Cardiology Laboratory, Bayer US LLC" + }, + { + "author_name": "- Human Cell Atlas Lung Biological Network", + "author_inst": "" + }, + { + "author_name": "Kenneth B Margulies", + "author_inst": "Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Patrick T Ellinor", + "author_inst": "Precision Cardiology Laboratory, The Broad Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.04.09.20059055", "rel_title": "Forecasting Covid-19 Outbreak Progression in Italian Regions: A model based on neural network training from Chinese data", @@ -1558850,149 +1560643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.10.20059121", - "rel_title": "ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20059121", - "rel_abs": "ObjectivesTo use human genetic variants that proxy angiotensin-converting enzyme (ACE) inhibitor drug effects and cardiovascular risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 gene expression and circulating ACE2 levels.\n\nDesignTwo-sample Mendelian randomization (MR) analysis.\n\nSettingSummary-level genetic association data.\n\nParticipantsParticipants were predominantly of European ancestry. Variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors (body mass index, chronic obstructive pulmonary disease, lifetime smoking index, low-density lipoprotein cholesterol, systolic blood pressure and type 2 diabetes mellitus) were selected from publicly available genome-wide association study data (sample sizes ranging from 188,577 to 898,130 participants). Genetic association estimates for lung expression of ACE2 and TMPRSS2 were obtained from the Gene-Tissue Expression (GTEx) project (515 participants) and the Lung eQTL Consortium (1,038 participants). Genetic association estimates for circulating plasma ACE2 levels were obtained from the INTERVAL study (4,947 participants).\n\nMain outcomes and measuresLung ACE2 and TMPRSS2 expression and plasma ACE2 levels.\n\nResultsThere were no association of genetically proxied ACE inhibition with any of the outcomes considered here. There was evidence of a positive association of genetic liability to type 2 diabetes mellitus with lung ACE2 gene expression in GTEx (p = 4x10-4) and with circulating plasma ACE2 levels in INTERVAL (p = 0.03), but not with lung ACE2 expression in the Lung eQTL Consortium study (p = 0.68). There were no associations between genetically predicted levels of the other cardiometabolic traits with the outcomes.\n\nConclusionsThis study does not provide evidence to support that ACE inhibitor antihypertensive drugs affect lung ACE2 and TMPRSS2 expression or plasma ACE2 levels. In the current COVID-19 pandemic, our findings do not support a change in ACE inhibitor medication use without clinical justification.\n\nSummary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current coronavirus disease 2019 (COVID-19) pandemic.\nC_LIO_LISerine protease TMPRSS2 is involved in priming the SARS-CoV-2 spike protein for cellular entry through the angiotensin-converting enzyme 2 (ACE2) receptor.\nC_LIO_LIExpression of ACE2 and TMPRSS2 in the lung epithelium might have implications for risk of SARS-CoV-2 infection and severity of COVID-19.\nC_LI\n\nWhat this study addsO_LIWe used human genetic variants that proxy ACE inhibitor drug effects and cardiometabolic risk factors to provide insight into how these exposures affect lung ACE2 and TMPRSS2 expression and circulating ACE2 levels.\nC_LIO_LIOur findings do not support the hypothesis that ACE inhibitors have effects on ACE2 expression.\nC_LIO_LIWe found some support for an association of genetic liability to type 2 diabetes mellitus with higher lung ACE2 expression and plasma ACE2 levels, but evidence was inconsistent across studies.\nC_LI", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Dipender Gill", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marios Arvanitis", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Paul Carter", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ana I Hernandez Cordero", - "author_inst": "The University of British Columbia Center for Heart Lung Innovation" - }, - { - "author_name": "Brian Jo", - "author_inst": "Lewis Sigler Institute for Integrative Biology" - }, - { - "author_name": "Ville Karhunen", - "author_inst": "Imperial College London" - }, - { - "author_name": "Susanna C Larsson", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Xuan Li", - "author_inst": "The University of British Columbia Center for Heart Lung Innovation" - }, - { - "author_name": "Sam M Lockhart", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Amy M Mason", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Evanthia Pashos", - "author_inst": "Pfizer" - }, - { - "author_name": "Ashis Saha", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Vanessa Tan", - "author_inst": "University of Bristol" - }, - { - "author_name": "Verena Zuber", - "author_inst": "Imperial College London" - }, - { - "author_name": "Yohan Bosse", - "author_inst": "Laval University, Quebec" - }, - { - "author_name": "Sarah Fahle", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ke Hao", - "author_inst": "School of Medicine at Mount Sinai" - }, - { - "author_name": "Tao Jiang", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Philippe Joubert", - "author_inst": "Laval University, Quebec" - }, - { - "author_name": "Alan C Lunt", - "author_inst": "Imperial College London" - }, - { - "author_name": "Willem hendrik Ouwehand", - "author_inst": "University of Cambridge" - }, - { - "author_name": "David J Roberts", - "author_inst": "University of Oxford" - }, - { - "author_name": "Wim Timens", - "author_inst": "University of Groningen" - }, - { - "author_name": "Maarten van den Berge", - "author_inst": "University of Groningen" - }, - { - "author_name": "Nicholas A Watkins", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Alexis Battle", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Adam S Butterworth", - "author_inst": "University of Cambridge" - }, - { - "author_name": "John Danesh", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Barbara E Engelhard", - "author_inst": "Princeton University" - }, - { - "author_name": "James E Peters", - "author_inst": "Imperial College London" - }, - { - "author_name": "Don Sin", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Stephen Burgess", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.04.10.20061192", "rel_title": "COVID-19 most vulnerable Mexican cities lack the public health infrastructure to face the pandemic: a new temporally-explicit model", @@ -1559172,6 +1560822,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.09.20059824", + "rel_title": "Recovery Ratios Reliably Anticipate COVID-19 Pandemic Progression", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059824", + "rel_abs": "The COVID-19 pandemic is placing unprecedented demands on healthcare systems worldwide and exacting a massive humanitarian toll. This makes the development of accurate predictive models imperative, not just for understanding the course of the pandemic but more importantly for gaining insight into the efficacy of public health measures and planning accordingly. Epidemiological models are forced to make assumptions about many unknowns and therefore can be unreliable. Here, taking an empirical approach, we report a 20-30 day lag between the peak of confirmed to recovered cases and the peak of daily deaths in each country, independent of the epoch of that country in its pandemic cycle. This analysis is expected to be largely independent of the proportion of the population being tested and therefore should aid in planning around the timing and easing of public health measures. Our data also suggests broad predictions for the number of fatalities, generally somewhat lower than most other models. Finally, our model suggests that the world as a whole is shortly to enter a recovery phase, at least as far as the first pandemic wave is concerned.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Dan Valeriu Nicolau", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Alexander Hasson", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Mona Bafadhel", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.09.20057802", "rel_title": "COVID-19 pandemic and lockdown measures impact on mental health among the general population in Italy. An N=18147 web-based survey.", @@ -1560352,41 +1562029,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.13.039263", - "rel_title": "Comparative in vitro transcriptomic analyses of COVID-19 candidate therapy hydroxychloroquine suggest limited immunomodulatory evidence of SARS-CoV-2 host response genes.", - "rel_date": "2020-04-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.13.039263", - "rel_abs": "Hydroxychloroquine (HCQ) has emerged as a potential and controversial antiviral candidate therapy for COVID-19. While many clinical trials are underway to test the efficacy of HCQ as a treatment for COVID-19, underlying mechanisms of HCQ in the setting of COVID-19 remain unclear. Hence, we examined differential gene expression signatures of HCQ exposure, in vitro SARS-CoV-2 infection, and host signatures of COVID-19 in blood, bronchoalveolar lavage, and postmortem lung to evaluate whether HCQ transcriptome signatures associate with restoration of SARS-CoV-2-related host transcriptional responses. Here, we show that 24 hours of in vitro treatment of peripheral blood mononuclear cells(PBMC) with HCQ significantly impacted transcription of 16 genes involved in immune regulation and lipid metabolism. Using transcriptome data from in vitro SARS-CoV-2 infected NHBE and A549 cells and PBMC derived from confirmed COVID-19 infected patients, we determined that only 0.24% of the COVID-19 PBMC differentially expressed gene set and 0.39% of the in vitro SARS-CoV-2 cells differentially expressed gene set overlapped with HCQ-related differentially expressed genes. Moreover, we observed that HCQ treatment significantly impacted transcription of 159 genes in human primary monocyte-derived macrophages involved in cholesterol biosynthetic process and chemokine activity. Notably, when we compared the macrophage HCQ-related gene lists with genes transcriptionally altered during SARS-CoV-2 infection and in bronchoalveolar lavage of COVID-19+ patients, the CXCL6 gene was impacted in all three transcriptional signatures revealing evidence in favor of chemokine modulation. HCQ-related transcriptional changes minimally overlapped with host genes altered in postmortem lung biopsies from COVID-19 participants. These results may provide insight into the immunomodulation mechanisms of HCQ treatment in the setting of COVID-19 and suggest HCQ is not a panacea to SARS-CoV-2 infection.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Michael Jay Corley", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Christopher Sugai", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Michael Schotsaert", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Robert E. Schwartz", - "author_inst": "Weill Cornell Graduate School of Medical Sciences" - }, - { - "author_name": "Lishomwa C Ndhlovu", - "author_inst": "Weill Cornell Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.04.09.20059345", "rel_title": "Chasing the ghost of infection past: identifying thresholds of change during the COVID-19 infection in Spain", @@ -1560606,6 +1562248,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.10.20060376", + "rel_title": "Molecular mechanism of action of repurposed drugs and traditional Chinese medicine used for the treatment of patients infected with COVID-19: A systematic review", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060376", + "rel_abs": "BackgroundThe emergence of COVID-19 as a pandemic has resulted in the need for urgent development of vaccines and drugs and the conduction of clinical trials to fight the outbreak. Because of the time constraints associated with the development of vaccines and effective drugs, drug repurposing and other alternative treatment methods have been used to treat patients that have been infected by the SARS-CoV-2 virus and have acquired COVID-19.\n\nObjectiveThe objective of this systematic scoping review is to provide an overview of the molecular mechanism of action of repurposed drugs or alternative treatment medicines used to attenuate COVID-19 disease.\n\nData SourcesThe research articles or grey literature, including theses, government reports, and official news online, were identified from 4 databases and 1 search engine. The full content of a total of 160 articles that fulfilled our inclusion criteria was analyzed and information about 6 drugs (ritonavir, lopinavir, oseltamivir, remdesivir, favipiravir, and chloroquine) and 4 traditional Chinese medicines (Shuang Huang Lian Kou Fu Ye, TCM combination of Bu Huan Jin Zheng Qi San and Da Yuan Yin, Xue Bi Jing Injection and Qing Fei Pai Du Tang) were extracted.\n\nConclusionsAll of the repurposed drugs that have been used for the treatment of COVID-19 depend on the ability of the drug to inhibit the proliferation of the SARS-CoV-2 virus by binding to enzyme active sites, viral chain termination, or triggering of the molecular pathway, whereas traditional Chinese medicine has a pivotal role in triggering the inflammation pathway, such as the neuraminidase blocker, to fight the SARS-CoV-2 virus. This review provides an insight to experimental validation of drugs and alternative medicine used for the treatment and control of COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Fui Fui Lem", + "author_inst": "Ministry of Health Malaysia" + }, + { + "author_name": "Fernandes Opook", + "author_inst": "Wildlife Health Genetic and Forensic Laboratory, Wildlife and Health Department" + }, + { + "author_name": "Dexter Lee Jiunn Herng", + "author_inst": "Universiti Malaysia Sabah" + }, + { + "author_name": "Chee Fong Tyng", + "author_inst": "Universiti Malaysia Sabah" + }, + { + "author_name": "Fahcina P Lawson", + "author_inst": "The Johns Hopkins University" + }, + { + "author_name": "Chin Su Na", + "author_inst": "Universiti Malaysia Sabah" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.10.20061150", "rel_title": "Immunological assays for SARS-CoV-2: an analysis of available commercial tests to measure antigen and antibodies", @@ -1561830,45 +1563511,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.04.10.036335", - "rel_title": "A Computational Approach to Design Potential siRNA Molecules as a Prospective Tool for Silencing Nucleocapsid Phosphoprotein and Surface Glycoprotein Gene of SARS-CoV-2", - "rel_date": "2020-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.10.036335", - "rel_abs": "An outbreak, caused by a RNA virus, SARS-CoV-2 named COVID-19 has become pandemic with a magnitude which is daunting to all public health institutions in the absence of specific antiviral treatment. Surface glycoprotein and nucleocapsid phosphoprotein are two important proteins of this virus facilitating its entry into host cell and genome replication. Small interfering RNA (siRNA) is a prospective tool of the RNA interference (RNAi) pathway for the control of human viral infections by suppressing viral gene expression through hybridization and neutralization of target complementary mRNA. So, in this study, the power of RNA interference technology was harnessed to develop siRNA molecules against specific target genes namely, nucleocapsid phosphoprotein gene and surface glycoprotein gene. Conserved sequence from 139 SARS-CoV-2 strains from around the globe was collected to construct 78 siRNA that can inactivate nucleocapsid phosphoprotein and surface glycoprotein genes. Finally, based on GC content, free energy of folding, free energy of binding, melting temperature and efficacy prediction process 8 siRNA molecules were selected which are proposed to exerts the best action. These predicted siRNAs should effectively silence the genes of SARS-CoV-2 during siRNA mediated treatment assisting in the response against SARS-CoV-2", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Umar Faruq Chowdhury", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh" - }, - { - "author_name": "Mohammad Umer Sharif Shohan", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh" - }, - { - "author_name": "Kazi Injamamul Hoque", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh" - }, - { - "author_name": "Mirza Ashikul Beg", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh" - }, - { - "author_name": "Mohammad Kawsar Sharif Siam", - "author_inst": "Department of Pharmacy, Brac University, Dhaka, Bangladesh" - }, - { - "author_name": "Mohammad Ali Moni", - "author_inst": "The University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.05.026005", "rel_title": "Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine", @@ -1562104,6 +1563746,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.06.20055236", + "rel_title": "Oxygen transfer characteristics of a hollow fiber dialyser: toward possible repurposing of dialysers as blood oxygenators in the context of constrained availability of respiratory support", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20055236", + "rel_abs": "The COVID-19 pandemic has highlighted resource constraints in respiratory support. The oxygen transfer characteristics of a hollow fiber membrane dialyser were investigated with a view to repurposing the device as a low-cost, readily available blood oxygenator. Oxygen transfer in a low-flux hollow fiber dialyser with a polysulfone membrane was studied by passing first water and then blood through the dialyser in counter-current to high-purity oxygen. Oxygen transfer rates of about 15% of the nominal 250 ml(STP)/min of a typical adult oxygen consumption rate were achieved for blood flow rates of 500ml/min. Using two such dialysis devices in parallel could provide up to 30% of the nominal oxygen consumption. Specific hollow fiber dialysis devices operating with suitable pumps in a veno-venous access configuration, could provide a cost-effective and readily available supplementation of respiratory support in the face of severe resource constraints.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "David M Rubin", + "author_inst": "Biomedical Engineering Research Group, School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg" + }, + { + "author_name": "Neil T Stacey", + "author_inst": "School of Chemical and Metallurgical Engineering, University of the Witwatersrand, Johannesburg" + }, + { + "author_name": "Tonderayi Matambo", + "author_inst": "Institute for the Development of Energy for African Sustainability, University of South Africa" + }, + { + "author_name": "Claudia Do Vale", + "author_inst": "Morningside Clinic, Johannesburg and Department of Medicine, Division of Nephrology, University of the Witwatersrand, Johannesburg" + }, + { + "author_name": "Martin Sussman", + "author_inst": "Cardiothoracic Surgery, Milpark Hospital, Johannesburg" + }, + { + "author_name": "Tracy Snyman", + "author_inst": "National Health Laboratory Service and Department of Chemical Pathology, University of the Witwatersrand, Johannesburg" + }, + { + "author_name": "Mervyn Mer", + "author_inst": "Charlotte Maxeke Johannesburg Academic Hospital and Department of Medicine, Divisions of Critical Care and Pulmonology, University of the Witwatersrand, Johanne" + }, + { + "author_name": "Diane Hildebrandt", + "author_inst": "Institute for the Development of Energy for African Sustainability, University of South Africa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.04.07.20056671", "rel_title": "Use of a Single Ventilator to Support Multiple Patients: Modeling Tidal Volume Response to Heterogeneous Lung Mechanics", @@ -1563020,49 +1564709,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.04.07.20056390", - "rel_title": "Adjuvant corticosteroid therapy for critically ill patients with COVID-19", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056390", - "rel_abs": "Addition of adjuvant corticosteroid therapy to standard antiviral treatment of patients with coronavirus disease (COVID-19) is common in clinical practice. However, evidence is scarce regarding the efficacy of adjuvant corticosteroids in patients who are critically ill. We retrospectively evaluated the effects of adjuvant corticosteroid treatment on the outcome of 244 critically ill patients with COVID-19, using a risk stratification model that adjusts for potential differences between the steroid group (n=151) and the non-steroid group (n=93). We observed that adjuvant corticosteroid therapy was independent from 28-day mortality, either in multivariate logistic regression of the entire cohort after adjustment for major mortality-associated variables (age, SpO2/FiO2, and lymphocyte count) and individual propensity score (adjusted OR: 1.05; 95% CI: -1.92-2.01), or in propensity score-matched (1:1 without replacement) case-control analysis (62 patients in 31 pairs; log-rank test P=0.17). Additionally, subgroup analyses of 147 (60%) patients who had dyspnea and 87 (36%) patients who had ARDS revealed corticosteroid treatment was not associated with clinical outcome (both, P>0.3). However, increased corticosteroids dosage was significantly associated with elevated mortality risk after adjustment for administration duration (P=0.003); every ten-milligram increase in hydrocortisone-equivalent dosage was associated with additional 4% mortality risk (adjusted HR: 1.04, 95% CI: 1.01-1.07). Our findings indicated that limited effect of corticosteroid therapy could pose to overall survival and prudent dose within effective limits may be recommended for critically ill patients under certain circumstances.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Xiaofan Lu", - "author_inst": "State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China" - }, - { - "author_name": "Taige Chen", - "author_inst": "Medical School of Nanjing University" - }, - { - "author_name": "Yang Wang", - "author_inst": "Department of Radiology, The Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China" - }, - { - "author_name": "Jun Wang", - "author_inst": "The First Affiliated Hospital of Soochow University, Suzhou, China" - }, - { - "author_name": "Bing Zhang", - "author_inst": "Department of Radiology, The Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China" - }, - { - "author_name": "Yongsheng Li", - "author_inst": "Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan 430030" - }, - { - "author_name": "Fangrong Yan", - "author_inst": "State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.04.06.20055640", "rel_title": "Gaussian Statistics and Data-Assimilated Model of Mortality due to COVID-19: China, USA, Italy, Spain, UK, Iran, and the World Total", @@ -1563242,6 +1564888,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.08.20056598", + "rel_title": "Prognostic factors for severity and mortality in patients infected with COVID-19: A living systematic review protocol", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20056598", + "rel_abs": "ObjectiveThe objective of our systematic review is to identify prognostic factors that can potentially be used in decision-making related to the care of patients infected with COVID-19.\n\nDesignThis is the protocol of a living systematic review.\n\nData sourcesWe will conduct searches in PubMed/Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), grey literature and in a centralised repository in L{middle dot}OVE (Living OVerview of Evidence). L{middle dot}OVE is a platform that maps PICO questions to evidence from Epistemonikos database. In response to the COVID-19 emergency, L{middle dot}OVE was adapted to expand the range of evidence covered and customised to group all COVID-19 evidence in one place. The search will continue until the day before submission to a journal.\n\nEligibility criteria for selecting studies and methodsWe will follow a common protocol for multiple parallel systematic reviews, already published and submitted to PROSPERO (awaiting ID allocation).\n\nWe will include studies that assess patients with confirmed or suspected SARS-CoV-2 infection and inform the relation between potential prognostic factors and death or disease severity. Two groups of two reviewers will independently screen studies for eligibility, extract data and assess the risk of bias. We will perform meta-analyses and use GRADE to assess the certainty of evidence for each prognostic factor and outcome.\n\nA living, web-based version of this review will be openly available during the COVID-19 pandemic. We will resubmit it if the conclusions change or there are substantial updates.\n\nEthics and disseminationNo ethics approval is considered necessary. The results of this review will be widely disseminated via peer-reviewed publications, social networks and traditional media.\n\nPROSPERO RegistrationSubmitted to PROSPERO (awaiting ID allocation).", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ariel Izcovich", + "author_inst": "Hospital Alem\u00e1n de Buenos Aires, Argentina" + }, + { + "author_name": "Mart\u00edn Ragusa", + "author_inst": "Hospital Alem\u00e1n de Buenos Aires, Argentina" + }, + { + "author_name": "Ver\u00f3nica Sanguine", + "author_inst": "Ministerio de Salud de la Naci\u00f3n, Argentina" + }, + { + "author_name": "Fernando Tortosa", + "author_inst": "Hospital Ram\u00f3n Carrillo, San Carlos de Bariloche, Rio Negro, Argentina" + }, + { + "author_name": "Federico Espinosa", + "author_inst": "Hospital Alem\u00e1n de Buenos Aires, Argentina" + }, + { + "author_name": "Camila Agnoletti", + "author_inst": "Hospital Alem\u00e1n de Buenos Aires, Argentina" + }, + { + "author_name": "Mar\u00eda Andrea Lavena Marzio", + "author_inst": "Hospital Alem\u00e1n de Buenos Aires, Argentina" + }, + { + "author_name": "Agust\u00edn Bengolea", + "author_inst": "Hospital Alem\u00e1n de Buenos Aires, Argentina" + }, + { + "author_name": "Ezequiel Saavedra", + "author_inst": "Hospital Alem\u00e1n de Buenos Aires, Argentina" + }, + { + "author_name": "Hugo Norberto Catalano", + "author_inst": "Hospital Alem\u00e1n de Buenos Aires, Argentina" + }, + { + "author_name": "Gabriel Rada", + "author_inst": "Fundaci\u00f3n Epistemonikos, Santiago, Chile" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.08.20056986", "rel_title": "Development of a dual-gene loop-mediated isothermal amplification (LAMP) detection assay for SARS-CoV-2: A preliminary study", @@ -1564314,49 +1566019,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.08.20057919", - "rel_title": "Burden and prevalence of prognostic factors for severe covid-19 disease in Sweden", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057919", - "rel_abs": "ObjectivesDescribe the burden and prevalence of prognostic factors of severe COVID-19 disease at national and county level in Sweden.\n\nDesignCross sectional study\n\nSettingSweden\n\nParticipants9,624,428 individuals living in Sweden on 31st December 2014 and alive on 1st January 2016\n\nMain outcome measuresBurden and prevalence of prognostic factors for severe COVID-19 based on the guidelines from the World Health Organization and European Centre for Disease Prevention and Control, which are age 70 years and older, cardiovascular disease, cancer, chronic obstructive pulmonary disease, severe asthma, and diabetes. Prognostic factors were identified based on records for three years before 1st January 2016 from the Swedish National Inpatient and Outpatient Specialist Care Register, Prescribed Drug Register, and Cancer Register.\n\nResults22.1% of the study population had at least one prognostic factor for severe COVID-19 (2,131,319 individuals), and 1.6% had at least three factors (154,746 individuals). The prevalence of underlying medical conditions in the whole study population ranged from 0.8% with chronic obstructive pulmonary disease (78,516 individuals) to 7.4% with cardiovascular disease (708,090 individuals), and the county specific prevalence of at least one prognostic factor ranged from 19.2% in Stockholm (416,988 individuals) to 25.9% in Kalmar (60,005 individuals).\n\nConclusionsThe prevalence of prognostic factors for severe COVID-19 disease will aid authorities in optimally planning healthcare resources during the ongoing pandemic. Results can also be applied to underlying assumptions of disease burden in modelling efforts to support COVID-19 planning. This information is crucial when deciding appropriate strategies to mitigate the pandemic and reduce both the direct mortality burden from the disease itself, and the indirect mortality burden from potentially overwhelmed health systems.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Katalin Gemes", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Mats Talback", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Karin Modig", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Anders Ahlbom", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Anita Berglund", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Maria Feychting", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Anthony Matthews", - "author_inst": "Karolinska Institutet" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.09.033910", "rel_title": "Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis", @@ -1564576,6 +1566238,25 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.08.20058123", + "rel_title": "Long-term predictions for COVID-19 pandemic dynamics in Ukraine, Austria and Italy", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058123", + "rel_abs": "The SIR (susceptible-infected-removed) model, statistical approach to the parameter identification and the official WHO daily data about the confirmed cumulative number of cases were used to make some estimations for the dynamics of the coronavirus pandemic dynamics in Ukraine, Italy and Austria. The volume of the data sets and the influence of the information about the initial stages of the epidemics were discussed in order to have reliable long-time predictions. The final sizes and durations for the pandemic in these countries are estimated.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Igor Nesteruk", + "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.07.029132", "rel_title": "A virus that has gone viral: Amino acid mutation in S protein of Indian isolate of Coronavirus COVID-19 might impact receptor binding and thus infectivity", @@ -1565611,57 +1567292,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.08.20057794", - "rel_title": "Factors associated with hospitalization and critical illness among 4,103 patients with COVID-19 disease in New York City", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057794", - "rel_abs": "BackgroundLittle is known about factors associated with hospitalization and critical illness in Covid-19 positive patients.\n\nMethodsWe conducted a cross-sectional analysis of all patients with laboratory-confirmed Covid-19 treated at an academic health system in New York City between March 1, 2020 and April 2, 2020, with follow up through April 7, 2020. Primary outcomes were hospitalization and critical illness (intensive care, mechanical ventilation, hospice and/or death). We conducted multivariable logistic regression to identify risk factors for adverse outcomes, and maximum information gain decision tree classifications to identify key splitters.\n\nResultsAmong 4,103 Covid-19 patients, 1,999 (48.7%) were hospitalized, of whom 981/1,999 (49.1%) have been discharged, and 292/1,999 (14.6%) have died or been discharged to hospice. Of 445 patients requiring mechanical ventilation, 162/445 (36.4%) have died. Strongest hospitalization risks were age [≥]75 years (OR 66.8, 95% CI, 44.7-102.6), age 65-74 (OR 10.9, 95% CI, 8.35-14.34), BMI>40 (OR 6.2, 95% CI, 4.2-9.3), and heart failure (OR 4.3 95% CI, 1.9-11.2). Strongest critical illness risks were admission oxygen saturation <88% (OR 6.99, 95% CI 4.5-11.0), d-dimer>2500 (OR 6.9, 95% CI, 3.2-15.2), ferritin >2500 (OR 6.9, 95% CI, 3.2-15.2), and C-reactive protein (CRP) >200 (OR 5.78, 95% CI, 2.6-13.8). In the decision tree for admission, the most important features were age >65 and obesity; for critical illness, the most important was SpO2<88, followed by procalcitonin >0.5, troponin <0.1 (protective), age >64 and CRP>200.\n\nConclusionsAge and comorbidities are powerful predictors of hospitalization; however, admission oxygen impairment and markers of inflammation are most strongly associated with critical illness.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Christopher M. Petrilli", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Simon A. Jones", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Jie Yang", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Harish Rajagopalan", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Yelena Chernyak", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Katie Tobin", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Robert J. Cerfolio", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Fritz Francois", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Leora I. Horwitz", - "author_inst": "NYU Grossman School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.04.08.20057588", "rel_title": "On the corona infection model with contact restriction", @@ -1565789,6 +1567419,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.08.20057463", + "rel_title": "COVID-19 epidemic in Malaysia: Impact of lock-down on infection dynamics", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057463", + "rel_abs": "COVID-19 epidemic in Malaysia started as a small wave of 22 cases in January 2020 through imported cases. It was followed by a bigger wave mainly from local transmissions resulting in 651 cases. The following wave saw unexpectedly three digit number of daily cases following a mass gathering urged the government to choose a more stringent measure. A limited lock-down approach called Movement Control Order (MCO) was immediately initiated to the whole country as a way to suppress the epidemic trajectory. The lock-down causes a major socio-economic disruption thus the ability to forecast the infection dynamic is urgently required to assist the government on timely decisions. Limited testing capacity and limited epidemiological data complicate the understanding of the future infection dynamic of the COVID-19 epidemic. Three different epidemic forecasting models was used to generate forecasts of COVID-19 cases in Malaysia using daily reported cumulative case data up until 1st April 2020 from the Malaysia Ministry of Health. The forecasts were generated using a Curve Fitting Model with Probability Density Function and Skewness Effect, the SIR Model, and a System Dynamic Model. Method one based on curve fitting with probability density function estimated that the peak will be on 19th April 2020 with an estimation of 5,637 infected persons. Method two based on SIR Model estimated that the peak will be on 20th - 31st May 2020 if Movement Contro (MCO) is in place with an estimation of 630,000 to 800,000 infected persons. Method three based on System Dynamic Model estimated that the peak will be on 17th May 2020 with an estimation of 22,421 infected persons. Forecasts from each of model suggested the epidemic may peak between middle of April to end of May 2020.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Naomie Salim", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Weng Howe Chan", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Shuhaimi Mansor", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Nor Erne Nazira Bazin", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Safiya Amaran", + "author_inst": "Universiti Sultan Zainal Abidin" + }, + { + "author_name": "Ahmad Athif Mohd Faudzi", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Anazida Zainal", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Sharin Hazlin Huspi", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Eric Jiun Hooi Khoo", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Shaekh Mohammad Shithil", + "author_inst": "Universiti Teknologi Malaysia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.06.20054239", "rel_title": "Making sense of the Global Coronavirus Data: The role of testing rates in understanding the pandemic and our exit strategy", @@ -1566685,33 +1568370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.20058974", - "rel_title": "Predicting the number of reported and unreported cases for the COVID-19 epidemics in China, South Korea, Italy, France, Germany and United Kingdom", - "rel_date": "2020-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20058974", - "rel_abs": "We model the COVID-19 coronavirus epidemics in China, South Korea, Italy, France, Germany and United Kingdom. We use early reported case data to predict the cumulative number of reported cases to a final size in each country. The key features of our model are the timing of implementation of major public policies restricting social movement, the identification and isolation of unreported cases, and the impact of asymptomatic infectious cases.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Zhihua Liu", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Pierre Magal", - "author_inst": "University of Bordeaux" - }, - { - "author_name": "Glenn F Webb", - "author_inst": "Vanderbilt University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.06.20042580", "rel_title": "Interferon-a2b treatment for COVID-19", @@ -1566923,6 +1568581,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.08.20040907", + "rel_title": "Artificial intelligence applied on chest X-ray can aid in the diagnosis of COVID-19 infection: a first experience from Lombardy, Italy", + "rel_date": "2020-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20040907", + "rel_abs": "ObjectivesWe tested artificial intelligence (AI) to support the diagnosis of COVID-19 using chest X-ray (CXR). Diagnostic performance was computed for a system trained on CXRs of Italian subjects from two hospitals in Lombardy, Italy.\n\nMethodsWe used for training and internal testing an ensemble of ten convolutional neural networks (CNNs) with mainly bedside CXRs of 250 COVID-19 and 250 non-COVID-19 subjects from two hospitals. We then tested such system on bedside CXRs of an independent group of 110 patients (74 COVID-19, 36 non-COVID-19) from one of the two hospitals. A retrospective reading was performed by two radiologists in the absence of any clinical information, with the aim to differentiate COVID-19 from non-COVID-19 patients. Real-time polymerase chain reaction served as reference standard.\n\nResultsAt 10-fold cross-validation, our AI model classified COVID-19 and non COVID-19 patients with 0.78 sensitivity (95% confidence interval [CI] 0.74-0.81), 0.82 specificity (95% CI 0.78-0.85) and 0.89 area under the curve (AUC) (95% CI 0.86-0.91). For the independent dataset, AI showed 0.80 sensitivity (95% CI 0.72-0.86) (59/74), 0.81 specificity (29/36) (95% CI 0.73-0.87), and 0.81 AUC (95% CI 0.73- 0.87). Radiologists reading obtained 0.63 sensitivity (95% CI 0.52-0.74) and 0.78 specificity (95% CI 0.61-0.90) in one centre and 0.64 sensitivity (95% CI 0.52-0.74) and 0.86 specificity (95% CI 0.71-0.95) in the other.\n\nConclusionsThis preliminary experience based on ten CNNs trained on a limited training dataset shows an interesting potential of AI for COVID-19 diagnosis. Such tool is in training with new CXRs to further increase its performance.\n\nKey pointsO_LIArtificial intelligence based on convolutional neural networks was preliminary applied to chest-X-rays of patients suspected to be infected by COVID-19.\nC_LIO_LIConvolutional neural networks trained on a limited dataset of 250 COVID-19 and 250 non-COVID-19 were tested on an independent dataset of 110 patients suspected for COVID-19 infection and provided a balanced performance with 0.80 sensitivity and 0.81 specificity.\nC_LIO_LITraining on larger multi-institutional datasets may allow this tool to increase its performance.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Isabella Castiglioni", + "author_inst": "Department of Physics, Universita degli Studi di Milano-Bicocca, Piazza della Scienza 3, 20126 Milano, Italy" + }, + { + "author_name": "Davide Ippolito", + "author_inst": "Department of Radiology, San Gerardo Hospital, Via Pergolesi 33, 20900 Monza, Italy" + }, + { + "author_name": "Matteo Interlenghi", + "author_inst": "Institute of Biomedical Imaging and Physiology, National Research Council, Segrate, Milan, Italy." + }, + { + "author_name": "Caterina Beatrice Monti", + "author_inst": "Department of Biomedical Sciences for Health, Universita degli Studi di Milano, Via Mangiagalli 31, 20133, Milan, Italy" + }, + { + "author_name": "Christian Salvatore", + "author_inst": "Scuola Universitaria Superiore IUSS Pavia, Piazza della Vittoria 15, 27100 Pavia, Italy; DeepTrace Technologies S.R.L., Via Conservatorio 17, 20122, Milan, Ital" + }, + { + "author_name": "Simone Schiaffino", + "author_inst": "Department of Radiology, IRCCS Policlinico San Donato, Via Morandi 30, 20097 San Donato Milanese, Milan, Italy." + }, + { + "author_name": "Annalisa Polidori", + "author_inst": "DeepTrace Technologies S.r.l., Via Conservatorio 17, 20122 Milan, Italy." + }, + { + "author_name": "Davide Gandola", + "author_inst": "Department of Radiology, San Gerardo Hospital, Via Pergolesi 33, 20900 Monza, Italy." + }, + { + "author_name": "Cristina Messa", + "author_inst": "Fondazione Tecnomed, Universita di Milano-Bicocca, Palazzina Ciclotrone, Via Pergolesi 33,, 20126 Milano, Italy." + }, + { + "author_name": "Francesco Sardanelli", + "author_inst": "Department of Biomedical Sciences for Health, Universita degli Studi di Milano, Via Mangiagalli 31, 20133, Milan, Italy; Department of Radiology, IRCCS Policlin" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.04.07.20049049", "rel_title": "Is the impact of social distancing on coronavirus growth rates effective across different settings? A non-parametric and local regression approach to test and compare the growth rate", @@ -1567887,29 +1569600,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.07.20057356", - "rel_title": "The Immediate Effect of COVID-19 Policies on Social Distancing Behavior in the United States", - "rel_date": "2020-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20057356", - "rel_abs": "Anecdotal evidence points to the effectiveness of COVID-19 social distancing policies, however, their effectiveness vis-a-vis what is driven by public awareness and voluntary actions have not been studied. Policy variations across US states create a natural experiment to study the causal impact of each policy. Using a difference-in-differences methodology, location-based mobility, and daily state-level data on COVID-19 tests and confirmed cases, we rank policies based on their effectiveness. We show that statewide stay-at-home orders had the strongest causal impact on reducing social interactions. In contrast, most of the expected impact of more lenient policies were already reaped from non-policy mechanisms. Moreover, stay-at-home policy results in a steady decline in confirmed cases, starting from ten days after implementation and reaching a 37% decrease after fifteen days, consistent with the testing practices and incubation period of the disease.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rahi Abouk", - "author_inst": "William Paterson University" - }, - { - "author_name": "Babak Heydari", - "author_inst": "Northeastern University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.05.026377", "rel_title": "On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2", @@ -1568057,6 +1569747,45 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.04.08.20057430", + "rel_title": "Anticipating the novel coronavirus disease (COVID-19) pandemic", + "rel_date": "2020-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057430", + "rel_abs": "COVID-19 outbreak has been declared as a public health emergency of international concern, and later as a pandemic. In most countries, the COVID-19 incidence curve rises sharply in a short period, suggesting a transition from a disease-free (or low-burden disease) equilibrium state to a sustained infected (or high-burden disease) state. Such a transition is often known to exhibit characteristics of critical slowing down. Critical slowing down can be, in general, successfully detected using many statistical measures such as variance, lag-1 autocorrelation, density ratio, and skewness. Here, we report an empirical test of this phenomena on the COVID-19 data sets for nine countries, including India, China, and the United States. For most of the data sets, increase in variance and autocorrelation predict the onset of a critical transition. Our analysis suggests two key features in predicting the COVID-19 incidence curve for a specific country: a) the timing of strict social distancing and/or lockdown interventions implemented, and b) the fraction of a nations population being affected by COVID-19 at that time. Further, using satellite data of nitrogen dioxide, as an indicator of lockdown efficacy, we find that in countries where the lockdown was implemented early and firmly have been successful in reducing the COVID-19 spread. These results are essential for designing effective strategies to control the spread/resurgence of infectious pandemics.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Taranjot Kaur", + "author_inst": "Indian Institute of Technology Ropar" + }, + { + "author_name": "Sukanta Sarkar", + "author_inst": "Indian Institute of Technology Ropar" + }, + { + "author_name": "Sourangsu Chowdhury", + "author_inst": "Max Planck Institute for Chemistry, 55128 Mainz, Germany" + }, + { + "author_name": "Sudipta Kumar Sinha", + "author_inst": "Indian Institute of Technology Ropar" + }, + { + "author_name": "Mohit Kumar Jolly", + "author_inst": "Indian Institute of Science Bangalore" + }, + { + "author_name": "Partha Sharathi Dutta", + "author_inst": "Indian Institute of Technology Ropar" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.07.024752", "rel_title": "Human ACE2 receptor polymorphisms predict SARS-CoV-2 susceptibility", @@ -1569793,109 +1571522,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.04.07.030742", - "rel_title": "Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue", - "rel_date": "2020-04-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.07.030742", - "rel_abs": "In December 2019, SARS-CoV-2 emerged causing the COVID-19 pandemic. SARS-CoV, the agent responsible for the 2003 SARS outbreak, utilizes ACE2 and TMPRSS2 host molecules for viral entry. ACE2 and TMPRSS2 have recently been implicated in SARS-CoV-2 viral infection. Additional host molecules including ADAM17, cathepsin L, CD147, and GRP78 may also function as receptors for SARS-CoV-2.\n\nTo determine the expression and in situ localization of candidate SARS-CoV-2 receptors in the respiratory mucosa, we analyzed gene expression datasets from airway epithelial cells of 515 healthy subjects, gene promoter activity analysis using the FANTOM5 dataset containing 120 distinct sample types, single cell RNA sequencing (scRNAseq) of 10 healthy subjects, immunoblots on multiple airway epithelial cell types, and immunohistochemistry on 98 human lung samples.\n\nWe demonstrate absent to low ACE2 promoter activity in a variety of lung epithelial cell samples and low ACE2 gene expression in both microarray and scRNAseq datasets of epithelial cell populations. Consistent with gene expression, rare ACE2 protein expression was observed in the airway epithelium and alveoli of human lung. We present confirmatory evidence for the presence of TMPRSS2, CD147, and GRP78 protein in vitro in airway epithelial cells and confirm broad in situ protein expression of CD147 in the respiratory mucosa.\n\nCollectively, our data suggest the presence of a mechanism dynamically regulating ACE2 expression in human lung, perhaps in periods of SARS-CoV-2 infection, and also suggest that alternate receptors for SARS-CoV-2 exist to facilitate initial host cell infection.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Jennifer A Aguiar", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Benjamin Jean-Marie Tremblay", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Michael J Mansfield", - "author_inst": "Okinawa Institute of Science and Technology" - }, - { - "author_name": "Owen Woody", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Briallen Lobb", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Arinjay Banerjee", - "author_inst": "McMaster University" - }, - { - "author_name": "Abiram Chandiramohan", - "author_inst": "McMaster University" - }, - { - "author_name": "Nicholas Tiessen", - "author_inst": "McMaster University" - }, - { - "author_name": "Anna Dvorkin-Gheva", - "author_inst": "McMaster University" - }, - { - "author_name": "Spencer Revill", - "author_inst": "McMaster University" - }, - { - "author_name": "Matthew S Miller", - "author_inst": "McMaster University" - }, - { - "author_name": "Christopher Carlsten", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Louise Organ", - "author_inst": "The University of Nottingham" - }, - { - "author_name": "Chitra Joseph", - "author_inst": "The University of Nottingham" - }, - { - "author_name": "Alison John", - "author_inst": "The University of Nottingham" - }, - { - "author_name": "Paul J Hanson", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Bruce M McManus", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Gisli Jenkins", - "author_inst": "The University of Nottingham" - }, - { - "author_name": "Karen Mossman", - "author_inst": "McMaster University" - }, - { - "author_name": "Kjetil Ask", - "author_inst": "McMaster University" - }, - { - "author_name": "Andrew C Doxey", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Jeremy A Hirota", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.04.07.030650", "rel_title": "The spatial and cell-type distribution of SARS-CoV-2 receptor ACE2 in human and mouse brain", @@ -1570179,6 +1571805,109 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.08.032763", + "rel_title": "Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS-CoV-2 by Remdesivir", + "rel_date": "2020-04-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.08.032763", + "rel_abs": "The pandemic of Corona Virus Disease 2019 (COVID-19) caused by SARS-CoV-2 has become a global crisis. The replication of SARS-CoV-2 requires the viral RNA-dependent RNA polymerase (RdRp), a direct target of the antiviral drug, Remdesivir. Here we report the structure of the SARS-CoV-2 RdRp either in the apo form or in complex with a 50-base template-primer RNA and Remdesivir at a resolution range of 2.5-2.8 [A]. The complex structure reveals that the partial double-stranded RNA template is inserted into the central channel of the RdRp where Remdesivir is incorporated into the first replicated base pair and terminates the chain elongation. Our structures provide critical insights into the working mechanism of viral RNA replication and a rational template for drug design to combat the viral infection.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Wanchao Yin", + "author_inst": "Shanghai Institute of Materia Medica" + }, + { + "author_name": "Chunyou Mao", + "author_inst": "Zhejiang University School of Medicine" + }, + { + "author_name": "Xiaodong Luan", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Dan-Dan Shen", + "author_inst": "Zhejiang University School of Medicine" + }, + { + "author_name": "Qingya Shen", + "author_inst": "Zhejiang University School of Medicine" + }, + { + "author_name": "Haixia Su", + "author_inst": "Shanghai Institute of Materia Medica" + }, + { + "author_name": "Xiaoxi Wang", + "author_inst": "Shanghai Institute of Materia Medica Chinese Academy of Sciences" + }, + { + "author_name": "Fulai Zhou", + "author_inst": "Shanghai Institute of Materia Medica" + }, + { + "author_name": "Wenfeng Zhao", + "author_inst": "Shanghai Institute of Materia Medica" + }, + { + "author_name": "Minqi Gao", + "author_inst": "Wuxi Biortus Biosciences Co. Ltd" + }, + { + "author_name": "Shenghai Chang", + "author_inst": "Zhejiang University School of Medicine" + }, + { + "author_name": "Yuan-Chao Xie", + "author_inst": "Shanghai Institute of Materia Medica" + }, + { + "author_name": "Guanghui Tian", + "author_inst": "Shanghai Institute of Materia Medica" + }, + { + "author_name": "He-Wei Jiang", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Sheng-Ce Tao", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Jingshan Shen", + "author_inst": "Shanghai Institute of Materia Medica" + }, + { + "author_name": "Yi Jiang", + "author_inst": "Shanghai Institute of Materia Medica Chinese Academy of Sciences" + }, + { + "author_name": "Hualiang Jiang", + "author_inst": "Shanghai Institute of Materia Medica" + }, + { + "author_name": "Yechun Xu", + "author_inst": "Shanghai Institute of Materia Medica" + }, + { + "author_name": "Shuyang Zhang", + "author_inst": "Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijin" + }, + { + "author_name": "Yan Zhang", + "author_inst": "Zhejiang University School of Medicine" + }, + { + "author_name": "H. Eric Xu", + "author_inst": "Shanghai Institute of Materia Medica" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.04.08.031856", "rel_title": "SARS-CoV-2 might manipulate against its host the immunity RNAi/Dicer/Ago system", @@ -1571186,33 +1572915,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.06.026765", - "rel_title": "Noisy Pooled PCR for Virus Testing", - "rel_date": "2020-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.06.026765", - "rel_abs": "Fast testing can help mitigate the coronavirus disease 2019 (COVID-19) pandemic. Despite their accuracy for single sample analysis, infectious diseases diagnostic tools, like RT-PCR, require substantial resources to test large populations. We develop a scalable approach for determining the viral status of pooled patient samples. Our approach converts group testing to a linear inverse problem, where false positives and negatives are interpreted as generated by a noisy communication channel, and a message passing algorithm estimates the illness status of patients. Numerical results reveal that our approach estimates patient illness using fewer pooled measurements than existing noisy group testing algorithms. Our approach can easily be extended to various applications, including where false negatives must be minimized. Finally, in a Utopian world we would have collaborated with RT-PCR experts; it is difficult to form such connections during a pandemic. We welcome new collaborators to reach out and help improve this work!", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Junan Zhu", - "author_inst": "Harvest Fund Management" - }, - { - "author_name": "Kristina Rivera", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Dror Baron", - "author_inst": "North Carolina State University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.04.03.20052548", "rel_title": "Lack of Antiviral Activity of Darunavir against SARS-CoV-2", @@ -1571404,6 +1573106,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.06.028316", + "rel_title": "Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic", + "rel_date": "2020-04-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.06.028316", + "rel_abs": "Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus disease 2019 (COVID-19), a respiratory tract infection. The standard molecular diagnostic test is a multistep process involving viral RNA extraction and real-time quantitative reverse transcriptase PCR (qRT-PCR). Laboratories across the globe face constraints on equipment and reagents during the COVID-19 pandemic. We have developed a simplified qRT-PCR assay that removes the need for an RNA extraction process and can be run on a real-time thermal cycler. The assay uses custom primers and probes, and maintains diagnostic sensitivity within 98.0% compared to the assay run on a high-throughput, random-access automated platform, the Panther Fusion (Hologic). This assay can be used to increase capacity for COVID-19 testing for national programmes worldwide.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Paul R Grant", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Melanie A Turner", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Gee Yen Shin", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Eleni Nastouli", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Lisa J Levett", + "author_inst": "Health Services Laboratories" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.04.02.20051565", "rel_title": "Targeting the catecholamine-cytokine axis to prevent SARS-CoV-2 cytokine storm syndrome", @@ -1572496,49 +1574233,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.04.03.20051649", - "rel_title": "Efficacy of face mask in preventing respiratory virus transmission: a systematic review and meta-analysis", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20051649", - "rel_abs": "BackgroundConflicting recommendations exist related to whether masks have a protective effect on the spread of respiratory viruses.\n\nMethodsThe Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement was consulted to report this systematic review. Relevant articles were retrieved from PubMed, Web of Science, ScienceDirect, Cochrane Library, and Chinese National Knowledge Infrastructure (CNKI), VIP (Chinese) database.\n\nResultsA total of 21 studies met our inclusion criteria. Meta-analyses suggest that mask use provided a significant protective effect (OR=0.35 and 95% CI=0.24-0.51). Use of masks by healthcare workers (HCWs) and non-healthcare workers (Non-HCWs) can reduce the risk of respiratory virus infection by 80% (OR=0.20, 95% CI=0.11-0.37) and 47% (OR=0.53, 95% CI=0.36-0.79). The protective effect of wearing masks in Asia (OR=0.31) appeared to be higher than that of Western countries (OR=0.45). Masks had a protective effect against influenza viruses (OR=0.55), SARS (OR=0.26), and SARS-CoV-2 (OR=0.04). In the subgroups based on different study designs, protective effects of wearing mask were significant in cluster randomized trials and observational studies.\n\nConclusionsThis study adds additional evidence of the enhanced protective value of masks, we stress that the use masks serve as an adjunctive method regarding the COVID-19 outbreak.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mingming Liang", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "Liang Gao", - "author_inst": "Saarland University Medical Center" - }, - { - "author_name": "Ce Cheng", - "author_inst": "Cape Fear Valley Medical Center" - }, - { - "author_name": "Qin Zhou", - "author_inst": "Mayo clinic" - }, - { - "author_name": "John Patrick Uy", - "author_inst": "AMITA Health Saint Joseph Hospital Chicago" - }, - { - "author_name": "Kurt Heiner", - "author_inst": "Dignity Health Mercy Hospital" - }, - { - "author_name": "Chenyu Sun", - "author_inst": "AMITA Health Saint Joseph Hospital Chicago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.02.20050914", "rel_title": "A statistical method of batch screening entrying population from abroad by stages and groups in COVID-19 nucleic acid testing", @@ -1572722,6 +1574416,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.04.02.20048793", + "rel_title": "A globally available COVID-19 - Template for clinical imaging studies", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20048793", + "rel_abs": "BackgroundThe pandemic spread of COVID-19 has caused worldwide implications on societies and economies. Chest computed tomography (CT) has been found to support both, current diagnostic and disease monitoring. A joint approach to collect, analyze and share clinical and imaging information about COVID-19 in the highest quality possible is urgently needed.\n\nMethodsAn evidence-based reporting template was developed for assessing COVID-19 pneumonia using an FDA-approved medical software. The annotation of qualitative and quantitative findings including radiomics features is performed directly on primary imaging data. For data collection, secondary information from the patient history and clinical data such as symptoms and comorbidities are queried.\n\nResultsLicense-royalty free, cloud-based web platform and on-premise deployments are offered. Hospitals can upload, assess, report and if pseudonymized share their COVID-19 cases. The aggregation of radiomics in correlation with rt-PCR, patient history, clinical and radiological findings, systematically documented in a single database, will lead to optimized diagnosis, risk stratification and response evaluation. A customizable analytics dashboard allows the explorative real-time data analysis of imaging features and clinical information.\n\nConclusionsThe COVID-19-Template is based on a systematic, computer-assisted and context-guided approach to collect, analyze and share data. Epidemiological and clinical studies for therapies and vaccine candidates can be implemented in compliance with high data quality, integrity and traceability.\n\nAn additional explanation video of the COVID-19-Template video is provided via:http://cloud1.mint-medical.de/downloads/player/index.html?v=Covid19StandardizedAssessmentWeb\n\nHighlightsO_LIDynamic evidence-based electronic case report form (eCRF) for COVID-19 including documentation of primary imaging data, secondary clinical data and patient history including radiomics features\nC_LIO_LIComputer-assisted, context-guided reporting approach based on FDA approved medical product software package available free of charge\nC_LIO_LIData quality, traceability, integrity in open-access web platform\nC_LIO_LICustomizable analytics dashboard for explorative real-time data analysis of imaging features and clinical information\nC_LIO_LIHuman and machine-readable data export for clinical trials\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Gabriel Alexander Salg", + "author_inst": "University Hospital Heidelberg, Department of Surgery, New Technologies and Data Science, Heidelberg, Germany" + }, + { + "author_name": "Maria Katharina Ganten", + "author_inst": "Mint Medical GmbH, Heidelberg, Germany" + }, + { + "author_name": "Matthias Baumhauer", + "author_inst": "Mint Medical GmbH, Heidelberg, Germany" + }, + { + "author_name": "Claus Peter Heussel", + "author_inst": "University Hospital Heidelberg, Department of Diagnostic and Interventional Radiology, Heidelberg, Germany" + }, + { + "author_name": "Jens Kleesiek", + "author_inst": "German Cancer Research Center (DKFZ), Department of Radiology, Computational Radiology, Heidelberg, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.04.01.20050443", "rel_title": "Can N95 respirators be reused after disinfection? And for how many times?", @@ -1573714,33 +1575443,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.03.20052878", - "rel_title": "Search for trends of Covid-19 infection in India, China, Denmark, Brazil, France. Germany and the USA on the basis of power law scaling", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20052878", - "rel_abs": "The corona virus (SARS-CoV-2) or Covid-19 pandemic is growing alarmingly throughout the whole world. Using the power law scaling we analyze the data of different countries and three states of India up to 1st April, 2020 and explain in terms of power law exponent. We find significant reduction in growth of infections in China and Denmark ({gamma} reduced from approximately 2.18 to 0.05 and 11.41 to 6.95, respectively). Very slow reduction is also seen in Brazil and Germany ({gamma} reduced from approximately 6 to 4 and 11 to 7, respectively). Infection in India is growing ({gamma}=9.23) though lesser in number than that in the USA (highest {gamma} of 16 approximately, studied so far), Italy and a few other countries. Among three Indian states the growth in West Bengal ({gamma}=0.64) is much slower than other states like Maharashtra and Kerala ({gamma}=3.23 and 3.32, respectively). Some future predictions, though not rigid, has also been incorporated in our analysis. The earlier lock-down and stricter measures from the Governments concerned are being thought to be the only possible solutions, in the present situation, to fight against this virus.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "SRIJIT BHATTACHARYA", - "author_inst": "DEPARTMENT OF PHYSICS, BARASAT GOVERNMENT COLLEGE" - }, - { - "author_name": "MD MOINUL ISLAM", - "author_inst": "DEPARTMENT OF PHYSICS, APC COLLEGE" - }, - { - "author_name": "ALOKKUMAR DE", - "author_inst": "DEPT OF PHYSICS, RANIGANJ GIRLS COLLEGE" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.04.20053629", "rel_title": "Association of COVID-19 Infections in San Francisco in Early March 2020 with Travel to New York and Europe", @@ -1573960,6 +1575662,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.05.20053355", + "rel_title": "Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20053355", + "rel_abs": "Reverse transcription-polymerase chain reaction (RT-PCR) assays are used to test patients and key workers for infection with the causative SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives can occur if the sample contains insufficient quantities of the virus to be successfully amplified and detected. The amount of virus in a swab is likely to vary between patients, sample location (nasal, throat or sputum) and through time as infection progresses. Here, we analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once. We identify that the probability of a positive test decreases with time after symptom onset, with throat samples less likely to yield a positive result relative to nasal samples. Empirically derived distributions of the time between symptom onset and hospitalisation allowed us to comment on the likely false negative rates in cohorts of patients who present for testing at different clinical stages. We further estimate the expected numbers of false negative tests in a group of tested individuals and show how this is affected by the timing of the tests. Finally, we assessed the robustness of these estimates of false negative rates to the probability of false positive tests. This work has implications both for the identification of infected patients and for the discharge of convalescing patients who are potentially still infectious.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Paul Wikramaratna", + "author_inst": "None." + }, + { + "author_name": "Robert S Paton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Mahan Ghafari", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jose Lourenco", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.04.20053595", "rel_title": "Initial evidence of higher morbidity and mortality due to SARS-CoV-2 in regions with lower air quality", @@ -1575160,25 +1576893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.02.20051466", - "rel_title": "Predictions for COVID-19 outbreak in India using Epidemiological models", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051466", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWCOVID-19 data from India is compared against several countries as well as key states in the US with a major outbreak, and it is found that the basic reproduction number R0 for India is in the expected range of 1.4-3.9. Further, the rate of growth of infections in India is very close to that in Washington and California. Exponential and classic susceptible-infected-recovered (SIR) models based on available data are used to make short and long-term predictions on a daily basis. Based on the SIR model, it is estimated that India will enter equilibrium by the end of May 2020 with the final epidemic size of approximately 13,000. However, this estimation will be invalid if India enters the stage of community transmission. The impact of social distancing, again with the assumption of no community transmission, is also assessed by comparing data from different geographical locations.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Rajesh Ranjan", - "author_inst": "The Ohio State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.02.20051680", "rel_title": "COVID-19 epidemic: Power law spread and flattening of the curve", @@ -1575362,6 +1577076,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.03.30.20047969", + "rel_title": "COVID-19 and maternal mental health: Are we getting the balance right?", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047969", + "rel_abs": "This paper presents a rapid evidence review into the clinical and psychological impacts of COVID-19 on perinatal women and their infants. Literature search revealed that there is very little formal evidence on the impact of COVID-19 on pregnant, labouring and postnatal women or their babies. The clinical evidence to date suggests that pregnant and childbearing women, and their babies are not at increased risk of either getting infected, or of having severe symptoms or consequences than the population as a whole. There is no evidence on the short- and longer-term psychological impacts of restrictive practices or social and personal constraints for childbearing women during COVID-19 in particular, or infection pandemics in general. The potential for adverse mental health consequences of the pandemic should be recognised as a critical public health concern, together with appropriate care and support to prevent and ameliorate any negative impacts.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Anastasia Topalidou", + "author_inst": "THRIVE Centre, Faculty of Health and Wellbeing, University of Central Lancashire, UK" + }, + { + "author_name": "Gill Thomson", + "author_inst": "THRIVE Centre, Faculty of Health and Wellbeing, University of Central Lancashire, UK" + }, + { + "author_name": "Soo Downe", + "author_inst": "THRIVE Centre, Faculty of Health and Wellbeing, University of Central Lancashire, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.05.026146", "rel_title": "CovProfile: profiling the viral genome and gene expressions of SARS-COV2", @@ -1576354,73 +1578095,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.02.20050997", - "rel_title": "Acute liver injury and its association with death risk of patients with COVID-19: a hospital-based prospective case-cohort study", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050997", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is a newly respiratory infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with multiple organ injuries. The aim of this study was to analyze SARS-CoV-2-induced acute liver injury (ALI), its association with death risk and prognosis after discharge.\n\nMethodsThree-hundred and fifty-five COVID-19 patients were recruited. Clinical data were collected from electronic medical records. ALI was evaluated and its prognosis was tracked. The association between ALI and death risk was analyzed.\n\nResultsOf 355 COVID-19 patients, 211 were common, 88 severe, and 51 critical ill cases, respectively. On admission, 223 (62.8%) patients were with hypoproteinemia, 151(42.5%) with cholestasis, and 101 (28.5%) with hepatocellular injury. As expected, ALI was more common in critical ill patients. By multivariate logistic regression, male, older age and lymphocyte reduction were three important independent risk factors predicting ALI among COVID-19 patients. Death risk analysis shows that fatality rate was higher among patients with hypoproteinemia than those without hypoproteinemia (RR=9.471, P<0.001). Moreover, fatality rate was higher among patients with cholestasis than those without cholestasis (RR=2.182, P<0.05). Follow-up observation found that more than one hepatic functional indexes of two-third patients remained abnormal 14 days after discharge.\n\nConclusionsALI at early stage elevates death risk of COVID-19 patients. SARS-CoV-2-induced ALI has not recovered completely 14 days after discharge.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Lin Fu", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "Jun Fei", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "Shen Xu", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "Hui-Xian Xiang", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "Ying Xiang", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "Zhu-Xia Tan", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "Meng-Die Li", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "Fang-Fang Liu", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "Ying Li", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Ming-Feng Han", - "author_inst": "Fuyang Second People's Hospital" - }, - { - "author_name": "Xiu-Yong Li", - "author_inst": "Fuyang Second People's Hospital" - }, - { - "author_name": "Hui Zhao", - "author_inst": "Anhui Medical University" - }, - { - "author_name": "De-Xiang Xu", - "author_inst": "Anhui Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.02.20050955", "rel_title": "Reduction of lymphocyte at early stage elevates severity and death risk of COVID-19 patients: a hospital-based case-cohort study", @@ -1576572,6 +1578246,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.02.20050666", + "rel_title": "COVID-19 Outbreak in Oman: Model-Driven Impact Analysis and Challenges", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050666", + "rel_abs": "Motivated by the rapid spread of COVID-19 all across the globe, we have performed simulations of a system dynamic epidemic spread model in different possible situations. The simulation, not only captures the model dynamic of the spread of the virus, but also, takes care of population and mobility data. The model is calibrated based on epidemic data and events specifically of Sultanate of Oman, which can easily be generalized. The simulation results are quite disturbing, indicating that, during a process of stringent social distancing and testing strategies, a small perturbation can lead to quite undesirable outcomes. The simulation results, although consistent in expected outcomes across changing parameters values, also indicate a substantial mismatch with real numbers. An analysis of what can be the reason of this mismatch is also performed. Within these contradictions, for Oman, regarding the eradication of epidemic, the future is not extremely alarming.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kashif Zia", + "author_inst": "Sohar University, Oman" + }, + { + "author_name": "Umar Farooq", + "author_inst": "University of Science and Technology Bannu, Pakistan" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.02.20050633", "rel_title": "Explaining national differences in the mortality of Covid-19: individual patient simulation model to investigate the effects of testing policy and other factors on apparent mortality.", @@ -1577504,37 +1579201,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.01.20047373", - "rel_title": "Frequency of testing for COVID 19 infection and the presence of higher number of available beds per country predict outcomes with the infection, not the GDP of the country - A descriptive statistical analysis", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20047373", - "rel_abs": "IntroductionThe novel coronavirus epidemic which originated in late 2019 from China has wreaked havoc on millions across the world with illness, death and socioeconomic recession. As of now no valid treatment or preventative strategy has evolved worldwide and governments across the world have been forced to take the draconian step of social isolation in communities by enforcing \"lockdowns\".\n\nAim of this StudyThis study aims to correlate the rates of infection with the novel coronavirus and total deaths as the primary output variable. In addition the strength of association between infection rates and total death in comparison to GDP share of the respective countries, physicians, hospital beds and rates of testing for COVID 19 infection per thousand patients, is being assessed, in a bid to develop a model which would help to develop tools to reduce the impact of this disease.\n\nMaterial & MethodsData relating to number of cases, severity, cases recovered and deaths worldwide and specifically for the top six countries affected was collected from the WHO COVID-19 situation report which is being updated on a daily basis till 22nd March 2020, the date of analysis. Additional data related to GDP, physician and hospital bed per 1000 patients were procured from the World Bank database. All data were collected in a file in CSV format. Analysis was conducted in Jupyter notebook with Python 3.8.2 software and also with XL-Stat statistical software for excel. The analytical strategy was descriptive with no inferential overtones.\n\nResultsCOVID 19 infection strongly correlates with total deaths (r : 0.89), with a predicted death rate of 25 patients per 1000 affected. There was no correlation between the GDP growth of the country and number of treating physicians/1000 patient population with any COVID 19 related outcome. However there was a negative correlation between COVID 19-related deaths and the number of beds available per 1000 population [r=-0.34]. Importantly there is an inverse correlation between the number of tests conducted per million population with the rates of active infections [r=-0.12], new cases [r=-0.38] and new deaths [r=-0.28] in COVID 19.\n\nConclusionThis is the first study to assess parameters other than age and sex and sets out a robust dataset which indicates an increased risk of worsening outcomes with lesser number of beds and testing, suggesting that the need of the hour is to increase available bed numbers and to increase rates of testing.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "SAMIT GHOSAL", - "author_inst": "Nightingale Hospital" - }, - { - "author_name": "Binayak Sinha", - "author_inst": "AMRI Hospitals" - }, - { - "author_name": "Sumit Sengupta", - "author_inst": "AMRI Hospitals" - }, - { - "author_name": "Milan Majumder", - "author_inst": "Independent Biostatistician" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.03.20051722", "rel_title": "Urinalysis, but not blood biochemistry, detects the early renal-impairment in patients with COVID-19", @@ -1577854,6 +1579520,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.02.20051342", + "rel_title": "How to quit confinement? French scenarios face to COVID-19", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051342", + "rel_abs": "A mathematical model is developed to study the spread of the COVID-19 epidemics in France. Data from French Public Agency of Health are considered to calibrate the model. The spread of the epidemics strongly depends on confinement measures. The aim of the paper is to predict the evolution of the epidemics under various scenarios that could be taken to quit confinement. The spread of the disease and its re-emergence strongly depends on these scenarios.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Emmanuelle Augeraud-Veron", + "author_inst": "University of Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.02.20051318", "rel_title": "Estimating the presymptomatic transmission of COVID19 using incubation period and serial interval data", @@ -1578938,65 +1580623,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.03.31.20038935", - "rel_title": "Angiotensin II Receptor Blockers and Angiotensin-Converting Enzyme Inhibitors Usage is Associated with Improved Inflammatory Status and Clinical Outcomes in COVID-19 Patients With Hypertension", - "rel_date": "2020-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20038935", - "rel_abs": "With the capability of inducing elevated expression of ACE2, the cellular receptor for SARS-CoV-2, angiotensin II receptor blockers or angiotensin-converting enzyme inhibitors (ARBs/ACEIs) treatment may have a controversial role in both facilitating virus infection and reducing pathogenic inflammation. We aimed to evaluate the correlation of ARBs/ACEIs usage with the pathogenesis of COVID-19 in a retrospective, single-center study. 126 COVID-19 patients with preexisting hypertension at Hubei Provincial Hospital of Traditional Chinese Medicine (HPHTCM) in Wuhan from January 5 to February 22, 2020 were retrospectively allocated to ARBs/ACEIs group (n=43) and non-ARBs/ACEIs group (n=83) according to their antihypertensive medication. 125 age- and sex-matched COVID-19 patients without hypertension were randomly selected as non-hypertension controls. In addition, the medication history of 1942 hypertension patients that were admitted to HPHTCM from November 1 to December 31, 2019 before COVID-19 outbreak were also reviewed for external comparison. Epidemiological, demographic, clinical and laboratory data were collected, analyzed and compared between these groups. The frequency of ARBs/ACEIs usage in hypertension patients with or without COVID-19 were comparable. Among COVID-19 patients with hypertension, those received either ARBs/ACEIs or non-ARBs/ACEIs had comparable blood pressure. However, ARBs/ACEIs group had significantly lower concentrations of CRP (p=0.049) and procalcitonin (PCT, p=0.008). Furthermore, much lower proportion of critical patients (9.3% vs 22.9%; p=0.061), and a lower death rate (4.7% vs 13.3%; p=0.216) were observed in ARBs/ACEIs group than non-ARBs/ACEIs group, although these differences failed to reach statistical significance. Our findings thus support the use of ARBs/ACEIs in COVID-19 patients with preexisting hypertension.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Guang Yang", - "author_inst": "Department of Geriatrics, Hubei Provincial Hospital of Traditional Chinese Medicine; Hubei Provincial Academy of Traditional Chinese Medicine." - }, - { - "author_name": "Zihu Tan", - "author_inst": "Department of Geriatrics, Hubei Provincial Hospital of Traditional Chinese Medicine; Hubei Provincial Academy of Traditional Chinese Medicine" - }, - { - "author_name": "Ling Zhou", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Min Yang", - "author_inst": "Department of Preventive Medicine, School of Basic Medicine, Hubei University of Chinese Medicine" - }, - { - "author_name": "Lang Peng", - "author_inst": "Department of Geriatrics, Hubei Provincial Hospital of Traditional Chinese Medicine; Hubei Provincial Academy of Traditional Chinese Medicine" - }, - { - "author_name": "Jinjin Liu", - "author_inst": "Department of Geriatrics, Hubei Provincial Hospital of Traditional Chinese Medicine; Hubei Provincial Academy of Traditional Chinese Medicine" - }, - { - "author_name": "Jingling Cai", - "author_inst": "Department of Geriatrics, Hubei Provincial Hospital of Traditional Chinese Medicine; Hubei Provincial Academy of Traditional Chinese Medicine" - }, - { - "author_name": "Ru Yang", - "author_inst": "Wuhan Blood Center" - }, - { - "author_name": "Junyan Han", - "author_inst": "Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Yafei Huang", - "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Shaobin He", - "author_inst": "Department of Geriatrics, Hubei Provincial Hospital of Traditional Chinese Medicine; Hubei Provincial Academy of Traditional Chinese Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.01.20041186", "rel_title": "Countrywide quarantine only mildly increased anxiety level during COVID-19 outbreak in China", @@ -1579220,6 +1580846,185 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.01.20047076", + "rel_title": "Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China", + "rel_date": "2020-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20047076", + "rel_abs": "COVID-19 is caused by the SARS-CoV-2 coronavirus and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, Chinas most populous province, during early 2020 resulted in 1,388 reported RNA positive cases from 1.6 million tests. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. Combined epidemiological and phylogenetic analyses indicate multiple independent introductions to Guangdong, although phylogenetic clustering is uncertain due to low virus genetic variation early in the pandemic. Our results illustrate how the timing, size and duration of putative local transmission chains were constrained by national travel restrictions and by the provinces large-scale intensive surveillance and intervention measures. Despite these successes, COVID-19 surveillance in Guangdong is still required as the number of cases imported from other countries is increasing.\n\nHighlightsO_LI1.6 million molecular diagnostic tests identified 1,388 SARS-CoV-2 infections in Guangdong Province, China, by 19th March 2020\nC_LIO_LIVirus genomes can be recovered using a variety of sequencing approaches from a range of patient samples.\nC_LIO_LIGenomic analyses reveal multiple virus importations into Guangdong Province, resulting in genetically distinct clusters that require careful interpretation.\nC_LIO_LILarge-scale epidemiological surveillance and intervention measures were effective in interrupting community transmission in Guangdong\nC_LI", + "rel_num_authors": 41, + "rel_authors": [ + { + "author_name": "Jing Lu", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Louis du Plessis", + "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" + }, + { + "author_name": "Zhe Liu", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Verity Hill", + "author_inst": "University of Edinburgh, UK" + }, + { + "author_name": "Min Kang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Huifang Lin", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Jiufeng Sun", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Sarah Francois", + "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" + }, + { + "author_name": "Moritz U G Kraemer", + "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" + }, + { + "author_name": "Nuno R Faria", + "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" + }, + { + "author_name": "John T McCrone", + "author_inst": "University of Edinburgh, UK" + }, + { + "author_name": "Jinju Peng", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Qianling Xiong", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Runyu Yuan", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Lilian Zeng", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Pingping Zhou", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Chuming Liang", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Lina Yi", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Jun Liu", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Jianpeng Xiao", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Jianxiong Hu", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Tao Liu", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Wenjun Ma", + "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Wei Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Juan Su", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Huanying Zheng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Bo Peng", + "author_inst": "Shenzhen Center for Disease Control and Prevention, China" + }, + { + "author_name": "Shisong Fang", + "author_inst": "Shenzhen Center for Disease Control and Prevention, China" + }, + { + "author_name": "Wenzhe Su", + "author_inst": "Guangzhou Center for Disease Control and Prevention, China" + }, + { + "author_name": "Kuibiao Li", + "author_inst": "Guangzhou Center for Disease Control and Prevention, China" + }, + { + "author_name": "Ruilin Sun", + "author_inst": "Guangdong Provincial Second People's Hospital, Guangzhou, China" + }, + { + "author_name": "Ru Bai", + "author_inst": "Guangdong Provincial Second People's Hospital, Guangzhou, China" + }, + { + "author_name": "Xi Tang", + "author_inst": "Foshan First People's Hospital, Foshan, China" + }, + { + "author_name": "Minfeng Liang", + "author_inst": "Foshan First People's Hospital, Foshan, China" + }, + { + "author_name": "Josh Quick", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, UK" + }, + { + "author_name": "Tie Song", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + }, + { + "author_name": "Andrew Rambaut", + "author_inst": "University of Edinburgh, UK" + }, + { + "author_name": "Nick Loman", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, UK" + }, + { + "author_name": "Jayna Raghwani", + "author_inst": "Department of Zoology, University of Oxford, Oxford, UK" + }, + { + "author_name": "Oliver Pybus", + "author_inst": "University of Oxford" + }, + { + "author_name": "Changwen Ke", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.31.20042333", "rel_title": "Detection of 2019 novel coronavirus in semen and testicular biopsy specimen of COVID-19 patients", @@ -1580136,53 +1581941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.31.20049312", - "rel_title": "Projected ICU and Mortuary load due to COVID-19 in Sydney", - "rel_date": "2020-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049312", - "rel_abs": "The spread of COVID-19 is expected to put a large strain on many hospital resources, including ICU bed space, and mortuary capacity. In this report we study the possible demands on ICU and mortuary capacity in Sydney, Australia, using an adapted SEIR epidemiological model.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Andrew Francis", - "author_inst": "Western Sydney University" - }, - { - "author_name": "Yi Guo", - "author_inst": "Western Sydney University" - }, - { - "author_name": "Paul Hurley", - "author_inst": "Western Sydney University" - }, - { - "author_name": "Oliver Obst", - "author_inst": "Western Sydney University" - }, - { - "author_name": "Laurence A. F. Park", - "author_inst": "Western Sydney University" - }, - { - "author_name": "Mark Tanaka", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Russell Thomson", - "author_inst": "Western Sydney University" - }, - { - "author_name": "Rosalind Wang", - "author_inst": "Western Sydney University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.01.20050526", "rel_title": "Meteorological factors correlate with transmission of 2019-nCoV: Proof of incidence of novel coronavirus pneumonia in Hubei Province, China", @@ -1580314,6 +1582072,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.01.20049767", + "rel_title": "Intervention Serology and Interaction Substitution: Modeling the Role of 'Shield Immunity' in Reducing COVID-19 Epidemic Spread", + "rel_date": "2020-04-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20049767", + "rel_abs": "The COVID-19 pandemic has precipitated a global crisis, with more than 690,000 confirmed cases and more than 33,000 confirmed deaths globally as of March 30, 2020 [1-4]. At present two central public health control strategies have emerged: mitigation and suppression (e.g, [5]). Both strategies focus on reducing new infections by reducing interactions (and both raise questions of sustainability and long-term tactics). Complementary to those approaches, here we develop and analyze an epidemiological intervention model that leverages serological tests [6, 7] to identify and deploy recovered individuals as focal points for sustaining safer interactions via interaction substitution, i.e., to develop what we term shield immunity at the population scale. Recovered individuals, in the present context, represent those who have developed protective, antibodies to SARS-CoV-2 and are no longer shedding virus [8]. The objective of a shield immunity strategy is to help sustain the interactions necessary for the functioning of essential goods and services (including but not limited to tending to the elderly [9], hospital care, schools, and food supply) while decreasing the probability of transmission during such essential interactions. We show that a shield immunity approach may significantly reduce the length and reduce the overall burden of an outbreak, and can work synergistically with social distancing. The present model highlights the value of serological testing as part of intervention strategies, in addition to its well recognized roles in estimating prevalence [10, 11] and in the potential development of plasma-based therapies [12-15].", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Joshua S Weitz", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Stephen J Beckett", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Ashley R Coenen", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "David Demory", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Marian Dominguez-Mirazo", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Jonathan Dushoff", + "author_inst": "McMaster University" + }, + { + "author_name": "Chung-Yin Leung", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Guanlin Li", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Andreea Magalie", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Sang Woo Park", + "author_inst": "Princeton University" + }, + { + "author_name": "Rogelio Rodriguez-Gonzalez", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Shashwat Shivam", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Conan Zhao", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.01.20049692", "rel_title": "The Effectiveness of Targeted Quarantine for Minimising Impact of COVID-19", @@ -1581218,89 +1583043,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2020.03.31.017889", - "rel_title": "Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia", - "rel_date": "2020-04-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.31.017889", - "rel_abs": "In the current COVID-19 pandemic context, proposing and validating effective treatments represents a major challenge. However, the lack of biologically relevant pre-clinical experimental models of SARS-CoV-2 infection as a complement of classic cell lines represents a major barrier for scientific and medical progress. Here, we advantageously used human reconstituted airway epithelial models of nasal or bronchial origin to characterize viral infection kinetics, tissue-level remodeling of the cellular ultrastructure and transcriptional immune signatures induced by SARS-CoV-2. Our results underline the relevance of this model for the preclinical evaluation of antiviral candidates. Foremost, we provide evidence on the antiviral efficacy of remdesivir and the therapeutic potential of the remdesivir-diltiazem combination as a rapidly available option to respond to the current unmet medical need imposed by COVID-19.\n\nOne Sentence SummaryNew insights on SARS-CoV-2 biology and drug combination therapies against COVID-19.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Andres Pizzorno", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Blandine Padey", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Thomas Julien", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Sophie Trouillet-Assant", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Aurelien Traversier", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Julien Fouret", - "author_inst": "Signia Therapeutics SA" - }, - { - "author_name": "Julia Dubois", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Alexandre Gaymard", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Xavier Lescure", - "author_inst": "AP-HP, Infectious and Tropical Diseases Department, Bichat-Claude Bernard University Hospital" - }, - { - "author_name": "Victoria Duliere", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Pauline Brun", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Samuel Constant", - "author_inst": "Epithelix Sarl, Geneva, Switzerland" - }, - { - "author_name": "Julien Poissy", - "author_inst": "Pole de Reanimation, Hopital Roger Salengro, Centre Hospitalier Regional et Universitaire de Lille, Universite de Lille 2" - }, - { - "author_name": "Bruno Lina", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Yazdan Yazdanpanah", - "author_inst": "AP-HP, Infectious and Tropical Diseases Department, Bichat-Claude Bernard University Hospital" - }, - { - "author_name": "Olivier Terrier", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Manuel Rosa-Calatrava", - "author_inst": "Centre International de Recherche en Infectiologie" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.31.019216", "rel_title": "Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis", @@ -1581512,6 +1583254,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.03.30.20048264", + "rel_title": "Estimating the risk of COVID-19 death during the course of the outbreak in Korea, February-March, 2020", + "rel_date": "2020-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20048264", + "rel_abs": "Background: In Korea, a total of 10,840 confirmed cases of COVID-19 including 256 deaths have been recorded as of May 9, 2020. The time-delay adjusted case fatality risk (CFR) of COVID-19 in Korea is yet to be estimated. Methods: We obtained the daily series of confirmed cases and deaths in Korea reported prior to May 9, 2020. Using statistical methods, we estimated the time-delay adjusted risk for death from COVID-19 in Daegu, Gyeongsangbuk-do, other regions in Korea, as well as the entire country. Results: Our model-based crude CFR fitted the observed data well throughout the course of the epidemic except for the very early stage in Gyeongsangbuk-do; this was partially due to the reporting delay. Our estimates of the risk of death in Gyeongsangbuk-do reached 25.9% (95% CrI: 19.6%-33.6%), 20.8% (95% CrI: 18.1%-24.0%) in Daegu and 1.7% (95% CrI: 1.1%-2.5%) in other regions, whereas the national estimate was 10.2% (95% CrI: 9.0%-11.5%). Conclusions: The latest estimates of CFR of COVID-19 in Korea are considerably high, even with the early implementation of public health interventions including widespread testing, social distancing, and delayed school openings. Geographic differences in the CFR are likely influenced by clusters tied to hospitals and nursing homes.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eunha Shim", + "author_inst": "Soongsil University" + }, + { + "author_name": "Kenji Mizumoto", + "author_inst": "Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University" + }, + { + "author_name": "Wongyeong Choi", + "author_inst": "Soongsil University" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.30.20047985", "rel_title": "Why is chest CT important for early diagnosis of COVID-19? Prevalence matters", @@ -1582452,29 +1584225,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.03.30.20047308", - "rel_title": "Predicting Mortality Risk in Patients with COVID-19 Using Artificial Intelligence to Help Medical Decision-Making", - "rel_date": "2020-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047308", - "rel_abs": "In the wake of COVID-19 disease, caused by the SARS-CoV-2 virus, we designed and developed a predictive model based on Artificial Intelligence (AI) and Machine Learning algorithms to determine the health risk and predict the mortality risk of patients with COVID-19. In this study, we used documented data of 117,000 patients world-wide with laboratory-confirmed COVID-19. This study proposes an AI model to help hospitals and medical facilities decide who needs to get attention first, who has higher priority to be hospitalized, triage patients when the system is overwhelmed by overcrowding, and eliminate delays in providing the necessary care. The results demonstrate 93% overall accuracy in predicting the mortality rate. We used several machine learning algorithms including Support Vector Machine (SVM), Artificial Neural Networks, Random Forest, Decision Tree, Logistic Regression, and K-Nearest Neighbor (KNN) to predict the mortality rate in patients with COVID-19. In this study, the most alarming symptoms and features were also identified. Finally, we used a separate dataset of COVID-19 patients to evaluate our developed model accuracy, and used confusion matrix to make an in-depth analysis of our classifiers and calculate the sensitivity and specificity of our model.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mohammad Pourhomayoun", - "author_inst": "California State University Los Angeles" - }, - { - "author_name": "Mahdi Shakibi", - "author_inst": "California State University Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.03.27.20045062", "rel_title": "How lethal is the novel coronavirus, and how many undetected cases there are? The importance of being tested.", @@ -1582634,6 +1584384,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.29.20046557", + "rel_title": "Detection of Air and Surface Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Hospital Rooms of Infected Patients", + "rel_date": "2020-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20046557", + "rel_abs": "Understanding the particle size distribution in the air and patterns of environmental contamination of SARS-CoV-2 is essential for infection prevention policies. We aimed to detect SARS-CoV-2 surface and air contamination and study associated patient-level factors. 245 surface samples were collected from 30 airborne infection isolation rooms of COVID-19 patients, and air sampling was conducted in 3 rooms.\n\nAir sampling detected SARS-CoV-2 PCR-positive particles of sizes >4 {micro}m and 1-4 {micro}m in two rooms, which warrants further study of the airborne transmission potential of SARS-CoV-2. 56.7% of rooms had at least one environmental surface contaminated. High touch surface contamination was shown in ten (66.7%) out of 15 patients in the first week of illness, and three (20%) beyond the first week of illness (p = 0.010).", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Po Ying Chia", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Kristen K Coleman", + "author_inst": "Duke-NUS Medical School, National University of Singapore" + }, + { + "author_name": "Yian Kim Tan", + "author_inst": "DSO National Laboratories, Singapore" + }, + { + "author_name": "Sean Wei Xiang Ong", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Marcus Gum", + "author_inst": "DSO National Laboratories, Singapore" + }, + { + "author_name": "Sok Kiang Lau", + "author_inst": "DSO National Laboratories, Singapore" + }, + { + "author_name": "Stephanie Sutjipto", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Pei Hua Lee", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Than The Son", + "author_inst": "Duke-NUS Medical School, National University of Singapore" + }, + { + "author_name": "Barnaby E. Young", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Donald K. Milton", + "author_inst": "Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, USA" + }, + { + "author_name": "Gregory C. Gray", + "author_inst": "Duke-NUS Medical School, National University of Singapore" + }, + { + "author_name": "Stephan Schuster", + "author_inst": "Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore" + }, + { + "author_name": "Timothy Barkham", + "author_inst": "Tan Tock Seng Hospital, Singapore" + }, + { + "author_name": "Partha Prathim De", + "author_inst": "Tan Tock Seng Hospital, Singapore" + }, + { + "author_name": "Shawn Vasoo", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Monica Chan", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Brenda Sze Peng Ang", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Boon Huan Tan", + "author_inst": "DSO National Laboratories, Singapore" + }, + { + "author_name": "Yee Sin Leo", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Oon-Tek Ng", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Michelle Su Yen Wong", + "author_inst": "DSO National Laboratories, Singapore" + }, + { + "author_name": "Kalisvar Marimuthu", + "author_inst": "National Centre for Infectious Diseases, Singapore" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.27.20044974", "rel_title": "Guideline-based Chinese herbal medicine treatment plus standard care for severe coronavirus disease 2019 (G-CHAMPS): evidence from China", @@ -1583581,45 +1585438,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.28.013672", - "rel_title": "Cigarette smoke triggers the expansion of a subpopulation of respiratory epithelial cells that express the SARS-CoV-2 receptor ACE2", - "rel_date": "2020-03-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.28.013672", - "rel_abs": "The factors mediating fatal SARS-CoV-2 infections are poorly understood. Here, we show that cigarette smoke causes a dose-dependent upregulation of Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV-2 receptor, in rodent and human lungs. Using single-cell sequencing data, we demonstrate that ACE2 is expressed in a subset of secretory cells in the respiratory tract. Chronic smoke exposure triggers the expansion of this cell population and a concomitant increase in ACE2 expression. In contrast, quitting smoking decreases the abundance of these secretory cells and reduces ACE2 levels. Finally, we demonstrate that ACE2 expression is responsive to inflammatory signaling and can be upregulated by viral infections or interferon treatment. Taken together, these results may partially explain why smokers are particularly susceptible to severe SARS-CoV-2 infections. Furthermore, our work identifies ACE2 as an interferon-stimulated gene in lung cells, suggesting that SARS-CoV-2 infections could create positive-feedback loops that increase ACE2 levels and facilitate viral dissemination.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Joan C Smith", - "author_inst": "Cold Spring Harbor Laboratory" - }, - { - "author_name": "Erin L. Sausville", - "author_inst": "Cold Spring Harbor Laboratory" - }, - { - "author_name": "Vishruth Girish", - "author_inst": "Cold Spring Harbor Laboratory" - }, - { - "author_name": "Monet Lou Yuan", - "author_inst": "Cold Spring Harbor Laboratory" - }, - { - "author_name": "Kristen M. John", - "author_inst": "Cold Spring Harbor Laboratory" - }, - { - "author_name": "Jason Meyer Sheltzer", - "author_inst": "Cold Spring Harbor Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.03.28.013607", "rel_title": "Computational Design of Peptides to Block Binding of the SARS-CoV-2 Spike Protein to Human ACE2", @@ -1583819,6 +1585637,57 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.03.28.013789", + "rel_title": "Structural analysis of SARS-CoV-2 andprediction of the human interactome", + "rel_date": "2020-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.28.013789", + "rel_abs": "Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic regions display different degrees of conservation. SARS-CoV-2 domain encompassing nucleotides 22500 - 23000 is conserved both at the sequence and structural level. The regions upstream and downstream, however, vary significantly. This part codes for the Spike S protein that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2). Thus, variability of Spike S may be connected to different levels of viral entry in human cells within the population.\n\nOur predictions indicate that the 5 end of SARS-CoV-2 is highly structured and interacts with several human proteins. The binding proteins are involved in viral RNA processing such as double-stranded RNA specific editases and ATP-dependent RNA-helicases and have strong propensity to form stress granules and phase-separated complexes. We propose that these proteins, also implicated in viral infections such as HIV, are selectively recruited by SARS-CoV-2 genome to alter transcriptional and post-transcriptional regulation of host cells and to promote viral replication.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Andrea Vandelli", + "author_inst": "Autonomous University of Barcelona" + }, + { + "author_name": "Michele Monti", + "author_inst": "Italian Institute of Technology" + }, + { + "author_name": "Edoardo Milanetti", + "author_inst": "University \"Sapienza\" of Rome" + }, + { + "author_name": "Alex Armaos", + "author_inst": "Italian Institute of Technology" + }, + { + "author_name": "Jakob Rupert", + "author_inst": "Sapienza University Rome" + }, + { + "author_name": "Elsa Zacco", + "author_inst": "Italian Institute of Technology" + }, + { + "author_name": "Elias Bechara", + "author_inst": "Italian Institute of Techonology" + }, + { + "author_name": "Riccardo Delli Ponti", + "author_inst": "University of Singapore" + }, + { + "author_name": "Gian Gaetano Tartaglia", + "author_inst": "University of Rome Sapienza and Italian Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.03.30.015685", "rel_title": "Re-insights into origin and adaptation of SARS-CoV-2", @@ -1585179,53 +1587048,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.27.20045807", - "rel_title": "The psychological distress and coping styles in the early stages of the 2019 coronavirus disease (COVID-19) epidemic in the general mainland Chinese population: a web-based survey", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045807", - "rel_abs": "BackgroundAs the epidemic outbreak of 2019 coronavirus disease (COVID-19), general population may experience psychological distress. Evidence has suggested that negative coping styles may be related to subsequent mental illness. Therefore, we investigate the general populations psychological distress and coping styles in the early stages of the COVID-19 outbreak.\n\nMethodsA cross-sectional battery of surveys was conducted from February 1-4, 2020. The Kessler 6 psychological distress scale, the simplified coping style questionnaire and a general information questionnaire were administered on-line to a convenience sample of 1599 in China. Spearmans correlation was used to measure the correlations among category variables.\n\nResultsGeneral populations psychological distress were significant differences based on age, marriage, epidemic contact characteristics, concern with media reports, and perceived impacts of the epidemic outbreak (all p <0.001) except gender (p=0.316). Those with a history of visiting Wuhan and a history of epidemics occurring in the community, more concern with media reports, perceived more severe impacts and negative coping style had a higher level of psychological distress, which was significantly positively correlated with a history of visiting Wuhan (r=0.548, p<0.001), a history of epidemics occurring in the community (r=0.219, p<0.001), and concern with media reports (r=0.192, p<0.001). Coping styles were significantly different across all category variables (all p <0.001), and negatively correlated with other category variables (all p<0.01) except age and marriage. Psychological distress was significantly negatively correlated with the coping style (r=-0.573, p<0.01).\n\nConclusionsIn the early stages of COVID-19, general population with epidemic contact characteristics, excessive concern with media reports, and perceived more severe impacts have higher levels of psychological distress. Psychological distress was significantly negatively correlated with the coping style. Interventions should be implemented early, especially for those population with a high level of psychological distress and/or with a negative coping style.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Hui-yao Wang", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Qian Xia", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Zhen-zhen Xiong", - "author_inst": "Chengdu Medical College" - }, - { - "author_name": "Zhi-xiong Li", - "author_inst": "Karamay Municipal People's Hospital" - }, - { - "author_name": "Wei-yi Xiang", - "author_inst": "The West China College of Medicine, Sichuan University" - }, - { - "author_name": "Yi-wen Yuan", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Ya-ya Liu", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "zhe li", - "author_inst": "West China Hospital, Sichuan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.03.27.20045757", "rel_title": "Changing transmission dynamics of COVID-19 in China: a nationwide population-based piecewise mathematical modelling study", @@ -1585457,6 +1587279,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.27.20045575", + "rel_title": "Basic prediction methodology for covid-19: estimation and sensitivity considerations", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045575", + "rel_abs": "The purpose of the present paper is to present simple estimation and prediction methods for basic quantities in an emerging epidemic like the ongoing covid-10 pandemic. The simple methods have the advantage that relations between basic quantities become more transparent, thus shedding light to which quantities have biggest impact on predictions, with the additional conclusion that uncertainties in these quantities carry over to high uncertainty also in predictions.\n\nA simple non-parametric prediction method for future cumulative case fatalities, as well as future cumulative incidence of infections (assuming a given infection fatality risk f), is presented. The method uses cumulative reported case fatalities up to present time as input data. It is also described how the introduction of preventive measures of a given magnitude{rho} will affect the two incidence predictions, using basic theory of epidemic models. This methodology is then reversed, thus enabling estimation of the preventive magnitude{rho} , and of the resulting effective reproduction number RE. However, the effects of preventive measures only start affecting case fatalities some 3-4 weeks later, so estimates are only available after this time has elapsed. The methodology is applicable in the early stage of an outbreak, before, say, 10% of the community have been infected.\n\nBeside giving simple estimation and prediction tools for an ongoing epidemic, another important conclusion lies in the observation that the two quantities f (infection fatality risk) and{rho} (the magnitude of preventive measures) have very big impact on predictions. Further, both of these quantities currently have very high uncertainty: current estimates of f lie in the range 0.2% up to 2% ([9], [7]), and the overall effect of several combined preventive measures is clearly very uncertain.\n\nThe two main findings from the paper are hence that, a) any prediction containing f, and/or some preventive measures, contain a large amount of uncertainty (which is usually not acknowledged well enough), and b) obtaining more accurate estimates of in particular f, should be highly prioritized. Seroprevalence testing of random samples in a community where the epidemic has ended are urgently needed.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Tom Britton", + "author_inst": "Stockholm University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.27.20040816", "rel_title": "Correlation between hypophosphatemia and the severity of Corona Virus Disease 2019 patients", @@ -1586393,37 +1588234,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.27.20045302", - "rel_title": "Mobility traces and spreading of COVID-19", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045302", - "rel_abs": "1Executive summaryWe use human mobility models, for which we are experts, and attach a virus infection dynamics to it, for which we are not experts but have taken it from the literature, including recent publications. This results in a virus spreading dynamics model. The results should be verified, but because of the current time pressure, we publish them in their current state. Recommendations for improvement are welcome. We come to the following conclusions:\n\nO_LIComplete lockdown works. About 10 days after lockdown, the infection dynamics dies down. This assumes that lockdown is complete, which can be guaranteed in the simulation, but not in reality. Still, it gives strong support to the argument that it is never too late for complete lockdown.\nC_LIO_LIAs a rule of thumb, we would suggest complete lockdown no later than once 10% of hospital capacities available for COVID-19 are in use, and possibly much earlier. This is based on the following insights:\nO_LIEven after lockdown, the infection dynamics continues at home, leading to another tripling of the cases before the dynamics is slowed.\nC_LIO_LIThere will be many critical cases coming from people who were infected before lockdown. Because of the exponential growth dynamics, their number will be large.\nC_LIO_LIResearchers with more detailed disease progression models should improve upon these statements.\nC_LI\nC_LIO_LIOur simulations say that complete removal of infections at child care, primary schools, workplaces and during leisure activities will not be enough to sufficiently slow down the infection dynamics. It would have been better, but still not sufficient, if initiated earlier.\nC_LIO_LIInfections in public transport play an important role. In the simulations shown later, removing infections in the public transport system reduces the infection speed and the height of the peak by approximately 20%. Evidently, this depends on the infection parameters, which are not well known. - This does not point to reducing public transport capacities as a reaction to the reduced demand, but rather use it for lower densities of passengers and thus reduced infection rates.\nC_LIO_LIIn our simulations, removal of infections at child care, primary schools, workplaces, leisure activities, and in public transport may barely have been sufficient to control the infection dynamics if implemented early on. Now according to our simulations it is too late for this, and (even) harsher measures will have to be initiated until possibly a return to such a restrictive, but still somewhat functional regime will again be possible.\nC_LI\n\nEvidently, all of these results have to be taken with care. They are based on preliminary infection parameters taken from the literature, used inside a model that has more transport/movement details than all others that we are aware of but still not enough to describe all aspects of reality, and suffer from having to write computer code under time pressure. Optimally, they should be confirmed independently. Short of that, given current knowledge we believe that they provide justification for \"complete lockdown\" at the latest when about 10% of available hospital capacities for COVID-19 are in use (and possibly earlier; we are no experts of hospital capabilities).1\n\nWhat was not investigated in detail in our simulations was contact tracing, i.e. tracking down the infection chains and moving all people along infection chains into quarantine. The case of Singapore has so far shown that this may be successful. Preliminary simulation of that tactic shows that it is difficult to implement for COVID-19, since the incubation time is rather long, people are contagious before they feel sick, or maybe never feel sufficiently sick at all. We will investigate in future work if and how contact tracing can be used together with a restrictive, but not totally locked down regime.\n\nWhen opening up after lockdown, it would be important to know the true fraction of people who are already immune, since that would slow down the infection dynamics by itself. For Wuhan, the currently available numbers report that only about 0.1% of the population was infected, which would be very far away from \"herd immunity\". However, there have been and still may be many unknown infections (Frankfurter Allgemeine Zeitung GmbH 2020).", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sebastian Alexander Muller", - "author_inst": "TU Berlin" - }, - { - "author_name": "Michael Balmer", - "author_inst": "Senozon AG, Switzerland" - }, - { - "author_name": "Andreas Neumann", - "author_inst": "Senozon GmbH, Germany" - }, - { - "author_name": "Kai Nagel", - "author_inst": "TU Berlin" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.27.20045005", "rel_title": "A modified SEIR model to predict the COVID-19 outbreak in Spain: simulating control scenarios and multi-scale epidemics", @@ -1586603,6 +1588413,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.28.20046045", + "rel_title": "Deep Learning-Based Recognizing COVID-19 and other Common Infectious Diseases of the Lung by Chest CT Scan Images", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.28.20046045", + "rel_abs": "PurposeCOVID-19 has become global threaten. CT acts as an important method of diagnosis. However, human-based interpretation of CT imaging is time consuming. More than that, substantial inter-observer-variation cannot be ignored. We aim at developing a diagnostic tool for artificial intelligence (AI)-based classification of CT images for recognizing COVID-19 and other common infectious diseases of the lung.\n\nExperimental DesignIn this study, images were retrospectively collected and prospectively analyzed using machine learning. CT scan images of the lung that show or do not show COVID-19 were used to train and validate a classification framework based on convolutional neural network. Five conditions including COVID-19 pneumonia, non-COVID-19 viral pneumonia, bacterial pneumonia, pulmonary tuberculosis, and normal lung were evaluated. Training and validation set of images were collected from Wuhan Jin Yin-Tan Hospital whereas test set of images were collected from Zhongshan Hospital Xiamen University and the fifth Hospital of Wuhan.\n\nResultsAccuracy, sensitivity, and specificity of the AI framework were reported. For test dataset, accuracies for recognizing normal lung, COVID-19 pneumonia, non-COVID-19 viral pneumonia, bacterial pneumonia, and pulmonary tuberculosis were 99.4%, 98.8%, 98.5%, 98.3%, and 98.6%, respectively. For the test dataset, accuracy, sensitivity, specificity, PPV, and NPV of recognizing COVID-19 were 98.8%, 98.2%, 98.9%, 94.5%, and 99.7%, respectively.\n\nConclusionsThe performance of the proposed AI framework has excellent performance of recognizing COVID-19 and other common infectious diseases of the lung, which also has balanced sensitivity and specificity.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Min Fu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Shuang-Lian Yi", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Yuanfeng Zeng", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Feng Ye", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Yuxuan Li", + "author_inst": "Hubei University of Technology" + }, + { + "author_name": "Xuan Dong", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Yan-Dan Ren", + "author_inst": "Zhongshan Hospital Affiliated to Xiamen University" + }, + { + "author_name": "Linkai Luo", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jin-Shui Pan", + "author_inst": "Zhongshan Hospital Xiamen University" + }, + { + "author_name": "Qi Zhang", + "author_inst": "Jin Yin-Tan Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.26.20044768", "rel_title": "Persistent SARS-CoV-2 presence is companied with defects in adaptive immune system in non-severe COVID-19 patients", @@ -1587707,89 +1589572,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.29.014209", - "rel_title": "Orthogonal genome-wide screenings in bat cells identify MTHFD1 as a target of broad antiviral therapy", - "rel_date": "2020-03-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.29.014209", - "rel_abs": "Bats are responsible for the zoonotic transmission of several major viral diseases including the 2003 SARS outbreak and the ongoing COVID-19 pandemic. While bat genomic sequencing studies have revealed characteristic adaptations of the innate immune system, functional genomic studies are urgently needed to provide a foundation for the molecular dissection of the tolerance of viral infections in bats. Here we report the establishment and screening of genome-wide RNAi library and CRISPR library for the model megabat, Pteropus Alecto. We used the complementary RNAi and CRISPR libraries to interrogate Pteropus Alecto cells for infection with two different viruses, mumps virus and Influenza A virus, respectively. Screening results converged on the endocytosis pathway and the protein secretory pathway as required for both viral infections. Additionally, we revealed a general dependence of the C-1-tetrahydrofolate synthase gene, MTHFD1, for viral replication in bat cells as well as in human cells. MTHFD1 inhibitor carolacton potently blocked replication of several RNA viruses including SARS-CoV-2. Our studies provide a resource for systematic inquiry into the genetic underpinnings of bat biology and a potential target for developing broad spectrum antiviral therapy.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Danielle E Anderson", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Jin Cui", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Qian Ye", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Baoying Huang", - "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" - }, - { - "author_name": "Wenhong Zu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Jing Gong", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Weiqiang Liu", - "author_inst": "Institute of Zoology, Chinese Academy of Science" - }, - { - "author_name": "So Young Kim", - "author_inst": "Duke University" - }, - { - "author_name": "Biao Guo Yan", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Kristmundur Sigmundsson", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Xiao Fang Lim", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Fei Ye", - "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" - }, - { - "author_name": "Peihua Niu", - "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" - }, - { - "author_name": "Xuming Zhou", - "author_inst": "Institute of Zoology, Chinese Academy of Science" - }, - { - "author_name": "Wenjie Tan", - "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" - }, - { - "author_name": "Lin-Fa Wang", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Xu Tan", - "author_inst": "Tsinghua University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.26.20043042", "rel_title": "Analysis and Prediction of False Negative Results for SARS-CoV-2 Detection with Pharyngeal Swab Specimen in COVID-19 Patients: A Retrospective Study", @@ -1588029,6 +1589811,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.28.20046136", + "rel_title": "EARLY ESTIMATION OF REPRODUCTION NUMBER OF COVID-19 IN VIETNAM", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.28.20046136", + "rel_abs": "Reproduction number is an epidemiologic indicator that reflects the contagiousness and transmissibility of infectious agents. This paper aims to estimate the reproduction number of in the early phase of COVID-19 outbreak in Vietnam.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Long Viet Bui", + "author_inst": "Center for Research - Consulting and Support of Community Health" + }, + { + "author_name": "Truong Thanh Nguyen", + "author_inst": "Vietnam Ministry of Scinceand Technology" + }, + { + "author_name": "Ha Nguyen", + "author_inst": "People's Police Academy of Vietnam" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.28.20045989", "rel_title": "Prognostic factors for COVID-19 pneumonia progression to severe symptom based on the earlier clinical features: a retrospective analysis", @@ -1589049,53 +1590858,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "urology" }, - { - "rel_doi": "10.1101/2020.03.28.20043471", - "rel_title": "Disposable N95 Masks Pass Qualitative Fit-Test But Have Decreased Filtration Efficiency after Cobalt-60 Gamma Irradiation", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.28.20043471", - "rel_abs": "The current COVID-19 pandemic has led to a dramatic shortage of masks and other personal protective equipment (PPE) in hospitals around the globe [1]. One component of PPE that is in particular demand are disposable N95 face masks. To alleviate this, many methods of N95 mask sterilization have been studied and proposed with the hope of being able to safely reuse masks [2]. Two major considerations must be made when re-sterilizing masks: (1) the sterilization method effectively kills pathogens, penetrating into the fibers of the mask, and (2) the method does not degrade the operational integrity of the N95 filters.\n\nWe studied Cobalt-60 (60Co) gamma irradiation as a method of effective sterilization without inducing mask degradation. Significant literature exists supporting the use of gamma radiation as a sterilization method, with viral inactivation of SARS-CoV reported at doses of at most 10 kGy [3], with other studies supporting 5 kGy for many types of viruses [4]. However, concerns have been raised about the radiation damaging the fiber material within the mask, specifically by causing cross-linking of polymers, leading to cracking and degradation during fitting and/or deployment [5, 6].\n\nA set of 3M 8210 and 9105 masks were irradiated using MITs 60Co irradiator. Three masks of each type received 0 kiloGray (kGy), 10 kGy and 50 kGy of approximately 1.3 MeV gamma radiation from the circular cobalt sources, at a dose rate of 2.2kGy per hour.\n\nFollowing this sterilization procedure, the irradiated masks passed a OSHA Gerson Qualitative Fit Test QLFT 50 (saccharin apparatus) [7] when donned correctly, performed at the Brigham and Womens Hospital, in a blinded study repeated in triplicate. However, the masks filtration of 0.3 {micro}m particles was significantly degraded, even at 10 kGy.\n\nThese results suggest against gamma, and possibly all ionizing radiation, as a method of disposable N95 sterilization. Even more importantly, they argue against using the qualitative fit test alone to assess mask integrity.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Avilash Cramer", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Enze Tian", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Sherryl H Yu", - "author_inst": "Harvard Combined Dermatology Residency Training Program" - }, - { - "author_name": "Mitchell Galanek", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Edward Lamere", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ju Li", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Rajiv Gupta", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Michael P Short", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.03.26.20044214", "rel_title": "Projecting the Spread of COVID19 for Germany", @@ -1589259,6 +1591021,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.26.20044164", + "rel_title": "Understand Research Hotspots Surrounding COVID-19 and Other Coronavirus Infections Using Topic Modeling", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044164", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that causes severe respiratory illness in humans, which results in global outbreak of novel coronavirus disease (COVID-19) currently. This study aimed to evaluate the characteristics of publications involving coronaviruses as well as COVID-19 by using topic modeling.\n\nMethodsWe extracted all abstracts and retained the most informative words from the COVID-19 Open Research Dataset, which contains 35,092 pieces of coronavirus related literature published up to March 20, 2020. Using Latent Dirichlet Allocation modeling, we trained a topic model from the corpus, analyzed the semantic relationships between topics and compared the topic distribution between COVID-19 and other CoV infections.\n\nResultsEight topics emerged overall: clinical characterization, pathogenesis research, therapeutics research, epidemiological study, virus transmission, vaccines research, virus diagnostics, and viral genomics. It was observed that current COVID-19 research puts more emphasis on clinical characterization, epidemiological study, and virus transmission. In contrast, topics about diagnostics, therapeutics, vaccines, genomics and pathogenesis only account for less than 10% or even 4% of all the COVID-19 publications, much lower than those of other CoV infections.\n\nConclusionsThese results identified knowledge gaps in the area of COVID-19 and offered directions for future research.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mengying Dong", + "author_inst": "University of Queensland" + }, + { + "author_name": "Xiaojun Cao", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Mingbiao Liang", + "author_inst": "Guangzhou College of Commerce" + }, + { + "author_name": "Lijuan Li", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Guangjian Liu", + "author_inst": "Guangzhou Medical University" + }, + { + "author_name": "Huiying Liang", + "author_inst": "Guangzhou Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.26.20044057", "rel_title": "Clinical and Paraclinical Characteristics of COVID-19 patients: A systematic review and meta-analysis", @@ -1590379,61 +1592180,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.03.24.20041087", - "rel_title": "Hydrogen Peroxide Vapor sterilization of N95 respirators for reuse", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20041087", - "rel_abs": "Reprocessing of used N95 respirators may ameliorate supply chain constraints during the COVID-19 pandemic and provide a higher filtration crisis alternative. The FDA Medical Countermeasures Initiative previously funded a study of HP vapor decontamination of respirators using a Clarus C system (Bioquell, Horsham, PA) which normally is used to fumigate hospital rooms. The process preserved respirator function, but it is unknown if HP vapor would be virucidal since respirators have porous fabric that may harbor virus.\n\nWe evaluated the virucidal activity of HP vapor using a BQ-50 system (Bioquell, Horsham, PA) after inoculating 3M 1870 N95 respirators (3M, St. Paul, MN) with 3 aerosolized bacteriophage that are a reasonable proxy for SARS-CoV-2. Inoculation resulted in contamination of the respirator with 9.87e4 plaque forming units (PFU) of phage phi-6, 4.17e7 PFU of phage T7 and 1.35e7 PFU of phage T1. Respirators were reprocessed with BQ-50 with a long aeration phase to reduce HP vapors. Virucidal activity was measured by a standard plaquing assay prior to and after sterilization. A single HP vapor cycle resulted in complete eradication of phage from masks (limit of detection 10 PFU, lower than the infectious dose of the majority of respiratory viral pathogens). After 5 cycles, the respirators appeared similar to new with no deformity.\n\nUse of a Bioquell machine can be scaled to permit simultaneous sterilization of a large number of used but otherwise intact respirators. HP vapor reprocessing may ease shortages and provide a higher filtration crisis alternative to non-NIOSH masks.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Patrick Kenney", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Benjamin K Chan", - "author_inst": "Yale University" - }, - { - "author_name": "Kaitlyn Kortright", - "author_inst": "Yale University" - }, - { - "author_name": "Margaret Cintron", - "author_inst": "Yale New Haven Health" - }, - { - "author_name": "Nancy Havill", - "author_inst": "Yale New Haven Health" - }, - { - "author_name": "Mark Russi", - "author_inst": "Yale University" - }, - { - "author_name": "Jaqueline Epright", - "author_inst": "Yale New Haven Health" - }, - { - "author_name": "Lorraine Lee", - "author_inst": "Yale New Haven Health" - }, - { - "author_name": "Thomas Balcezak", - "author_inst": "Yale New Haven Health System" - }, - { - "author_name": "Richard Martinello", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.23.20040998", "rel_title": "A demographic adjustment to improve measurement of COVID-19 severity at the developing stage of the pandemic", @@ -1590653,6 +1592399,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.22.20040832", + "rel_title": "Factors associated with prolonged viral shedding and impact of Lopinavir/Ritonavir treatment in patients with SARS-CoV-2 infection", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20040832", + "rel_abs": "BackgroundThe duration of viral shedding is central to guide decisions around isolation precautions and antiviral treatment. However, studies about risk factors associated with prolonged SARS-CoV-2 shedding and the potential impact of Lopinavir/Ritonavir (LPV/r) treatment remain scarce.\n\nMethodsIn this retrospective study, data were collected from all SARS-CoV-2 infected patients who were admitted to isolation wards and had RT-PCR conversion at the NO.3 Peoples hospital of Hubei province between 31 January and 09 March 2020. We compared clinical features and SARS-CoV-2 RNA shedding between patients with LPV/r treatment and those without. Logistic regression analysis was employed to evaluate risk factors associated with prolonged viral shedding.\n\nResultsOf 120 patients, the median age was 52 years, 54 (45%) were male and 78 (65%) received LPV/r treatment. The median duration of SARS-CoV-2 RNA detection from symptom onset was 23 days (IQR, 18-32 days). Older age (odd ratio [OR] 1.03, 95% confidence interval [CI] 1.00-1.05, p=0.03) and lack of LPV/r treatment (OR 2.42, 95% CI 1.10-5.36, p=0.029) were independent risk factors for prolonged SARS-CoV-2 RNA shedding in multivariate logistic regression analysis. The median duration of viral shedding was shorter in the LPV/r treatment group (n=78) than that in no LPV/r treatment group (n=42) (median, 22 days vs. 28.5 days, p=0.02). Only earlier administration of LPV/r treatment ([≤]10 days from symptom onset) could shorten the duration of viral shedding.\n\nConclusionsOlder age and lack of LPV/r treatment were independently associated with prolonged SARS-CoV-2 RNA shedding in patients with COVID-19. Earlier administration of LPV/r treatment could shorten viral shedding.\n\nTake home messageRisk factors for prolonged SARS-CoV-2 shedding included older age and lack of Lopinavir/Ritonavir treatment. Earlier administration of Lopinavir/Ritonavir treatment could shorten the duration of SARS-CoV-2 RNA shedding.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Dan Yan", + "author_inst": "Hubei NO.3 People Hospital of Jianghan University, Wuhan, Hubei, China" + }, + { + "author_name": "Xiao-yan Liu", + "author_inst": "Hubei NO.3 People Hospital of Jianghan University, Wuhan, Hubei, China" + }, + { + "author_name": "Ya-nan Zhu", + "author_inst": "The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China" + }, + { + "author_name": "Li Huang", + "author_inst": "The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China" + }, + { + "author_name": "Bi-tang Dan", + "author_inst": "Hubei NO.3 People Hospital of Jianghan University, Wuhan, Hubei, China" + }, + { + "author_name": "Guo-jun Zhang", + "author_inst": "The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China" + }, + { + "author_name": "Yong-hua Gao", + "author_inst": "The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.23.20041970", "rel_title": "Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak", @@ -1592033,25 +1593822,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2020.03.25.20043893", - "rel_title": "A Simple Mathematical Model for Estimating the Inflection Points of COVID-19 Outbreaks", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20043893", - "rel_abs": "BackgroundExponential-like infection growths leading to peaks (which could be the inflection points or turning points) are usually the hallmarks of infectious disease outbreaks including coronaviruses. To predict the inflection points, i.e., inflection time (Tmax) & maximal infection number (Imax) of the novel coronavirus (COVID-19), we adopted a trial and error strategy and explored a series of approaches from simple logistic modeling (that has an asymptomatic line) to sophisticated tipping point detection techniques for detecting phase transitions but failed to obtain satisfactory results.\n\nMethodInspired by its success in diversity-time relationship (DTR), we apply the PLEC (power law with exponential cutoff) model for detecting the inflection points of COVID-19 outbreaks. The model was previously used to extend the classic species-time relationship (STR) for general DTR (Ma 2018), and it has two \"secondary\" parameters (computed from its 3 parameters including power law scaling parameter w, taper-off parameter d to overwhelm virtually exponential growth ultimately, and a parameter c related to initial infections): one that was originally used for estimating the potential or dark biodiversity is proposed to estimate the maximal infection number (Imax) and another is proposed to determine the corresponding inflection time point (Tmax).\n\nResultsWe successfully estimated the inflection points [Imax, Tmax] for most provinces ({approx}85%) in China with error rates <5% in both Imax and Tmax. We also discussed the constraints and limitations of the proposed approach, including (i) sensitive to disruptive jumps, (ii) requiring sufficiently long datasets, and (iii) limited to unimodal outbreaks.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Zhanshan (Sam) Ma", - "author_inst": "Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.03.23.20039362", "rel_title": "Immune Cell Profiling of COVID-19 Patients in the Recovery Stage by Single-Cell Sequencing", @@ -1592307,6 +1594077,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.03.21.20040261", + "rel_title": "ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20040261", + "rel_abs": "The pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS- CoV-2) has resulted in several thousand deaths worldwide in just a few months. Patients who died from Coronavirus disease 2019 (COVID-19) often had comorbidities, such as hypertension, diabetes, and chronic obstructive lung disease. The angiotensin-converting enzyme 2 (ACE2) was identified as a crucial factor that facilitates SARS-CoV2 to bind and enter host cells. To date, no study has assessed the ACE2 expression in the lungs of patients with these diseases. Here, we analyzed over 700 lung transcriptome samples of patients with comorbidities associated with severe COVID-19 and found that ACE2 was highly expressed in these patients, compared to control individuals. This finding suggests that patients with such comorbidities may have higher chances of developing severe COVID-19. We also found other genes, such as RAB1A, that can be important for SARS-CoV-2 infection in the lung. Correlation and network analyses revealed many potential regulators of ACE2 in the human lung, including genes related to histone modifications, such as HAT1, HDAC2, and KDM5B. In fact, epigenetic marks found in ACE2 locus were compatible to with those promoted by KDM5B. Our systems biology approach offers a possible explanation for increase of COVID-19 severity in patients with certain comorbidities.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bruna GG Pinto", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Antonio ER Oliveira", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Youvika Singh", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Leandro Jimenez", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Andre NA Goncalves", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Rodrigo LT Ogava", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Rachel Creighton", + "author_inst": "University of Washington" + }, + { + "author_name": "Jean PS Peron", + "author_inst": "University of Sao Paulo" + }, + { + "author_name": "Helder I Nakaya", + "author_inst": "University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.03.25.20043562", "rel_title": "On the assessment of more reliable COVID-19 infected number: the italian case.", @@ -1593499,81 +1595320,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.22.20040642", - "rel_title": "The Effect of Large-Scale Anti-Contagion Policies on the Coronavirus (COVID-19) Pandemic", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20040642", - "rel_abs": "Governments around the world are responding to the novel coronavirus (COVID-19) pandemic1 with unprecedented policies designed to slow the growth rate of infections. Many actions, such as closing schools and restricting populations to their homes, impose large and visible costs on society, but their benefits cannot be directly observed and are currently understood only through process-based simulations.2-4 Here, we compile new data on 1,717 local, regional, and national non-pharmaceutical interventions deployed in the ongoing pandemic across localities in China, South Korea, Italy, Iran, France, and the United States (US). We then apply reduced-form econometric methods, commonly used to measure the effect of policies on economic growth, 5,6 to empirically evaluate the effect that these anti-contagion policies have had on the growth rate of infections. In the absence of policy actions, we estimate that early infections of COVID-19 exhibit exponential growth rates of roughly 38% per day. We find that anti-contagion policies have significantly and substantially slowed this growth. Some policies have different impacts on different populations, but we obtain consistent evidence that the policy packages now deployed are achieving large, beneficial, and measurable health outcomes. We estimate that across these six countries, interventions prevented or delayed on the order of 62 million confirmed cases, corresponding to averting roughly 530 million total infections. These findings may help inform whether or when these policies should be deployed, intensified, or lifted, and they can support decision-making in the other 180+ countries where COVID-19 has been reported.7", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Solomon Hsiang", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Daniel Allen", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Sebastien Annan-Phan", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Kendon Bell", - "author_inst": "Manaaki Whenua Landcare Research" - }, - { - "author_name": "Ian Bolliger", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Trinetta Chong", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Hannah Druckenmiller", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Andrew Hultgren", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Luna Yue Huang", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Emma Krasovich", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Peiley Lau", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Jaecheol Lee", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Esther Rolf", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Jeanette Tseng", - "author_inst": "UC Berkeley" - }, - { - "author_name": "Tiffany Wu", - "author_inst": "UC Berkeley" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.21.20040667", "rel_title": "COVID-19 in Canada: Predictions for the future and control lessons from Asia", @@ -1593793,6 +1595539,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20042176", + "rel_title": "Anaesthetic managment and clinical outcomes of parturients with COVID-19: a multicentre, retrospective, propensity score matched cohort study", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042176", + "rel_abs": "ObjectiveTo analyse the clinical features of COVID-19 parturients, and to compare anaesthetic regimen and clinical outcomes in parturients with or without COVID-19 undergoing cesarean delivery.\n\nMethodData were extracted from the electronic medical record of 3 medical institutions in Hubei Province, China, from June 1, 2019 to March 20, 2020 according to inclusion and exclusion criteria. After propensity score matching with demographics, the clinical and laboratory characteristics of parturients with or without COVID-19 were analysed. The anaesthetic regimen and clinical outcomes of themselves and their infants were compared in these two groups of parturients.\n\nResultsA total of 1,588 patients without SARS-CoV-2 infection undergoing cesarean delivery were retrospectively included. After achieving a balanced cohort through propensity score matching, 89 patients (COVID-19 group), who were diagnosed with COVID-19 by SARS-CoV-2 nucleic acid test and CT scan matched with 173 patients without COVID-19 (Control group). The SARS-CoV-2 infected parturients in the early stages of COVID-19 outbreak was much more than during the later stage. The main clinical characteristics of parturients with COVID-19 were fever (34.8%), cough (33.7%), an increased plasma CRP (52.8%) and a decreased lymphocyte counting (33.7%). A high rate of emergency and a high incidence of anaesthesia-related complications, such as pharyngalgia, multiple puncture, intraoperative hypotension, nausea, vomiting, vertigo and chills in the COVID-19 parturients. In addition, the parturients with COVID-19 had a long duration of operation and hospital stay, and an increased intraoperative oxytocin utilization and postoperative oxygen therapy. The newborns from the SARS-CoV-2 infected mothers, who received general anaesthesia, had a high risk of Apgar score [≤] 8 at 1 and 5 minutes after delivery and a higher rate of neonatal intensive care unit (NICU) admission.\n\nConclusionsAnaesthesia-related complications occur more frequently in the COVID-19 parturients and their newborns have a high risk of distress.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yuan Zhang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Rong Chen", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Jie Wang", + "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology," + }, + { + "author_name": "Yuan Gong", + "author_inst": "Yichang Central People's Hospital" + }, + { + "author_name": "Qin Zhou", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Hui-hui Cheng", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Zhong-yuan Xia", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Xiangdong Chen", + "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Qing-tao Meng", + "author_inst": "Department of Anaesthesiology, Renmin Hospital of Wuhan University, Wuhan, China" + }, + { + "author_name": "Daqing Ma", + "author_inst": "Imperial College London, Chelsea & Westminster Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "anesthesia" + }, { "rel_doi": "10.1101/2020.03.22.20040949", "rel_title": "Quantifying treatment effects of hydroxychloroquine and azithromycin for COVID-19: a secondary analysis of an open label non-randomized clinical trial (Gautret et al, 2020)", @@ -1595081,49 +1596882,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2020.03.22.20040600", - "rel_title": "Human leukocyte antigen susceptibility map for SARS-CoV-2", - "rel_date": "2020-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20040600", - "rel_abs": "Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen [HLA] A, B, and C) may affect susceptibility to and severity of severe acute respiratory syndrome 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We execute a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA -A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explore the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome is successfully sampled and presented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (1). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting it could enable cross-protective T-cell based immunity. Finally, we report global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic.\n\nIMPORTANCEIndividual genetic variation may help to explain different immune responses to a virus across a population. In particular, understanding how variation in HLA may affect the course of COVID-19 could help identify individuals at higher risk from the disease. HLA typing can be fast and inexpensive. Pairing HLA typing with COVID-19 testing where feasible could improve assessment of viral severity in the population. Following the development of a vaccine against SARS-CoV-2, the virus that causes COVID-19, individuals with high-risk HLA types could be prioritized for vaccination.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Austin Nguyen", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Julianne K David", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Sean K Maden", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Mary A Wood", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Benjamin R Weeder", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Abhinav Nellore", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Reid F Thompson", - "author_inst": "Oregon Health & Science University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.24.20042903", "rel_title": "COVID-19 clinical characteristics, and sex-specific risk of mortality: Systematic Review and Meta-analysis", @@ -1595507,6 +1597265,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.03.25.20041475", + "rel_title": "An international comparison of the second derivative of COVID-19 deaths after implementation of social distancing measures", + "rel_date": "2020-03-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20041475", + "rel_abs": "This work compares deaths for confirmed COVID-19 cases in China to eight other countries, Italy, Spain, France, USA, UK, Germany, Netherlands and South Korea. After implementing varying intensities and timing of social distancing measures, several appear to be converging onto the decline in the daily growth rate of deaths, or relative second derivative of total deaths, seen in China after the implementation an aggressive social distancing policy. By calculating future trajectories in these countries based on the observed Chinese fatality statistics, an estimate of the total deaths and maximum daily death rates over a defined period of time is made. Our lower bound estimate for the United Kingdom based on the real data approximates the lower bound estimate of the recent modelling study of Ferguson et al. [1]. These results suggest there may be a threshold of effective public health intervention. Our method of viewing the data may be helpful in monitoring the course of the epidemic, judging the effectiveness of implementation, and monitoring the relaxation of social distancing.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "William Thomas Pike", + "author_inst": "Imperial College London" + }, + { + "author_name": "Vikas Saini", + "author_inst": "Lown Institute" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.25.007898", "rel_title": "Computational analysis of SARS-CoV-2 S1 protein O-glycosylation and phosphorylation modifications and identifying potential target positions against CD209L-mannose interaction to inhibit initial binding of the virus", @@ -1596623,149 +1598404,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.21.20040691", - "rel_title": "Meplazumab treats COVID-19 pneumonia: an open-labelled, concurrent controlled add-on clinical trial", - "rel_date": "2020-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20040691", - "rel_abs": "BackgroundSARS-CoV-2 is a novel human coronavirus, there is no specific antiviral drugs. It has been proved that host-cell-expressed CD147 could bind spike protein of SARS-CoV-2 and involve in host cell invasion. Antibody against CD147 could block the infection of SARS-CoV-2. We aimed to assess the efficacy and safety of meplazumab, a humanized anti-CD147 antibody, as add-on therapy in patients with COVID-19 pneumonia.\n\nMethodsAll patients received recommended strategy from Diagnosis and Treatment for 2019 Novel Coronavirus Diseases released by National Health Commission of China. Eligible patients were add-on administered 10 mg meplazumab intravenously at days 1, 2, and 5. Patients hospitalized in the same period were observed as concurrent control. The endpoints include virological clearance rate, case severity, chest radiographic, and laboratory test. This trial was approved by the Ethics Committee of Institution at the Tangdu hospital, and registered with ClinicalTrials.gov, NCT 04275245.\n\nFindings17 patients were enrolled and assigned to meplazumab group between Feb 3, 2020 and Feb 10, 2020. 11 hospitalized patients served as concurrent control. Baseline characteristics were generally balanced across two groups. Compared to control group, meplazumab treatment significantly improved the discharged (p=0.006) and case severity (p=0.021) in critical and severe patients. The time to virus negative in meplazumab group was reduced than that in control group (median 3, 95%CI[1.5-4.5] vs. 13, [6.5-19.5]; p=0.014, HR=0.37, 95%CI[0.155-0.833]). The percentages of patients recovered to the normal lymphocyte count and CRP concentration were also increased remarkably and rapidly in meplazumab group. No adverse effect was found in meplazumab-treated patients.\n\nInterpretationMeplazumab efficiently improved the recovery of patients with SARS-CoV-2 pneumonia with a favorable safety profile. Our results support to carry out a large-scale investigation of meplazumab as a treatment for COVID-19 pneumonia.\n\nFundingNational Science and Technology Major Project.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Huijie Bian", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Zhao-Hui Zheng", - "author_inst": "Xijing Hospital, Fourth Military Medical University" - }, - { - "author_name": "Ding Wei", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Zheng Zhang", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Wen-Zhen Kang", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Chun-Qiu Hao", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Ke Dong", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Wen Kang", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Jie-Lai Xia", - "author_inst": "College of Military Preventive Medicine, Fourth Military Medical University" - }, - { - "author_name": "Jin-Lin Miao", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Rong-Hua Xie", - "author_inst": "Xijing Hospital, Fourth Military Medical University" - }, - { - "author_name": "Bin Wang", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Xiu-Xuan Sun", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Xiang-Min Yang", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Peng Lin", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Jie-Jie Geng", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Ke Wang", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Hong-Yong Cui", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Kui Zhang", - "author_inst": "Xijing Hospital, Fourth Military Medical University" - }, - { - "author_name": "Xiao-Chun Chen", - "author_inst": "Jiangsu Pacific Meinuoke Biopharmceuticals Co. Ltd." - }, - { - "author_name": "Hao Tang", - "author_inst": "Jiangsu Pacific Meinuoke Biopharmceuticals Co. Ltd." - }, - { - "author_name": "Hong Du", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Na Yao", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Shuang-Shuang Liu", - "author_inst": "Jiangsu Pacific Meinuoke Biopharmceuticals Co. Ltd." - }, - { - "author_name": "Lin-Na Liu", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Zhe Zhang", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Zhao-Wei Gao", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Gang Nan", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Qing-Yi Wang", - "author_inst": "Fourth Military Medical University" - }, - { - "author_name": "Jian-Qi Lian", - "author_inst": "Tangdu Hospital, Fourth Military Medical University" - }, - { - "author_name": "Zhi-Nan Chen", - "author_inst": "National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University" - }, - { - "author_name": "Ping Zhu", - "author_inst": "Xijing Hospital, Fourth Military Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.22.002204", "rel_title": "Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site.", @@ -1597129,6 +1598767,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.21.20039065", + "rel_title": "Optimization of Microbiological Laboratory Detection Strategy for Patients in A Designated Hospital Treating Novel Coronavirus Pneumonia in Anhui Province", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20039065", + "rel_abs": "Novel coronavirus pneumonia (NCP) is an emerging, highly contagious community acquired pneumonia (CAP) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Highly efficient and accurate microbiological laboratory assay is essential to confirm the SARS-CoV-2 infection, rule out other pathogens that can cause CAP, and monitor secondary infections. Here, we enrolled and provide microbiological analysis for 129 suspected and 52 transferred confirmed NCP patients hospitalized in the First Affiliated Hospital of University of Science and Technology of China (USTC) from Jan 21 to Feb 29, 2020. By analyzing the dual swab samples (sputum and pharyngeal) from 129 suspected patients with realtime RT-PCR, we confirmed 33 SARS-CoV-2 infections, with two co-infection cases with adenovirus or rhinovirus. We also used multiplex PCR to detect 13 common respiratory tract pathogens in 96 non-NCP patients, and found that 30 patients (31.25%) were infected with at least one respiratory tract pathogen that may cause CAP. Further, we performed bacterial and fungal cultures as well as fungal serologic tests and found that there is no secondary bacterial/fungal infections in confirmed NCP patients. Our studies suggest that, during the epidemic of NCP in Anhui province, there was a certain proportion of infection and co-infection of other common pathogens of CAP, and the secondary bacterial and fungal infection is not detectable in NCP patients. In comparison with SARS-CoV-2 detection alone, this optimized strategy combining multiple pathogen detection for identification of NCP and other CAP patients as well as cultures and serologic tests for confirmed patients increases the diagnosis efficiency and facilitates the personalized medication.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Wenjiao Chang", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Yuru Shi", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Yingjie Qi", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Jiaxing Liu", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Ting Liu", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Zhaowu Chen", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Wenjing Zhang", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Mengmeng Wang", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Dongfeng Liu", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Ming Yin", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Jing Xu", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Yun Yang", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Xiaowu Zhu", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Jing Ge", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Shu Zhu", + "author_inst": "Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine" + }, + { + "author_name": "Yong Gao", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of " + }, + { + "author_name": "Xiaoling Ma", + "author_inst": "The First Affiliated Hospital of University of Science and Technology of China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.20.20039024", "rel_title": "COVID-19: Modelling Local Transmission and Morbidity effects to provide an estimate of overall Relative Healthcare Resource Impact by General Practice Granularity", @@ -1598185,29 +1599906,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.20.20038422", - "rel_title": "Estimating the reproduction number of COVID-19 in Iran using epidemic modeling", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20038422", - "rel_abs": "BackgroundAs reported by Iranian governments, the first cases of coronavirus (COVID-19) infections confirmed in Qom, Iran on February 19, 2020 (30 Bahman 1398). The number of identified cases afterward increased rapidly and the novel coronavirus spread to all provinces of the country. This study aimed to fit an epidemic model to the reported cases data to estimate the basic reproduction number (R0) of COVID-19 in Iran.\n\nMethodsWe used data from February 21, 2020, to April 21, 2020, on the number of cases reported by Iranian governments and we employed the SIR (Susceptible-Infectious-Removed) epidemic spreading model to fit the transmission model to the reported cases data by tuning the parameters in order to estimate the basic reproduction number of COVID-19 in Iran.\n\nResultsThe value of reproduction number was estimated 4.86 in the first week and 4.5 in the second week. it decreased from 4.29 to 2.37 in the next four weeks. At the seventh week of the outbreak the reproduction number was reduced below one.\n\nConclusionsThe results indicate that the basic reproduction number of COVID-19 was significantly larger than one in the early stages of the outbreak. However, implementing social distancing and preventing travelling on Nowruz (Persian New Year) effectively reduced the reproduction number. Although the results indicate that reproduction number is below one, it is necessary to continue social distancing and control travelling to prevent causing a second wave of outbreak.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ebrahim Sahafizadeh", - "author_inst": "Payame Noor University" - }, - { - "author_name": "Samaneh Sartoli", - "author_inst": "Payame Noor University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.19.20038315", "rel_title": "Association between Clinical, Laboratory and CT Characteristics and RT-PCR Results in the Follow-up of COVID-19 patients", @@ -1598479,6 +1600177,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.20.20038141", + "rel_title": "Covid-19 dynamics in Albania: first estimates and projections", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20038141", + "rel_abs": "The SARS-CoV-2 epidemic is one of the biggest challenges healthcare systems worldwide have ever had to face. To curb transmission many countries have adopted social distancing measures and travel restrictions. Estimating the effect of these measures in each context is challenging and requires mathematical models of the transmission dynamics. Projections for the future course of the epidemic strongly rely on model predictions and accurate representation of real-time data as they accumulate. Here I develop an SEIR modeling framework for Covid-19, to evaluate reported cases and fatalities, and to enable forecasting using evidence-based Bayesian parameter estimation. This Bayesian framework offers a tool to parametrize real-time dynamics of Covid-19 cases, and explore the effect of control as it unfolds in any setting. I apply the model to Covid-19 data from Albania, where drastic control measures were put in place already on the day of the first confirmed case. Evaluating the dynamics of reported cases 9-31 March 2020, I estimate parameters and make preliminary projections. Three weeks into the measures, Albanian data already indicate a strong signature of more than 40% transmission reduction, and lend support to a progressively increasing effect of control measures rather than a static one. In the Albanian setting, the model and data match well, projecting the peak of the outbreak may be around 5-15 April, and be contained within 300 active confirmed cases if control continues with the same trend. This framework can be used to understand the quantitative effects of different control measures in real-time, and inform adaptive intervention for success in other settings.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Erida Gjini", + "author_inst": "Instituto Gulbenkian de Ciencia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.19.20038158", "rel_title": "Climatic influences on the worldwide spread of SARS-CoV-2", @@ -1600087,37 +1601804,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.03.19.998724", - "rel_title": "All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus", - "rel_date": "2020-03-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.19.998724", - "rel_abs": "A recent outbreak of novel coronavirus (SARS-CoV-2), the causative agent of COVID-19, has spread rapidly all over the world. Human immunodeficiency virus (HIV) is another deadly virus and causes acquired immunodeficiency syndrome (AIDS). Rapid and early detection of these viruses will facilitate early intervention and reduce disease transmission risk. Here, we present an All-In-One Dual CRISPR-Cas12a (termed \"AIOD-CRISPR\") assay method for simple, rapid, ultrasensitive, one-pot, and visual detection of coronavirus SARS-CoV-2 and HIV virus. In our AIOD CRISPR assay, a pair of crRNAs was introduced to initiate dual CRISPR-Cas12a detection and improve detection sensitivity. The AIOD-CRISPR assay system was successfully utilized to detect nucleic acids (DNA and RNA) of SARS-CoV-2 and HIV with a sensitivity of few copies. Also, it was evaluated by detecting HIV-1 RNA extracted from human plasma samples, achieving a comparable sensitivity with real-time RT-PCR method. Thus, our method has a great potential for developing next-generation point-of-care molecular diagnostics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Xiong Ding", - "author_inst": "Univerisity of Connecticut Health Center" - }, - { - "author_name": "Kun Yin", - "author_inst": "University of Connecticut Health Center" - }, - { - "author_name": "Ziyue Li", - "author_inst": "University of Connecticut Health Center" - }, - { - "author_name": "Changchun Liu", - "author_inst": "University of Connecticut Health Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.03.21.001628", "rel_title": "Respiratory disease and virus shedding in rhesus macaques inoculated with SARS-CoV-2", @@ -1600409,6 +1602095,117 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.03.19.997890", + "rel_title": "An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 and multiple endemic, epidemic and bat coronavirus", + "rel_date": "2020-03-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.19.997890", + "rel_abs": "Coronaviruses (CoVs) traffic frequently between species resulting in novel disease outbreaks, most recently exemplified by the newly emerged SARS-CoV-2. Herein, we show that the ribonucleoside analog {beta}-D-N4-hydroxycytidine (NHC, EIDD-1931) has broad spectrum antiviral activity against SARS-CoV 2, MERS-CoV, SARS-CoV, and related zoonotic group 2b or 2c Bat-CoVs, as well as increased potency against a coronavirus bearing resistance mutations to another nucleoside analog inhibitor. In mice infected with SARS-CoV or MERS-CoV, both prophylactic and therapeutic administration of EIDD-2801, an orally bioavailable NHC-prodrug (b-D-N4-hydroxycytidine-5-isopropyl ester), improved pulmonary function, and reduced virus titer and body weight loss. Decreased MERS-CoV yields in vitro and in vivo were associated with increased transition mutation frequency in viral but not host cell RNA, supporting a mechanism of lethal mutagenesis. The potency of NHC/EIDD-2801 against multiple coronaviruses, its therapeutic efficacy, and oral bioavailability in vivo, all highlight its potential utility as an effective antiviral against SARS-CoV-2 and other future zoonotic coronaviruses.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Timothy P Sheahan", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Amy C Sims", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Shuntai Zhou", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Collin Hill", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Sarah R Leist", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Alexandra Schaefer", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Maria Agostini", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Andrea Pruijssers", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Ariane J Brown", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Gregory Bluemling", + "author_inst": "Emory University" + }, + { + "author_name": "Michael Natchus", + "author_inst": "Emory University" + }, + { + "author_name": "Manohar Saindane", + "author_inst": "Emory University" + }, + { + "author_name": "Alexander Kolykhalov", + "author_inst": "Emory University" + }, + { + "author_name": "George Painter", + "author_inst": "Emory University" + }, + { + "author_name": "Ronald Swanstrom", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kenneth Dinnon III", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Rachel Graham", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Jennifer Harcourt", + "author_inst": "Centers for Disease Control" + }, + { + "author_name": "Azaibi Tamin", + "author_inst": "Centers for Disease Control" + }, + { + "author_name": "Natalie J. Thornburg", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Stephanie A. Montgomery", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "James Chappell", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Mark Denison", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.03.14.992156", "rel_title": "Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning", @@ -1601429,89 +1603226,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.17.20036640", - "rel_title": "Characterization of anti-viral immunity in recovered individuals infected by SARS-CoV-2", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20036640", - "rel_abs": "The WHO has declared SARS-CoV-2 outbreak a public health emergency of international concern. However, to date, there was hardly any study in characterizing the immune responses, especially adaptive immune responses to SARS-CoV-2 infection. In this study, we collected blood from COVID-19 patients who have recently become virus-free and therefore were discharged, and analyzed their SARS-CoV-2-specific antibody and T cell responses. We observed SARS-CoV-2-specific humoral and cellular immunity in the patients. Both were detected in newly discharged patients, suggesting both participate in immune-mediated protection to viral infection. However, follow-up patients (2 weeks post discharge) exhibited high titers of IgG antibodies, but with low levels of virus-specific T cells, suggesting that they may enter a quiescent state. Our work has thus provided a basis for further analysis of protective immunity to SARS-CoV-2, and understanding the pathogenesis of COVID-19, especially in the severe cases. It has also implications in designing an effective vaccine to protect and treat SARS-CoV-2 infection.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Chen Dong", - "author_inst": "Institute for immunology, School of Medicine, Tsinghua University" - }, - { - "author_name": "Ling Ni", - "author_inst": "Institute for immunology, School of medicine, Tsinghua University" - }, - { - "author_name": "Fang Ye", - "author_inst": "Department of Hematology, Chui Yang Liu Hospital affiliated to Tsinghua University" - }, - { - "author_name": "Meng-Li Chen", - "author_inst": "Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" - }, - { - "author_name": "Yu Feng", - "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" - }, - { - "author_name": "Yong-Qiang Deng", - "author_inst": "Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" - }, - { - "author_name": "Hui Zhao", - "author_inst": "Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" - }, - { - "author_name": "Peng Wei", - "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" - }, - { - "author_name": "Jiwan Ge", - "author_inst": "School of Life Sciences, Tsinghua University" - }, - { - "author_name": "Xiaoli Li", - "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" - }, - { - "author_name": "Lin Sun", - "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" - }, - { - "author_name": "Pengzhi Wang", - "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" - }, - { - "author_name": "Peng Liang", - "author_inst": "Department of Cardiology, Chui Yang Liu Hospital affiliated to Tsinghua University" - }, - { - "author_name": "Han Guo", - "author_inst": "Department of Orthopedics, Chui Yang Liu Hospital affiliated to Tsinghua University" - }, - { - "author_name": "Xinquan Wang", - "author_inst": "School of Life Sciences, Tsinghua University" - }, - { - "author_name": "Cheng-Feng Qin", - "author_inst": "Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" - }, - { - "author_name": "Fang Chen", - "author_inst": "Department of Cardiology, Chui Yang Liu Hospital affiliated to Tsinghua University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.03.16.20037176", "rel_title": "Hundreds of severe pediatric COVID-19 infections in Wuhan prior to the lockdown", @@ -1601695,6 +1603409,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.03.19.20039099", + "rel_title": "A Novel Triage Tool of Artificial Intelligence Assisted Diagnosis Aid System for Suspected COVID-19 pneumonia In Fever Clinics", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20039099", + "rel_abs": "BackgroundCurrently, the prevention and control of the novel coronavirus disease (COVID-19) outside Hubei province in China, and other countries have become more and more critically serious. We developed and validated a diagnosis aid model without computed tomography (CT) images for early identification of suspected COVID-19 pneumonia (S-COVID-19-P) on admission in adult fever patients and made the validated model available via an online triage calculator.\n\nMethodsPatients admitted from Jan 14 to February 26, 2020 with the epidemiological history of exposure to COVID-19 were included [Model development (n = 132) and validation (n = 32)]. Candidate features included clinical symptoms, routine laboratory tests, and other clinical information on admission. Features selection and model development were based on the least absolute shrinkage and selection operator (LASSO) regression. The primary outcome was the development and validation of a diagnostic aid model for S-COVID-19-P early identification on admission.\n\nResultsThe development cohort contained 26 S-COVID-19-P and 7 confirmed COVID-19 pneumonia cases. The final selected features included 1 variable of demographic information, 4 variables of vital signs, 5 variables of blood routine values, 7 variables of clinical signs and symptoms, and 1 infection-related biomarker. The model performance in the testing set and the validation cohort resulted in the area under the receiver operating characteristic (ROC) curves (AUCs) of 0.841 and 0.938, the F-1 score of 0.571 and 0.667, the recall of 1.000 and 1.000, the specificity of 0.727 and 0.778, and the precision of 0.400 and 0.500. The top 5 most important features were Age, IL-6, SYS_BP, MONO%, and Fever classification. Based on this model, an optimized strategy for S-COVID-19-P early identification in fever clinics has also been designed.\n\nConclusionsS-COVID-19-P could be identified early by a machine-learning model only used collected clinical information without CT images on admission in fever clinics with a 100% recall score. The well-performed and validated model has been deployed as an online triage tool, which is available at https://intensivecare.shinyapps.io/COVID19/.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Cong Feng", + "author_inst": "PLA general hospital" + }, + { + "author_name": "Lili Wang", + "author_inst": "PLAGH" + }, + { + "author_name": "Xin Chen", + "author_inst": "PLAGH" + }, + { + "author_name": "Yongzhi Zhai", + "author_inst": "PLAGH" + }, + { + "author_name": "Feng Zhu", + "author_inst": "PLAGH" + }, + { + "author_name": "Hua Chen", + "author_inst": "PLAGH" + }, + { + "author_name": "Yingchan Wang", + "author_inst": "PLAGH" + }, + { + "author_name": "Xiangzheng Su", + "author_inst": "PLAGH" + }, + { + "author_name": "Sai Huang", + "author_inst": "PLAGH" + }, + { + "author_name": "Lin Tian", + "author_inst": "PLAGH" + }, + { + "author_name": "Weixiu Zhu", + "author_inst": "PLAGH" + }, + { + "author_name": "Wenzheng Sun", + "author_inst": "PLAGH" + }, + { + "author_name": "Liping Zhang", + "author_inst": "PLAGH" + }, + { + "author_name": "Qingru Han", + "author_inst": "PLAGH" + }, + { + "author_name": "Juan Zhang", + "author_inst": "PLAGH" + }, + { + "author_name": "Fei Pan", + "author_inst": "PLAGH" + }, + { + "author_name": "Li Chen", + "author_inst": "PLAGH" + }, + { + "author_name": "Zhihong Zhu", + "author_inst": "PLAGH" + }, + { + "author_name": "Hongju Xiao", + "author_inst": "PLAGH" + }, + { + "author_name": "Yu Liu", + "author_inst": "PLAGH" + }, + { + "author_name": "Gang Liu", + "author_inst": "PLAGH" + }, + { + "author_name": "Wei Chen", + "author_inst": "PLAGH" + }, + { + "author_name": "Tanshi Li", + "author_inst": "PLAGH" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.03.19.20039107", "rel_title": "Age profile of susceptibility, mixing, and social distancing shape the dynamics of the novel coronavirus disease 2019 outbreak in China", @@ -1602683,33 +1604504,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.03.17.20037788", - "rel_title": "Intensive Care Unit Resource Planning During COVID-19 Emergency at the Regional Level: the Italian case.", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20037788", - "rel_abs": "Severe acute respiratory syndrome COVID-19 (SARS-CoV-2) has been declared a worldwide emergency and a pandemic disease by the World Health Organisation (WHO). It started in China in December 2019, and it is currently rapidly spreading throughout Italy, which is now the most affected country after China. There is great attention for the diffusion and evolution of the COVID-19 infection which started from the north (particularly in the Lombardia region) and it is now rapidly affecting other Italian regions. We investigate on the impact of patients hospitalisation in Intensive Care Units (ICUs) at a regional and subregional granularity. We propose a model derived from well-known models in epidemic to estimate the needed number of places in intensive care units. The model will help decision-makers to plan resources in the short and medium-term in order to guarantee appropriate treatments to all patients needing it. We analyse Italian data at regional level up to March 15th aiming to: (i) support health and government decision-makers in gathering rapid and efficient decisions on increasing health structures capacities (in terms of ICU slots) and (ii) define a scalable geographic model to plan emergency and future COVID-19 patients management using reallocating them among health structures. Finally, the here proposed model can be useful in countries where COVID-19 is not yet strongly diffused.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pietro Hiram Guzzi", - "author_inst": "University of Catanzaro" - }, - { - "author_name": "Giuseppe Tradigo", - "author_inst": "University of Catanzaro" - }, - { - "author_name": "Pierangelo Veltri", - "author_inst": "University of Catanzaro" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.03.16.20037291", "rel_title": "Short-range airborne route dominates exposure of respiratory infection during close contact", @@ -1603085,6 +1604879,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.18.20034561", + "rel_title": "High transmissibility of COVID-19 near symptom onset", + "rel_date": "2020-03-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20034561", + "rel_abs": "BackgroundThe dynamics of coronavirus disease 2019 (COVID-19) transmissibility after symptom onset remains unknown.\n\nMethodsWe conducted a prospective case-ascertained study on laboratory-confirmed COVID-19 cases and their contacts. Secondary clinical attack rate (considering symptomatic cases only) was analyzed for different exposure windows after symptom onset of index cases and for different exposure settings.\n\nResultsThirty-two confirmed patients were enrolled and 12 paired data (index-secondary cases) were identified among the 1,043 contacts. The secondary clinical attack rate was 0.9% (95% CI 0.5-1.7%). The attack rate was higher among those whose exposure to index cases started within five days of symptom onset (2.4%, 95% CI 1.1-4.5%) than those who were exposed later (zero case from 605 close contacts, 95% CI 0-0.61%). The attack rate was also higher among household contacts (13.6%, 95% CI 4.7-29.5%) and non- household family contacts (8.5%, 95% CI 2.4-20.3%) than that in healthcare or other settings. The higher secondary clinical attack rate for contacts near symptom onset remained when the analysis was restricted to household and family contacts. There was a trend of increasing attack rate with the age of contacts (p for trend < 0.001).\n\nConclusionsHigh transmissibility of COVID-19 near symptom onset suggests that finding and isolating symptomatic patients alone may not suffice to contain the epidemic, and more generalized social distancing measures are required. Rapid reduction of transmissibility over time implies that prolonged hospitalization of mild cases might not be necessary in large epidemics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Hao-Yuan Cheng", + "author_inst": "Taiwan Centers for Disease Control" + }, + { + "author_name": "Shu-Wan Jian", + "author_inst": "Taiwan Centers for Disease Control" + }, + { + "author_name": "Ding-Ping Liu", + "author_inst": "Taiwan Centers for Disease Control, Division of Acute Infectious Disease & Immunization" + }, + { + "author_name": "Ta-Chou Ng", + "author_inst": "Institute of Epidemiology and Preventive Medicine, National Taiwan University" + }, + { + "author_name": "Wan-Ting Huang", + "author_inst": "Taiwan Centers for Disease Control" + }, + { + "author_name": "Taiwan COVID-19 outbreak investigation team", + "author_inst": "" + }, + { + "author_name": "Hsien-Ho Lin", + "author_inst": "Institute of Epidemiology and Preventive Medicine, National Taiwan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.14.20036129", "rel_title": "Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR", @@ -1604313,73 +1606150,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.12.20027185", - "rel_title": "Deep Learning-based Detection for COVID-19 from Chest CT using Weak Label", - "rel_date": "2020-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.12.20027185", - "rel_abs": "Accurate and rapid diagnosis of COVID-19 suspected cases plays a crucial role in timely quarantine and medical treatment. Developing a deep learning-based model for automatic COVID-19 detection on chest CT is helpful to counter the outbreak of SARS-CoV-2. A weakly-supervised deep learning-based software system was developed using 3D CT volumes to detect COVID-19. For each patient, the lung region was segmented using a pre-trained UNet; then the segmented 3D lung region was fed into a 3D deep neural network to predict the probability of COVID-19 infectious. 499 CT volumes collected from Dec. 13, 2019, to Jan. 23, 2020, were used for training and 131 CT volumes collected from Jan 24, 2020, to Feb 6, 2020, were used for testing. The deep learning algorithm obtained 0.959 ROC AUC and 0.976 PR AUC. There was an operating point with 0.907 sensitivity and 0.911 specificity in the ROC curve. When using a probability threshold of 0.5 to classify COVID-positive and COVID-negative, the algorithm obtained an accuracy of 0.901, a positive predictive value of 0.840 and a very high negative predictive value of 0.982. The algorithm took only 1.93 seconds to process a single patients CT volume using a dedicated GPU. Our weakly-supervised deep learning model can accurately predict the COVID-19 infectious probability in chest CT volumes without the need for annotating the lesions for training. The easily-trained and highperformance deep learning algorithm provides a fast way to identify COVID-19 patients, which is beneficial to control the outbreak of SARS-CoV-2. The developed deep learning software is available at https://github.com/sydney0zq/covid-19-detection.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Chuansheng Zheng", - "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China" - }, - { - "author_name": "Xianbo Deng", - "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China" - }, - { - "author_name": "Qing Fu", - "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China" - }, - { - "author_name": "Qiang Zhou", - "author_inst": "Artificial Intelligence Institute, School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, 430074, China" - }, - { - "author_name": "Jiapei Feng", - "author_inst": "Artificial Intelligence Institute, School of Electronic Information and Communications,} \\\\ \\normalsize{Huazhong University of Science and Technology, Wuhan, 4" - }, - { - "author_name": "Revision Created", - "author_inst": "" - }, - { - "author_name": "Revision Converted", - "author_inst": "[View Correspondence]" - }, - { - "author_name": "Newly Submitted Revision", - "author_inst": "[View Correspondence]" - }, - { - "author_name": "Newly Submitted Revision", - "author_inst": "" - }, - { - "author_name": "Final Decision", - "author_inst": "[View Correspondence]" - }, - { - "author_name": "Final Decision", - "author_inst": "" - }, - { - "author_name": "Final Decision", - "author_inst": "" - }, - { - "author_name": "Final Decision", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.16.994152", "rel_title": "Characterization of the SARS-CoV-2 Spike in an Early Prefusion Conformation", @@ -1604715,6 +1606485,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.13.20035410", + "rel_title": "Wuhan and Hubei COVID-19 mortality analysis reveals the critical role of timely supply of medical resources", + "rel_date": "2020-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035410", + "rel_abs": "We report that COVID-19 mortality and recovery rates in Hubei Province, China exponentially decays (R2>0.93) and grows (R2>0.95), respectively. A great number of newly supplied medical resources, including more than 42000 aided health workers, over 26000 makeshift beds and 23000 acute care beds, enabled overwhelming patients to be treated effectively in hospitals. This may inform other countries to deal with the coming COVID-19 pandemic when patients are overwhelming the local health care system.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Zuqin Zhang", + "author_inst": "Fujian Normal University" + }, + { + "author_name": "Wei Yao", + "author_inst": "Fujian Normal University" + }, + { + "author_name": "Yan Wang", + "author_inst": "Fujian Normal University" + }, + { + "author_name": "Cheng Long", + "author_inst": "Sichuan University West China Hospital" + }, + { + "author_name": "XINMIAO FU", + "author_inst": "Fujian Normal University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.16.993386", "rel_title": "Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target", @@ -1606019,29 +1607824,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.14.20035741", - "rel_title": "Excess cases of Influenza like illnesses in France synchronous with COVID19 invasion.", - "rel_date": "2020-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.14.20035741", - "rel_abs": "Several French regions where COVID19 has been reported currently show a renewed increase in ILI cases in the general practice based Sentinelles network. Here we computed the number of excess cases by region and found correlation with the number of reported COVID19 cases so far. These data suggest larger circulation of SARS-CoV-2 in the French population than apparent from confirmed cases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Pierre-Yves BOELLE", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Sentinelles syndromic and viral surveillance group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.14.20035873", "rel_title": "Expected impact of COVID-19 outbreak in a major metropolitan area in Brazil", @@ -1606273,6 +1608055,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.13.20035329", + "rel_title": "Influence factors of death risk among COVID-19 patients in Wuhan, China: a hospital-based case-cohort study", + "rel_date": "2020-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035329", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) triggered by infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been widely pandemic all over the world. The aim of this study was to analyze the influence factors of death risk among 200 COVID-19 patients.\n\nMethodsTwo hundred patients with confirmed SARS-CoV-2 infection were recruited. Demographic data and clinical characteristics were collected from electronic medical records. Biochemical indexes on admission were measured and patients prognosis was tracked. The association of demographic data, clinical characteristics and biochemical indexes with death risk was analyzed.\n\nResultsOf 200 COVID-19 patients, 163 (81.5%) had at least one of comorbidities, including diabetes, hypertension, hepatic disease, cardiac disease, chronic pulmonary disease and others. Among all patients, critical cases, defined as oxygenation index lower than 200, accounted for 26.2%. Severe cases, oxygenation index from 200 to 300, were 29.7%. Besides, common cases, oxygenation index higher than 300, accounted for 44.1%. At the end of follow-up, 34 (17%) were died on mean 10.9 day after hospitalization. Stratified analysis revealed that older ages, lower oxygenation index and comorbidities elevated death risk of COVID-19 patients. On admission, 85.5% COVID-19 patients were with at least one of extrapulmonary organ injuries. Univariable logistic regression showed that ALT and TBIL, two indexes of hepatic injury, AST, myoglobin and LDH, AST/ALT ratio, several markers of myocardial injury, creatinine, urea nitrogen and uric acid, three indexes of renal injury, were positively associated with death risk of COVID-19 patients. Multivariable logistic regression revealed that AST/ALT ratio, urea nitrogen, TBIL and LDH on admission were positively correlated with death risk of COVID-19 patients.\n\nConclusionOlder age, lower oxygenation index and comorbidities on admission elevate death risk of COVID-19 patients. AST/ALT ratio, urea nitrogen, TBIL and LDH on admission may be potential prognostic indicators. Early hospitalization is of great significance to prevent multiple organ damage and improve the survival of COVID-19 patients.\n\nSummaryIn this hospital-based case-cohort study, we found that serum urea nitrogen, TBIL, LDH and AST/ALT ratio, several markers of extrapulmonary organ injuries, were positively correlated with death risk of COVID-19 patients. We provide evidence for the first time that multiple organ damage on admission influences the prognosis of COVID-19 patients. Early hospitalization is beneficial for elevating the survival rate of COVID-19 patients especially critical ill patients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Lin Fu", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Jun Fei", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Hui-Xian Xiang", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Ying Xiang", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Zhu-Xia Tan", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Meng-Die Li", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Fang-Fang Liu", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Hong-Yan Liu", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Ling Zheng", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "Ying Li", + "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Hui Zhao", + "author_inst": "Anhui Medical University" + }, + { + "author_name": "De-xiang Xu", + "author_inst": "Anhui Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.13.20035212", "rel_title": "Triaging patients in the outbreak of the 2019 novel coronavirus", @@ -1607496,85 +1609341,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2020.03.12.988246", - "rel_title": "High sensitivity detection of SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method", - "rel_date": "2020-03-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.12.988246", - "rel_abs": "Many detection methods have been used or reported for the diagnosis and/or surveillance of COVID-19. Among them, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used because of its high sensitivity, typically claiming detection of about 5 copies of viruses. However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. Therefore, alternative and highly sensitive methods are imperative. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. The assay produced clean characteristic target peaks of defined sizes, which allowed for direct identification of positives by electrophoresis. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Chenyu Li", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "David N. Debruyne", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Julia Spencer", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Vidushi Kapoor", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Lily Y. Liu", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Bo Zhou", - "author_inst": "Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University, CA 94305 USA" - }, - { - "author_name": "Lucie Lee", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Rounak Feigelman", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Grayson Burdon", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Jeffrey Liu", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Alejandra Oliva", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Adam Borcherding", - "author_inst": "MGI, BGI-Shenzhen, Shenzhen 518083 China" - }, - { - "author_name": "Hongdong Tan", - "author_inst": "MGI, BGI-Shenzhen, Shenzhen 518083 China; BGI-Shenzhen, Shenzhen 518083 China" - }, - { - "author_name": "Alexander E. Urban", - "author_inst": "Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University, CA 94305 USA" - }, - { - "author_name": "Guoying Liu", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - }, - { - "author_name": "Zhitong Liu", - "author_inst": "Paragon Genomics Inc., Hayward, CA 94545 USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.03.13.990226", "rel_title": "Reinfection could not occur in SARS-CoV-2 infected rhesus macaques", @@ -1607858,6 +1609624,77 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.03.13.991455", + "rel_title": "SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches", + "rel_date": "2020-03-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.13.991455", + "rel_abs": "The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigate ACE2 and TMPRSS2 expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. While TMPRSS2 is expressed in both tissues, in the subsegmental bronchial branches ACE2 is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Soeren Lukassen", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Charitepl" + }, + { + "author_name": "Robert Lorenz Chua", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Charitepl" + }, + { + "author_name": "Timo Trefzer", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Charitepl" + }, + { + "author_name": "Nicolas C Kahn", + "author_inst": "Thoraxklinik, Heidelberg University Hospital, Department of Pneumology and Critical Care Medicine, Roentgenstrasse 1, 69126 Heidelberg, Germany" + }, + { + "author_name": "Marc A Schneider", + "author_inst": "Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Im Neuenheimer Feld 156, 69120 Heidelberg, Germany" + }, + { + "author_name": "Thomas Muley", + "author_inst": "Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Im Neuenheimer Feld 156, 69120 Heidelberg, Germany" + }, + { + "author_name": "Hauke Winter", + "author_inst": "Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Im Neuenheimer Feld 156, 69120 Heidelberg, Germany" + }, + { + "author_name": "Michael Meister", + "author_inst": "Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Im Neuenheimer Feld 156, 69120 Heidelberg, Germany" + }, + { + "author_name": "Carmen Veith", + "author_inst": "Division of Redox Regulation, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany" + }, + { + "author_name": "Agnes W Boots", + "author_inst": "Department of Pharmacology and Toxicology, NUTRIM School of Nutrition, Translational Research and Metabolism. Faculty of Health, Medicine and Life Sciences, Maa" + }, + { + "author_name": "Bianca P Hennig", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Charitepl" + }, + { + "author_name": "Michael Kreuter", + "author_inst": "Thoraxklinik, Heidelberg University Hospital, Department of Pneumology and Critical Care Medicine, Roentgenstrasse 1, 69126 Heidelberg, Germany" + }, + { + "author_name": "Christian Conrad", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Charitepl" + }, + { + "author_name": "Roland Eils", + "author_inst": "Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Charitepl" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.03.13.991307", "rel_title": "Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza", @@ -1609200,65 +1611037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.10.20033605", - "rel_title": "Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study", - "rel_date": "2020-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.10.20033605", - "rel_abs": "BackgroundThe ongoing epidemics of coronavirus disease 2019 (COVID-19) have caused serious concerns about its potential adverse effects on pregnancy. There are limited data on maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia.\n\nMethodsWe conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia.\n\nResultsDuring January 24 to February 29, 2020, there were sixteen pregnant women with confirmed COVID-19 pneumonia and eighteen suspected cases who were admitted to labor in the third trimester. Two had vaginal delivery and the rest took cesarean section. Few patients presented respiratory symptoms (fever and cough) on admission, but most had typical chest CT images of COVID-19 pneumonia. Compared to the controls, COVID-19 pneumonia patients had lower counts of white blood cells (WBC), neutrophils, C-reactive protein (CRP), and alanine aminotransferase (ALT) on admission. Increased levels of WBC, neutrophils, eosinophils, and CRP were found in postpartum blood tests of pneumonia patients. There were three (18.8%) and two (10.5%) of the mothers with confirmed or suspected COVID-19 pneumonia had preterm delivery due to maternal complications, which were significantly higher than the control group. None experienced respiratory failure during hospital stay. COVID-19 infection was not found in the newborns and none developed severe neonatal complications.\n\nConclusionSevere maternal and neonatal complications were not observed in pregnant women with COVID-19 pneumonia who had vaginal delivery or caesarean section. Mild respiratory symptoms of pregnant women with COVID-19 pneumonia highlight the need of effective screening on admission.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Na Li", - "author_inst": "Maternal and Child Health Hospital of Hubei Province" - }, - { - "author_name": "Lefei Han", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Min Peng", - "author_inst": "Maternal and Child Health Hospital of Hubei Province" - }, - { - "author_name": "Yuxia Lv", - "author_inst": "Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China" - }, - { - "author_name": "Yin Ouyang", - "author_inst": "Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China" - }, - { - "author_name": "Kui Liu", - "author_inst": "Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China" - }, - { - "author_name": "Linli Yue", - "author_inst": "Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China" - }, - { - "author_name": "Qiannan Li", - "author_inst": "Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China" - }, - { - "author_name": "Guoqiang Sun", - "author_inst": "Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China" - }, - { - "author_name": "Lin Chen", - "author_inst": "Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China" - }, - { - "author_name": "Lin Yang", - "author_inst": "The Hong Kong Polytechnic University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.10.20033738", "rel_title": "Effectiveness of isolation and contact tracing for containment and slowing down a COVID-19 epidemic: a modelling study", @@ -1609550,6 +1611328,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.10.986398", + "rel_title": "The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor", + "rel_date": "2020-03-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.10.986398", + "rel_abs": "The COVID-19 disease has plagued over 110 countries and has resulted in over 4,000 deaths within 10 weeks. We compare the interaction between the human ACE2 receptor and the SARS-CoV-2 spike protein with that of other pathogenic coronaviruses using molecular dynamics simulations. SARS-CoV, SARS-CoV-2, and HCoV-NL63 recognize ACE2 as the natural receptor but present a distinct binding interface to ACE2 and a different network of residue-residue contacts. SARS-CoV and SARS-CoV-2 have comparable binding affinities achieved by balancing energetics and dynamics. The SARS-CoV-2-ACE2 complex contains a higher number of contacts, a larger interface area, and decreased interface residue fluctuations relative to SARS-CoV. These findings expose an exceptional evolutionary exploration exerted by coronaviruses toward host recognition. We postulate that the versatility of cell receptor binding strategies has immediate implications on therapeutic strategies.\n\nOne Sentence SummaryMolecular dynamics simulations reveal a temporal dimension of coronaviruses interactions with the host receptor.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Esther S Brielle", + "author_inst": "The Hebrew University of Jerusalem" + }, + { + "author_name": "Dina Schneidman", + "author_inst": "The Hebrew University of Jerusalem" + }, + { + "author_name": "Michal Linial", + "author_inst": "The Hebrew University of Jerusalem" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.03.11.987958", "rel_title": "A human monoclonal 1 antibody blocking SARS-CoV-2 infection", @@ -1611525,45 +1613330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.07.20031393", - "rel_title": "The epidemiological characteristics of 2019 novel coronavirus diseases (COVID-19) in Jingmen,Hubei,China", - "rel_date": "2020-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.07.20031393", - "rel_abs": "BackgroundThere is currently a global outbreak of coronavirus disease 2019 (COVID-19),and its epidemic characteristics in the areas where the outbreak has been successfully controlled are rarely reported.\n\nObjectiveDescribe the epidemic characteristics of COVID-19 in Jingmen,Hubei,introduce the local prevention and control experience,and observe the impact of various prevention and control measures on the number of new cases.\n\nMethodsAll the COVID-19 patients diagnosed in the municipal districts of Jingmen from January 12 to February 29,2020 were enrolled in this study. We described epidemiological data and observed the impact of control measures on the epidemic.\n\nFindingsOf the 219 cases (110 men and 109 women), 88 (40%) had exposure to Wuhan. The median age was 48 years (range,2-88 years;IQR,35-60). Thirty-three severe patients with a median age of 66 years(range,33-82 years,IQR,57-76) were treated in intensive care units; out of these patients, 66.7 %(22) were men and 19 (57.5%) had chronic diseases, including hypertension, diabetes, heart failure, stroke, and renal insufficiency. Under the control measures, the number of new patients gradually decreased and nearly disappeared after 18 days. Wearing masks in all kinds of situations prevents most infections and is one of the most effective prevention and control measures.\n\nInterpretationIn conclusion,all people are susceptible to COVID-19, and older males and those with comorbid conditions are more likely to become severe cases. Even though COVID-19 is highly contagious,control measures have proven to be very effective, particularly wearing masks,which could prevent most infections.\n\nFundingSupported by the Major Program of Technological Innovation of Hubei Province.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Qijun Gao", - "author_inst": "the first hospital of Jingmen" - }, - { - "author_name": "yingfu hu", - "author_inst": "the first hospital of Jingmen" - }, - { - "author_name": "zhiguo dai Sr.", - "author_inst": "the first hospital of Jingmen" - }, - { - "author_name": "Jing wu", - "author_inst": "the first hospital of Jingmen" - }, - { - "author_name": "Feng Xiao", - "author_inst": "the first hostial of Jingmen" - }, - { - "author_name": "Jing wang", - "author_inst": "the fisrt hospital ofJingmen" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.08.20031229", "rel_title": "Mortality of COVID-19 is Associated with Cellular Immune Function Compared to Immune Function in Chinese Han Population", @@ -1611819,6 +1613585,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.06.20032417", + "rel_title": "Estimation of incubation period distribution of COVID-19 using disease onset forward time: a novel cross-sectional and forward follow-up study", + "rel_date": "2020-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.06.20032417", + "rel_abs": "BackgroundThe current outbreak of coronavirus disease 2019 (COVID-19) has quickly spread across countries and become a global crisis. However, one of the most important clinical characteristics in epidemiology, the distribution of the incubation period, remains unclear. Different estimates of the incubation period of COVID-19 were reported in recent published studies, but all have their own limitations. In this study, we propose a novel low-cost and accurate method to estimate the incubation distribution.\n\nMethodsWe have conducted a cross-sectional and forward follow-up study by identifying those asymptomatic individuals at their time of departure from Wuhan and then following them until their symptoms developed. The renewal process is hence adopted by considering the incubation period as a renewal and the duration between departure and symptom onset as a forward recurrence time. Under mild assumptions, the observations of selected forward times can be used to consistently estimate the parameters in the distribution of the incubation period. Such a method enhances the accuracy of estimation by reducing recall bias and utilizing the abundant and readily available forward time data.\n\nFindingsThe estimated distribution of forward time fits the observations in the collected data well. The estimated median of incubation period is 8{middle dot}13 days (95% confidence interval [CI]: 7{middle dot}37-8{middle dot}91), the mean is 8{middle dot}62 days (95% CI: 8{middle dot}02-9{middle dot}28), the 90th percentile is 14{middle dot}65 days (95% CI: 14{middle dot}00-15{middle dot}26), and the 99th percentile is 20{middle dot}59 days (95% CI: 19{middle dot}47, 21{middle dot}62). Compared with results in other studies, the incubation period estimated in this study is longer.\n\nInterpretationBased on the estimated incubation distribution in this study, about 10% of patients with COVID-19 would not develop symptoms until 14 days after infection. Further study of the incubation distribution is warranted to directly estimate the proportion with long incubation periods.\n\nFundingThis research is supported by National Natural Science Foundation of China grant 8204100362 and Zhejiang University special scientific research fund for COVID-19 prevention and control.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSBefore the current outbreak of coronavirus disease (COVID-19) in China, there were two other coronaviruses that have caused major global epidemics over the last two decades. Severe acute respiratory syndrome (SARS) spread to 37 countries and caused 8424 cases and 919 deaths in 2002-03, while Middle East respiratory syndrome (MERS) spread to 27 countries, causing 2494 cases and 858 deaths worldwide to date. Precise knowledge of the incubation period is crucial for the prevention and control of these diseases. We have searched PubMed and preprint archives for articles published as of February 22, 2020, which contain information about these diseases by using the key words of \"COVID-19\", \"SARS\", \"MERS\", \"2019-nCoV\", \"coronavirus\", and \"incubation\". We have found 15 studies that estimated the distribution of the incubation period. There are four articles focused on COVID-19, five on MERS, and six on SARS. Most of these studies had limited sample sizes and were potentially influenced by recall bias. The estimates for mean, median, and percentiles of the incubation period from these articles are summarized in Table 1.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@119cb07org.highwire.dtl.DTLVardef@605c02org.highwire.dtl.DTLVardef@3897e9org.highwire.dtl.DTLVardef@17d4d64org.highwire.dtl.DTLVardef@164102f_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONEstimates for the incubation periods of SARS, MERS, and COVID-19.\n\nC_TABLECAPTION C_TBL Added value of this studyIn the absence of complete and robust contact-tracing data, we have inferred the distribution of the incubation period of COVID-19 from the durations between departure from Wuhan and symptom onset for the confirmed cases. More than 1000 cases were collected from publicly available data. The proposed approach has a solid theoretical foundation and enhances the accuracy of estimation by reducing recall bias and utilizing a large pool of samples.\n\nImplications of all the available evidenceBased on our model, about 10% of patients with COVID-19 do not develop symptoms until 14 days after infection. Further study of individuals with long incubation periods is warranted.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Qin Jing", + "author_inst": "Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institute of Health" + }, + { + "author_name": "Chong You", + "author_inst": "Beijing International Center for Mathematical Research, Peking University" + }, + { + "author_name": "Qiushi Lin", + "author_inst": "Peking University" + }, + { + "author_name": "Taojun Hu", + "author_inst": "Peking University" + }, + { + "author_name": "Shicheng Yu", + "author_inst": "Office for Epidemiology, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Xiao-Hua Zhou", + "author_inst": "Beijing International Center for Mathematical Research, Peking University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.07.20032573", "rel_title": "Clinical Characteristics of 2019 Coronavirus Pneumonia (COVID-19): An Updated Systematic Review", @@ -1613059,49 +1614864,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.06.20031880", - "rel_title": "Estimating the scale of COVID-19 Epidemic in the United States: Simulations Based on Air Traffic directly from Wuhan, China", - "rel_date": "2020-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.06.20031880", - "rel_abs": "IntroductionCoronavirus Disease 2019 (COVID-19) infection has been characterized by rapid spread and unusually large case clusters. It is important to have an estimate of the current state of COVID-19 epidemic in the U.S. to help develop informed public health strategies.\n\nMethodsWe estimated the potential scale of the COVID-19 epidemic (as of 03/01/2020) in the U.S. from cases imported directly from Wuhan area. We used simulations based on transmission dynamics parameters estimated from previous studies and air traffic data from Wuhan to the U.S and deliberately built our model based on conservative assumptions. Detection and quarantine of individual COVID-19 cases in the U.S before 03/01/2020 were also taken into account. A SEIR model was used to simulate the growth of the number of infected individuals in Wuhan area and in the U.S.\n\nResultsWith the most likely model, we estimated that there would be 9,484 infected cases (90%CI 2,054-24,241) as of 03/01/2020 if no successful intervention procedure had been taken to reduce the transmissibility in unidentified cases. Assuming current preventive procedures have reduced 25% of the transmissibility in unidentified cases, the number of infected cases would be 1,043 (90%CI 107-2,474).\n\nConclusionOur research indicates that, as of 03/01/2020., it is likely that there are already thousands of individuals in the US infected with SARS-CoV-2. Our model is dynamic and is available to the research community to further evaluate as the situation becomes clearer.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Dalin Li", - "author_inst": "IBIRI institute, Cedars-Sinai Medical Center" - }, - { - "author_name": "Jun Lv", - "author_inst": "Department of Epidemiology and Biostatistics, Peking University Health Science Center" - }, - { - "author_name": "Gregory Botwin", - "author_inst": "IBIRI Institute, Cedars-Sinai Medical Center" - }, - { - "author_name": "Jonathan Braun", - "author_inst": "IBIRI Institute, Cedars-Sinai Medical Center" - }, - { - "author_name": "Weihua Cao", - "author_inst": "Department of Epidemiology and Biostatistics, Peking University Health Science Center" - }, - { - "author_name": "Liming Li", - "author_inst": "Department of Epidemiology and Biostatistics, Peking University Health Science Center" - }, - { - "author_name": "Dermot P.B. McGovern", - "author_inst": "IBIRI Institute, Cedars-Sinai Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.05.20031591", "rel_title": "Acute Myocardial Injury of Patients with Coronavirus Disease 2019", @@ -1613352,6 +1615114,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.03.05.20031088", + "rel_title": "Modeling the Comparative Impact of Individual Quarantine vs. Active Monitoring of Contacts for the Mitigation of COVID-19", + "rel_date": "2020-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031088", + "rel_abs": "BackgroundVoluntary individual quarantine and voluntary active monitoring of contacts are core disease control strategies for emerging infectious diseases, such as COVID-19. Given the impact of quarantine on resources and individual liberty, it is vital to assess under what conditions individual quarantine can more effectively control COVID-19 than active monitoring. As an epidemic grows, it is also important to consider when these interventions are no longer feasible, and broader mitigation measures must be implemented.\n\nMethodsTo estimate the comparative efficacy of these case-based interventions to control COVID-19, we fit a stochastic branching model to reported parameters for the dynamics of the disease. Specifically, we fit to the incubation period distribution and each of two sets of the serial interval distribution: a shorter one with a mean serial interval of 4.8 days and a longer one with a mean of 7.5 days. To assess variable resource settings, we consider two feasibility settings: a high feasibility setting with 90% of contacts traced, a half-day average delay in tracing and symptom recognition, and 90% effective isolation; and low feasibility setting with 50% of contacts traced, a two-day average delay, and 50% effective isolation.\n\nFindingsOur results suggest that individual quarantine in high feasibility settings where at least three-quarters of infected contacts are individually quarantined contains an outbreak of COVID-19 with a short serial interval (4.8 days) 84% of the time. However, in settings where this performance is unrealistically high and the outbreak continues to grow, so too will the burden of the number of contacts traced for active monitoring or quarantine. When resources are prioritized for scalable interventions such as social distancing, we show active monitoring or individual quarantine of high-risk contacts can contribute synergistically to mitigation efforts.\n\nInterpretationOur model highlights the urgent need for more data on the serial interval and the extent of presymptomatic transmission in order to make data-driven policy decisions regarding the cost-benefit comparisons of individual quarantine vs. active monitoring of contacts. To the extent these interventions can be implemented they can help mitigate the spread of COVID-19.\n\nFundingThis work was supported in part by Award Number U54GM088558 from the US National Institute Of General Medical Sciences.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Corey M Peak", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Rebecca Kahn", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Yonatan H Grad", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Lauren M Childs", + "author_inst": "Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Ruoran Li", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Marc Lipsitch", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Caroline O Buckee", + "author_inst": "Harvard T.H. Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.05.20030502", "rel_title": "Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster", @@ -1614672,37 +1616477,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.03.20030775", - "rel_title": "Key Points of Clinical and CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV) Imported Pneumonia Based On 21 Cases Analysis", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.03.20030775", - "rel_abs": "Background and ObjectiveWHO Director-General declared that the 2019-nCoV outbreak constitutes a Public Health Emergency of International Concern,and the outbreak is still on-going.Chest CT had been a key component of the diagnostic workup for patients with suspected infection. In this retrospective study, we attempt to summarize and analyze the chest CT features of 2019-nCov infections, and to identify the typical features to improved the diagnostic accuracy of new coronavirus pneumonia (NCP).\n\nMethodsChest CT scans and Clinical data of 21 patients confirmed NCP in our hospital were enrolled.These patients were divided into mild and sever group according to clinical manifestations described by the 6th clinical practice guideline of NCP in China. Main clinical and chest CT features were analyzed and identify.\n\nResultsFever (85.7%) and cough (80.9%) were the two main symptoms of NCP patients.More significantly higher incidence (85.7%) of shortness of breath in the severe cases. Multiple lesions in both lungs and with incidence of GGO(100%),vascular enlargement (76.5%) and cobblestone/reticular pattern(70.6%) were the major feature.The incidence of consolidation, mixed pattern and vascular enlargement features were up to 100% in the severe group, significantly higher than that of patients in mild group. In addition, the incidence of air-bronchogram, dilated bronchi with thickened wall and fibrosis in the severe group was significantly higher than that in the mild group.\n\nConclusionsFever and cough are the typical clinical features of NCP patients, and chest CT mainly manifested as multiple lesions in both lungs, often accompanied by GGO, vascular enlargement and cobblestone/reticular pattern.Changes in these main CT features can indicate development of the disease\n\nSummary2019 novel Coronavirus (2019-nCov) had typical clinical manifestations (fever and cough), and presented with characteristic chest CT imaging features (multiple lesions in both lungs, often accompanied by GGO, vascular enlargement and cobblestone/reticular pattern), which are helpful to the radiologist in the early detection and diagnosis of this emerging global health emergency. In addition, changes in these main CT features can indicate development of the disease.\n\nHighlightsO_LIFever (85.7%) and cough (80.9%) were the two main symptoms of NCP patients.The incidence of shortness of breath was 85.7% in the severe cases, significantly higher than 21.4% in the mild cases.\nC_LIO_LIMultiple lesions in both lungs and with incidence of GGO (100%), vascular enlargement (76.5%) and cobblestone/reticular pattern (70.6%) were the major features of NCP patients. 85.7% of cases in serve group displayed 4-5 lobes were involved simultaneously.\nC_LIO_LIChanges in these main CT imaging features can indicate development of the disease. About 19.1% of patients (4 of 21) presented with a normal CT.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "wenxiu Wu", - "author_inst": "The First People Hospital of Foshan" - }, - { - "author_name": "zhifeng xu", - "author_inst": "first people's hospital of Foshan" - }, - { - "author_name": "yabin Jin", - "author_inst": "The First People Hospital of Foshan" - }, - { - "author_name": "aizhen Pan", - "author_inst": "The First People Hospital of Foshan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.03.03.20030858", "rel_title": "Prediction of New Coronavirus Infection Based on a Modified SEIR Model", @@ -1614926,6 +1616700,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.03.20030668", + "rel_title": "Clinical findings in critical ill patients infected with SARS-Cov-2 in Guangdong Province, China: a multi-center, retrospective, observational study", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.03.20030668", + "rel_abs": "BackgroundIn December 2019, human infection with a novel coronavirus, known as SARS-CoV-2, was identified in Wuhan, China. The mortality of critical illness was high in Wuhan. Information about critically ill patients with SARS-CoV-2 infection outside of Wuhan is scarce. We aimed to provide the clinical features, treatment, and prognosis of the critically ill patients with SARS-CoV-2 infection in Guangdong Province.\n\nMethodsIn this multi-centered, retrospective, observational study, we enrolled critically ill patients with SARS-CoV-2 pneumonia who were admitted to the intensive care unit (ICU) in Guangdong Province. Demographic data, symptoms, laboratory findings, comorbidities, treatments, and prognosis were collected. Data were compared between patients with and without intubation.\n\nResultsForty-five critically ill patients with SARS-CoV-2 pneumonia were identified in 7 ICUs in Guangdong Province. The mean age was 56.7 years, and 29 patients (64.4%) were men. The most common symptoms at the onset of illness were high fever and cough. Majority of patients presented with lymphopenia and elevated lactate dehydrogenase. Treatment with antiviral drugs was initiated in all the patients. Thirty-seven patients (82.2%) had developed acute respiratory distress syndrome, and 13 (28.9%) septic shock. A total of 20 (44.4%) patients required intubation and 9 (20%) required extracorporeal membrane oxygenation. As of February 28th 2020, only one patient (2.2%) had died and half of them had discharged of ICU.\n\nConclusionsInfection with SARS-CoV-2 in critical illness is characterized by fever, lymphopenia, acute respiratory failure and multiple organ dysfunction. Compared with critically ill patients infected with SARS-CoV-2 in Wuhan, the mortality of critically ill patients in Guangdong Province was relatively low. These data provide some general understandings and experience for the critical patients with SARS-CoV-2 outside of Wuhan.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Yonghao Xu", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Zhiheng Xu", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Xuesong Liu", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Lihua Cai", + "author_inst": "Dongguan People's Hospital, Department of Intensive Care" + }, + { + "author_name": "Haichong Zheng", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Yongbo Huang", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Lixin Zhou", + "author_inst": "Foshan First People's Hospital, Department of Intensive Care" + }, + { + "author_name": "Linxi Huang", + "author_inst": "The First Affiliated Hospital of Shantou University Medical College, Department of Intensive Care" + }, + { + "author_name": "Yun Lin", + "author_inst": "Huizhou Municipal Central Hospital, Department of Intensive Care" + }, + { + "author_name": "Liehua Deng", + "author_inst": "Affiliated Hospital of Guangdong Medical University, Department of Intensive Care" + }, + { + "author_name": "Jianwei Li", + "author_inst": "Zhongshan City People's Hospital, Department of Intensive Care" + }, + { + "author_name": "Sibei Chen", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Dongdong Liu", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Zhimin Lin", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Liang Zhou", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Weiqun He", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Xiaoqing Liu", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + }, + { + "author_name": "Yimin Li", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Department o" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.03.03.20030445", "rel_title": "Modelling-based evaluation of the effect of quarantine control by the Chinese government in the coronavirus disease 2019 outbreak", @@ -1616338,29 +1618199,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.01.20029801", - "rel_title": "Evaluation of the incidence of COVID-19 and of the efficacy of contention measures in Spain: a data-driven approach.", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.01.20029801", - "rel_abs": "Our society is currently experiencing an unprecedented challenge, managing and containing an outbreak of a new coronavirus disease known as COVID-19. While China - where the outbreak started - seems to have been able to contain the growth of the epidemic, different outbreaks are nowadays being detected in multiple countries. Much is currently unknown about the natural history of the disease, such as a possible asymptomatic spreading or the role of age in both the susceptibility and mortality of the disease. Nonetheless, authorities have to take action and implement contention measures, even if not everything is known. To facilitate this task, we have studied the effect of different containment strategies that can be put into effect. Our work specifically refers to the situation in Spain as of February 28th, 2020, where a few dozens of cases have been detected. We implemented an SEIR-metapopulation model that allows tracing explicitly the spatial spread of the disease through data-driven stochastic simulations. Our results are in line with the most recent recommendations from the World Health Organization, namely, that the best strategy is the early detection and isolation of individuals with symptoms, followed by interventions and public recommendations aimed at reducing the transmissibility of the disease, which although not efficacious for disease eradication, would produce as a second order effect a delay of several days in the raise of the number of infected cases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Alberto Aleta", - "author_inst": "ISI Foundation,Turin, Italy" - }, - { - "author_name": "Yamir Moreno", - "author_inst": "University of Zaragoza" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.29.20029462", "rel_title": "68 Consecutive patients assessed for COVID-19 infection; experience from a UK regional infectious disease unit", @@ -1616636,6 +1618474,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.02.968818", + "rel_title": "Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia", + "rel_date": "2020-03-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.02.968818", + "rel_abs": "Rapid production and publication of pathogen genome sequences during emerging disease outbreaks provide crucial public health information. In resource-limited settings, especially near an outbreak epicenter, conventional deep sequencing or bioinformatics are often challenging. Here we successfully used metagenomic next generation sequencing on an iSeq100 Illumina platform paired with an open-source bioinformatics pipeline to quickly characterize Cambodias first case of COVID-2019.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Jessica E Manning", + "author_inst": "Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia" + }, + { + "author_name": "Jennifer A Bohl", + "author_inst": "Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia" + }, + { + "author_name": "Sreyngim Lay", + "author_inst": "Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia" + }, + { + "author_name": "Sophana Chea", + "author_inst": "Laboratory of Malaria and Vector Research, US National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia" + }, + { + "author_name": "Sovann Ly", + "author_inst": "Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia" + }, + { + "author_name": "Yi Sengdoeurn", + "author_inst": "Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia" + }, + { + "author_name": "Seng Heng", + "author_inst": "Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia" + }, + { + "author_name": "Chan Vuthy", + "author_inst": "Cambodian Center for Disease Control, Ministry of Health, Phnom Penh, Cambodia" + }, + { + "author_name": "Katarina Kalantar", + "author_inst": "Chan Zuckerberg Initiative, Redwood City, California, USA" + }, + { + "author_name": "Vida Ahyong", + "author_inst": "Chan Zuckerberg Biohub, San Francisco, California, USA" + }, + { + "author_name": "Michelle Tan", + "author_inst": "Chan Zuckerberg Biohub, San Francisco, California, USA" + }, + { + "author_name": "Jonathan Sheu", + "author_inst": "Chan Zuckerberg Biohub, San Francisco, California, USA" + }, + { + "author_name": "Christina M Tato", + "author_inst": "Chan Zuckerberg Biohub, San Francisco, California, USA" + }, + { + "author_name": "Joseph DeRisi", + "author_inst": "UC San Francisco" + }, + { + "author_name": "Laurence Baril", + "author_inst": "Institut Pasteur du Cambodge, Phnom Penh, Cambodia" + }, + { + "author_name": "Philippe Dussart", + "author_inst": "Virology Unit, Insititut Pasteur du Cambodge, Phnom Penh, Cambodia" + }, + { + "author_name": "Veasna Duong", + "author_inst": "Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia" + }, + { + "author_name": "Erik A Karlsson", + "author_inst": "Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.03.02.974139", "rel_title": "A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19", @@ -1618203,57 +1620128,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.28.20029272", - "rel_title": "Closed environments facilitate secondary transmission of coronavirus disease 2019 (COVID-19)", - "rel_date": "2020-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.28.20029272", - "rel_abs": "ObjectiveTo identify common features of cases with novel coronavirus disease (COVID-19) so as to better understand what factors promote secondary transmission including superspreading events.\n\nMethodsA total of 110 cases were examined among eleven clusters and sporadic cases, and investigated who acquired infection from whom. The clusters included four in Tokyo and one each in Aichi, Fukuoka, Hokkaido, Ishikawa, Kanagawa and Wakayama prefectures. The number of secondary cases generated by each primary case was calculated using contact tracing data.\n\nResultsOf the 110 cases examined, 27 (24.6%) were primary cases who generated secondary cases. The odds that a primary case transmitted COVID-19 in a closed environment was 18.7 times greater compared to an open-air environment (95% confidence interval [CI]: 6.0, 57.9).\n\nConclusionsIt is plausible that closed environments contribute to secondary transmission of COVID-19 and promote superspreading events. Our findings are also consistent with the declining incidence of COVID-19 cases in China, as gathering in closed environments was prohibited in the wake of the rapid spread of the disease.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hiroshi Nishiura", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Hitoshi Oshitani", - "author_inst": "Tohoku University" - }, - { - "author_name": "Tetsuro Kobayashi", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Tomoya Saito", - "author_inst": "National Institute of Public Health" - }, - { - "author_name": "Tomimasa Sunagawa", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Tamano Matsui", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Takaji Wakita", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "MHLW COVID-19 Response Team", - "author_inst": "" - }, - { - "author_name": "Motoi Suzuki", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.02.20030064", "rel_title": "Forecasting the Cumulative Number of COVID-19 Deaths in China: Can More Lives Be Saved?", @@ -1618489,6 +1620363,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.28.20029199", + "rel_title": "The Impact of the COVID-19 Outbreak on the Medical Treatment of Chinese Children with Chronic Kidney Disease (CKD)\uff1aA Multicenter Cross-section Study in the Context of a Public Health Emergency of International Concern", + "rel_date": "2020-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.28.20029199", + "rel_abs": "ObjectiveTo investigate the impact of the COVID-19 outbreak on the medical advice seeking of Chinese children with chronic kidney disease (CKD).\n\nMaterials and MethodsAn anonymous online questionnaire survey was conducted in 17 pediatric nephropathy diagnosis and treatment centers in China. The questions collected basic information on the patients and their parents and data on changes in the approach to medical treatment and their needs in the context of the outbreak etc. This is a Multicenter Cross-section Study.\n\nResultsA total of 735 valid questionnaires were collected. 555 patients (75.5%) and their parents said that the outbreak had a significant influence on their medical treatment: 264 patients (47.6%) said that it would be delayed by 2 to 4 weeks and 199 patients (35.9%) by 4 to 8 weeks. 510 patients (84.16%) hoped to get in touch with specialists through online consultation, and 528 patients (84.5%) hoped that online consultation could be implemented and that medication could be delivered to them.. A total of 458 patients (62.3%) said that their greatest concern was that the CKD would be aggravated or that they would experience a relapse; only 203 patients were infected by 2019-nCoV. A total of 313 patients (42.5%) experienced anxiety and thus required the intervention of psychologists.\n\nConclusionThe COVID-19 outbreak has affected the medical treatment of children with CKD. Online consultation, medication delivery and psychological counselling are the greatest needs reported by patients and their families and could especially provide solutions for the management of low income children with CKD in remote rural areas in the context of the COVID-19 epidemic.\n\nStrengths and limitations of this studyThe study is a Multicenter Cross-section Study in the Context of a Public Health Emergency of International Concern.\n\nThe study can well explore the impact of COVID-19 outbreak on the medical treatment of CKD children in China and the needs of current patients.\n\nThe study explored ways to meet the medical needs of CKD children in the context of a public health emergency of international concern, which provides a method support for all countries in the world experiencing COVID-19 outbreak.\n\nThe study is an exploration of the coping strategies for CKD management in China.\n\nThe limitations of this study is that it is quite simple and descriptive, and many studies need to be further carried out.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Gaofu Zhang", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing, 400014, China" + }, + { + "author_name": "Haiping Yang", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Aihua Zhang", + "author_inst": "Children's Hospital of Nanjing Medical University, Nanjing. 210008, China" + }, + { + "author_name": "Qian Shen", + "author_inst": "Children's Hospital of Fudan University, Shanghai 201102, China" + }, + { + "author_name": "Li Wang", + "author_inst": "Chengdu Women's and Children's Central Hospital, Chengdu, 611731, China." + }, + { + "author_name": "Zhijuan Li", + "author_inst": "Xi'an children's Hospital, Xi'an, 710003, China" + }, + { + "author_name": "Yuhong Li", + "author_inst": "Guiyang children's Hospital, Guiyang, 550003, China" + }, + { + "author_name": "Lijun Zhao", + "author_inst": "Shanxi children's Hospital, Taiyuan, 300013, China" + }, + { + "author_name": "Yue Du", + "author_inst": "Shengjing Hospital of China Medical University, Shenyang, 110004, China" + }, + { + "author_name": "Liangzhong Sun", + "author_inst": "Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China" + }, + { + "author_name": "Bo Zhao", + "author_inst": "Kunming children's Hospital, Kunming, 650000, China" + }, + { + "author_name": "Hongtao Zhu", + "author_inst": "The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830000, China" + }, + { + "author_name": "Haidong Fu", + "author_inst": "The Children Hospital of Zhejiang University School of Medicine, Hangzhou 310053, China" + }, + { + "author_name": "Xiaoyan Li", + "author_inst": "The Second Xiangya Hospital of Central South University, Changsha 410011, China" + }, + { + "author_name": "Xiaojie Gao", + "author_inst": "Shenzhen children's hospital, Shenzhen,518038, China" + }, + { + "author_name": "Sheng Hao", + "author_inst": "Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, China" + }, + { + "author_name": "Juanjuan Ding", + "author_inst": "Wuhan Children's Hospital, Wuhan, 430016, China" + }, + { + "author_name": "Zongwen Chen", + "author_inst": "Chongqing Three Gorges Central Hospital Chongqing 400014, China" + }, + { + "author_name": "Zhiquan Xu", + "author_inst": "Hainan Women and Children's Medical Center, Haikou , 570300, China" + }, + { + "author_name": "Xiaorong Liu", + "author_inst": "Beijing Children's Hospital, Capital Medical University, Beijing 100045, China" + }, + { + "author_name": "Daoqi Wu", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Mingsi Gao", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Mo Wang", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Qiu Li", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.01.20029074", "rel_title": "Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study", @@ -1619496,37 +1621481,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.27.20028928", - "rel_title": "A simple ecological model captures the transmission pattern of the coronavirus COVID-19 outbreak in China", - "rel_date": "2020-02-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.27.20028928", - "rel_abs": "The rapid spread of the 2019 novel coronavirus (COVID-19), initially reported in the city of Wuhan in China, and quickly transmitted to the entire nation and beyond, has become an international public health emergency. Estimating the final number of infection cases and the turning point (time with the fastest spreading rate) is crucial to assessing and improving the national and international control measures currently being applied. In this paper we develop a simple model based on infectious growth with a time-varying infection rate, and estimate the final number of infections and the turning point using data updated daily from 3 February 2020, when China escalated its initial public health measures, to 10 February. Our model provides an extremely good fit to the existing data and therefore a reasonable estimate of the time-varying infection rate that has largely captured the transmission pattern of this epidemic outbreak. Our estimation suggests that (i) the final number of infections in China could reach 78,000 with an upper 95% confidence limit of 88,880; (ii) the turning point of the fastest spread was on the 4th or the 5th of February; and (iii) the projected period for the end of the outbreak (i.e., when 95% of the final predicted number of infection is reached) will be the 24th of February, with an upper 95% confidence limit on the 19th of March. This suggests that the current control measures in China are excellent, and more than sufficient to contain the spread of this highly infectious novel coronavirus, and that the application of such measures could be considered internationally for the global control of this outbreak.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Feng Zhang", - "author_inst": "Anhui University" - }, - { - "author_name": "Jinmei Zhang", - "author_inst": "Xiguan Community Health Center of Liangzhou" - }, - { - "author_name": "Menglan Cao", - "author_inst": "Anhui University" - }, - { - "author_name": "Cang Hui", - "author_inst": "Stellenbosch University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.27.20027524", "rel_title": "Sex differences in clinical findings among patients with coronavirus disease 2019 (COVID-19) and severe condition", @@ -1619874,6 +1621828,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.26.20028373", + "rel_title": "Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP", + "rel_date": "2020-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.26.20028373", + "rel_abs": "The ability to detect an infectious agent in a widespread epidemic is crucial to the success of quarantine efforts in addition to sensitive and accurate screening of potential cases of infection from patients in a clinical setting. Enabling testing outside of sophisticated laboratories broadens the scope of control and surveillance efforts, but also requires robust and simple methods that can be used without expensive instrumentation. Here we report a method to identify SARS-CoV-2 (COVID-19) virus RNA from purified RNA or cell lysis using loop-mediated isothermal amplification (LAMP) using a visual, colorimetric detection. This test was additionally verified using RNA samples purified from respiratory swabs collected from COVID-19 patients in Wuhan, China with equivalent performance to a commercial RT-qPCR test while requiring only heating and visual inspection. This simple and sensitive method provides an opportunity to facilitate virus detection in the field without a requirement for complex diagnostic infrastructure.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Yinhua Zhang", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Nelson Odiwuor", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Jin Xiong", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Luo Sun", + "author_inst": "New England Biolabs" + }, + { + "author_name": "Raphael Ohuru Nyaruaba", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Hongping Wei", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Nathan A Tanner", + "author_inst": "New England Biolabs" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.27.20028530", "rel_title": "Hypokalemia and Clinical Implications in Patients with Coronavirus Disease 2019 (COVID-19)", @@ -1621274,61 +1623271,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.22.951178", - "rel_title": "Spike protein binding prediction with neutralizing antibodies of SARS-CoV-2", - "rel_date": "2020-02-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.22.951178", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is a new emerging human infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, also previously known as 2019-nCoV), originated in Wuhan seafood and animal market, China. Since December 2019, more than 69,000 cases of COVID-19 have been confirmed in China and quickly spreads to other counties. Currently, researchers put their best efforts to identify effective drugs for COVID-19. The neutralizing antibody, which binds to viral capsid in a manner that inhibits cellular entry of virus and uncoating of the genome, is the specific defense against viral invaders. In this study, we investigate to identify neutralizing antibodies that can bind to SARS-CoV-2 Sipke (S) protein and interfere with the interaction between viral S protein and a host receptor by bioinformatic methods. The sequence analysis of S protein showed two major differences in the RBD region of the SARS-CoV-2 S protein compared to SARS-CoV and SARS-CoV related bat viruses (btSARS-CoV). The insertion regions were close to interacting residues with the human ACE2 receptor. Epitope analysis of neutralizing antibodies revealed that SARS-CoV neutralizing antibodies used conformational epitopes, whereas MERS-CoV neutralizing antibodies used a common linear epitope region, which contributes to form the {beta}-sheet structure in MERS-CoV S protein and deleted in SARS-CoV-2 S protein. To identify effective neutralizing antibodies for SARS-CoV-2, the binding affinities of neutralizing antibodies with SARS-CoV-2 S protein were predicted and compared by antibody-antigen docking simulation. The result showed that CR3022 neutralizing antibody from human may have higher binding affinity with SARS-CoV-2 S protein than SARS-CoV S protein. We also found that F26G19 and D12 mouse antibodies could bind to SARS-CoV S protein with high affinity. Our findings provide crucial clues towards the development of antigen diagnosis, therapeutic antibody, and the vaccine against SARS-CoV-2.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Tamina Park", - "author_inst": "University of Science and Technology" - }, - { - "author_name": "Sang-Yeop Lee", - "author_inst": "Korea Basic Science Institute" - }, - { - "author_name": "Seil Kim", - "author_inst": "Korea Research Institute of Standards and Science" - }, - { - "author_name": "Mi Jeong Kim", - "author_inst": "Korea Basic Science Institute" - }, - { - "author_name": "Hong Gi Kim", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Sangmi Jun", - "author_inst": "Korea Basic Science Institute" - }, - { - "author_name": "Seung Il Kim", - "author_inst": "Korea Basic Science Institute" - }, - { - "author_name": "Bum Tae Kim", - "author_inst": "Korea Research Institute of Chemical Technology" - }, - { - "author_name": "Edmond Changkyun Park", - "author_inst": "Korea Basic Science Institute" - }, - { - "author_name": "Daeui Park", - "author_inst": "Center for Convergent Research of Emerging Virus Infection" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.02.22.961268", "rel_title": "A simple magnetic nanoparticles-based viral RNA extraction method for efficient detection of SARS-CoV-2", @@ -1621644,6 +1623586,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.02.25.964775", + "rel_title": "Comparative analysis of primer-probe sets for the laboratory confirmation of SARS-CoV-2", + "rel_date": "2020-02-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.25.964775", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is newly emerging human infectious diseases, which is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, also previously known as 2019-nCoV). Within two months of the outbreak, more than 80,000 cases of COVID-19 have been confirmed worldwide. Since the human to human transmission occurred easily and the human infection is rapidly increasing, the sensitive and early diagnosis is essential to prevent the global outbreak. Recently, World Health Organization (WHO) announced various primer and probe sets for SARS-CoV-2 previously developed in China, Germany, Hong Kong, Japan, Thailand, and USA. In this study, we compared the ability to detect SARS-CoV-2 RNA among the seven primer-probe sets for N gene and the three primer-probe sets for Orf1 gene. The result of the comparative analysis represented that the 2019-nCoV_N2, N3 of USA and the ORF1ab of China are the most sensitive primer-probe sets for N and Orf1 genes, respectively. Therefore, the appropriate combination from ORF1ab (China), 2019-nCoV_N2, N3 (USA), and NIID_2019-nCOV_N (Japan) sets should be selected for the sensitive and reliable laboratory confirmation of SARS-CoV-2.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Yu Jin Jung", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Gun-Soo Park", + "author_inst": "Korea Food Research Institute" + }, + { + "author_name": "Jun Hye Moon", + "author_inst": "WELLS BIO, INC." + }, + { + "author_name": "Keunbon Ku", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Seung-Hwa Beak", + "author_inst": "Korea Institute of Toxicology" + }, + { + "author_name": "Seil Kim", + "author_inst": "Korea Research Institute of Standards and Science" + }, + { + "author_name": "Edmond Changkyun Park", + "author_inst": "Korea Basic Science Institute" + }, + { + "author_name": "Daeui Park", + "author_inst": "Center for Convergent Research of Emerging Virus Infection" + }, + { + "author_name": "Jong-Hwan Lee", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Cheol Woo Byeon", + "author_inst": "WELLS BIO, INC." + }, + { + "author_name": "Joong Jin Lee", + "author_inst": "WELLS BIO, INC." + }, + { + "author_name": "Jin-soo Maeng", + "author_inst": "Korea Food Research Institute" + }, + { + "author_name": "Seong Jun Kim", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Seung Il Kim", + "author_inst": "Korea Basic Science Institute" + }, + { + "author_name": "Bum-Tae Kim", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Min Jun Lee", + "author_inst": "WELLS BIO, INC." + }, + { + "author_name": "Hong Gi Kim", + "author_inst": "Korea Institute of Chemical Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.02.27.967760", "rel_title": "The ACE2 expression of maternal-fetal interface and fetal organs indicates potential risk of vertical transmission of SARS-COV-2", @@ -1622940,33 +1624965,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.23.20024802", - "rel_title": "Intrinsic growth rules of patients infected, dead and cured with 2019 novel coronavirus in mainland China", - "rel_date": "2020-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.23.20024802", - "rel_abs": "An outbreak of a novel coronavirus (SARS-CoV-2)-infected pneumonia (COVID-19) was first diagnosed in Wuhan, China, in December 2019 and then spread rapidly to other regions. We collected the time series data of the cumulative number of confirmed infected, dead, and cured cases from the health commissions in 31 provinces in mainland China. A descriptive model in a logistic form was formulated to infer the intrinsic epidemic rules of COVID-19, which illustrates robustness spatially and temporally. Our model is robust (R2>0.95) to depict the intrinsic growth rule for the cumulative number of confirmed infected, dead, and cured cases in 31 provinces in mainland China. Furthermore, we compared the intrinsic epidemic rules of COVID-19 in Hubei with that of severe acute respiratory syndrome (SARS) in Beijing, which was obtained from the Ministry of Public Health of China in 2003. We found that the infected case is the earliest to be saturated and has the lowest semi-saturation period compared with deaths and cured cases for both COVID-19 and SARS. All the three types of SARS cases are later to saturate and have longer semi-saturation period than that of COVID-19. Despite the virus caused SARS (SARS-CoV) and the virus caused COVID-19 (SARS-CoV-2) are homologous, the duration of the outbreak would be shorter for COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Chuanliang Han", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Yimeng Liu", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Saini Yang", - "author_inst": "Beijing Normal University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.24.20026773", "rel_title": "Characterizing the transmission and identifying the control strategy for COVID-19 through epidemiological modeling", @@ -1623150,6 +1625148,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.22.20023267", + "rel_title": "A Novel Method for the Estimation of a Dynamic Effective Reproduction Number (Dynamic-R) in the CoViD-19 Outbreak", + "rel_date": "2020-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.22.20023267", + "rel_abs": "The CoViD-19 outbreak has escalated to a pandemic in the last few months. Pharmaceutical solutions based upon virologic studies, at this point, remain inconclusive, with no proven pharmaceutical solution so far. In contrast, this paper looks towards creating more accurate epidemiological models during this phase of viral growth in order to provide better feedback measures to public health officials and agencies, in particular, by providing a responsive, timely model of the R value based on the previous few days results.\n\nSuch an R value, although bearing less statistical precision due to limited sampling, could allow R to become a more effective, responsive standalone measure of infectious transmission. It demonstrates that the R value can be used as a dynamic, time-dependent indicator without the use of curve-fitting, and also estimates the most recent R-value of the CoViD-19 outbreak to be between 1.32 and 1.35.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Yi Chen Chong", + "author_inst": "Independent" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.23.20026872", "rel_title": "Mental health status and coping strategy of medical workers in China during The COVID-19 outbreak", @@ -1624670,77 +1626687,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.20.20025619", - "rel_title": "Clinical Characteristics of 24 Asymptomatic Infections with COVID-19 Screened among Close Contacts in Nanjing, China", - "rel_date": "2020-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025619", - "rel_abs": "BackgroundPrevious studies have showed clinical characteristics of patients with the 2019 novel coronavirus disease (COVID-19) and the evidence of person-to-person transmission. Limited data are available for asymptomatic infections. This study aims to present the clinical characteristics of 24 cases with asymptomatic infection screened from close contacts and to show the transmission potential of asymptomatic COVID-19 virus carriers.\n\nMethodsEpidemiological investigations were conducted among all close contacts of COVID-19 patients (or suspected patients) in Nanjing, Jiangsu Province, China, from Jan 28 to Feb 9, 2020, both in clinic and in community. Asymptomatic carriers were laboratory-confirmed positive for the COVID-19 virus by testing the nucleic acid of the pharyngeal swab samples. Their clinical records, laboratory assessments, and chest CT scans were reviewed.\n\nFindingsNone of the 24 asymptomatic cases presented any obvious symptoms before nucleic acid screening. Five cases (20.8%) developed symptoms (fever, cough, fatigue, etc.) during hospitalization. Twelve (50.0%) cases showed typical CT images of ground-glass chest and 5 (20.8%) presented stripe shadowing in the lungs. The remaining 7 (29.2%) cases showed normal CT image and had no symptoms during hospitalization. These 7 cases were younger (median age: 14.0 years; P = 0.012) than the rest. None of the 24 cases developed severe COVID-19 pneumonia or died. The median communicable period, defined as the interval from the first day of positive nucleic acid tests to the first day of continuous negative tests, was 9.5 days (up to 21 days among the 24 asymptomatic cases). Through epidemiological investigation, we observed a typical asymptomatic transmission to the cohabiting family members, which even caused severe COVID-19 pneumonia.\n\nInterpretationThe asymptomatic carriers identified from close contacts were prone to be mildly ill during hospitalization. However, the communicable period could be up to three weeks and the communicated patients could develop severe illness. These results highlighted the importance of close contact tracing and longitudinally surveillance via virus nucleic acid tests. Further isolation recommendation and continuous nucleic acid tests may also be recommended to the patients discharged.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Zhiliang Hu", - "author_inst": "Nanjing Infectious Disease Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China." - }, - { - "author_name": "Ci Song", - "author_inst": "Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China." - }, - { - "author_name": "Chuanjun Xu", - "author_inst": "Department of Radiology, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China." - }, - { - "author_name": "Guangfu Jin", - "author_inst": "Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China." - }, - { - "author_name": "Yaling Chen", - "author_inst": "Nanjing Infectious Disease Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China." - }, - { - "author_name": "Xin Xu", - "author_inst": "Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China." - }, - { - "author_name": "Hongxia Ma", - "author_inst": "Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China." - }, - { - "author_name": "Wei Chen", - "author_inst": "Department of Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China." - }, - { - "author_name": "Yuan Lin", - "author_inst": "Department of Maternal, Child and Adolescent Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China." - }, - { - "author_name": "Yishan Zheng", - "author_inst": "Department of Critical Medicine, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China." - }, - { - "author_name": "Jianming Wang", - "author_inst": "Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China." - }, - { - "author_name": "zhibin hu", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Yongxiang Yi", - "author_inst": "Nanjing Infectious Disease Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China." - }, - { - "author_name": "Hongbing Shen", - "author_inst": "Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.18.20024281", "rel_title": "Phase adjusted estimation of the number of 2019 novel coronavirus cases in Wuhan, China", @@ -1624948,6 +1626894,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.19.20025262", + "rel_title": "A Note on NCP Diagnosis Number Prediction Model", + "rel_date": "2020-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.19.20025262", + "rel_abs": "ImportanceTo predict the diagnosed COVID-19 patients and the trend of the epidemic in China. It may give the public some scientific information to ease the fear of the epidemic.\n\nObjectiveIn December 2019, pneumonia infected with the novel coronavirus burst in Wuhan, China. We aimed to use a mathematical model to predict number of diagnosed patients in future to ease anxiety on the emergent situation.\n\nDesignAccording to all diagnosis number from WHO website and combining with the transmission mode of infectious diseases, the mathematical model was fitted to predict future trend of outbreak.\n\nSettingOur model was based on the epidemic situation in China, which could provide referential significance for disease prediction in other countries, and provide clues for prevention and intervention of relevant health authorities.\n\nParticipantsIn this retrospective, all diagnosis number from Jan 21 to Feb 10, 2020 reported from China was included and downloaded from WHO website.\n\nMain Outcome(s) and Measure(s)We develop a simple but accurate formula to predict the next day diagnosis number:[Formula],where Ni is the total diagnosed patient till the ith day, and was estimated as 0.904 at Feb 10.\n\nResultsBased on this model, it is predicted that the rate of disease infection will decrease exponentially. The total number of infected people is limited; thus, the disease will have limited impact. However, new diagnosis will last to March.\n\nConclusions and RelevanceThrough the establishment of our model, we can better predict the trend of the epidemic in China.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.19.20025395", "rel_title": "Generalized anxiety disorder, depressive symptoms and sleep quality during COVID-19 epidemic in China: a web-based cross-sectional survey", @@ -1626272,65 +1628232,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.02.19.957118", - "rel_title": "Mucin 4 Protects Female Mice from Coronavirus Pathogenesis", - "rel_date": "2020-02-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.19.957118", - "rel_abs": "Using incipient lines of the Collaborative Cross (CC), a murine genetic reference population, we previously identified a quantitative trait loci (QTL) associated with low SARS-CoV titer. In this study, we integrated sequence information and RNA expression of genes within the QTL to identify mucin 4 (Muc4) as a high priority candidate for controlling SARS-CoV titer in the lung. To test this hypothesis, we infected Muc4-/- mice and found that female, but not male, Muc4-/- mice developed more weight loss and disease following infection with SARS-CoV. Female Muc4-/- mice also had more difficulty breathing despite reduced lung pathology; however, no change in viral titers was observed. Comparing across viral families, studies with chikungunya virus, a mosquito-borne arthralgic virus, suggests that Muc4s impact on viral pathogenesis may be widespread. Although not confirming the original titer QTL, our data identifies a role for Muc4 in the SARS-CoV disease and viral pathogenesis.\n\nImportanceGiven the recent emergence of SARS-CoV-2, this work suggest that Muc4 expression plays a protective role in female mice not conserved in male mice following SARS-CoV infection. With the SARS-CoV-2 outbreak continuing, treatments that modulate or enhance Muc4 activity may provide an avenue for treatment and improved outcomes. In addition, the work highlights the importance of studying host factors including host genetics and biological sex as key parameters influencing infection and disease outcomes.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jessica A Plante", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Kenneth Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Lisa Gralinski", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Anne Beall", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Martin T. Ferris", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Daniel Bottomly", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Richard R Green", - "author_inst": "University of Washington" - }, - { - "author_name": "Shannon McWeeney", - "author_inst": "Oregon Health and Sciences University" - }, - { - "author_name": "Mark T. Heise", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Ralph S. Baric", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Vineet D. Menachery", - "author_inst": "University of Texas Medical Branch at Galveston" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.02.19.950253", "rel_title": "Pangolin homology associated with 2019-nCoV", @@ -1626538,6 +1628439,33 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.02.16.20023655", + "rel_title": "SEIR Transmission dynamics model of 2019 nCoV coronavirus with considering the weak infectious ability and changes in latency duration", + "rel_date": "2020-02-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.16.20023655", + "rel_abs": "Pneumonia patients of 2019-ncov in latent period are not easy to be effectively quarantined, but there is evidence that they have strong infectious ability. Here, the infectious ability of patients during the latent period is slightly less than that of the infected patients was assumed. We established a new SEIR propagation dynamics model, that considered the weak transmission ability of the incubation period, the variation of the incubation period length, and the government intervention measures to track and isolate comprehensively. Based on the raw epidemic data of China from January 23, 2020 to February 10, 2020, the dynamic parameters of the new present SEIR model are fitted. Through the Euler integration algorithm to solve the model, the effect of infectious ability of incubation patients on the theoretical estimation of the present SEIR model was analyzed, and the occurrence time of peak number in China was predicted.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Pengpeng Shi", + "author_inst": "Xian University of Architecture and Technology" + }, + { + "author_name": "Shengli Cao", + "author_inst": "Xian Jiaotong University" + }, + { + "author_name": "Peihua Feng", + "author_inst": "Xian Jiaotong University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.17.20023630", "rel_title": "Estimating the case fatality ratio of the COVID-19 epidemic in China", @@ -1627750,49 +1629678,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.02.10.942748", - "rel_title": "Recombination and convergent evolution led to the emergence of 2019 Wuhan coronavirus", - "rel_date": "2020-02-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.10.942748", - "rel_abs": "The emergence of SARS-CoV-2 underscores the need to better understand the evolutionary processes that drive the emergence and adaptation of zoonotic viruses in humans. In the betacoronavirus genus, which also includes SARS-CoV and MERS-CoV, recombination frequently encompasses the Receptor Binding Domain (RBD) of the Spike protein, which, in turn, is responsible for viral binding to host cell receptors. Here, we find evidence of a recombination event in the RBD involving ancestral linages to both SARS-CoV and SARS-CoV-2. Although we cannot specify the recombinant nor the parental strains, likely due to the ancestry of the event and potential undersampling, our statistical analyses in the space of phylogenetic trees support such an ancestral recombination. Consequently, SARS-CoV and SARS-CoV-2 share an RBD sequence that includes two insertions (positions 432-436 and 460-472), as well as the variants 427N and 436Y. Both 427N and 436Y belong to a helix that interacts directly with the human ACE2 (hACE2) receptor. Reconstruction of ancestral states, combined with protein-binding affinity analyses using the physics-based trRosetta algorithm, reveal that the recombination event involving ancestral strains of SARS-CoV and SARS-CoV-2 led to an increased affinity for hACE2 binding, and that alleles 427N and 436Y significantly enhanced affinity as well. Structural modeling indicates that ancestors of SARS-CoV-2 may have acquired the ability to infect humans decades ago. The binding affinity with the human receptor was subsequently boosted in SARS-CoV and SARS-CoV-2 through further mutations in RBD. In sum, we report an ancestral recombination event affecting the RBD of both SARS-CoV and SARS-CoV-2 that was associated with an increased binding affinity to hACE2.\n\nImportanceThis paper addresses critical questions about the origin of the SARS-CoV-2 virus: what are the evolutionary mechanisms that led to the emergence of the virus, and how can we leverage such knowledge to assess the potential of SARS-like viruses to become pandemic strains? In this work, we demonstrate common mechanisms involved in the emergence of human-infecting SARS-like viruses: first, by acquiring a common haplotype in the RBD through recombination, and further, through increased specificity to the human ACE2 receptor through lineage specific mutations. We also show that the ancestors of SARS-CoV-2 already had the potential to infect humans at least a decade ago, suggesting that SARS-like viruses currently circulating in wild animal species constitute a source of potential pandemic re-emergence.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Juan Angel Patino-Galindo", - "author_inst": "Columbia University" - }, - { - "author_name": "Ioan Filip", - "author_inst": "Columbia University" - }, - { - "author_name": "Ratul Chowdhury", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Costas D. Maranas", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Peter Karl Sorger", - "author_inst": "Harvard University" - }, - { - "author_name": "Mohammed AlQuraishi", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Raul Rabadan", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.02.10.942185", "rel_title": "Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses", @@ -1627940,6 +1629825,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.14.20022939", + "rel_title": "A new transmission route for the propagation of the SARS-CoV-2 coronavirus", + "rel_date": "2020-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.14.20022939", + "rel_abs": "BackgroundA novel coronavirus (SARS-CoV-2) spread from the capital of the Hubei province in China to the rest of the country, then to most of the world. To anticipate future trends in the development of the epidemic, we explore here, based on public records of infected persons how variation in the virus tropism could end up in different patterns, warranting specific way to handle the epidemic.\n\nMethodsWe use a compartmental model to describe the evolution of an individual through several possible states: susceptible, infected, alternative infection, detected and removed. We fit the parameters of the model to the existing data taking into account significant quarantine changes where necessary.\n\nResultsThe model indicates that Wuhan quarantine measures were effective but that alternative virus forms and a second propagation route are compatible with available data. For Singapore and Shenzhen region the secondary route does not seem to be active yet and the epidemic size limited.\n\nConclusionsThe alternative infection tropism (the gut tropism) and a secondary propagation route are validated hypotheses using a model fitted by the available data. Corresponding prevention measures that take into account both routes should be implemented to the benefit of epidemic control.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Antoine Danchin", + "author_inst": "Institut Cochin _ INSERM U1016 - CNRS UMR8104 - Universite de Paris, FRANCE and School of Biomedical Sciences Li Kashing Faculty of Medicine, University of Hong" + }, + { + "author_name": "Tuen Wai Patrick Ng", + "author_inst": "Department of Mathematics, University of Hong Kong, SAR Hong Kong, CHINA" + }, + { + "author_name": "Gabriel TURINICI", + "author_inst": "Universite Paris Dauphine - PSL" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.16.20023770", "rel_title": "Study on SARS-COV-2 transmission and the effects of control measures in China", @@ -1629064,25 +1630976,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.13.20022251", - "rel_title": "Understanding the present status and forecasting of COVID-19 in Wuhan", - "rel_date": "2020-02-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.13.20022251", - "rel_abs": "The present status of COVID[-]19 is analyzed and the end of the disease is forecasted. The peak of the epidemic is different in three regions, Wuhan, Hubei province except Wuhan, and mainland China except Hubei. In two regions except Wuhan, the peak of the epidemic passed ten days ago. If the trend until February 11 does not change, the disease may end by the end of February. In Wuhan, the epidemic reached a peak but the reported number of newly infected patients fluctuates largely. We need to know the reason for the big fluctuation to forecast the end of the disease.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Toshihisa Tomie", - "author_inst": "Changchun University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.12.20021386", "rel_title": "Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers", @@ -1629302,6 +1631195,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.02.12.20022426", + "rel_title": "Interventions targeting air travellers early in the pandemic may delay local outbreaks of SARS-CoV-2", + "rel_date": "2020-02-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.12.20022426", + "rel_abs": "BackgroundWe evaluated if interventions aimed at air travellers can delay local SARS-CoV-2 community transmission in a previously unaffected country.\n\nMethodsWe simulated infected air travellers arriving into countries with no sustained SARS-CoV-2 transmission or other introduction routes from affected regions. We assessed the effectiveness of syndromic screening at departure and/or arrival & traveller sensitisation to the COVID-2019-like symptoms with the aim to trigger rapid self-isolation and reporting on symptom onset to enable contact tracing. We assumed that syndromic screening would reduce the number of infected arrivals and that traveller sensitisation reduces the average number of secondary cases. We use stochastic simulations to account for uncertainty in both arrival and secondary infections rates, and present sensitivity analyses on arrival rates of infected travellers and the effectiveness of traveller sensitisation. We report the median expected delay achievable in each scenario and an inner 50% interval.\n\nResultsUnder baseline assumptions, introducing exit and entry screening in combination with traveller sensitisation can delay a local SARS-CoV-2 outbreak by 8 days (50% interval: 3-14 days) when the rate of importation is 1 infected traveller per week at time of introduction. The additional benefit of entry screening is small if exit screening is effective: the combination of only exit screening and traveller sensitisation can delay an outbreak by 7 days (50% interval: 2-13 days). In the absence of screening, with less effective sensitisation, or a higher rate of importation, these delays shrink rapidly to less than 4 days.\n\nConclusionSyndromic screening and traveller sensitisation in combination may have marginally delayed SARS-CoV-2 outbreaks in unaffected countries.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Samuel J Clifford", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Carl A B Pearson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Petra Klepac", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Kevin Van Zandvoort", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Billy J Quilty", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "- CMMID COVID-19 working group", + "author_inst": "-" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Stefan Flasche", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.12.20021931", "rel_title": "Statistics based predictions of coronavirus 2019-nCoV spreading in mainland China", @@ -1630466,25 +1632406,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.05.20020107", - "rel_title": "Tobacco-use disparity in gene expression of ACE2, the receptor of 2019-nCov", - "rel_date": "2020-02-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.05.20020107", - "rel_abs": "In current severe global emergency situation of 2019-nCov outbreak, it is imperative to identify vulnerable and susceptible groups for effective protection and care. Recently, studies found that 2019-nCov and SARS-nCov share the same receptor, ACE2. In this study, we analyzed five large-scale bulk transcriptomic datasets of normal lung tissue and two single-cell transcriptomic datasets to investigate the disparities related to race, age, gender and smoking status in ACE2 gene expression and its distribution among cell types. We didnt find significant disparities in ACE2 gene expression between racial groups (Asian vs Caucasian), age groups (>60 vs <60) or gender groups (male vs female). However, we observed significantly higher ACE2 gene expression in former smokers lung compared to non-smokers lung. Also, we found higher ACE2 gene expression in Asian current smokers compared to non-smokers but not in Caucasian current smokers, which may indicate an existence of gene-smoking interaction. In addition, we found that ACE2 gene is expressed in specific cell types related to smoking history and location. In bronchial epithelium, ACE2 is actively expressed in goblet cells of current smokers and club cells of non-smokers. In alveoli, ACE2 is actively expressed in remodelled AT2 cells of former smokers. Together, this study indicates that smokers especially former smokers may be more susceptible to 2019-nCov and have infection paths different with non-smokers. Thus, smoking history may provide valuable information in identifying susceptible population and standardizing treatment regimen.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Guoshuai Cai", - "author_inst": "University of South Carolina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.07.20021196", "rel_title": "Tracking the spread of novel coronavirus (2019-nCoV) based on big data", @@ -1630672,6 +1632593,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2020.02.07.20021188", + "rel_title": "Transmission Dynamics of 2019-nCoV in Malaysia", + "rel_date": "2020-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.07.20021188", + "rel_abs": "This paper focuses on the formulation of a deterministic COVID-19 transmission model by considering the exposed and recovered populations with immunity. The scenario of the simulation is depicted based on the patient zero in Malaysia. The transmission model is found to be able to predict the next confirmed case given a single case is introduced in a fully susceptible population. The mathematical model is developed based on the SEIR model which has susceptible, exposed, infectious and recovered populations. The system of equations which were obtained were solved numerically and the simulation results were analyzed. The analysis includes the impact of the disease if no control is taken.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jane Labadin", + "author_inst": "Universiti Malaysia Sarawak" + }, + { + "author_name": "Boon Hao Hong", + "author_inst": "Universiti Malaysia Sarawak" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.02.08.20021162", "rel_title": "Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts", @@ -1632156,45 +1634100,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.04.20020503", - "rel_title": "Risk assessment of novel coronavirus 2019-nCoVoutbreaks outside China", - "rel_date": "2020-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.04.20020503", - "rel_abs": "We developed a computational tool to assess the risks of novel coronavirus outbreaks outside of China. We estimate the dependence of the risk of a major outbreak in a country from imported cases on key parameters such as: (i) the evolution of the cumulative number of cases in mainland China outside the closed areas; (ii) the connectivity of the destination country with China, including baseline travel frequencies, the effect of travel restrictions, and the efficacy of entry screening at destination; and (iii) the efficacy of control measures in the destination country (expressed by the local reproduction number Rloc). We found that in countries with low connectivity to China but with relatively high Rloc, the most beneficial control measure to reduce the risk of outbreaks is a further reduction in their importation number either by entry screening or travel restrictions. Countries with high connectivity but low Rloc benefit the most from policies that further reduce Rloc. Countries in the middle should consider a combination of such policies. Risk assessments were illustrated for selected groups of countries from America, Asia, and Europe. We investigated how their risks depend on those parameters, and how the risk is increasing in time as the number of cases in China is growing.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Peter Boldog", - "author_inst": "University of Szeged" - }, - { - "author_name": "Tamas Tekeli", - "author_inst": "University of Szeged" - }, - { - "author_name": "Zsolt Vizi", - "author_inst": "University of Szeged" - }, - { - "author_name": "Attila Denes", - "author_inst": "University of Szeged" - }, - { - "author_name": "Ferenc Bartha", - "author_inst": "University of Szeged" - }, - { - "author_name": "Gergely Rost", - "author_inst": "University of Szeged" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.03.20020263", "rel_title": "Network-based Drug Repurposing for Human Coronavirus", @@ -1632382,6 +1634287,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.04.20020339", + "rel_title": "Population movement, city closure and spatial transmission of the 2019-nCoV infection in China", + "rel_date": "2020-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.04.20020339", + "rel_abs": "The outbreak of pneumonia caused by a novel coronavirus (2019-nCoV) in Wuhan City of China obtained global concern, the population outflow from Wuhan has contributed to spatial expansion in other parts of China. We examined the effects of population outflow from Wuhan on the 2019-nCoV transmission in other provinces and cities of China, as well as the impacts of the city closure in Wuhan. We observed a significantly positive association between population movement and the number of cases. Further analysis revealed that if the city closure policy was implemented two days earlier, 1420 (95% CI: 1059, 1833) cases could be prevented, and if two days later, 1462 (95% CI: 1090, 1886) more cases would be possible. Our findings suggest that population movement might be one important trigger of the 2019-nCoV infection transmission in China, and the policy of city closure is effective to prevent the epidemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Siqi Ai", + "author_inst": "Department of Epidemiology, School of Public Health, Sun Yat-sen University" + }, + { + "author_name": "Guanghu Zhu", + "author_inst": "School of Mathematics and Computing Science, Guilin University of Electronic Technology" + }, + { + "author_name": "Fei Tian", + "author_inst": "Department of Epidemiology, School of Public Health, Sun Yat-sen University" + }, + { + "author_name": "Huan Li", + "author_inst": "Department of Epidemiology, School of Public Health, Sun Yat-sen University" + }, + { + "author_name": "Yuan Gao", + "author_inst": "Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Instit" + }, + { + "author_name": "Yinglin Wu", + "author_inst": "Department of Epidemiology, School of Public Health, Sun Yat-sen University" + }, + { + "author_name": "Qiyong Liu", + "author_inst": "Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Instit" + }, + { + "author_name": "Hualiang Lin", + "author_inst": "Department of Epidemiology, School of Public Health, Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.03.20020271", "rel_title": "Getting to zero quickly in the 2019-nCov epidemic with vaccines or rapid testing", @@ -1633454,41 +1635406,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.01.31.929497", - "rel_title": "Highly Distinguished Amino Acid Sequences of 2019-nCoV (Wuhan Coronavirus)", - "rel_date": "2020-02-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.31.929497", - "rel_abs": "Using a method for pathogen screening in DNA synthesis orders, we have identified a number of amino acid sequences that distinguish 2019-nCoV (Wuhan Coronavirus) from all other known viruses in Coronaviridae. We find three main regions of unique sequence: two in the 1ab polyprotein QHO60603.1, one in surface glycoprotein QHO60594.1.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jacob Beal", - "author_inst": "Raytheon BBN Technologies" - }, - { - "author_name": "Thomas Mitchell", - "author_inst": "Raytheon BBN Technologies" - }, - { - "author_name": "Daniel Wyschogrod", - "author_inst": "Raytheon BBN Technologies" - }, - { - "author_name": "Jeff Manthey", - "author_inst": "Integrated DNA Technologies" - }, - { - "author_name": "Adam Clore", - "author_inst": "Integrated DNA Technologies" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.01.30.926881", "rel_title": "Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes", @@ -1633708,6 +1635625,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.01.28.20019224", + "rel_title": "Estimated effectiveness of traveller screening to prevent international spread of 2019 novel coronavirus (2019-nCoV)", + "rel_date": "2020-01-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.28.20019224", + "rel_abs": "Traveller screening is being used to limit further global spread of 2019 novel coronavirus (nCoV) following its recent emergence. Here, we project the impact of different travel screening programs given remaining uncertainty around the values of key nCoV life history and epidemiological parameters. Even under best-case assumptions, we estimate that screening will miss more than half of infected travellers. Breaking down the factors leading to screening successes and failures, we find that most cases missed by screening are fundamentally undetectable, because they have not yet developed symptoms and are unaware they were exposed. These findings emphasize the need for measures to track travellers who become ill after being missed by a travel screening program. We make our model available for interactive use so stakeholders can explore scenarios of interest using the most up-to-date information. We hope these findings contribute to evidence-based policy to combat the spread of nCoV, and to prospective planning to mitigate future emerging pathogens.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Katelyn Gostic", + "author_inst": "The University of Chicago, United States" + }, + { + "author_name": "Ana C. R. Gomez", + "author_inst": "University of California Los Angeles, United States" + }, + { + "author_name": "Riley O. Mummah", + "author_inst": "University of California Los Angeles, United States" + }, + { + "author_name": "Adam J. Kucharski", + "author_inst": "London School of Tropical Hygiene and Medicine, United Kingdom" + }, + { + "author_name": "James O. Lloyd-Smith", + "author_inst": "University of California Los Angeles; Fogarty International Center, National Institutes of Health, United States" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.01.29.925867", "rel_title": "Insights into Cross-species Evolution of Novel Human Coronavirus 2019-nCoV and Defining Immune Determinants for Vaccine Development", @@ -1634711,29 +1636663,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2020.01.23.917351", - "rel_title": "Pattern of early human-to-human transmission of Wuhan 2019-nCoV", - "rel_date": "2020-01-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.23.917351", - "rel_abs": "On December 31, 2019, the World Health Organization was notified about a cluster of pneumonia of unknown aetiology in the city of Wuhan, China. Chinese authorities later identified a new coronavirus (2019-nCoV) as the causative agent of the outbreak. As of January 23, 2020, 655 cases have been confirmed in China and several other countries. Understanding the transmission characteristics and the potential for sustained human-to-human transmission of 2019-nCoV is critically important for coordinating current screening and containment strategies, and determining whether the outbreak constitutes a public health emergency of international concern (PHEIC). We performed stochastic simulations of early outbreak trajectories that are consistent with the epidemiological findings to date. We found the basic reproduction number, R0, to be around 2.2 (90% high density interval 1.4--3.8), indicating the potential for sustained human-to-human transmission. Transmission characteristics appear to be of a similar magnitude to severe acute respiratory syndrome-related coronavirus (SARS-CoV) and the 1918 pandemic influenza. These findings underline the importance of heightened screening, surveillance and control efforts, particularly at airports and other travel hubs, in order to prevent further international spread of 2019-nCoV.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Julien Riou", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Christian L Althaus", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.01.21.914044", "rel_title": "Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm", @@ -1635008,5 +1636937,44 @@ "license": "cc_no", "type": "new results", "category": "microbiology" + }, + { + "rel_doi": "10.1101/2020.01.19.911669", + "rel_title": "A mathematical model for simulating the transmission of Wuhan novel Coronavirus", + "rel_date": "2020-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.19.911669", + "rel_abs": "As reported by the World Health Organization, a novel coronavirus (2019-nCoV) was identified as the causative virus of Wuhan pneumonia of unknown etiology by Chinese authorities on 7 January, 2020. In this study, we developed a Bats-Hosts-Reservoir-People transmission network model for simulating the potential transmission from the infection source (probable be bats) to the human infection. Since the Bats-Hosts-Reservoir network was hard to explore clearly and public concerns were focusing on the transmission from a seafood market (reservoir) to people, we simplified the model as Reservoir-People transmission network model. The basic reproduction number (R0) was calculated from the RP model to assess the transmissibility of the 2019-nCoV.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Tianmu Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jia Rui", + "author_inst": "Xiamen University" + }, + { + "author_name": "Qiupeng Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Zeyu Zhao", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jing-An Cui", + "author_inst": "Beijing University of Civil Engineering and Architecture" + }, + { + "author_name": "Ling Yin", + "author_inst": "Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" } ] \ No newline at end of file